Month: May 2022

JUNIOR STAR projects

23. 05. 2022

JUNIOR STAR grants are intended for excellent scientists in their early careers within 8 years of receiving their PhDs who have published in prestigious international journals before, and have had substantial experience abroad. The 5-year project allows them to receive up to CZK 25 million and gives them an opportunity to attain scientific independence or even start their own research team, which can bring new areas of research into Czech science. Only a fraction of submitted projects receive funding.

JUNIOR STAR 2024

High-throughput host detection and cultivation of freshwater CPRs (‘Ca. Patescibacteria’)

Maria-Cecilia Chiriac | Biology Centre of the CAS

Abstract

One of the most important discoveries in microbiology in the last decade was Candidate Phyla Radiation (CPR) or ‘Ca. Patescibacteria’, a recently described phylum of mostly episymbionts that include up to 26% of bacterial diversity. Although >2400 representative genomes are available, less than a dozen members were cultivated to date, belonging to just two out of 24 CPR classes. Because to their prevalence in the environment, cultivating ‘Ca. Patescibacteria’ is important, but notoriously difficult due to their complex nutrition needs and reliance on other microorganisms, and new strategies and techniques are needed to understand their ecophysiology. In our project, we propose to target both partners with metatranscriptomics and EpicPCR to assess the functional potential and host range of CPRs. Further, we aim to obtain episymbionts – hosts co-cultures by combining reverse metagenomics and high-throughput cultivation. These approaches represent the necessary steps that will advance the understanding of CPRs biology.

Project Aims

The project aims 1) to understand the functional potential of ‘Ca. Patescibacteria’ members in the environment; 2) to assess the host range of these epi- and endo-symbiotic bacteria; and 3) to obtain new enrichment cultures and co-cultures.

Model theory, structural combinatorics, and algorithms

Samuel Walker Braunfeld | Charles University, Faculty of Mathematics and Physics

Abstract

Our research will study the emerging connections between model theory and structural graph theory. Model theory provides a collection of concepts and tools for analyzing the complexity of infinite structures, and these are mirrored in the analysis of finite structures. For some time, this similarity seemed only analogical, but recent results have shown that the model-theoretic machinery can be finitized, and doing so recovers key definitions from structural graph theory and provides new and unified tools for proving results about them. The main conjecture that serves to focus our efforts is algorithmic in nature: it identifies a certain model-theoretic property as characterizing the graph classes on which a wide swath of algorithmic problems (namely, those expressible in first-order logic) can be efficiently solved. While most researchers active in the area approach from the combinatorial viewpoint, we plan to use our expertise to take a model-theoretic approach to this problem, and also to see how the combinatorial concepts can feed back into model theory

Project Aims

We plan to develop the interaction between model theory and structural graph theory, and in particular to (try to) solve a conjecture about graph classes that admit efficient algorithms.

The Sociology of Literature Revisited: Towards Epistemological Symmetry within Literature-and-Society Research

Mgr. Jan Váňa, Ph.D. | Institute of Czech Literature of the CAS

Abstract

In this interdisciplinary project, we will develop a research model for studying the relationship between literature and society through a critical discussion of relevant paradigms in literary theory and sociology from their foundation to the present. The project consists of two parts: First, we will conduct metatheoretical research on how the relationship between literature and society has been studied throughout the history of literary theory and sociology. We will focus on the epistemological and ontological assumptions of the most dominant approaches and investigate how these assumptions determine the treatment of the literary-social link. Second, we will synthesize selected approaches and construct a theoretical hypothesis, which will be empirically tested on five distinct case studies. The goal is to design a model of literary communication that combines micro- and macro-perspectives to study literary production, reception, internal textual structure, and their interconnectedness, thus granting literature and society equal valence in the analysis—epistemological symmetry.

Project Aims

1. Identify and make transparent the asymmetries between the “literary” and the “social” in previous literature-and-society research. 2. Employ this knowledge to design a model of literary communication that grants the “literary” and “social” epistemological symmetry and develop it on case studies.

Innovative synthetic methods enabled by transition metal catalysis and electrochemistry

Ing. Rafael Navrátil, Ph.D. | Charles University, Faculty of Science

Abstract

Advances in organic chemistry have enabled life-changing discoveries and fostered key developments in medicinal, agricultural and materials chemistry. However, bridging fundamental knowledge gaps and meeting increasing demands for more safe, practical, and easily scalable organic syntheses while also reducing their step-count, cost, and environmental impact requires developing innovative synthetic methods. The research proposal tackles these challenges by developing conceptually innovate and unprecedented synthetic methods based on two emerging research areas: 1) molecular editing, for predictive and selective manipulation (e.g., migration) of native functional groups, and 2) radical-based C–C/C–N cross-coupling, for bond formation at sp3-hybridized carbon centers. To this end, this research will tap into the potential of transition metal catalysis, electrochemical activation, and radical chemistry approaches. The resulting methods will be then applied to overcome current limitations in the synthesis of bioactive compounds and natural products.

Project Aims

Development of novel catalytic and electrochemical synthetic methods for 1) migration of functional groups in organic compounds, 2) radical-based C–C a C–N cross-coupling reactions. Application of developed methods in the synthesis of bioactive compounds and natural products.

Control of quantum phases and entanglement by magnetic field in molecular systems

Dr Vinicius Tadeu Santana | Brno University of Technology, Central European Institute of Technology

Abstract

Electronic spin in molecules of coordination compounds is promising as the basic logic unit of quantum computers. This technology will transform various aspects of society by enabling faster and more efficient computation, secure communication, and precise sensing. Molecules can be tailored to achieve specific magnetic properties through simple ligand substitution. Among the desired features is quantum entanglement, which interconnects the molecular quantum states for quantum information processing. Molecular crystals are formed through hydrogen bonds or other weak interactions between neighbor molecules, resulting in a structure that gives rise to spin lattices and spin-spin couplings. We will use electron spin resonance (ESR) to explain the crucial role of weak intermolecular interactions in determining the entanglement phenomenon in molecular crystals. A thorough understanding of these interactions is essential to successfully implement molecular crystals in future quantum devices.

Project Aims

Investigate the effect of the weak exchange and the control of quantum entanglement in molecular crystals by screening new coordination compounds and pushing forward the state-ofthe-art in electron spin resonance, envisioning possible applications in quantum devices.

Transposons and ovulatory cycles – key players in long-term female fertility?

Mgr. Lenka Gahurová, Ph.D. | University of South Bohemia in České Budějovice, Faculty of Science

Abstract

In mammalian female foetuses, the oocytes are established as a finite pool. They enter meiosis I before birth and remain arrested until the meiotic resumption during the reproductive period, leading to ovulation. Oocytes of long-lived species can be arrested for decades while maintaining the quality to support embryonic development. To understand the mechanisms of long-term female fertility, we study naked mole rat (NMR) and giant mole rat (GMR), rodents with reproductive span greater than 20 and 15 years, respectively. Decreased oocyte quality in aged mice was linked with transposon (TE) dysregulation and deleterious effect of ovulations. Low genomic content of potentially active TEs and social system comprising ovulating and nonovulating females make NMR and GMR suitable models to study the effect of TEs and ovulatory cycles on oocyte and ovarian quality. By combining the latest genomics and imaging technologies, we will assess the consequences of low TE activity on the oocyte transcriptome and epigenome, and the effect of ovulations on the aging-associated decline of the quality.

Project Aims

We aim to determine the role of transposons and ovulatory cycles on female fertility by studying the effect of low transposable element activity and natural absence of ovulations on oocyte and ovarian quality in mole-rats, long-living rodents with long-term female fertility.

Tunable graphene/SiC optoelectronics

RNDr. Martin Rejhon, Ph.D. | Charles University, Faculty of Mathematics and Physics

Abstract

ABC-stacked trilayer graphene is known to exhibit a clean tunable energy bandgap by a perpendicular field, an important feature for its future applications in electronics and optoelectronics. However, the major techniques used to prepare ABC graphene struggle with a maximal size of ABC graphene, which is around 100 nm, making any future applications impossible. Therefore, we propose to use ABC-stacked epitaxial graphene on a silicon carbide substrate grown by silicon sublimation, which enables the preparation of homogeneous graphene on a large scale, for the development of tunable electronic and optoelectronic devices. In particular, we aim to develop a detector of terahertz and far-infrared radiation based on ABC-stacked graphene by tailoring the energy bandgap with a perpendicular electric field. The detection performance will be tested at temperatures from cryogenic to room temperature, and compared with conventional liquid-helium-cooled bolometers.

Project Aims

The project’s goal is to fabricate and characterize tunable electronic and optoelectronic components based on ABC-stacked trilayer epitaxial graphene on SiC substrate. We aim to optimize the growth technique and comprehensively study the tunable properties of ABC graphene.

Prenatal Programming of Child's Brain and Behavior: Novel Insights into the Mechanisms of the Intergenerational Transmission

Klára Marečková, Ph.D., M.Sc. | Masaryk University, Central European Institute of Technology

Abstract

Maternal stress, anxiety, and depression during pregnancy have long-lasting consequences for the child, manifesting as emotional and behavioral problems. Still, the mechanisms of this intergenerational transmission are not well understood. The ambition of the current project is to identify the mechanisms underlying the relationships between maternal health during pregnancy and brain structure, function and behavior in the child. We aim to test the mediatory role of inflammation and accelerated aging in these relationships and demonstrate what environmental factors might magnify or protect against the negative impact of maternal illness during pregnancy. This high-risk/high-gain project would provide ground-breaking new insights into the mechanisms of prenatal programming and allow the development of targeted interventions that would reduce the odds of mental illness in the new generations. Our findings will thus contribute to two areas of the national priority Healthy Population: (1) Origin and Development of Diseases and (2) Epidemiology and Prevention of the Most Serious Diseases.

Project Aims

ChiBra project aims to identify the mechanisms underlying the relationships between maternal mental health during pregnancy and child’s brain and behavior. We will test the mediatory role of inflammation and accelerated aging and demonstrate what environmental factors moderate these relationships.

Computing Religious Devotion: How Reinforcing Supernatural Beliefs Affects Normative Models in the Mind

Mgr. Martin Lang, Ph.D. | Masaryk University, Faculty of Arts

Abstract

Religions permeate the lives of billions and are hypothesised to play an essential role in normative behaviour. Yet, little is known about how religious devotion penetrates cognitive computations during decision-making. I fill this lacuna by proposing a computational model of religious decision-making. In this model, religious belief, forged through religious practice, forms strong priors in the mind. When the mind simulates possible actions during decision-making, religious actions become readily available and likely selected due to their high value. To empirically develop the model, I will determine how religious belief affects the strength of religious priors during normative decision-making in various laboratory and field studies. Moreover, in a large-scale cross-cultural study, I will establish how beliefs and practices of different religious traditions affect cognitive computations during normative decisions. The project will producing one-of-a-kind, comprehensive model of how religions shape the mind, and document the workings of this model across at least 12 articles.

Project Aims

The CREDO project aims to devise and test a computational model that will explain how religious devotion affects normative decision-making. The long-term vision is to provide a formal computational platform offering a deeper understanding of the workings of human mind within cultural complexity.

Catalytic Stereoselective Synthesis of Elusive Atropisomers for Accelerating Drug Discovery

Paulo Paioti | Institute of Organic Chemistry and Biochemistry of the CAS

Abstract

Atropisomers are separable conformational isomers arising from restricted rotation around a single bond which revolutionized drug discovery. The main goal herein is inducing conformational restriction to create new drugs by developing catalytic stereoselective synthesis methods toward difficult-to-access drug-like atropisomers. We will study how conformational changes, from achiral and flexible to chiral and more rigid atropisomeric forms, impact a molecule’s ability to interact with biological receptors. To accomplish this, we will introduce three new catalytic atroposelective methods. 1) We will develop the first atroposelective amidebond formation toward atropisomeric peptidomimetics. (2) We will generate sphere-shaped atropisomers. This rarely investigated area of molecular shape is sought-after in drug discovery. (3) We will develop the first atroposelective decarboxylation of esters. Collectively, the resulting knowledge will shed light on differences between pharmacological properties of achiral and chiral atropisomers, constituting an invaluable insight for drug discovery.

Project Aims

Discovery of new atropisomeric drugs by development of unprecedented catalytic stereoselective synthesis methods toward difficult-to-access drug-like atropisomers.

Salmonella effector network inhibiting T cell immunity

RNDr. Ondřej Černý, Ph.D. | Institute of Microbiology of the CAS

Abstract In this project we will identify the network of effectors enabling Salmonella to establish a longlasting niche in its host by inhibiting crucial T cell response. The Salmonella pathogenicity island 2-encoded type III secretion system (SPI-2 T3SS) is known to translocate effectors inhibiting migration of dendritic cells, inducing anti-inflammatory conditions, and blocking antigen presentation. However, my preliminary data show that only a subpopulation of intracellular bacteria express effectors involved in subversion of the T cell immunity. This leads to formation of distinct populations of infected antigen-presenting cells that induce different T cell phenotypes. Using the effector network approach, we will identify contribution of individual effectors to inhibition of T cell response. We will examine how the effectors influence interaction between dendritic cells and T cells and describe the heterogeneity in the T cell response. Our results might provide us with new markers for infection outcome and help to develop new vaccination strategy in the future.

Project Aims

The aim of this project is to determine the impact of heterogeneous modulation of dendritic cells by Salmonella effectors on the establishment of chronic infection and superspreader phenotype of infected host. This may open new avenues in design of chronic bacterial infection therapies.

The effect of bilingualism on speech perception and production in the first year of life

Nikola Paillereau, Ph. D. | Institute of Psychology of the CAS

Abstract

Many infants in the world acquire two languages from birth and yet, the population of bilingual children is under-represented in scientific studies on early speech acquisition. The fundamental aim of this research project is to investigate the effect of bilingualism on the course of speech perception and production in the first year of infants’ lives, and render existing theoretical accounts on early speech development more comprehensive and generalisable. Babbling will be analysed in infants aged 8-14 months. Auditory discrimination between languages and speech sounds will be examined at 4, 6, and 12 months, using advanced neuroimaging (EEG and fNIRS) and cognitive-behavioural methods. Neurophysiological data on speech processing during the initial months of life are expected to be particularly illuminating as they should help provide deeper understanding of the developing brain’s exposure to the infant’s native language (s). The project will help to understand whether the established developmental milestones in early speech acquisition can be considered universal.

Project Aims

Run four perception and one production studies with monolingual and bilingual infants between 4 and 14 months. Check milestones in language acquisition. Gain unique insight into developmental differences and point to possible applications. Form a research team. Report findings in IF journals

Design and optimization of 3D printable oxide-dispersion-strengthened multi-principal element alloys for extreme environments

Mgr. Milan Heczko, Ph.D. | Institute of Physics of Materials of the CAS

Abstract

The future of sustainable development of human society directly depends on improvement in energetic and economic efficiency. Such advancement in electric power generation or propulsion requires discovery and development of high-performance materials. Following-up our recent revolutionary work (Nature, 2023) the goal is to explore a newly opened compositional space for design and optimization of cost-effective and sustainable 3D printable oxide-dispersion-strengthened multi-principal element alloys (ODS-MPEAs). The predictive power of thermodynamic calculations will be combined with rapid alloy production by additive manufacturing. Promising candidate materials will undergo accelerated mechanical testing in terms of monotonic load, creep and fatigue. Complemented by state-of-the-art multi-scale characterization and supported by the atomistic simulations, the key design aspects determining alloy performance will be assessed. Proposed multi-layered optimization approach will result in the development of new 3D printable ODS-MPEAs for use in the targeted temperature range of 800-1000°C.

Project Aims

Identification of critical aspects of material design determining behavior of 3D printable ODSMPEAs under monotonic, creep and cyclic loading at high temperatures (800-1000°C). Development of new cost-effective and sustainable 3D printable ODS-MPEA for use in extreme environment.

Inductive Biases of Deep Neural Networks in Computer Vision

Ing. Lukáš Neumann, Ph.D. | Czech Technical University in Prague, Faculty of Electrical Engineering

Abstract

Deep Neural Network models have in the recent years dominated virtually all areas of Artificial Intelligence and Computer Vision. Despite the recent success, the models are easily confused by trivial samples not present in the training set and even the largest models lack basic generalisation and reasoning abilities despite having hundreds of millions of parameters and being trained on millions of very diverse data samples – suggesting that a fundamental piece of understanding is still missing. We propose that one of the missing pieces in current models is an appropriate inductive bias – the set of prior assumptions used to generalise and make a prediction based on a finite set of training samples – and therefore in this project, we want to study inductive biases for common Computer Vision tasks and incorporate them into modern Deep Neural Networks. This will result in Deep Neural Network models which require less parameters, which are more efficient, which are less confused by out-of-distribution data samples and which require less training data.

Project Aims

1) discover existing and search for new symmetries for modern computer vision models 2) discover novel topological representations as another form of inductive bias encoding 3) introduce novel indirect low-dimensional representations 4) make the search for inductive bias more efficient

Stars in galactic nuclei: interrelation with massive black holes

RNDr. Michal Zajaček, Ph.D. | Masaryk University, Faculty of Science

Abstract

The goal of the project is to study the mutual interaction between stars and supermassive black holes (SBHs) in galactic nuclei. Previously, we showed that the interaction with the nuclear jet can substantially affect stellar characteristics. Here we propose to extend previous studies by analyzing systematically the combined interaction of stars with both the accretion disk and the jet. Repetitive encounters will enhance stellar mass loss and hence, in addition to modifying stellar evolution, they inevitably change the accretion state of the SBH. Traditional unified models of active galactic nuclei (AGN) neglect the effect of stars. However, they can not only perturb the accretion state of SBHs, but eventually also determine it via dense concentrations – nuclear star clusters (NSCs). Comparison of the NSC properties, radio emission characteristics on smaller and larger scales as well as X-ray emission properties within the Bondi radius of the SBH are needed to comprehend the link between the NSC modulation of the SMBH accretion state and large-scale AGN feedback.

Project Aims

We will compute the effect of repetitive stellar passages through the nuclear disk-jet on both the star and the accretion of the supermassive black hole (SBH). We will compare the nuclear star cluster (NSC) properties with the SBH emission to understand the NSC effect on the large-scale feedback.

Probing Chiral Dynamics on Femtosecond Timescales

Ing. Vít Svoboda, Dr. sc. ETH Zurich | University of Chemistry and Technology Prague, Faculty of Chemical Engineering

Abstract

Chirality plays an important role in chemistry, physics, and biology. Reactions involving chiral molecules often entail changes in molecular chirality. One way to visualize photo-induced chiral dynamics during chemical transformations in real time is time-resolved photoelectron circular dichroism (TRPECD). The PECD manifests itself as an asymmetry in a photoelectron angular distribution (PAD) when an ensemble of randomly oriented chiral molecules is ionized with circularly polarized (CP) radiation. The PAD is measured by time-resolved photoelectron spectroscopy combined with extreme ultraviolet CP femtosecond pulses obtained through high harmonic generation. The project aims to study chiral dynamics on femtosecond timescales, thereby advancing several research disciplines such as excited-state photochemistry and femtochirality and entails the following major goals: probing electron correlations during double ionization of chiral molecules, probing chiral changes during the photo-switching of helicenes, and the development of a theoretical framework for calculating the TRPECD.

Project Aims

1) Founding of a new research group 2) Study of chiral dynamics during chemical transformations in real time by measuring static and time-resolved PECD and PICD of doubly charged cations and helicenes 3) Development of advanced experimental setup with 3D VMI and circularly polarized high harmonics

Titles and bones of ancient Egyptian officials: New mathematical approach to analysing Old Kingdom data

Mgr. et Mgr. Veronika Dulíková, Ph.D. | Charles University, Faculty of Philosophy and Art

Abstract

The analysis of extensive data of prospographical, administrative and anthropological character using advanced mathematical methods reveals changes in Old Kingdom society (2700–2180 BC) and differences between individuals in relation to their social status. The combined use of a database of officials and their titles (Maat-base) and an anthropological database (AnuBase) containing the detailed evaluation of hundreds of morphological and metric features is the initial resource in the analyses and mathematical processing. The interdisciplinary project integrating the methods of systematic data collecting and complex network analysis with anthropological study of particular individuals buried at Giza and Abusir enables us to view, newly interconnect and evaluate known data using new perspectives that significantly expand and deepen our knowledge of ancient Egyptian society at a number of levels: an individual (physical appearance, physical activity, career length) – the family or community (family ties, nepotism) – the whole society/population (demography, changes over time).

Project Aims

The main goal is to study individuals and the operation of society in Egypt in the third millennium BC. The principal task is to define possible relations and links between anthropological data and the social status, family kinship or demographic profile of the population using mathematical methods.

JUNIOR STAR 2023

Particle identification in high-energy physics experiments and space with advanced detection systems

Dr. rer. nat. Benedikt Bergmann | České vysoké učení technické v Praze, Ústav technické a experimentální fyziky ČVUT

Abstract

The proposed project addresses the development of radiation detection systems for real-time measurement of radiation field characteristics, based on hybrid pixel detectors of the Timepix family. This development is driven by the needs of physics experiments at accelerators and in space. Particle type identification accuracy and precision of trajectory reconstruction shall be improved by utilizing novel chip technology and sensor materials in combination with state-ofthe-art computer science methods. Artificial intelligence will be used for exploiting the characteristic features of particle traces in the sensors. Besides 3D particle trajectory and dE/dX measurement, detector segmentation and an expected time resolution of 200 ps also provide information about the direction of particle flight. Developed detection systems and data evaluation methodology will be applied also to the mixed radiation fields found in the ATLAS and MoEDAL experiments at the LHC, and in Space. The expected outputs are 10-15 publications in impacted journals and 2-3 conference proceedings.

Project Aims

Develop novel detector systems and algorithms for real-time particle identification and trajectory reconstruction;
• Use the developed detector system and evaluation methodology for fundamental research in high-energy physics and space applications.

Shaped beams for a new era of electron microscopy and spectroscopy

Ing. Andrea Konečná, Ph.D. | Vysoké učení technické v Brně, Fakulta strojního inženýrství

Abstract

“With recent developments in instrumentation, phase plates and machine learning algorithms, the field of electron microscopy and spectroscopy is at the edge of a new era. In this project, we will study shaped electron beams as revolutionary probes, which will make electron microscopes more versatile and cheaper, and enable novel applications. We will theoretically explore phase plates needed for the preparation of shaped beams and alternative imaging and spectroscopic methods available with these unconventional probes. We will introduce and optimise designs of tunable light- or microelectronics-based electron phase concerning selected applications. We will focus on fast and damage-free imaging and spectroscopy, probing lowenergy excitations beyond the usual selection rules and studying optical dichroism, everything down to the atomic scale. Since electron microscopes are essential diagnostic tools in many areas of research and development, the achievements of the project will have a significant impact on the whole society.”

Project Aims

Theoretical development and optimisation of fast and versatile electron phase plates for generation of shaped beams. Theoretical proposal of applications of such beams in fast electron imaging and spectroscopy of low-energy optical and vibrational excitations.

Development of actin polymerization inhibitors as potential migrastatics

Mgr. et Mgr. Pavla Perlíková, Ph.D. | Vysoká škola chemicko-technologická v Praze, Fakulta chemické technologie

Abstract

Migrastatics represent a new class of drugs with great potential to improve the outcome of current cancer treatment strategies by inhibiting the metastatic behaviour of cancer cells. Actin polymerization is one of the potential targets for migrastatics. The aim of the project is to develop new compounds with antimetastatic activity based on inhibition of actin polymerization (direct or indirect). Analogues of cytochalasins, that directly inhibit actin polymerization, will be developed based on virtual screening and fragment growing. Inhibitors of ARPC1, a subunit of the Arp2/3 complex and actin polymerization regulator, will be developed including specific inhibitors of ARPC1 isoforms. Finally, PROTACs targeting the Arp2/3 complex and its subunits will be synthesized and their effect on cancer cell invasion will be studied. The screening of the new compounds will be performed in close collaboration with Prof. Jan Brábek (BIOCEV, Vestec, Czech Republic).

Project Aims

Development of cytochalasin analogs Development of Arp2/3 complex inhibitors that target an ARPC1 subunit Development of specific binders to ARPC1 subunit isoforms Development of proteolysis-targeting chimeras to modulate the function of the Arp2/3 complex

NMDA receptor conformational dynamics: from structure to function and pharmacology

RNDr. Vojtěch Vyklický, Ph.D. | Fyziologický ústav AV ČR, v.v.i.

Abstract

“N-methyl-D-aspartate receptors (NMDARs), a subtype of ionotropic glutamate receptors, bin synaptically released neurotransmitter glutamate and mediate fast excitatory synaptic transmission at the majority of synapses in the mammalian central nervous system. NMDARs play a key role in synaptic plasticity and neuronal development. We will use a combination of single-molecule FRET, electrophysiology, molecular biology and computational methods to study human NMDAR conformational rearrangements underlying receptor activation and desensitization. On this basis the project aims to build a quantitative model of NMDAR activation, reveal how the individual conformational states and transitions in the receptor activation pathway are affected by human de novo disease-associated mutations of the GRIN genes and how this relates to altered receptor cell-surface expression. Finally we aim to reveal how the impaired NMDAR signaling can be rectified by novel subunit-selective modulators.”

Project Aims

To quantitatively characterize NMDAR conformational changes in the course of receptor activation and desensitization, to uncover the structural basis of human GRIN diseaseassociated mutations, and to explore how the impaired NMDAR signaling can be rectified by novel subunit-selective modulators.

Mechanisms driving convergent genome evolution in natural populations

RNDr. Filip Kolář, Ph.D. | Univerzita Karlova, Přírodovědecká fakulta

Abstract

“Determining genetic underpinnings of adaptation is a major challenge of evolutionary biology. Repeated environmental adaptation offers powerful naturally replicated study systems, yet varying fraction of the genome exhibiting convergence precludes generalization. Multiple genomic and functional factors have been proposed to determine genomic convergence, but their relative importance is blurred by case-specific focus of the studies and varying evolutionary timescales. Leveraging 13-fold independent colonization of challenging toxic soil by model family Brassicaceae, I aim at systematic assessment of the factors underlying genome convergence and thus evolutionary predictability. We will combine population and structural genomics with transcriptomic and reverse genetic validations to characterize the factors determining genomic hotspots of convergence and test the hypothesis of their varying importance with divergence. The project will identify general drivers of convergent genome evolution in nature and inform evolutionary predictions essential for efficient breeding and conservation.”

Project Aims

Identify candidate hotspots of convergent adaptation along a broad divergence continuum. Quantify relative importance of the genomic and functional predictors of convergent hotspot loci. Functionally validate phenotypic and fitness effects of the convergent hotspot loci.

Spurious Precision in Meta-Analysis of Social Science Research (METASPUR)

doc. PhDr. Zuzana Iršová Havránková, Ph.D. | Univerzita Karlova, Fakulta sociálních věd

Abstract

“I argue that the meta-analysis methodology used in observational research entails a bias, one that stems from a reliance on reported precision which often exaggerates real precision. I will show that, when applied to all meta-analysis contexts, a method inspired by instrumentál variables used in economics corrects for the bias. In meta-analysis, studies reporting more precision get more weight. Yet more than 20,000 metaanalyses have been conducted in social sciences, mostly synthesizing observational research, where researchers have control over the precision measure they report. Hence, reported precision is endogenous. I challenge the assumption that observational studies reporting more precision are more informative and less biased. While I focus on social sciences, the results will apply to the 100,000+ meta-analyses in other fields that have also relied on observational research. Spurious precision has dramatic consequences not only for meta-analysis methodology and structural models calibrated using meta-analyses but also for the entire practice of evidence based policy.

Project Aims

“I will present a novel meta-analysis estimator and gauge its performance using i) Monte Carlo simulations, ii) comparisons of meta-analyses with pre-registered Many Labs replications, and iii) comparisons among many meta-analysis estimators applied to a large number of metaanalysis datasets”

Normalisation and Emergence: Rethinking the Dynamics of Mathematics The case of Prague in the First Half of the 19th Century

Elías Fuentes Guillén | Filosofický ústav AV ČR, v.v.i.

Abstract

“The purpose of this project is to better understand the development of mathematics in Prague during the first half of the 19th century by elucidating the motives (e.g., practical) and factors (e.g., socio-institutional) that led to certain practices being set as a norm but also to the emergence of new mathematical knowledge. For this we take as case study the University of Prague and Bernard Bolzano, both of which were sui generis actors at the time, and we propose a methodological approach to study the dynamics of mathematics that brings together elements from the latest trends in the history of mathematics and mathematics education, the philosophy of mathematical practices, the studies on mathematical cultures and the textual studies.”

Project Aims

“Study the mathematical practices in Prague and in Bolzano’s work in the context of European mathematics of the first half of the 19th century. Create a Digital Archive of Bolzano’s mathematical manuscripts. Encouragement of ‘citizen science’ and education through public engagement.”

Inexact Matrix Computations for the Exascale Era

Dr. Erin Claire Carson, Ph.D. | Univerzita Karlova, Matematicko-fyzikální fakulta

Abstract

“Scientific computing inherently involves multiple sources of inexactness, from discretization or simplification of the problem, to noisy data, to rounding errors, to stopping computations intentionally to improve efficiency. The state-of-the-art approach is to analyze different sources of error separately. This modular approach is not only potentially hazardous, but also misses potential opportunities to improve performance by combining multiple sources of inexactness. Developing reliable, efficient approaches for exascale matrix computations requires filling this gap. This project will break the modular approach to the analysis and design of algorithms for inexact matrix computations by rigorously analyzing how different errors interact while being propagated through a computation and their effect on numerical behavior and solution quality. Our holistic approach, rooted in rigorous theoretical analysis, will lead to new algorithms for exascale problems that exploit inexactness to balance performance and accuracy. ”

Project Aims

“This project will: 1) rigorously analyze matrix computations subject to multiple sources of inexactness and 2) to build on insights from this analysis to develop new algorithms targeting exascale machines that exploit inexactness to achieve both performance and accuracy. ”

TOPFLIGHT: Trajectory and Mission Planning for Agile Flight of Aerial Robots in Cluttered Environments

Ing. Robert Pěnička, Ph.D. | České vysoké učení technické v Praze, Fakulta elektrotechnická

Abstract

“Drones are already changing many industries like package delivery, inspection, or search and rescue. This research project will focus on answering fundamental questions that arise from high-speed flight of quadrotors in cluttered environments. The motivation for this project is the search and rescue scenario which requires the drones to be as fast as possible to quickly find survivors after natural disasters. We will focus on pushing the boundaries of the drones’ autonomy in planning and control for agile quadrotor flight. Current approaches struggle with online trajectory planning and control that would use full agility of the quadrotors and thus minimize the time of flight. We plan to developt planning and control methods that overcome this limitation and thus significantly improve the efficiency of drones in such tasks. Furthermore, we will develop novel approaches for online mission planning over multiple targets, e.g. estimated locations of survivors in the search and rescue, that would (contrary to existing work) account for cluttered environments and limited battery capacity.”

Project Aims

“We will develop novel methods in

1)Online trajectory planning for minimum-time flight in cluttered environments

2)Robust model-based and learning-based control approaches for an agile flight amongobstacles

3)Multi-goal mission planning with minimum-time objective and constrained battery capacity”

Analysis of the craniofacial skeletal stem cell niche

Peter Fabian | Masarykova univerzita, Přírodovědecká fakulta

Abstract

Stem cells reside in specialized microenvironments or “niches” that maintain stem cell function during the growth, maintenance, and repair of tissues. My project aims to leverage powerful genetic, imaging, and lineage tracing tools of zebrafish with single-cell sequencing to investigate a recently discovered specialized fibroblast population (Fabian et al, NatCom, 2022) that may act as a niche for long-term skeletal health. As several of the genes enriched in this niche cause craniofacial malformations when mutated in humans, my work will provide an important new insight into how proper niche function ensures normal development and maintenance of the head skeleton.

Project Aims

“This proposal aims to characterize a novel population of cranial neural crest cells in the vertebrate face and describe their function as a niche supporting the skeletal stem cells.”

Making ab initio modelling possible for disordered molecular semi-conductive materials

Ing. Ctirad Červinka, Ph. D. | Vysoká škola chemicko-technologická v Praze, Fakulta chemicko-inženýrská

Abstract

“This proposal aims at development of novel ab initio simulation tools for treatment of amorphous and crystalline organic semiconductors. My research background enables me to target an unprecedented sub-chemical accuracy of predictions of structural properties and phase transitions. Exploitation of fragment-based ab initio Monte Carlo and quasi-harmonic models grants a sound physical consistency, minimizing any empiric inputs. I will address extending the applicability of the developed methodology to bulk phase of large molecules, typical for organic semiconductors. These compounds nicely illustrate the applicability and accuracy limits of the state-of-the-art ab initio modelling of molecular materials concerning molecular size, specific interactions, importance of the amorphous state, and dependence of the charge-carrier mobility on subtle variations of the structure. Proposed research will enable to accurately predict melting and vitrification points, polymorphism, crystallization driving force or conductivity of cutting-edge materials with optoelectronic relevance.”

Project Aims

Development of ab initio simulation tools to predict structure, phase behavior and chargé transfer of amorphous and crystalline organic semiconductors with an unprecedented subchemical accuracy, being applicable also for large molecules typical for real organic semiconductors.

The dynamics of adolescents‘ attitudes toward outgroups

Mgr. Aleš Kudrnáč, Ph.D. | Sociologický ústav AV ČR, v.v.i.

Abstract

The challenges related to integration of foreigners are very important and timely in various
societies. Negative attitudes toward out-groups are associated with social problems, such as
racism, discrimination, social exclusion, violent crime and extremism. Czech Republic is
currently facing unprecedented influx of refugees from Ukraine and most of the Czech
adolescents will start sharing classrooms with foreigners for the first time in their life. The main aim of this project is to examine the effect of education and classroom environment on the development of attitudes toward out-groups with a 4-wave panel survey that will track
individuals during their high school education. Literature on the liberalizing effect of education distinguishes three causal mechanisms: cognitive sophistication, learning liberal values, and gaining psychological security. This project aims to test the mechanisms on panel data that will include critical thinking assessment, sociometric status, dynamics of social relationships in classrooms, learning content, methods, and teachers’ characteristics.

Project Aims

“This project aims to employ a 4-wave Czech high school panel survey to examine the longitudinal effect of education, classmates and teachers on the development of attitudes towards out-groups in adolescence.”

Unravelling climate impacts of atmospheric internal gravity waves.

RNDr. Petr Šácha, Ph.D. | Univerzita Karlova, Matematicko-fyzikální fakulta

Abstract

“This research proposal employs state-of-the-art high-resolution atmospheric datasets and cutting-edge theoretical methods for internal gravity wave (GW) detection and wave-mean flow interaction to revisit and advance our understanding of GW effects on atmospheric dynamics, composition and coupling across atmospheric layers. GWs exist on a variety of scales, but typically a significant portion of the GW spectrum remains unresolved in global weather prediction or climate models and the GW impacts need to be parameterized. Our knowledge on GW impacts ranging from regionality of precipitation to the evolution of the ozone layer has been so-far based on their predominantly parameterized effects. Analyzing the resolved GW effects will improve our understanding on the forcing of selected atmospheric phenomena, but will also put additional constraints on the current GW parameterizations by showing to what extent their effects (and our current understanding) are artificial. This will help us to modify GW parameterization schemes with an ultimate goal of improving future climate predictions.”

Project Aims

“Evaluation of the parameterized gravity waves (GWs)-resolved dynamics interaction in models based on GW resolving simulations. Revision of climate GW effects based on GW resolving simulations. Development of GW parameterizations without artificial effects on model dynamics and transport.”

Hybrid biocompatible nanocatalysts for extracellular bioorthogonal activation of prodrugs

doc. Mgr. Zbyněk Heger, Ph.D. | Mendelova univerzita v Brně, Agronomická fakulta

Abstract

Targeted therapy is the golden grail of contemporary cancer chemotherapy. Despite that, the
use of targeted therapies in clinical practice is impeded by several drawbacks including
inadequate pharmacokinetics and side toxicity. These limitations might be circumvented by
enhancement of selectivity and efficiency of therapeutic modalities. Therefore, we plan to
benefit from a concept of bioorthogonal chemistry to develop biocompatible ferritin-based
nanocatalysts for in situ extracellular liberation of cytotoxicity of non-toxic prodrugs. To achieve this, we plan four work-packages: i) engineering and production of recombinant ferritins for delivery of catalysts, ii) synthesis of catalysts for BOOM and IEDDA reactions and their encapsulation into ferritins, and synthesis of prodrugs, iii) investigation of reactivity of nanocatalysts in cell-free and cell culture conditions. and iv) examination of an anticancer
efficiency of bioorthogonal pairs in murine model. The proposed project will open up new
avenues for exploitation of novel hybrid nanocatalysts in precise anticancer therapy.

Project Aims

“The proposed project aims on a design and functional validation of novel biocompatible hybrid ferritin-based nanocatalysts for in situ extracellular activation of prodrugs towards development of a new generation of efficient anticancer therapeutic modalities.”

Atomic-scale control and visualization of charge delocalization in light-harvesting molecular nanomodels

Bruno de la Torre, Ph.D. | Univerzita Palackého v Olomouci, Český institut výzkumu a pokročilých technologií

Abstract

“Organic solar cells exhibit remarkable optoelectronic properties similarly to naturally occurring light-harvesting complexes in photosynthesis. However, comparatively with their inorganic counterparts, they yield relatively low efficiency due to their short exciton and charge diffusion length. The project aims to investigate fundamental laws governing charge mobility in lightharvesting molecular nanomodels. To this ambition, I propose to combine templated-assisted synthesis of molecular nanorings and cryogenic atomic-scale probe microscopies for probing the effects of molecular organization on electronic communication, with single-electron sensitivity and sub-angstrom resolution for a complete control of their coherently delocalization of charge. This combination will allow us to understand the relation between structure, aromaticity, and charge mobility for single macrocycle. The proposal entails transformative potential for the field of organic solar cells down to the nanoscale.”

Project Aims

“To combine template-assisted synthesis with atomic-scale scanning probe techniques to experimentally control and visualize charge delocalization in molecular nanorings. Such combination will provide fundamental insights into the charge transfer processes of organic solar cell nanomodels.”

High-strength and water-resistant MOC composites with secondary fillers: contribution of 2D carbon-based nanomaterials and their combinations

doc. Ing. Ondřej Jankovský, Ph.D. | Vysoká škola chemicko-technologická v Praze, Fakulta chemické technologie

Abstract

The processes involved in Portland cement (PC) production account for around 7% of global
CO2 emissions. Reactive magnesia-based cements have comparable properties to PC, but
much lower environmental impact. In particular, magnesium oxychloride cement (MOC)
composites, with their CO2-neutral footprint, could provide the basis for a novel route to
sustainable construction materials. However, there are challenges to be overcome, the main
one of which is the poor water resistance of MOC, which results in the rapid degradation of its mechanical properties. The novelty of our approach lies in incorporating combinations of 2D carbon-based nanomaterials and selected secondary waste fillers into the MOC matrix in order to obtain high-strength and water-resistant composites. Furthermore, the excellent recycling potential of these MOC composites will be exploited by the design of thermal and mechanical methods that deliver a zero-waste cradle-to-cradle lifecycle. While this project is high-risk, success will offer an entirely new route in the design of sustainable construction materials.

Project Aims

“The main aim of the project is to develop high-strength, water-resistant, CO2-neutral, and completely recyclable magnesium oxychloride cement composites with 2D carbon nanoadditives and secondary fillers as a new group of materials for Portland cement replacement. ”

Trajectories of genome evolution in convergent organisms

Aleš Buček | Česká zemědělská univerzita v Praze, Fakulta tropického zemědělství

Abstract

“Organisms often evolve similar adaptations to similar environments in the process of convergent evolution, indicating that the trajectory of phenotypic evolution is amenable to predictions. Whether the genomic trajectories of convergent organisms are parallel – and thus predictable in principle – is unclear due to the scarcity of genomic evidence from convergent organismal groups. To answer these questions, I will establish a model system consisting of rove beetles (Staphylinidae) and scuttle flies (Phoridae) that adapted more than twenty times repeatedly to live in symbiosis with termites. Using phylogenetics, comparative genomics, transcriptomics, and microtomographic reconstructions of phenotypes, I will infer the extent and the timescale at which parallel patterns of genome evolution accompany the evolution of convergent adaptations. The integrative analytical approach applied to a massively convergent model group of organisms will give me an unprecedented capacity to assess the repeatability of evolution.”

Project Aims

“1) Uncover the extent, time-scale, and hierarchical level of genome sequence evolution accompanying convergent phenotype adaptation to a symbiotic lifestyle.

2) Determine whether the genetic changes in convergently adapted organisms are repeatable”

Synthesis and Property Tuning of Layered Low-Dimensional Materials Beyond Graphene – Utilization in Fundamental Research of Heterogeneous Catalysts

Ing. Martin Veselý, Ph.D. | Vysoká škola chemicko-technologická v Praze, Fakulta chemické technologie

Abstract

Layered low-dimensional materials are auspicious for application in all areas of nanotechnology since properties of these materials depend on the degree of exfoliation. Also, catalysis seems to be an exciting application as a superior effect of a two-dimensional (2D) support on the activity of metal nanoparticles due to specific metal-support interactions. This project is focused on preparation and chemical modification of layered materials based on Si, Ge, and SixGe(1-x) mixtures. The aim is to prepare 2D hundreds-of-micron-sized sheets and nanometer-sized quantum dots (QDs) with high optical and chemical uniformity. Functionalization of the prepared uniform low-dimensional materials allows the application of these materials in fundamental research of phenomena typical for heterogeneous catalysis: I) Study of the exclusive effect of 2D support on the enhanced activity of metal nanoparticles and II) Assessment of accessibility and interconnectivity of pores space in conventional catalysts using 0D QDs with varying size as a pore space probe.

Project Aims

Synthesis and chemical modification of layered materials based on Si, Ge, and SixGe(1-x) mixtures 2. Assessment of chemical and optical uniformity 3. Platinum nanoparticle deposition on 2D material 4. Study of the metal-2D support interaction 5. Mass transport visualization in pore space

Strong electromagnetic pulses: their generation, characterization and control

Ing. Jakub Cikhardt, Ph.D. | České vysoké učení technické v Praze, Fakulta elektrotechnická

Abstract

During the interaction of a high-power laser beam with a target, extreme intense electromagnetic pulses (EMP) in the MHz-THz band reaching up to hundreds of kV/m are emitted. Notwithstanding that such effects have been observed in recent decades, the physical mechanisms of EMP production still are not satisfactorily explained. Moreover, the strong EMP causes significant interferences in signals and damages the diagnostic systems. On the terawatt and petawatt laser facilities, these problems are so important that the systematic research of EMP was included in the scientific program of world-class institutions e.g. the Rutherford Appleton Laboratory and ENEA Frascati. The EMP is the current topic also in the Czech Republic due to the commissioning of the ELI Beamlines laser facility where highrepetition laser systems operate with a rate of tens or hundreds of pulses per second. Therefore, in the frame of this project, we will perform a systematic characterization of the EMP for various parameters of the laser beam and target using a comprehensive system of EMP and plasma diagnostics.

Project Aims

The aim is to understand the processes responsible for the EMP emission, characterization of the EMP for various parameters of the laser and target, optimization of established diagnostics and development of new diagnostics methods, improve measures against EMP, an effort to find an application.

Animal migrations in a changing world – Movements for reproduction to higher latitudes: still advantageous strategy or maladaptive behaviour?

RNDr. Vojtěch Kubelka, Ph.D. | Jihočeská univerzita v Českých Budějovicích, Přírodovědecká fakulta

Abstract

“We focus on a pressing question in evolutionary ecology: Is migratory behaviour to breed at higher latitudes still advantageous? Despite the historic benefits of migration, currently numerous migratory animals experience higher predation, more parasites but lower food supply on their breeding grounds than in earlier decades, questioning migration profitability. To address this emerging issue, we propose a comprehensive investigation of migration profitability, combining experimental, observational and comparative approaches, novel technologies and robust independent datasets. We will study latitudinal gradients in predation,

parasites and food supply in relation to migration profitability and population dynamics, using shorebirds as an excellent model system at 16 established study sites across both hemispheres. We anticipate uncovering the ecological and demographic drivers of changing benefits for migratory behaviour. This project is significant by disentangling the impacts of climate change and human pressure on a globally important issue as well as helping practical conservation.”

Project Aims

We will: 1) quantify predation, parasites and food supply using the same protocols across latitudes; 2) track breeding productivity and migration routes of individual birds from different populations; 3) combine experimental, observational and comparative investigations of migration profitability.

Human-Machine Transactions: Behavioral Micro-foundations and Legal Implications

Sven Hoeppner, M.Sc., LL.M., Ph.D. | Univerzita Karlova, Právnická fakulta

Abstract

More and more aspects of daily life, generally, and of contractual relations, specifically, are (partly) governed by artificially intelligent machines. Though the technology is still in its infancy, prominent examples that suggest the need for regulation are already emerging. Regulation, however, also requires a deep understanding about whether humans interact with machines differently as compared to their interactions with other humans, and if so, how. Research on behavioral micro-foundations of these human-machine transactions is surprisingly scarce. The proposed research project will contribute to closing this gap by conducting a set of experiments specifically designed to reveal how human behavior adapts to the presence of machines in social dilemma situations and coordination problems. The results will be used to draw conclusions for legal reform and, more broadly, for implications for institutional design.

Project Aims

The main goal of the research project is to quantify how human behavior changes when artificially intelligent machines are involved in social dilemma situations and coordination problems. A subsequent goal is to draw policy implications to smooth the transition to machinedriven economies/societies.

Extremal and probabilistic combinatorics

Dr. Jan Volec | České vysoké učení technické v Praze, Fakulta jaderná a fyzikálně inženýrská

Abstract

This project will create novel mathematical methods that facilitate a better understanding of the properties of massive networks. Such networks appear in many real-life situations including links between Internet routers, user connections on social networks, or protein-to-protein interactions inside a molecule. Large networks are, however, also fundamental to many open problems in pure mathematics. In particular, they are a central object in extremal combinatorics. One of the key elements of this project focuses on providing new techniques of using a computer in order to find mathematical proofs. Another important aspect of the project revolves around randomness, which turns out to be extremely effective in various mathematical and computer science scenarios. In fact, for many problems involving decisions that were solved in this randomized way, we currently do not know anything that would perform even nearly as good as random choices do. In this project, we will study so-called pseudorandomness – a systematic way that aims at catching up with the randomness by being smart.

Project Aims

Find novel and extend current methods for analyzing massive combinatorial structures (such as large networks), and apply these methods to open problems in discrete mathematics. Investigate new ways of using computers to prove theorems in mathematics.

Changing Adaptive Strategies of Mobile Pastoralists in Mongolia: Dynamics in Community Histories and Movement Patterns Documented Through Oral Sources

Mgr. Ondřej Srba, Ph.D. | Masarykova univerzita, Filozofická fakulta

Abstract

The project aims to analyse internal changes in the Mongol-Turkic multi-ethnic contact areas of Mongolia to the identities of rural communities as expressed in the memories of belonging and orally transmitted awareness of local geography and in relation to the land use strategies of mobile pastoralists (evolvement of movement patterns). The project is based on the innovative connection of methods of oral history and research of the oral tradition as a source of history in addressing changing identities and adaptive strategies of marginalized communities, ongoing metamorphoses in unprofessional parts of oral heritage and land use evolvement, which is expected to provide important data for current environmental issues. Outputs of the project include digital databases a) of seasonal moves of mobile pastoralists during the last hundred years, and b) of the endangered oral tradition, and c) an analysis of the main research problems in a comparative monograph assessing the current state of the local history-related oral tradition oscillating between transmitted and constructed memories.

Project Aims

The aim is basic interdisciplinary research of oral history and oral tradition. Based on data collected within own fieldwork, the project will analyse non-invasive methods to understand the dynamics of changes in the movement patterns and community identities of endangered ethnic groups in Mongolia.

JUNIOR STAR 2022

4D plate - Spatiotemporal dynamics of cell plate development

Roman Pleskot, Ph.D. | Ústav experimentální botaniky AV ČR, v.v.i.

Abstract

Cell division is an essential process for any living cell on Earth. Cell division is finalized by cytokinesis, which results in two daughter cells. Plant cytokinesis is fundamentally different from that of animal and fungal cells. Plant cells evolved a unique membranous compartment, the cell plate. The cell plate grows in an inside-out manner by which it separates two daughter nuclei. In this highly multidisciplinary project, we aim to unravel unprecedented details of cell plate development, which remain unknown. We will use cell plate development as a time axis to study the dynamic interplay between proteins, lipids and cell wall polysaccharides. We will use continuously dividing synchronized Arabidopsis cell culture. We will employ chemical crosslinking mass spectrometry, metabolic labelling and state-of-the-art fluorescence microscopy. We aim to solve the molecular architecture of the enigmatic callose synthase complex using an integrative structural approach. Our unique methodology will identify new players in plant cytokinesis and create a 4D map of cell plate development.

Aims

The overall aim of this research project is to describe the spatiotemporal dynamics of cell plate development at the level of individual proteins and construct a 4D map of cell plate development.

Investigation of the Terrestrial HydrologicAl Cycle Acceleration (ITHACA)

Ioannis Markonis | Česká zemědělská univerzita v Praze - Fakulta životního prostředí

Abstract

The changes in terrestrial hydrological cycle directly influence water availability. It is expected that global warming will accelerate the hydrological cycle, resulting to new challenges for human societies. In this project we will analyze and model the variability of the terrestrial hydrological cycle in a combination of multi-scale data-driven methods with process-based climate and hydrological modeling. Our aim is to assess the present and future acceleration rate and understand how it is connected to changes in water availability. We will combine paleoclimatic data and contemporary observations, develop new stochastic methods, and utilize the recent advances in process attribution to understand how water availability responds to the hydroclimatic fluctuations.

Aims

“1) Assessment of the current terrestrial water cycle acceleration and its statistical significance.
2) Development of a multi-scale stochastic model for hydroclimatic variability.
3) Attribution of changes in water availability to the processes affected by the acceleration of the hydrological cycle.”

Data, Algorithms, Power: Economic Theories of the Information Society

Ole Jann, PhD | Národohospodářský ústav AV ČR, v.v.i.

Abstract

This project is about developing insights in the most active research area in economic theory – information economics – to help understand the informational transformation that many sectors of the economy and society are undergoing. It will depart from previous research in this field by focusing on the interplay of information and power – such as in questions of privacy, of the ownership of data and algorithms, and the centralization or decentralization of data storage and processing. This includes understanding: (i) How the possibilities of the Internet can be harnessed for efficiency-enhancing information revelation and exchange, (ii) how the mandatory disclosure (or non-disclosure) of information shapes economic and societal outcomes, (iii) how we can most usefully model the economic value of data and algorithms and their ownership, and (iv) how the centralization of data storage and processing interacts with mechanisms of social and economic control.

Aims

To gain insights in the economic theory of information that can help harness the possibilities of the Internet for society and solve the problems it creates. To establish CERGE-EI and the Czech Republic as an international center of excellence and focal point for this research.

Cell*: a web platform for visualization, modelling and dynamics of organnel- and cell-sized structures

RNDr. David Sehnal, Ph.D. | Masarykova univerzita - Přírodovědecká fakulta

Abstract

Biomacromolecular structural data is a highly valuable research resource. Reconstruction of whole organelles and cells is the cutting-edge research in this area, but a community strongly lacks services for their efficient visualization and modelling. In this project, we will develop a Cell* web platform, which will solve this gap. Moreover, Cell* will show the structures in the context of experimental data and biological and chemical properties. It will provide an insight into organelle and cell biology through the integration of structural models. Cell* will be a breakthrough solution also due to its capabilities to visualize dynamics of cell-sized structures and perform their animations. In this project, I will use my experience with the development of LiteMol and Mol* web tools for the visualization of large biomacromolecular assemblies and complexes. LiteMol was published in Nature Methods and it was the main viewer in PDBe. LiteMol was replaced by Mol*, which is now a main structure visualization tool in PDBe and RCSB PDB. I have been a lead developer of both LiteMol and Mol*.

Aims

Develop a Cell* web platform for visualization, modelling, and dynamics of organelle- and cellsized structures. Cell* will also enable visualization of experimental data and biological and chemical properties (annotations).

Dynamics of the periglacial environment in the Antarctic Peninsula region under ongoing climate change

Mgr. Filip Hrbáček, Ph.D. | Masarykova univerzita - Přírodovědecká fakulta

Abstract

The active layer and permafrost are the building elements of the periglacial environment in polar regions. Their parameters like temperature, moisture, or active layer thickness respond very sensitively to climate oscillation, making them valuable indicators of the effect of climate change on terrestrial ecosystems in the polar environments. Therefore, a long-term monitoring of the active layer thickness and permafrost temperature belongs to principal questions of Antarctic research. The proposed project will assess the current state and evolution of periglacial dynamics in the ice-free areas of the Antarctic Peninsula. Extensive fieldwork, laboratory and analytical methods will provide a detailed evaluation of the ground physical properties (moisture, texture, thermal properties), ground temperature and active layer thickness. Available data will allow us to reconstruct the past state and predict the possible evolution of permafrost temperature and active layer thickness in the period 1950-2100 and determine the effect of ongoing climate change on these parameters.

Aims

The project aims to assess the dynamics of the periglacial environment at present, reconstruct its state in the past and predict its development in the future until 2100 in the Antarctic Peninsula region using monitoring of soil temperature variability, moisture and the active layer thickness.

Functional Genomics and Symbio-Genomics in Ticks

Jan Perner, Ph.D. | Biologické centrum AV ČR, v.v.i.

Abstract

Inter-species co-existence, between a microbe and its host, underpins much of the complexity of the natural world. Ticks, blood-feeding Arachnids, harbour a bacterial ally, residing within mitochondria of several tissues. Until now, ticks and symbionts have been rarely studied together as an interacting system. The functional context of this alliance is thus largely unexplored. This proposal aims to uncover the molecular interface of “species bridging”, i.e. integration of the symbiont metabolism in tick physiology. Using a holistic approach that blends state-of-the-art microscopy, multi-omics data, and RNAi with a newly developed comparative model of symbiont-free ticks, we propose to do an innovative structural and functional exploration into the interaction landscape of the bacterium and its host. This project will also provide an in-depth insight into the tolerance and resistance strategies of ticks against viruses and bacteria, allowing the multi-species co-existence.

Aims

“1) characterisation of symbiont-tick molecular and cellular interactions
2) identification of haem- and cholesterol-distribution network in ticks
3) development of Crispr-Cas9 delivery into ovaries using tick vitellogenin fragments”

High velocity impact dynamics with fast and flash X-ray radiography

Ing. Tomáš Fíla, Ph.D. | České vysoké učení technické v Praze - Fakulta dopravní

Abstract

In the project, the most recent methods of experimental dynamics will be combined with the state-of-the-art lab-based in-situ X-ray imaging to get an unprecedented insight into deformation behavior of complex materials at intermediate and high strain rates. A flash X-ray system and high power X-ray tube will be employed together with high speed imaging equipment (high speed cameras and detectors) to investigate the internal processes in the materials during dynamic loading. Significant effort will be aimed at novel cellular and layered materials filled with strain rate sensitive fillings while the effects of shear thickening fluids and fluids with nanoparticle inclusions will be investigated in particular. In this field, the combination of X-ray imaging with instrumented dynamic experiments will reveal fundamental aspects of the deformation response of the materials and their failure mechanisms. The results will be used to formulate and validate theoretical assumptions and models with a special aim on the internal processes that can be conventionally inspected only indirectly.

Aims

The main goal of the project is to reveal the crucial aspects of the deformation response in complex materials at intermediate and high strain rates through a combination of novel experimental methods and techniques in impact dynamics with state-of-the-art lab-based in-situ X-ray imaging.

Reaction networks at phase interfaces for dynamic self-assembly

Ing. Petr Kovaříček, Ph.D. | Vysoká škola chemicko-technologická v Praze - Fakulta chemické technologie

Abstract

This project will investigate reaction networks at phase interfaces and develop the concepts of molecular recognition, semiconductor electric polarization and molecular epitaxy towards enantioselective catalysis, photoredox catalysis and planar heterojunctions by doubly dynamic self-assembly. Phase interfaces are omnipresent and always dictate self-organization of species in their proximity. Here, I propose to take advantage of the interphase energy together with stimuli-responsive reaction networks to achieve a breakthrough concept: functionalitydriven dynamic self-assembly at phase interfaces. We will study how the molecules “feel” the presence of the phase interphase, the energy/charge transfer between them and the other phase and how they assemble to form a phase on their own. We will demonstrate the potential of this approach by achieving enantioselectivity in generally achiral transformations, electrochemically promoted reactions without applied electric potential and total self-assembly of planar heterojunctions from a single reaction network.

Aims

Develop methodology for stimuli and composition instructed self-assembly on surfaces and phase interfaces driven by functionality of the assembly, exploit the findings for heterogeneous organocatalysis, photoredox catalysis and optoelectronic devices (e.g. photovoltaics, diodes).

Deciphering Origins of DNA replication in genome integrity

Mgr. Hana Sedláčková, Ph.D. | Biofyzikální ústav AV ČR, v.v.i.

Abstract

DNA replication is fundamental to cell proliferation, but its malfunctions can cause genome instability and trigger diseases including cancer. DNA replication initiates at replication origins by the formation of pre-replicative complexes (pre-RCs). The pre-RCs are essential drivers of replication forks; however, the mechanism(s) of pre-RCs formation and their precise roles in safeguarding genome integrity is poorly understood. I have recently discovered a molecular pathway that couples pre-RC assembly with proper DNA replication dynamics. Building on these findings, I propose to address here a central hypothesis that ‘the molecular homeostasis of replication origins is a key component of error-free DNA replication’. Therefore, using mammalian cell culture models coupled to state-of-the-art set of coherent cell biology, genomics and proteomics-based experiments, I will investigate the maintenance, regulation, and novel functions of replication origins. These experiments will illuminate the fundaments of DNA replication and reveal mechanisms counteracting genome instability in disease.

Aims

“1) The role of pre-RCs in maintenance of replication origins in ensuing cellular generations
2) The determinants of distinct biochemical properties of parental and nascent DNA replication origins
3) The contribution of origin licensing pathways to the polyploidization during cardiomyocytes maturation”

Computer Aided Desing of Templated Assembling, Replication and Synthesis on Ionic Substrates

Ing Prokop Hapala, PhD | Fyzikální ústav AV ČR, v.v.i.

Abstract

The main obstacle which hinders humanity from building sophisticated nanomachines, such as molecular computers, is the lack of scaleable nanofabrication methods allowing precise assembly of many different molecular components. Living nature solves this problem using self-assembling and template-assisted synthesis driven by biopolymers such as DNA, RNA and proteins. In this project, I will develop methods for scalable bottom-up fabrication of molecular circuits on ionic substates in ultra high vacuum (UHV) inspired by these biological principles. This will be achieved by computational survey of templated synthesis pathways, and computer aided design of novel polymers (inspired by DNA) providing templates for the assembling and synthesis. To facilitate the design, I will create a multi-scale simulation software dedicated to exploration of self-assembling and template-synthesis pathways on ionic substrates. Such software will benefit the whole emerging field of on-surface chemistry, which currently lacks specialized tools comparable to those used for molecular docking in biochemistry.

Aims

“1) Develop specialized software for computational survey of templated synthesis processes on ionic substrate in vacuum
2) Design a polymer template applicable for driving templated synthesis and self-assembling of molecular circuits on ionic substrate”

Multipole antiferromagnets: New interlinked chapters in crystallography, band structure, and electronics

Dr. Dominik Kriegner | Fyzikální ústav AV ČR, v.v.i.

Abstract

The aim of our materials research project is to experimentally establish interlinked new paradigms in crystallography, band structure, and electronics in multipole collinear antiferromagnets. Using diffraction and microscopy measurements up to the ultimate atomic resolution, we will demonstrate unique crystallography signatures of the multipole antiferromagnets which are beyond the established nomenclature of magnetic symmetry groups. They result in a fundamentally new form of a wavevector-dependent spin-splitting, which has been omitted in the band theory of solids, and which we will elucidate by spectroscopy measurements and ab initio calculations. We will demonstrate that these spin-split bands in the dipole-free antiferromagnets generate conserved highly-polarized spin currents, which are analogous to spin currents driving reading and writing functionalities in ferromagnetic memory devices. Beyond spin-electronics, we envisage impact of the project on fields ranging from macroscopic quantum and topological phases to dissipationless microelectronics.

Aims

We will synthesize thin films of multipole collinear antiferromagnets, and by their experimental research establish new interlinked chapters in crystallography, band structure, and electronics, with the potential to outgrow science and technology fields based on traditional dipole ferromagnets.

JUNIOR STAR 2021

Advanced structures for thermal insulation in extreme conditions

Ing. Mohanapriya Venkataraman, Ph.D. | Technická univerzita v Liberci - Fakulta textilní

Abstract

The core of the project is to is to study the thermal behavior of high-performance textiles, describe the mechanism of heat transfer in fibrous structures under extreme conditions and developing a general, scientifically supported, methodology of constructing thermal insulation layers. To determine the heat resistance of the fabric in cold conditions in accordance with standards, the losses of heat conduction are negligible and convection and radiation have to be considered. Conventional devices for evaluation of thermal resistance of clothing are based on the measurement of thermal conductivity under standard climatic conditions, which is not useful for extreme conditions. For these reasons, the project also includes the development of the measuring tunnel, which can be used to measure the total heat loss of textiles below freezing temperatures. In construction of the new heat insulating layers, the materials which reduce heat transport by radiation will also be observed. A prediction system for thermal insulation properties of the textile layers will be created.

Aims

The aims of project are: solving of heat transfer problems in textiles; creation of system for construction of thermal insulation layers; development of devices for thermal characterization; advanced materials for effective thermal insulation; creation of thermal comfort prediction system.

The Lombard population in Moravia. Interdiciplinary research into Migration Period necropolises.

Mgr. Zuzana Loskotová, Ph.D. | Archeologický ústav AV ČR, Brno, v. v. i.

Abstract

The notion that groups of Elbe-German tribes were concentrated in a region north of the Danube has been contested by the discovery of vast necropolises, the study of which has great potential to shed light on cultural-historical developments in the 6th century. The subject of this project is interdisciplinary research into this population. The drawing of archaeological and historical conclusions will be preceded by non-destructive prospection, excavation, data heuristics and analytical evaluation using geographic information systems; a wide spectrum of natural-science analyses – standard anthropological analysis including paleopathology and carbon and nitrogen isotope analysis – will be applied to ascertain the population’s diet; strontium isotopes will be analysed to exactly prove migration of groups of population. At the same time, international collaboration, mainly in the area of genetic research, will take place. Regular presentation at international conferences is planned. The outputs will include three studies and a final summarising monograph in English by the proposer.

Aims

The aim of this project is to ascertain new crucial findings regarding the population and culturalhistorical development in 6th-century Moravia by means of a comprehensive assessment, employing the natural sciences to the maximum extent, of relevant co-called Lombard necropolises.

Learning Universal Visual Representation with Limited Supervision

Georgios Tolias | České vysoké učení technické v Praze - Fakulta elektrotechnická

Abstract

Machine-extracted representation of visual content in images and videos is used in computer vision to help estimating human-perceived visual similarity. Visual representation is important in a variety of domains and needs to capture multiple notions of visual similarity, each relying on different perceptual factors. These factors are typically captured by separate models, which results in systems that use model ensembles and are demanding in terms of processing power, processing time, and storage cost. One goal of the project is to propose new ways for designing and learning universal multi-purpose models to extract visual representation that is appropriate for a variety of cases. Representation models will be trained with deep learning, which is typically demanding in terms of labeled training data, especially if multiple purposes are targeted. Therefore, another goal of the project is to reduce the need for supervision by employing large collections of unlabeled examples and exploiting the structure of the representation space in semi-supervised and active learning.

Aims

“1) learn universal representation models that deliver high performance in a range of tasks and domains
2) learn representations that enable new ways of exploring large collections of visual content 3) perform deep representation learning with fewer labeled and more unlabeled data”

Lewis acids and frustrated Lewis pairs for reductive coupling reactions of carbon dioxide with amines

Martin Hulla, Ph.D. | Univerzita Karlova - Přírodovědecká fakulta

Abstract

Chemical industry heavily relies on petrochemical feedstock for raw materials. This puts strain on our natural resources and damages the environment. The use of carbon dioxide (CO2) in chemical synthesis can decrease our overreliance on petrochemicals, mitigate their devastating effects on the environment and help in the development of greener chemistry and circular economy. This project aims at the development of frustrated Lewis pair catalysts for reductive coupling reactions of CO2 with amines. Herein, CO2 replaces the industrially used petrochemical-based and toxic reagents such as carbon monoxide, formaldehyde, methanol and methyl iodide. Hydrogenation catalysts based on frustrated Lewis pairs are proposed as a bridge to main group hydrides, which recently proved as efficient reducing agents for the proposed reactions. Special attention will be given to the required properties of frustrated Lewis pairs for applications in CO2 reduction reactions and the mechanisms of the reactions.

Aims

The aim of the project is to develop and understand reductive coupling reactions of carbon dioxide with amines, which utilize dihydrogen as the reducing agent and frustrated Lewis pairs as hydrogenation catalysts.

Magnetoelastic Materials beyond Born-Oppenheimer Approximation

RNDr. Petr Čermák, Ph.D. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

The Born–Oppenheimer approximation simplified condensed matter physics by separating the motion of atomic nuclei and much lighter electrons. The violation of this concept was considered rare and lead to emergent functionalities such as multiferroicity, polar order and superconductivity. In a recent study, we have demonstrated an abundance of magnetoelastic (ME) interactions in common intermetallic compounds, revealing that interactions between nuclei and electrons are far more common. We believe that hidden ME modes are responsible for many unresolved inconsistencies across condensed matter physics. A detailed description of these phenomena will lead to rapid scientific progress. The project seeks to experimentally exploit ME modes in heavy fermion systems and iron pnictides, using inelastic neutron scattering (INS), which is able to uniquely unveil ME modes. Some compounds form only tiny crystals, too small for conventional INS. We will develop a bespoke device for their precise co-alignment, which will have an immense impact on neutron scattering beyond the scope of the project.

Aims

The project aims to show, that ME effects are a general property of condensed matter and the Born-Oppenheimer approximation is surpassed far more often than generally thought. To reach this goal we will build a unique device allowing neutron measurements on samples too small to measure before.

Hydrodynamic interactions of planets with protoplanetary disks and the origin of close-in exoplanetary systems

RNDr. Ondřej Chrenko, Ph.D. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

Close-in extrasolar systems of low-mass planets (super-Earths and mini-Neptunes) represent a substantial fraction of the exoplanet population discovered by recent astronomical observations. Our project aims to study hydrodynamic interactions between low-mass planets and their natal protoplanetary disk in order to constrain the processes which contributed to formation of closein exoplanets. First, we plan to analyze migration of low-mass planets towards the inner disk regions. We will explore the influence of gravitational torques induced by pebble accretion, gravity of a pebble disk, and pebble concentrations at pressure maxima. Second, we will focus on planet-disk interactions at the inner disk rim which is sculpted by stellar irradiation and viscosity transitions. Understanding the evolutionary phase at the inner disk rim represents a critical step in understanding the origin of close-in exoplanets. Our results will be obtained by means of 3D and 2D radiation hydrodynamic simulations and they will be confronted with existing theories of planet formation and observations

Aims

We will study interactions of planets and protoplanetary disks by means of numerical hydrodynamic simulations. The aim of the project is to improve the understanding of processes which led to the formation of close-in low-mass extrasolar planets.

Logical Structure of Information Channels

Mgr. Vít Punčochář, Ph.D. | Filosofický ústav AV ČR, v.v.i.

Abstract

The concept of information is ubiquitous in current logic. However, the informational interpretation of various logical approaches is rather scattered in the logical literature and a unification is needed. The main goal of this project is to develop unifying philosophical foundation for the logical concept of information based on Barwise’s theory of information channels. Special attention will be paid to the application of this general approach to two more specific areas of logical inquiry: fuzzy logic of graded information and epistemic logic of knowledge and belief. For these two distinct fields of logic a common semantic basis will be provided that will make possible transfer of results from one area into the other.

Aims

We will develop unifying philosophical foundation for the logical concept of information based on Barwise’s theory of information channels, and apply this general approach to two more specific areas of logical inquiry: fuzzy logic of graded information and epistemic logic.

The role of Aire-expressing ILC3 like cells in the regulation of Th17 response

Jan Dobeš | Univerzita Karlova - Přírodovědecká fakulta

Abstract

Autoimmune regulator (Aire) plays an essential role in the induction of self-tolerant T cells during their development in the thymus by generating a mirror image of the body’s own peripheral antigen repertoire within the medullary thymic epithelial cells (mTECs). Subsequent presentation of these self-antigens by mTECs is essential for deletion of self-reactive T-cell clones and prevention of autoimmunity. Interestingly, most AIRE-mutation bearing patients suffer from candidiasis, which represents one of the most common and earliest manifestations of this mutation. Recently, we were able to show that Aire is expressed in a rare extrathymic population of MHCII positive type-3 innate lymphoid cells (ILC3) and that these Aire-ILC3 like cells regulate the Th17 response to C. albicans. This project is focused on delineating the mechanisms imposed by Aire-ILC3 like cells to regulate the Th17 response in response to extracellular pathogens or during autoimmune reaction. Together, the proposed research project should help our understanding of the Aire role in regulation of Th17 response.

Aims

This project is focused on delineating the molecular mechanisms imposed by Aire-ILC3 like cells to regulate the Th17 response. Moreover, we would like to explore the role of Aire-ILC3 like cells in regulation of Th17 response to extracellular pathogens or during Th17-dependend autoimmune reaction

Effect of global changes on fungal biogeography and ecosystem functioning

Mgr. Petr Kohout, Ph.D. | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

Fungi are eukaryotic microorganisms that play fundamental roles in regulating key ecosystem processes. As major decomposers of organic matter as well as mutualists or pathogens of plants, soil fungi significantly influence plant primary production, carbon sequestration, and act as crucial regulators of the soil carbon balance, which is one of the greatest topics of human security. Although the wealth of our civilization profoundly depends on globalization and free market, there is also another side to this coin, represented by the global changes of environment and easier spread of pathogens of humans, animals and plants. Climate change and world biota globalization constitute most important challenges which affect the functioning of natural as well as agricultural ecosystems. Understanding the consequences of inevitable global changes on biota and ecosystem functioning have to be primary interest of current biological research.

Aims

In this project I aim to determine the effects of climate change and biological invasions on worldwide distribution of fungal species. I also aim to determine how these changes in fungal species distribution, caused by climate change or biological invasions, will affect ecosystem processes.

Specific bacterial strains and bacteria-derived postbiotics for amelioration of long-term sequelae of malnutrition

Mgr. Martin Schwarzer, Ph.D. | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

During the juvenile period the growth is determined by the nutrient intake and by production of growth hormones. Recently, we have identified intestinal bacteria as a key player in growth with specific Lactobacillus plantarum (Lp) strain being sufficient to reproduce the effect of the microbiota in monoassociated ex-germ-free mice. Our unpublished data show that Lp retains its growth promoting capacity after treatment of conventional mice and that this effect is Lp strain specific and independent of the Lp viability status. By using multilateral approach we will explore Lp- and Bifidobacteria-derived postbiotics and host receptors that are engaged in the molecular cross-talk resulting in the enhanced growth during chronic undernutrition. Further, we will characterize the impact of the protein undernutrition on the host immune system and its changes after treatment with selected postbiotics. Results of this project will shed light on the bacteria-host crosstalk during growth and pave way to amelioration of the long-term sequelae of undernutrition in children.

Aims

By using multilateral approach, this project aims at identification of lactobacillus- and bifidobacteria-derived postbiotics and host receptors that are engaged in the molecular crosstalk resulting in the enhanced host systemic growth during chronic undernutrition.

Response of microbial communities to changing climate in Arctic tundra soils

RNDr. Jana Voříšková, Ph.D. | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

Climate models predict substantial changes in temperature and precipitation patterns across the Arctic regions in future decades. Microbes are known to play key roles in determining the stability of soil carbon (C) and its possible release into the atmosphere as carbon dioxide and methane. Carbon-rich Arctic soil ecosystems are particularly vulnerable to C losses due to warming and subsequent ecosystem disturbances as wildfires. On the other hand, the release of C from soil to the atmosphere could be mitigated due to increased plant growth or reduced due to drought. Here we propose to characterize the response of soil microbes to the conditions caused by future climate change (increased winter precipitation, summer warming and wildfires); and to identify microbial processes affecting shrub expansion in Greenland. By combining soil, plant and microbial C pools and fluxes at the sites, the study will help in understanding whether Arctic soils will become C sink or source under future climate change.

Aims

The aim of the project is to comprehensively explore the response of soil microbial communities to the conditions caused by future climate change, specifically increased winter precipitation, summer warming and wildfire disturbance; and identify microbial drivers of shrub expansion in Arctic tundra.

Phosphonate biosynthesis and degradation – a novel mitochondrial pathway involved in global phosphorus turnover?

Jan Janouškovec | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

Phosphorus is a core, limiting macronutrient, but its global turnover is still little understood. For example, one quarter of all phosphorus in the ocean occurs as phosphonates, whose metabolism has only been thoroughly studied in bacteria. We identified unexpectedly widespread phosphonate enzymes in eukaryotic genomes and predict that they comprise a novel mitochondrial pathway. To test this, we will computationally map phosphonate enzyme distribution, expression, and cellular localization in all eukaryotes, then localize them subcellularly in two distantly related protists, Perkinsus and Capsaspora. We will next use labeled precursors to track phosphonate metabolism in both species, and measure the ability of a wide range of algae to utilize phosphonate substrates for growth. We will also reconstruct the evolutionary history of all phosphonate enzymes and how they relate to eukaryogenesis. Our findings will illuminate mitochondrial metabolism, eukaryotic evolution, and phosphorus turnover in cells and ecosystems, and identify new enzymes of potential commercial interest.

Aims

To illuminate the global phosphorus cycle, we will characterize the distribution, functionality, localization and evolution of phosphonate metabolism across the diversity of eukaryotes, a candidate novel and widespread mitochondrial pathway fundamental to phosphorus turnover in cells and ecosystems.

Optimal Electromagnetic Design Based on Exact Reanalysis

Ing. Miloslav Čapek, Ph.D. | České vysoké učení technické v Praze - Fakulta elektrotechnická

Abstract

The project aims to eliminate the gap between fundamental bounds and actual performance of inverse-designed devices in electromagnetism by revolutionizing approaches to design synthesis. A combination of local gradients of a performance metric over a fixed discretized model and the ability to avoid local minima are the main tools required to achieve this goal. Employing the exact reanalysis allows for unprecedented speed in evaluating full-wave models. A class of geometry- and topology-based operators is proposed to deal with regularity, conformity, and similarity of designs to act as constraints to remove highly irregular shapes, increase tolerance against manufacturing imperfections, and offer a full set of feasible designs. The proposed synthesis method is general and discoveries of structures with unique shapes and properties is expected from low to ultra-high frequencies. The project assumes intense collaboration with world-leading authorities and a multidisciplinary focus having the potential to open a new field of research.

Aims

O1: To formulate and solve the problem of shape synthesis using the exact reanalysis technique. O2: To develop geometry- and topology-based operators to regularize shapes. O3: To implement the theoretical findings of O1-O2 as a software package. O4: To experimentally verify O1-O3 on prototypes.

Transformation induced plasticity (TRIP) in titanium alloys and high entropy alloys

RNDr. PhDr. Josef Stráský, Ph.D. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

This junior project aims on the design and manufacturing of a new class of interstitial Ti alloys and refractory metals high entropy alloys (HEAs) exhibiting the transformation induced plasticity (TRIP) effect. To achieve the TRIP effect in Ti alloys with increased content of interstitial oxygen (i.e. increased strength) and in HEAs, the composition must be carefully tuned with respect to the stability of bcc phase. Main applicant will employ his experiences with developing new Ti alloys and the fact that metallurgy of bcc HEAs is strikingly similar to the metallurgy of bcc Ti alloys. Manufactured materials will be thoroughly characterized by a wide variety of experimental techniques including scanning and transmission electron microscopy, x-ray, electron and neutron diffraction. These results will be correlated with mechanical properties determined by tensile tests complemented by digital image correlation. The effect of composition variations on the TRIP effect will be assessed to obtain the material with the best combination of strength and ductility.

Aims

The aim of the project is to design, to manufacture and to characterize interstitial Ti alloys, high entropy alloys (HEAs) and interstitial HEAs exhibiting the TRIP effect and consequently both the high strength and ductility.

Nanoscale magnifiers: sub-diffraction manipulation of light by plasmons

Ing. Vladimíra Petráková, Ph.D. | Ústav fyzikální chemie J. Heyrovského AV ČR, v.v.i.

Abstract

This project will develop a new method for spatial manipulation of light at the nanoscale by assembly of plasmonic nanostructures. I propose to use this method to advance visualization of densely packed biomolecules and their dynamics. Metal nanostructures are capable of massive enhancements of optical response, which arise from collective electromagnetic resonances called plasmons. Here, I propose a radically new idea of understanding plasmonic nanoparticles as nanoscale spatial manipulators for light emitting fluorophores, opening a new dimension of diverse applications. We will use single molecule localization microscopy, DNA self-assembly, and machine learning to describe and reconstruct sub-diffraction limited shifts in the projection of plasmon-coupled fluorophores and determine how to control them by altering the enhancement mechanism, fluorophore-plasmon distance, and their dynamics. The experimental systems developed in this project will bring new routes to answering fundamental questions in plasmonic enhancement well beyond the scope of this project.

Aims

To alternate the enhancement mechanism of plasmon-coupled fluorophore. To control the shift in the projected position of plasmon coupled fluorophore by enhancement mechanism. To determine the distance-dependence of the fluorophore projection. To construct dynamic plasmonic system.

Kinases in endocytic membrane trafficking machinery : Key targets for therapeutic drug development

Ing. Zuzana Kadlecova, Ph.D. | Masarykova univerzita - Lékařská fakulta

Abstract

My research focuses on the regulation of protein trafficking at the cell surface by a highly dynamic process – endocytosis. This process determines the composition of the cellular plasma membrane and it is a major pathway for viral and pathogen entry, including Ebola and Coronovirus. The dysfunction of endocytosis is also a causal factor behind a number of human genetic diseases, and its dysregulation contributes to wide range of pathologies, including neuropathic pain. Despite its critical importance, surprisingly little is known about how it is regulated. A major regulation point is the dynamic phosphorylation of endocytic components by kinases. However, it is poorly understood which kinases (and phosphatases) control endocytosis even though they represent targets for disease-modifying therapies. My vision is to understand the regulatory role that protein kinases have in membrane-trafficking. My focus is on the Numb-Associated Kinase family (NAK) and their role in pain sensing.

Aims

“I seek to deliver a comprehensive, mechanistic model of the functioning of Numb-associated kinases (NAKs). Objective
1) Elucidating AAK1 and BMP2K related pathways,
2) Elucidating mechanisms of NAK regulation and
3) Determining the consequences of NAK deregulation for the plasma membrane proteome.”

Alchemies of Scent. Reconstructing the Practices of Ancient Greco-Egyptian Perfumery: An Experimental Approach to the History of Science

Sean Coughlin | Filosofický ústav AV ČR, v.v.i.

Abstract

Alchemies of Scent investigates how the quest to extract, concentrate, compound and preserve the essences of plants influenced natural philosophy, medicine and culture in the ancient world. It focuses on the encounter of ancient Greek philosophy with the technologies of Egyptian perfumery from the time of Alexander the Great to Cleopatra VII (fourth–first centuries BCE). Using experimental replications of Greco-Egyptian recipes, it reconstructs the practices of this ancestor to modern chemistry and studies the ways these practices were understood. It will produce a lexicon of Egyptian, Greek, and Latin perfumery; a manual of recipes and procedures; three monographic studies on perfume making in the context of the history of science and culture; and it will encourage citizen science and education through exciting social media content

Aims

“1. Produce a lexicon of ancient Egyptian–Greek–Latin perfumery
2. Replicate ancient Greco-Egyptian perfume-making methods
3. Study perfumery in ancient Egyptian and Greek science, medicine, and literary and material culture
4. Encourage citizen science and education through public engagement”

Molecular mechanisms of axon guidance

Daniel Rozbeský | Univerzita Karlova - Přírodovědecká fakulta

Abstract

The overarching aim of this proposal is to understand molecular mechanisms underlying semaphorin-plexin signalling. Semaphorin ligands and their plexin receptors are one of the classical cell guidance factors that play essential roles in cell processes requiring discrete changes in the cytoskeleton. Although the field has made enormous advances in understanding semaphorin function at the level of genetic and cellular experiments, our knowledge of the molecular-level mechanisms of semaphorin signalling is still lacking. My laboratory will address three fundamental questions: (1) How do proteoglycans modulate the axon navigation towards their target? (2) How does OTK co-receptor control semaphorin-plexin signalling? (3) How does a signal from outside the cell pass to cytoplasmic plexin domain? To address these challenges, we will use a hybrid approach integrating X-ray crystallography with cryo-electron microscopy and tomography. This approach will be further combined with biophysical and cellular experiments in neurons and transgenic flies.

Aims

“1. Dissect molecular mechanisms of proteoglycan-based modulation of semaphorin function 2. Elucidate the interplay OTK co-receptor and semaphorin-plexin signalling
3. Explore the molecular mechanisms through which the extracellular and cytoplasmic segments of plexins communicate”

Illuminating the interactions between nitrification and methane oxidation and the ensuing ecological impacts

Dr Anne Daebeler | Biologické centrum AV ČR, v.v.i.

Abstract

Nitrifiers and methanotrophs are microbial guilds responsible for aerobic transformation of reactive nitrogen and oxidation of methane, respectively. Both processes are fundamental ecosystem functions linked to nutrient cycling and global change. We hypothesize that interactions between these two guilds substantially contribute to the modulation of process rates. However, such interactions have hardly been investigated. The proposed line of research will expose the cause and nature of interactions between nitrifiers and methanotrophs and quantify their ecological impact. The project will employ a unique combination of multidisciplinary techniques, i.e. next generation sequencing, stable isotope incubations with integrated approaches of metagenomics and metatranscriptomics, single cell sorting, and metaproteomics with synthetic microbial consortia. Collectively, these approaches are poised to gather a deep understanding of the links between carbon and nitrogen cycling to eventually be able to predict and mitigate climate change and protect Earths ecosystems.

Aims

The project will resolve interactions between nitrifiers and methane oxidizers, quantify their ecological implications, and develop models for predictions. It will fill knowledge gaps on microbial ecogenomics and -physiology, establish a new stable isotope probing method, and isolate new organisms.

The Role of Institutional Factors and Information in Public Procurement Markets

Vítězslav Titl, MSc. et MSc. | Univerzita Karlova - Právnická fakulta

Abstract

Public procurement accounts for 12% of GDP in developed countries. Hence, the efficiency of procurement markets is a first-order issue in modern economies. The proposed research project will focus on three key understudied aspects of public procurement that likely influence procurement outcomes (such as prices, quality, and delays) and economic efficiency of procurement markets: (i) single-bidding in procurement contracts, (ii) the availability of information about public procurement contracts to firms, and (iii) public online oversight and monitoring. The first and the third objective will be conducted on high-quality administrative datasets from the Czech Republic and Ukraine, respectively. The second objective will be addressed by a field experiment. We aim to contribute to the academic literature by identifying causes of inefficiencies in the procurement markets and quantifying their extent. Our findings and the policy recommendations derived from them should, if implemented, result in a more efficient public sector.

Aims

The main goal of the research project is to quantify the extent of inefficiencies on public procurement markets caused by three understudied institutional factors and suggest policies which would result in savings and/or a more efficient public sector if they were implemented.

New avenues in the hunt for dark energy

Dr Ippocratis Saltas | Fyzikální ústav AV ČR, v.v.i.

Abstract

This is an interdisciplinary programme bridging cosmology, astrophysics and particle physics towards explaining dark energy in the Universe. The resolution of dark energy needs an extension of General Relativity. Theories aiming to explain it typically introduce new fields manifesting as a fifth force. The quest for their theoretical underpinning and observational imprints is currently paramount in cosmology. In the project’s first part, I will introduce helioseismology as a new precision probe for fifth forces in Nature. Within generic theories for dark energy, I will formulate the theory for solar pulsations, and with sophisticated simulations I will deliver the tightest constraints on the fifth force to date. In the second part, I will perform a complementary investigation of the fundamental character of general dark energy theories. With state-of-the-art field-theoretical methods I will deliver the first complete description of their quantum origin. With this, I will make robust predictions for gravitational waves for current and future surveys.

Aims

“Within generic dark energy theories:
1: Modelling of solar evolution in presence of the fifth force
2: Modelling of solar eigenspectrum and tight constraints on fifth force
3: Resolve their perturbative quantum structure and its phenomenology
4: Address their Wilsonian UV completion”

Vectors, symbionts and pathogens: a complex story of Triatominae microbiomes

RNDr Eva Novakova, PhD | Jihočeská univerzita v Českých Budějovicích - Přírodovědecká fakulta

Abstract

Triatominae are important blood feeding disease vectors. The project focuses on structure and development of their microbiomes, including interactions with transmitted pathogens. Recently, we identified several novel aspects of triatomine-bacteria associations, which point out unique potential of these vectors for entirely new insights into the principles of insect-bacteria symbiosis. We have proved that i) the microbiomes undergo ontogenetic diversity shift, ii) the dominant microbiome taxa enter intracellular symbiosis, and iii) the microbiomes of wild Triatoma populations encounter a complex pathobiome. The project builds on these novel findings and proposes to investigate microbiome development and bacteria transmission mechanism, functional analogies between the intracellular assemblies and bacteriomes of other hematophagous vectors, pangenomes of microbial communities found within US native Triatoma populations, and specific microbiome changes in respect to an underestimated complexity of the pathobiome, including T. cruzi DTUs, other eukaryotic, bacterial and viral pathogens.

Aims

“To reveal
i) specific changes of Triatoma microbiomes in respect to the complex pathobiome,
ii) characteristics of intracellular symbiosis found in R. prolixus and its functional analogies to tsetse bacteriomes,
iii) pangenome capacities of microbiota associated with wild Triatoma populations.”

Advanced analytical methods for soft locomotion

Paolo Gidoni, PhD | Ústav teorie informace a automatizace AV ČR, v.v.i.

Abstract

We propose to develop analytical tools to support the investigation of the locomotion of softbodied animals and robots. Our study will be focused on limbless locomotion, adopted in Nature by earthworms, snakes and snails, and inspiring a new generation of bio-mimetic soft robots, with applications in medical intervention and survey of complex environments. Instead of singularly studying specific models, we propose to build up general results in an abstract framework, where all the various mechanisms employed by such locomotors can be included. We study properties such as stabilization and optimality, and propose to rigorously derive some features of the models using multiscale convergence results. The main mathematical challenges in the analysis of such systems are the soft body, implying that its actual shape is not directly controlled, the presence of non-smooth friction laws, such as dry friction, and the absence of Dirichlet boundary conditions. Our approach combines techniques from nonsmooth analysis, dynamical systems, calculus of variation and optimal control.

Aims

– Development of analytical tools from nonsmooth analysis for the study of stabilitation and optimality in soft locomotors – Rigorous derivation of some properties of the locomotors using multiscale convergence methods.

Clarifying quantum limits in biomolecules by utilizing entangled photons generated from protein bound cofactor modeled on orange carotenoid protein

Mgr. Miroslav Kloz, Ph.D. | Fyzikální ústav AV ČR, v.v.i.

Abstract

Searching for quantum effects in biology is a grand topic of biophysics. On one hand, there are suggestions for quantum effects on such a macroscopic scale as a human brain; on the other hand, there are heated disputes over tiny localized intramolecular processes in proteins. There are experimental implications that certain quantum effects such as charge or exciton delocalization can indeed be purposely enhanced by the protein environment. Those are e.g. unusually long-lasting coherences observed by 2D spectroscopy in light-harvesting antennas of plants. Unfortunately, it has turned out that it is difficult to assess if the observed oscillations are genuine quantum effects. For assessing how “quantum” the nature of any molecular process is, we are missing “Occam’s razor” techniques. Here I propose that utilizing the deep connection between quantum decoherence and the entanglement collapse might provide such a tool. Generating and analyzing entangled bi-photons generated from chromophores in proteins (such as OCP) should provide direct insight into quantum effects in Biosystems.

Aims

The goal is to reliably set decoherence times of cofactors in proteins by generation of entangled photons in them. These times would be compared with decoherence times determined from free cofactors. This information should shed light on hypotheses about long living coherences in certain biosystems

Structural characterisation of the interplay between transcription and DNA repair

Mgr. Marek Šebesta, Ph.D. | Masarykova univerzita - Středoevropský technologický institut

Abstract

The interplay between DNA repair and transcription is a complex and poorly understood. On one hand, transcription is one of the mayor sources of DNA damage. On the other hand, under particular circumstances, cells use transcription machinery to efficiently initiate DNA repair. As the in vivo methods are inherently unable to uncover the causal relationships between DNA repair and transcription, we decided to study the above-mentioned processes by a combination of biochemical and structural approaches. The aim of the project is to determine the 3D structures of RNAPII with key factors promoting the cross-talk between transcription and DNA repair (BRCA1, SENATAXIN), coupled with a thorough biochemical analysis of the complexes. The combination of these approaches will provide a complex and detailed characterisation of the interplay between DNA repair and transcription.

Aims

“Our overall aim is to is to determine the molecular mechanism of the cross-talk between DNA repair and transcription. In particular:
(i) to solve the 3D structure of the complex between mammalian RNAPII with key DNA repair factors;
(ii) to biochemically characterise the abovementioned complexes.”

Taxing multinational corporations in the globalised world (CORPTAX)

Petr Janský, Ph.D. | Univerzita Karlova - Fakulta sociálních věd

Abstract

We hypothesise that multinational corporations (MNCs) avoid paying corporate income taxes by exploiting a combination of globalisation and countries’ sovereignty to set tax policies. Consistent with this hypothesis, we propose a new framework: the inescapable trilemma of corporate taxation. We argue that only two of three policy goals in this trilemma – globalisation, sovereignty, and revenue – can be achieved at any given time. We hypothesise that, at present, revenue is not being achieved. We aim to test it by determining the extent to which the existing limited evidence of MNCs’ tax avoidance represents a general pattern. Unlike previous research, we will overcome the limitations of currently available data. We propose a new empirical methodology and use two breakthrough ideas to establish how much MNCs pay in taxes, where and why. First, we will pioneer the use of country-by-country reporting data from large MNCs. Second, we will combine that data with other sources and leverage their respective strengths to create the most comprehensive data set on MNCs.

Aims

We aim to establish how much MNCs pay in taxes, to what extent these taxes are paid in tax havens, and which factors drive these patterns. Ultimately, we will use our theoretical, methodological and empirical innovations to transform the understanding of corporate taxation in the globalised world.

Latitudinal patterns in specialisation of interspecific interactions: Cross-continental geographical patterns in plant-pollinator networks

RNDr. Robert Tropek, Ph.D. | Univerzita Karlova - Přírodovědecká fakulta

Abstract

We will focus on the elementary question of ecology: Are niches of tropical species narrower than species in higher latitudes? The answer, although fundamental for understanding the global biodiversity organisation, lacks for pollination interactions, the key driver of most terrestrial ecosystems. We propose an intensive inter-continental study of latitudinal specialisation patterns by standardised sampling of interactions at a whole-community level along a large latitudinal gradient from tropical to subarctic biomes. Interactions will be recorded by our unique video-recording of floral visitors and modern NGS metabarcoding of pollen from pollinators. We will dissect the patterns for entire communities, and for particular groups of plants and pollinators, together with detailed analyses of plant traits related to their reproduction strategies. We hypothesise no simple answer, therefore such complex approach is necessary. The expected differences among groups of pollinators and plants be used for macroecological and macroevolutionary analyses of the global biodiversity patterns.

Aims

“1/ We will sample pollination interactions at 7 sites along latitude.
2/ We will combine ‚traditional‘ observation and experimental approaches with ‚modern‘ NGS metabarcoding.
3/ We will reveal latitudinal specialisation patterns of communities, as well as particular groups of plants and pollinators”

Extensive air showers as probes of hadronic interactions beyond the LHC energies

Eva Maria Martins dos Santos | Fyzikální ústav AV ČR, v.v.i.

Abstract

Above 1 PeV, the properties of cosmic rays can only be inferred indirectly through the detection of extensive air showers. The interpretation of air shower observables at 10 EeV relies on extrapolations of accelerator data by about one order of magnitude in energy, where a proper description of the very forward physics, most relevant for the shower development, is lacking. This leads to unknown systematic uncertainties in the predictions of hadronic interaction models and inconsistencies in the description of air shower data. We aim at improving the current situation through a comprehensive study of the main shower observables (lateral and longitudinal profiles of muon and electromagnetic components) and of the properties of current hadronic interaction models using data of several air shower experiments. The analysis will be based on several popular simulation codes and will include an unprecedented wide scan on the hadronic parameters (cross-section, multiplicity, elasticity, pion-charge ratio) placing constraints on the hadronic interaction models and exotic physics scenarios.

Aims

Reduction of the uncertainties of current simulation codes towards an improved description of various shower observables via analysis of public data from several air shower experiments. Adjustment of the interactions model parameters causing inconsistencies in the interpretation of data.

Universal Quadratic Forms and Class Numbers

doc. Mgr. Vítězslav Kala, Ph.D. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

We will establish a new connection between the multiplicative and additive structures of number fields. This will have important implications, e.g., for 1. universal quadratic forms over (totally real) number fields, estimating their ranks and proving 290-theorems, and 2. class numbers of number fields, determining their precise asymptotic growth in a wide class of families and discovering new techniques for dealing with the class number one problem. We aim at proving the following fundamental hypothesis: For a given number field K, the larger the class number of K is, the fewer indecomposable algebraic integers in K there are, and the smaller the ranks of universal quadratic forms over K are. Methodology is based on a combination of geometric (quadratic lattices), analytic (modular forms, L-functions), and arithmetic (indecomposables, generalized continued fractions) techniques. Despite promising preliminary results over real quadratic fields, further progress will require substantial effort to achieve much needed breakthroughs, starting with the case of cubic fields.

Aims

“Our main goals are to:
1. describe indecomposables using generalized continued fractions;
2. characterize corresponding families of number fields;
3. apply the results to universal quadratic forms;
4. refine the theory of infrastructure in number fields to obtain new connection with class numbers.”

Mapping the chemodiversity of Piperaceae plants using next-generation MZmine platform

Tomáš Pluskal, Ph.D. | Ústav organické chemie a biochemie AV ČR, v.v.i.

Abstract

Bioactive specialized metabolites from plants represent an essential source of chemical scaffolds for the development of new medicines, but new technological platforms are urgently needed to fully utilize this natural resource. In this project we will expand the capabilities of the popular MZmine platform for metabolomics into the domains of ion mobility separation and molecular networking, two state-of-the-art techniques that are essential for effective isolation and identification of diverse plant natural products. We will further develop and evaluate a novel bioinformatic approach based on genetic networking to associate plant natural products with their biosynthetic enzymes. We will demonstrate these technological advancements by mapping the chemodiversity of the Piperaceae plant family, widely recognized as a remarkable and underexplored reservoir of bioactive specialized metabolites.

Aims

“1. Expand the MZmine platform with ion mobility separation and molecular networking modules.
2. Develop a genetic networking approach to associate plant metabolites with their biosynthetic enzymes.
3. Map the chemodiversity and specialized biosynthetic networks of the Piperaceae plant family.”

SOUVISEJÍCÍ ČLÁNKY

Slovenian agency looking for foreign reviewers for panels

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Czech Science Foundation to Fund over 350 New Scientific Ideas

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EXPRO projects

23. 05. 2022

EXPRO grants provide funding to excellent scientists and their teams for five years. During this period they are able to draw up to 50 million CZK, i.e. an average of CZK ten million per year. The projects with the greatest potential to be part of a breakthrough in their fieldare selected for funding by international panels. One of the requirements for a successfully completed project is the submission of a project proposal to the European Research Council (ERC). Only a few EXPRO projects are funded each year.

EXPRO 2023

Fundamental questions of discrete geometry

doc. RNDr. Pavel Valtr, Dr.| Univerzita Karlova, Matematicko-fyzikální fakulta

Abstract

The project is focused on selected fundamental questions of discrete and computational geometry. These fundamental questions include questions around the Erdős-Szekeres Happy Ending theorem, on crossing numbers of graphs, on visibility in Euclidean space. The research team aims at a crucial contribution to a partial or full solution of at least one fundamental question in the field of discrete and computational geometry. The team members will look for ways how to obtain new important results with the use of new approaches and their interconnection with recently developed methods and tools, some of which were developed with a contribution of the team members. The prospective methods and tools are, for example, probabilistic methods, current state-of-the-art SAT solvers, or structural convexity results for planar point sets such as fractional or partitioned Erdős-Szekeres theorem.

Project aims

The goal is to obtain important results, some of which will lead to a partial or full solution of one or more fundamental questions in discrete and computational geometry, by means of a novel combination of new approaches with recently developed methods and tools.

Single-Atom-based 2D-Photocatalysts

Prof. Dr. Patrik Schmuki | Univerzita Palackého v Olomouci, Český institut výzkumu a pokročilých technologií

Abstract

Single atoms (SA) have shown great potential in heterogeneous catalysis due to their superior activity, utility, selectivity. The significance of SA became also recognized in photocatalysis, a heterogeneous catalysis where catalysts are activated by incident light. SA act as co-catalysts in reactions of technological significance (solar H2 generation from H2O, CO2 conversion to low-cost fuels). The project deals with exploitation the interplay of SA co-catalysts and photocatalytic surfaces on highly defined scalable semiconductor thin films. For this, magnetron sputtering techniques with elaborated Atomic Layer Deposition techniques are combined to design ionic, electronic and steric single-atom-traps (with atomic precision) to achieve mechanistic understanding about reactivity/stability of SA and their interaction with a wide range of trap-free and independently optimized photoabsorber and sensitizer surfaces. The selection of techniques enables the exploitation of the full potential of SA catalysis in photocatalytic devices, with focus on the photocatalytic production of solar H2.

Project aims

To exploit the interplay of single atom (SA) co-catalysts and photocatalytic surfaces on highly defined scalable semiconductor thin films, to elucidate fundamental aspects in SA configurations as co-catalysts, to establish most effective scaffold for photocatalyticphotoelectrochemical reactions.

Splitting of molecular nitrogen

Mgr. Jiří Dědeček, CSc., DSc.| Ústav fyzikální chemie J. Heyrovského AV ČR, v.v.i.

Abstract

The project aims to prove the possibility of N2 activation by its splitting over a new type of active sites – distant binuclear cationic sites, and to employ this activated nitrogen for the synthesis of nitrogen-containing compounds such as NH3 or NO/NO2. For this purpose, distant binuclear cationic sites capable of the 2+/5+ redox cycle will be prepared and stabilized in the aluminosilicate matrix of the ferrierite zeolite, which allows the stabilization of two cations in opposite cationic sites at the distance of 0.75 nm essential for the cooperation of two cations in the six-electron process of N2 splitting. Formation and structure of binuclear cationic sites in zeolite matrix, as well as splitting of N2 over these sites, will be monitored by a multispectroscopic approach (FTIR, UV-Vis, ss-NMR) supported by DFT. Interaction of O2 and H2 with the split N2 will be studied by FTIR spectroscopy of products adsorbed in the zeolite, further the evolution and presence of products in the gas phase will be studied by through-flow experiments monitored by FTIR, GC and mass spectrometry.

Project aims

The aim of the project is to prepare metal binuclear cationic sites stabilized in zeolite matrix and capable of 2 + / 5 + redox cycle, and to verify their ability to dissociate molecular nitrogen for the application in the synthesis of nitrogen compounds such as ammonia and NO / NO2.

Identification and characterization of a new pathway regulating pre-mRNA splicing

Mgr. et Mgr. Dalibor Blažek, Ph.D. | Masarykova univerzita, Středoevropský technologický institut

Abstract

Ability of cell to properly express its genes depends on optimal transcription and splicing. RNA polymerase II transcribes protein-coding genes and produces pre-mRNAs, which cotranscriptionally undergo intron excision by the spliceosome, a megadalton RNA-protein complex. Spliceosome activation is a major, but poorly characterized control step, leading to a catalytically active complex. Our unpublished data identified a new pathway that controls spliceosome activation and links the regulation of transcription to the regulation of splicing. Notably, the pathway links three important cancer-related and therapeutically attractive proteins. We propose to apply proteomics and chemical biology approaches coupled to state-of-the-art genomics to characterize how the pathway activates the spliceosome and orchestrates interplay between transcription and splicing. In addition, we have identified a family with a complex developmental disorder carrying aberrations in a component of the pathway. The molecular characterization of the family-derived cells will complement the above experiments.

Project aims

Aim 1. Characterization of a role of CDK11 and SF3B1 in spliceosome activation Aim 2. Identification and characterization of links between splicing and transcription Aim 3. Molecular characterization of a new complex developmental disorder caused by CDK11 aberrations.

What do the most abundant oceanic protistan proteins actually do?

prof. RNDr. Julius Lukeš, CSc. | Biologické centrum AV ČR, v.v.i.

Abstract

Protists represent the most speciose and abundant eukaryotes of the ocean, the largest ecosystem on Earth. Yet how they impact oceans remains enigmatic, primarily due to their extreme diversity and lack of cultivable and genetically tractable species. We know close to nothing about the proteins of marine protists, even though some of them represent the most abundant sequences in the ocean. Using advanced bioinformatics, we analysed millions of predicted proteins, to identify the most abundant ones having no projected function. We will introduce epitope tags to the most abundant proteins to establish their intracellular localization and interacting partners in model protists. A selected cohort of genes will be subsequently ablated for phenotypic analyses, with focus on cytosolic and mitochondrial ribosomes, as well as kinetochores, which remain unstudied in several ecologically and evolutionarily important supergroups. Using a library of monoclonal antibodies, we will visualize and characterize new protist lineages exceptionally important from the evolutionary perspective.

Project aims

Using advanced functional genomics, we aim to associate functions with the most abundant oceanic proteins derived from protists, with the focus on the composition of their ribosomes and kinetochores. We will also identify and analyze so far elusive, yet abundant and diverse protist lineages.

Pathways towards environmental sustainability

Jan Weinzettel, Ph.D. | Univerzita Karlova, Centrum pro otázky životního prostředí

Abstract

Human society risks exceeding the capacity of several Earth system processes, with the potential to cause irreversible environmental change. Nine planetary boundaries have been suggested to quantify this risk, which might in turn been “downscaled” to a national level to motivate political action. However, there is no systematic allocation of responsibility of nations, no insights into how fast we are approaching the boundaries, and limited foresight into actions that affect multiple earth system processes. In this project, we will explore a range of mitigation options by changing production technology and consumption on a global level. We will focus on the transgressed planetary boundaries from the consumer responsibility perspective. We will further develop state-of-the-art enviroeconomic models, and scenarios of future development. The outcomes will be policy relevant scenarios of potential future development of production technology and consumption within the capacity of the Earth systems and an insight into trade-offs and synergies of potential technical and behavioral changes.

Project aims

Determine the potential scenarios of future development in technology and consumption, which will ensure national footprints of all countries to be within the downscaled planetary boundaries.

Robots, Computing the Human, and Autism/Cultural Imaginations of Autism Diagnosis and Emotion AI

Mgr. Eva Šlesingerová, Ph.D. | Masarykova univerzita, Fakulta sociálních studií

Abstract

The project EMOROB analyses one of the most important challenges we are facing today – human/robot interaction. Specifically, the project explores the genealogy of the affective programming and social robotics field which started developing in the early1990s. Here, the imaginations relating to diagnosis and treatment of autism have played a crucial role as one of the first application domains of the social robotics. The EMOROB project aims to explore the field of emotional computing in the context of autism treatment, in particular with regard to cultural metaphors and codes. THE MAIN QUESTION is: How did the metaphors of social robotics and affective computing used in the context of autism treatment influence and mirror our view of human embodiment, agency, inequalities, and medical treatment itself? TO EXPLORE THIS QUESTION, the project carries out critical discourse analysis, archives research, and interviews with people in the field. Analytical reflections of EMOROB will contribute to the public debate on the societal impact of autism and affective computing cultural imagery.

Project aims

To analyse genealogy of the cultural imagery reflecting the diagnosis of autism and humanrobot interaction since 1990s – to explore epistemic maps interconnecting autism, robotics and ideas about normality, otherness, more-than-human sociality or bodies

A Unified 3D Map Representation

Dr. rer. nat. Torsten Sattler | České vysoké učení technické v Praze, Český institut informatiky, robotiky a kybernetiky

Abstract

3D scene representations, or 3D maps, are a key component of any type of intelligent system (agent). Significant progress has been made in terms of 3D mapping, enabling a wide range of applications, including self-driving cars and augmented reality systems. Yet the current generation of 3D maps have fundamental limitations that can be traced to the fact that mapping algorithms and scene representations are tailor-made for a specific sensor setup. This makes sharing 3D maps between intelligent systems with different sensor setups and true crowdsourced mapping essentially impossible. Further, algorithms and functionality such as visual localization, semantic segmentation, handling scene dynamics, and ensuring privacy need to be re-invented for each map representation. This project proposes an unified map representation to address these limitations. It will be able to integrate data captured from heterogeneous sources, handle the fact that the world is dynamic, and provide full privacy control. The unified map representation will thus enable the next generation of intelligent agents.

Project aims

The project will develop an unified 3D map representation that addresses the fundamental limitations of the current generation of 3D maps, including functionality to represent the fact that the world is dynamic, and that the next generation of 3D maps should be designed with user privacy in mind.

Biomolecular condensates in plant germline differentiation

Mgr. Karel Říha, Ph.D. | Masarykova univerzita, Středoevropský technologický institut

Abstract

Biomolecular condensates are membrane-less compartments that concentrate proteins and nucleic acids via multivalent interactions, and exhibit features of liquid-liquid phase separation. They have been implicated in number of cellular processes and list of their biological functions has rapidly grown over recent years. P-bodies are cytoplasmic condensates involved in translation repression, RNA storage and RNA decay, but how these opposite outcomes are achieved is not resolved. P-bodies are also important for differentiation of plant germline. We showed that P-bodies change composition and functional properties in the course of Arabidopsis meiosis, which represents unique system to study mechanisms of their action and regulation. In this application we propose to combine quantitative imaging and genomic approaches to study the function of P-bodies in plant meiosis. Gained knowledge will fundamentally advance our understanding of gene regulation in plant germline, and proposed technological developments will contribute to research on biomolecular condensates in plants.

Project aims

We will use advanced microscopy and genomic approaches to delineate function of P-bodies in plant meiosis. We will describe structure and dynamics of meiotic P-bodies, examine how they regulate translation and stability of mRNAs, and study kinases that regulate P-body assembly and function.

Rigorous Engineering of Data Analysis Pipelines (RiGiD)

Jan Vitek, Ph.D. | České vysoké učení technické v Praze, Fakulta informačních technologií

Abstract

Computer science, as a discipline, failed at producing tools and methodologies that can be adopted by working data scientists. This project takes the first steps of a long-term research program to remedy this situation. We will identify some of the most impactful errors in data science codes and to develop a methodology for rigorous engineering of data analysis pipelines that can be adopted in practice. We aim to reduce the potential for errors and increase our confidence in results while retaining ease of use. We will expose our ideas to working data scientists by developing usable tools and advocating their adoption. Our goal is to advance the state of the art in data science, software engineering and program analysis.

Project aims

Identify some of the most impactful errors in data science codes and to develop a methodology for rigorous engineering of data analysis pipelines that can be adopted in practice.

EXPRO 2021

Expertise in authoritarian societies. Human sciences in the socialist countries of East-Central Europe

doc. Kateřina Lišková, Ph.D. | Masarykova univerzita - Fakulta sociálních studií

Abstract

Expertise shapes modern forms of governance. Yet, we know significantly more about the postwar Western expertise than we know about the other side of the Iron Curtain. I will put expertise center stage and analyze socialist countries. Focusing on health and normalcy as discussed by the human sciences, I will study the negotiation of knowledge, analyzing how experts communicated with: other experts, the state and ordinary people in four neighboring countries: Czechoslovakia, Poland, Hungary and East Germany. While these countries shared the socialist path, they diverged in expertise institutionalization. My research stems from a post-totalitarian paradigm that refuses to perceive the state-socialist past as a monolith. Further, in contrast to prevailing views that communist ideology commanded human scientists and tainted their findings, my hypothesis is that it was expertise that shaped the ideas of health and normalcy that socialist governments subsequently implemented. Making this “expert turn” will bring a novel understanding of governance in modern, yet authoritarian societies.

Aims

Explain the character of governance through human-science expertise during state socialism in East-Central Europe. Analyze the role expertise played and the ways it intersected with the Party and the state. Comparatively analyze East-Central Europe focusing on transnational expert exchanges.

ADAR RNA editing; how immune systems and brains breach The Central Dogma

prof. Mary Anne O'Connell, PhD | Masarykova univerzita - Středoevropský technologický institut

Abstract

ADAR1 RNA editing in dsRNA inhibits activation of innate immune responses. We rescued Adar mutant mouse embryonic lethality in Adar1; Mavs double mutants that prevent the antiviral response. These mice die soon after birth and we will test whether removing the dsRNAactivated Protein Kinase R completes the rescue. ADAR2 RNA editing changes specific codons in neuronal transcripts. Human ADAR2 mutations cause infant epilepsy. We will use cell lines to investigate the molecular mechanisms. We will study changes in the glutamate receptors of Adar2 mutant mice that develop seizures. We will study changes in Adar2 as seizures progress in a similar Gria2 mutant seizure model. Drosophila Adar mutant brain defects are rescued by human ADAR2. There is also an innate immune induction in Adar mutant brains, paralleling the mouse Adar1 mutant. We will prevent the Adar mutant antiviral response in order to study how the Adar mutant affects circadian rhythms, sleep and other behaviors through editing of specific CNS transcripts. We plan bioinformatics projects across all ADAR RNA editing models.

Aims

“1. Study ADAR1 mutations and try to rescue Adar1, Mavs mice by PKR knockout.
2. Investigate ADAR2 mutations and study seizures in Adar2 and Gria2 mutant mice.
3. Elucidate how editing of Drosophila transcripts contribute to Adar mutant defects in circadian rhythms, sleep and other behaviors.”

Probing and Transforming Matter by Electrons in Liquid Jets

prof. RNDr. Petr Slavíček, Ph.D. | Vysoká škola chemicko-technologická v Praze - Fakulta chemicko-inženýrská

Abstract

The project aims at developing new concepts centered around electron interactions with liquid microjets. First, liquid microjets are a unique environment for spectroscopic techniques requiring vacuum. It is proposed in the present project to probe the liquid systems by the electron energy loss spectroscopy. The new technique will bring information that is otherwise inaccessible by optical or photoelectron spectroscopies, e.g., on optically dark states. Second, a liquid microjet will serve as an unusual reactor, exploring the reactivity of the dark states and exploring the electron-induced reactivity in the liquid phase in general. The project will be performed in a close synergy of experiment and theory, introducing novel approaches in both areas. The experimental and theoretical toolbox will allow us to explore the spectroscopy and reactivity of interfaces that play a role in atmospheric chemistry and in radiation chemistry. We also plan to explore electron analogs to photochemistry and photocatalysis, which may lead to new efficient ways how to trigger the chemical transformation.

Aims

“1) To develop novel concepts for the use of electrons in spectroscopy of liquids
2)To use this concepts for probing interfacial phenomena
3)To explore electron-induced reactivity in liquids by using liquid microjet technique”

Graph limits and beyond

Jan Hladký | Ústav informatiky AV ČR, v.v.i.

Abstract

The theory of graph limits is one of the most important recently emerged tools of discrete mathematics. It has led to breakthrough solutions of many old problems in extremal graph theory, theory of random graphs and in particular in connecting discrete mathematics to fields such as probability, real anf functional analysis and group theory. In the project, we will study the foundations of the limit theory of graphs, graph norms, and connections to mathematical models of statistical physics.

Aims

“1) introduction of a weak-star approach to hypegraph limits
2)graph, hypergraph and arithmetic norms
3) mathematical models of statistical physics in the context of dense graph limits
4) random processes connected with graph limits
5) limits of sparse graphs (local-global convergence, factors of iid)”

Identification and characterization of proteins involved in G-quadruplex and R-loop metabolism and their relationship with DNA replication

doc. Mgr. Lumír Krejčí, Ph.D. | Masarykova univerzita - Lékařská fakulta

Abstract

DNA replication is an essential and one of the most complex processes in the cell. Not only exogenous DNA damage but also intrinsic DNA structures including G-quadruplexes (G4) and R-loops, their stabilization or unscheduled formation represent major replication obstacles with possible detrimental effects on genome integrity. Not surprisingly, those processes are pharmacologically targeted in anticancer therapy, despite the fact that only little is known about the underlying molecular mechanisms. It becomes apparent that maintenance of processive DNA replication requires sophisticated protein networks beyond the core replisome. Whether there is a direct crosstalk between G4 and R-loops, what proteins are involved in their homeostasis and what are the factors diversifying between their beneficial and pathological roles is not well understood. The goals of our research are to identify proteins associated with G4 and R-loop structures and understand their roles in G4/R-loop formation and resolution as well as relationship to replication fork progression and associated repair.

Aims

Identify proteins contributing to the formation and processing of G-quadruplexes and R-loops, and by combining biochemical, biophysical and cell biological methods, characterize their role in the metabolism of these DNA structures and their physiological relationship to replication progression.

The Formation of Multi-ethnic Complex Societies in Early Medieval Moravia. Collective Action Theory and Interdisciplinary Approach

prof. Mgr. Jiří Macháček, Ph.D. | Masarykova univerzita - Filozofická fakulta

Abstract

The project is focused on social and ethnic groups building, social structure and behaviour, variation in the nature of leadership and on the collective–autocratic variability of governance in Early Mediaeval Central Europe. The paradigm shift to collective action theory allow us to explain diversity and changes in the early medieval society and integrate the data from Central Europe into the new stream of global comparative research into premodern state formations. The key variable for understanding such social processes will be the scale and the nature of socioeconomic networks–e.g. kinship or the interplay between the powerful and the disempowered. The basis of the project is the comprehensive analysis of early medieval settlements and burial grounds in Moravia (Czech Republic). The archaeological and anthropological research will be enriched with new interdisciplinary approaches, such as archeogenetics as well as digital morphometry.

Aims

The main objective of the project is to investigate the formation and dynamics of the early medieval polity and population in Central Europe over an extended period (from the 6th to 10th centuries AD) as well as empirical and theoretical shift in early medieval archaeology and anthropology.

Explaining the development of dual-tasking in children with and without motor difficulties: A mechanistic account

Prof. Peter Wilson, PhD, BAppSc(PE), BBSc(Hons), MAPS. | Univerzita Palackého v Olomouci - Fakulta tělesné kultury

Abstract

At a time when society is saturated with competing information, increasing demands are placed on children’s ability to perform motor and cognitive tasks at the same time (dual tasking). Our project will be the first to study the development of dual-tasking in children with and without motor difficulties from an ecological framework and using a longitudinal approach. We will test the novel causal hypothesis that (cognitive-motor) dual-task performance is explained by agerelated changes in predictive motor control and its integration with cognitive control. We will examine performance in a range of movement contexts that are representative of everyday life—when walking and stepping over obstacles, when performing manual actions, and when both actions are combined. This will enable us to understand how individual, task-related and environmental factors interact to influence dual-task performance, and how this interaction changes with age and experience. Results will directly benefit the design of safe and efficient learning environments for children

Aims

The broad aim of the project is map the development of dual-tasking in children from an ecological perspective (Wilson et al., 2017) and using a longitudinal approach. We will use this knowledge to design and test an intervention that will improve dual-task performance in children

Exploring the Hot Universe and Understanding Cosmic Feedback

Doc. Mgr. Norbert Werner, Phd | Masarykova univerzita - Přírodovědecká fakulta

Abstract

The Lambda Cold Dark Matter model has been shown to be remarkably successful in describing many aspects of our Universe, which is dominated by dark energy and dark matter. However, the physical processes associated with the evolution of the baryonic matter are complex and still poorly understood. In the course of structure formation, only a small fraction of the baryons turned into stars – most remain in a diffuse intergalactic medium (IGM). The growth of galaxies is regulated by feedback processes, such as energy and momentum input from supernovae, and jets and winds of accreting supermassive black holes. These processes, collectively called galactic feedback, can limit or even inhibit further gravitational collapse, and thus a detailed knowledge of how they work is essential for our understanding of galaxy formation and evolution. Here, I propose to take advantage of new observational opportunities to study the intimate connection between the IGM, star formation and the growth of supermassive black holes in groups, clusters, and massive galaxies.

Aims

“1) determine the role of the hot galactic atmospheres and accreting supermassive black holes in galaxy evolution
2) determine the physics of the hot intergalactic plasma by using multi-wavelength SZ, radio and X-ray observations, and by using new high resolution X-ray spectra”

Quantum non-Gaussian coherence

prof. Mgr. Radim Filip, Ph.D. | Univerzita Palackého v Olomouci - Přírodovědecká fakulta

Abstract

Photons and atoms are in the core of quantum physics and technology. They can be used to demonstrate a variety of quantum phenomena in the continuous-variable regime, and exhibit high potential for quantum sensing, communication, simulation and computing. However, many experiments only exploit the coherences provided by Gaussian states of light and atoms. Devising reliable and feasible generation and detection schemes for quantum non-Gaussian coherence in Fock-state superpositions remains however challenging, and as yet entirely unexplored. On top of this, we lack criteria capable of certifying quantum non-Gaussian coherences. This urges us to push in this research direction, the lack of which might severely hinder the development of quantum technologies relying on such continuous-variable systems. The project will clear this roadblock by providing conclusive criteria to detect quantum nonGaussian coherences, developing experimental platforms to test such criteria with photonic and atomic systems, and proposing applications allowed by these new quantum resources.

Aims

The project will deliver new theoretical methods and experimental verifications of the first conclusive observation of quantum non-Gaussian coherences of light and atoms necessary for many proof-of-principle tests and applications in quantum physics and technology with continuous variables.

Implementation of Frequency Rapid Scan Electron Spin Resonance Spectroscopy into Nuclear Magnetic Resonance Systems

Ing. Petr Neugebauer, Ph.D. | Vysoké učení technické v Brně - Středoevropský technologický institut

Abstract

Historically, even little progress in magnetic resonance have dramatically extended the field of its applications. Especially, this includes the use of nuclear magnetic resonance (NMR) in hospitals. Based on my recent developments in frequency rapid scan electron spin resonance (ESR) (ERC, GA714850), I intend to provide a working prototype of a combined high-field ESR /NMR system operating at the magnetic field of 11.75 T, which causes ESR and proton NMR at frequencies of 329 GHz and 500 MHz, respectively. The ESR/NMR concept will allow us to perform liquid state NMR hyperpolarization experiments (DNP) for such a desirable enhancement of inherently weak NMR signals, which limits progress in many today relevant biological studies. This will significantly increase the knowledge of complex systems, including the structure and dynamics of large biomolecules. The proposed system design can be easily modified to adjust to any high magnetic field NMR spectrometers. This will increase the functionality of the existing widespread NMR spectrometers, allowing more efficient use of resources.

Aims

“1. develop an ESR/NMR system for NMR spectrometers
2. provide theoretical studies of frequency rapid scan ESR
3. investigate electron dynamics directly in NMR systems
4. perform liquid state DNP at 500 MHz on real life samples
5. dissemination and steps towards commercialization”

Accreting Black Holes in the new era of X-ray polarimetry missions

RNDr. Michal Dovčiak, Ph.D. | Astronomický ústav AV ČR, v.v.i.

Abstract

The project will study the environment in the closest vicinity of accreting black holes in Galactic X-ray binaries. While the black hole form their fundamental element, these systems typically consist of two additional main constituents – an accretion disk and a corona. With the help of the most up-to-date methods in X-ray polarimetry and variability research, including traditional approach of spectroscopy, we will study these components and their mutual physical interactions in X-ray band. To this aim we will develop new numerical models that will link all the acting components together as a whole. In this project a compact team will be created, consisting of Czech scientists who actively participate on preparations of new X-ray polarimetric missions IXPE (NASA, 2021) and eXTP (China- Europe, 2027), including European large observatory Athena (ESA, 2031), and in this way the project will support Czech participation in the scientific programme of these space missions.

Aims

We will develop new relativistic models to compute polarimetric, timing and spectral properties of emission from black hole accretion disk and its corona, and we will use them to interpret data acquired with the new mission IXPE and for scientific preparations of planned missions eXTP and Athena

Nanocrystallography of molecular crystals

Dr.rer.nat. Lukáš Palatinus | Fyzikální ústav AV ČR, v.v.i.

Abstract

Structure analysis of molecular crystals is an important and powerful tool in many fields of chemistry and structural biology. Its power is, however, limited, if only nano- or microcrystals of the studied materials are available. The best method to study structures of such materials is electron diffraction. However, even this method suffers from a number of limitations, like the low accuracy of lattice parameters, difficulties with accuracy of structure models or inability to reliably determine the absolute structure of chiral compounds. These limitations severely restrict its applicability to many interesting scientific problems and consequently the general ability of scientists to understand molecular structures. The proposed project aims at removing these limitations. We will develop a set of protocols, methods and programs with the ambition to set new standards in the field and to make electron crystallography of molecular crystals a fully developed and generally accepted method of first choice for analysis of nano- and microcrystalline molecular materials.

Aims

The project aims to remove significant limitations in electron crystallography that severely restrict its potential in the structure analysis of molecular nanocrystals and thus its applicability to a variety of scientific problems, with the ambition of setting new standards in the field.

Horizontal transfer of mitochondria in cancer biology

prof. Ing. Jiří Neužil, CSc. | Biotechnologický ústav AV ČR, v.v.i.

Abstract

Mitochondria move from donor cells (mesenchymal stem cells, MSCs) to cancer cells with dysfunctional mitochondrial DNA (mtDNA) via tunnelling nanotubes (TNTs) with major role of the adaptor protein Miro1. Recruitment of MSCs to the site of pre-tumour plaque is driven by cytokines secreted by cancer cells with dysfunctional mitochondria. The result of mitochondrial repopulation is recovery of respiration needed for tumour cell proliferation, with respiration dependent on dihydroorotate dehydrogenase essential for de novo pyrimidine synthesis. We also propose that in case of low level of damage, the mtDNA repair system can ‘fix’ mitochondrial genome to promote tumour formation. We will define a novel, underexploited target for tumour therapy that can be used also in case of hard-to-treat tumours/resistant tumours.

Aims

Recruitment of donor cells to tumour stroma Molecular mechanism of intercellular movement of mitochondria Functional impact of horizontal transfer of mitochondria (HTM) The role of mitochondrial DNA repair in HTM Clinical relevance of HTM including hard-to-treat and resistant cancers

Beyond properties of current top performance alloys

RNDr. Jiří Svoboda, DSc. | Ústav fyziky materiálů AV ČR, v.v.i.

Abstract

Current top performance alloys still show a considerable potential to improve their properties. The project deals with two kinds of materials: (i) new-designed low alloyed martensitic steels with the goal to increase their ductility at room temperature while keeping their top strength and (ii) new-generation oxide dispersion strengthened (ODS) Fe-Al based alloys with the goal to increase their creep strength at 1100-1300 °C by tuning the grain morphology. The increase in ductility of the martensitic steels with a special chemical composition should be achieved by controlled heat treatment which allows tuning the morphology of strengthening C-based nanoclusters in martensite. Such a nanostructure can effectively block dislocation motion and activate deformation in nano-twining modes without formation of stress concentration initiating the fracture process. The optimal grain morphology of new-generation ODS alloys will be achieved by hot consolidation of ODS powders by rotary swaging (this method has never been used before) followed by annealing to provoke secondary recrystallization.

Aims

“1. To optimize mechanical properties of low alloyed martensitic steels strengthened by nanoclusters with respect to chemical composition and heat treatment.
2. To increase creep strength of new-generation oxidation dispersion strengthened Fe-Al based alloys by optimizing their grain morphology.”

The role of coevolution in ecological speciation

prof. RNDr. Martin Reichard, Ph.D. | Ústav biologie obratlovců AV ČR, v.v.i.

Abstract

This project aims to embrace a major question in ecological and evolutionary research – how coevolutionary processes and ecological interactions shape biodiversity at local and global scales. We will use brood parasitism, a unique study system in which interacting partners are readily identified and will take advantage of species that are highly amendable to laboratory and field studies. Using two understudied fish systems (cuckoo catfish and bitterling), we will employ comparative and experimental approaches to understand how coevolution drives and constrains diversification. This project will identify the conditions for the origin and evolution of host specificity, how it is maintained and constrained, and how it contributes to biological diversification. Field and lab studies will be combined with population genetics, phylogenetics and mathematical modelling. This project will contribute to resolving a central question about coevolution; how and why do some parasites become host specialists and its consequences for ecological speciation.

Aims

“1. Identify the origin and early evolution of host specificity.
2. Quantify large-scale patterns of host specificity and their association with parasite traits and diversification.
3. Measure the constraints and benefits of host specificity.”

EXPRO 2020

Abstract convergence schemes and their complexities

prof. Wieslaw Kubis | Matematický ústav AV ČR, v.v.i.

Abstract

Abstract convergence schemes are basic category-theoretic structures which serve as universes for studying infinite evolution-like processes and their limiting behavior. Convergence schemes endowed with extra structures provide an applicable framework for studying both discrete and continuous processes as well as their random variants. The main goal of the project is unifying and extending several concepts from model theory, algebra, topology and analysis, related to generic structures. We propose studying selected topics within the framework of abstract convergence schemes, addressing questions on their complexity and classification. One of our inspirations is the theory of universal homogeneous models, where convergence of finite structures is involved. Another motivation is set-theoretic forcing, where a convergence scheme is simply a partially ordered set of approximations of some “unreachable” objects, living outside of the universe of set theory.

Aims

Our goal is to study the complexity of convergence schemes and their limits. Sequences (viewed as evolutions) with the absorption property lead to so-called generic objects. One of our objectives is to extend this study in several directions.

Applied String Field Theory

Mgr. Martin Schnabl, Ph.D. | Fyzikální ústav AV ČR, v.v.i.

Abstract

String field theory has developed over the recent years into a potentially very useful tool for tackling some of the profound issues in string theory, namely how to connect classical open or closed string backgrounds via tachyon condensation and/or deduce the existence and study properties of new ones. It is also a longstanding idea that string theory possesses a huge underlying higher spin gauge symmetry which should become manifest in the tensionless limit of the theory, and recently impressive progress has been made in this direction. The structure of string field theory is expected to become especially simple and transparent in this limit, since all the fields should organize themselves into multiplets and gauge invariance strongly constrains the allowed interactions. In this project we will construct and explore the string field theory describing tensionless strings in Anti-de-Sitter backgrounds with the help of holographic duality.

Aims

“1) uncover new consistent open and closed string theory backgrounds, work out their properties and understand relations among them
2) develop string field theory for the tensionless string, elucidate the underlying gauge principle, and shed light on the holographic nature of quantum gravity”

Whole-body awareness for safe and natural interaction: from brains to collaborative robots

Mgr. Matěj Hoffmann, Ph.D. | České vysoké učení technické v Praze - Fakulta elektrotechnická

Abstract

As robots are leaving safety fences and starting to share workspaces and even living spaces with humans, they need to dynamically adapt to unpredictable interactions with people and guarantee safety at every moment. The rapidly growing market of collaborative robots ensures safety through specific technologies such as force limitations by design or contact detection and stopping relying on force measurements. Humans, however, possess whole-body awareness drawing on dynamic, context-dependent fusion of multimodal sensory information, which makes them adaptive, flexible, and versatile. The first goal of this project is thus to better understand the mechanisms of body and peripersonal space representations in the brain by building embodied computational models using humanoid robots. The modeling endeavor will inform the main goal of the project – designing new perception modules and robot controllers for humanrobot interaction – and also provide a proxy for what humans expect from a robot collaborator.

Aims

“1) Embodied computational models of body and peripersonal space representation
2) Computationally optimal and transparent representations of peripersonal space
3) Collaborative workspace representation and control framework for safe physical HRI complying with safety standards”

Novel biophotonic tools for investigation of cellular processes

prof. Ing. Jiří Homola, CSc., DSc. | Ústav fotoniky a elektroniky AV ČR, v.v.i.

Abstract

Understanding how life works on the cellular and molecular level is a major challenge for modern science with potential significant implications for the development of new drugs and diagnostic and treatment modalities. Therefore, the development of methods that will enable investigation of cellular processes presents an important research goal. The aim of the proposed project is to develop a new generation of label-free biophotonic tools that will enable investigation of cellular processes, especially cell secretion and interactions of cells with biomolecules, with an unprecedented spatio-temporal resolution. These new tools will combine advances in photonic and plasmonic nanostructures, plasmonic imaging and microscopy, and micro/nano-fluidics. Although the tools that will be developed in the project can be applied to a broad range of cellular processes, in this project, we plan to use them to investigate cellular processes related to a group of serious onco-hematological diseases – myelodysplastic syndromes and acute myeloid leukemia.

Aims

The main goal of the project is to advance science in the field of biophotonics, and to develop a new generation of biophotonic tools based on plasmonic imaging and microscopy, which will allow for real-time and label-free investigation of cellular processes.

Ferroelectric Perovskites for Energy Applications

Doc. Mgr. Martin Setvín, Ph.D. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

Ferroelectricity is an ability of certain materials to adopt spontaneous switchable electric polarization. While the bulk aspects of ferroelectricity are reasonably well-understood, there is very little direct evidence on how it manifests at surfaces. Ferroelectricity offers many opportunities for efficient generation of renewable fuels: It can aid electron-hole separation in photocatalysis, it can tune the reactivity and catalytic activity of materials surfaces, or, cycling through the ferroelectric phase transition can power redox reactions and generate fuels. The major issue is that ferroelectrics are mostly insulating ternary compounds and their surfaces are extremely difficult to study. I have recently solved the main impediment by preparing bulk-terminated surfaces of several relevant materials (KTaO3 and SrTiO3) and analysing them at the atomic level, using non-contact atomic force microscopy. This project will focus on fundamental aspects of using ferroelectricity and incipient-ferroelectricity in surface chemistry and fuel production.

Aims

Understand how ferroelectric polarization promotes the separation of photoexcited charge carriers and photocatalytic performance. Understand how the ferroelectric phase transition affects the surface, and use the transition for fuel generation. Use ferroelectricity for tuning co-catalyst performance

Social mobility of elites in the Central European regions (1861-1926) and transition of imperial experience and structures in nation-states

doc. PhDr. Alice Velková, Ph.D. | Univerzita Karlova - Přírodovědecká fakulta

Abstract

The interdisciplinary project analyses and compares transformation processes in modern European societies on the example of two non-central regions of the Habsburg Monarchy: Bohemia and Transylvania. It shows how social mobility, education, family and other ties of elite social groups contribute to de/stabilizing of the society as a whole. Research is conducted on two groups of members of the decision-making strata: higher-ranking state officials and deputies of the land diets, the Imperial Council in Vienna and the Hungarian Parliament. In an imaginative way, the project combines methods from both humanities and nature sciences. Its main goal is to investigate factors which had a significant impact on whether an individual would become member of the above mentioned elite groups, to clarify the process of circulation of elites and the transition of imperial experience and structures into the newly created succession states. It shows links between career of an individual and his family ties and sheds light on demographic factors influencing the modern European family.

Aims

The aim of project is to analyse factors which influenced social mobility and determined membership of decision-making strata in 1861-1926 and discuss whether there is transition of imperial experience and structures to the newly created nation states.

New challenges for spectral theory: geometry, advanced materials and complex fields

prof. Mgr. David Krejčiřík, Ph.D., DSc. | České vysoké učení technické v Praze - Fakulta jaderná a fyzikálně inženýrská

Abstract

The ultimate goal of the project is to develop unconventional tools in spectral theory in order to tackle various newly born, or more classical but recently revived, open problems in mathematics and physics. Among the variety of problems, I intend to particularly consider hot open questions in: spectral geometry of optimal shapes and eigenfunction properties; mathematical models of modern nanostructures, graphene and metamaterials; new concepts in quantum mechanics with non-self-adjoint operators, Schrödinger and Dirac operators with complex potentials, damped wave systems, non-standard stochastic processes and asymptotic distribution of eigenvalues of structured matrices. These apparently unrelated problems are in fact interlinked and a cross-fertilisation of ideas and techniques will constitute an important part of the project. As examples of the synergy, I propose to develop the method of multipliers to become a standard tool in spectral theory of differential operators with complex coefficients and explain the cloaking effect in metamaterials by operator-theoretic methods.

Aims

To develop unconventional tools in spectral theory in order to tackle hot open problems in mathematics and physics. To cross-fertilise various ideas and techniques from apparently unrelated branches of mathematics and physics, which are actually interlinked by spectral theory.

Language Understanding: from Syntax to Discourse

prof. RNDr. Jan Hajič, Dr. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

The project aims at developing and empirically verifying symbolic, formally defined, “universal” (in the multilingual sense) representation of textual communication, at the document (text) level. The project will build on the principles of the successful Universal Dependencies (UD) project in terms of methodology and scientific principles, but it will extend the current UD representation beyond morphology and syntax. The areas to be specified cover compositional and lexical semantics, discourse and information structure (including co-reference). Starting with existing semantic representations covering the above aspects, the new specification will be verified on real texts by (human) expert annotation and selected properties will also be confirmed by human-subject experiments. The resulting representations will be used for building ANN models by Deep Learning methods with properly analyzed results. All output (data, publications) will be published in Open Access mode using existing relevant Research Infrastructures and their repositories.

Aims

The goal is to publish fundamental research results (and open data) into natural language understanding, using empirically verified universal/multilingual symbolic and distributional representations of textual communication, and to formulate new fundamental research questions based on such findings.

1D molecular chains on surfaces

doc. Ing. Pavel Jelínek, Ph.D. | Fyzikální ústav AV ČR, v.v.i.

Abstract

We aim to design, synthetize and characterize 1D molecular chains on surfaces with the unique material properties. First, we will investigate organometallic polymers exploring their magnetic ordering and possibility to control redox states within the chain. Second, we will investigate a possibility to close the band gap of pi-conjugated polymers by proximity of the topological phase transition. In principle, this strategy should allow to overcome the problem of the Peirels transition (the dimerization) to form purely metallic pi-conjugated polymers. We will employ onsurface chemistry under UHV conditions to synthetize molecular chains of desired properties with lengths of tenth to hundreds of nanometers. Their chemical structure will be analyzed by the high-resolution scanning probe microscopy with functionalized probes providing the unprecedented spatial resolution. The scanning probe measurements will be complemented by other surface science techniques (electron diffraction and photoemission) and corroborated by theoretical analysis mainly based on density functional theory.

Aims

Goal of this project is to design, synthetize and characterize new 1D molecular chains on surfaces with the unique material properties and to explore their electronic and magnetic properties and investigating possibility to control charge states within chains.

Pan-European Lake Sampling - Microbial Eco-genomics (PELAGICS)

Dr. rer. nat. Rohit Ghai | Biologické centrum AV ČR, v.v.i.

Abstract

Freshwater habitats are critical for all terrestrial life, yet the vast majority of their microbial inhabitants (pro- and eukaryotes) remain enigmatic, outside the bounds of cultivation. The recent development of novel cultivation methods, coupled with advances in sequencing now provides an opportunity to finally unravel freshwater microbial diversity. The PELAGICS project plans a coordinated pan-European sampling campaign (70 lakes) with 24 collaborating scientists from 16 European countries. With novel media mimicking natural conditions and semiautomated high-throughput isolation we aim for stable cultivation and whole-genome sequencing of 500 prokaryotes and 50 unicellular eukaryotes. Moreover, terabyte scale deepmetagenomic sequencing (ca. 18 TB) will allow recovery of thousands of metagenomeassembled genomes for pro-, eukaryotes and viruses. This large-scale effort will finally uncover the microbial diversity (pro- and eukaryotes), their natural interactions and ecological roles in aquatic food webs.

Aims

A Pan-European microbial ecology network is proposed to sample 70 lakes towards the goal of stable cultivation, whole-genome sequencing (500 pro- and 50 unicellular eukaryotes) and terabyte-scale deep-metagenomic sequencing to obtain 1000s of genomes of freshwater pro-, eukaryotes and viruses.

Mathematical analysis of partial differential equations describing far-from-equilibrium open systems in continuum thermodynamics

Miroslav Bulíček | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

Most of the processes that are of interest in continuum thermodynamics take place far from equilibrium. These processes frequently give birth to dissipative structures that dominate the dynamical behaviour. The existing mathematical approaches applicable for the description of the dissipative structures however face principal difficulties. Either the physically relevant description is achieved at the price of sacrificing the mathematical rigour, or the existing approaches are fully rigorous, but they are of no physical relevance. Our aim is to overcome this gap. For the physically relevant models we will develop constructive methods for the description of the structures in terms of lower dimensional subsystems. Obstacles such as the lack of regularity of the solution operators will be dealt with the method of trajectories. The project is expected to open entirely new perspectives in the theory of dynamical systems and to considerably expand the understanding of complex behaviour of dynamical systems in continuum thermodynamics.

Aims

The goal of the project is to build the theory for behaviour of infinite-dimensional dynamical systems, which attractor set does not exist a priori. We focus on such systems that are used in continuum thermodynamics and allow the exchange of energy and matter with the surroundings.

The equilibrium theory of biodiversity dynamics - macroecological perspective

Prof. David Storch, Ph.D. | Univerzita Karlova - Centrum pro teoretická studia

Abstract

Variation of biological diversity in space and time is a main topic of ecology. During the last decade, evidence accumulated that diversity dynamics may be equilibrial, i.e. diversity has a tendency to stabilize at regional scales. Understanding the determinants of diversity equilibria and to what extent diversity deviates from equilibria is crucial for understanding future biodiversity changes. Recently, we have proposed a general species-based theory of diversity dynamics that makes predictions concerning the interplay between resource abundance (productivity), environmental stability and species origination rates in determining equilibrium diversity patterns. The aim of the project is to further develop the theory to address spatial dynamics and scale-dependence, to test its individual building blocks and assumptions, and to explore its consequences. We will employ a broad suite of methods, including mathematical analysis, computer simulations, macroecological analysis of large-scale biodiversity data, and analysis of paleontological time series.

Aims

To develop and test, using diverse data sets, the species-based equilibrium theory of biodiversity dynamics which states that macroecological diversity patterns are driven by regionspecific diversity equilibria given by the interplay of resources, environmental fluctuations and origination rates.

ÅrchitectRonics of Two-dimensional crystals via synergy of chiral electro-chemical and opto-electronic concepts on Å-scale

doc. RNDr. Ing. Martin Kalbáč, Ph.D. | Ústav fyzikální chemie J. Heyrovského AV ČR, v.v.i.

Abstract

The goal of the ÅRTdECO is to achieve a connection between intrinsic physics and the chemistry of Å-thin, two-dimensional (2D) crystals, which lay the foundation for groundbreaking concepts in opto-electronics. We formulate platforms that accommodate multiple intrinsic chirality, including geometric and Berry phase-induced chirality, using ultra-clean 2D lattices with chiral selectivity and a dynamic remote control. The valley-selective emissions and superradiance of the 2Ds are manipulated by electrochemical means by controlling carrier concentration. Next, selective interactions between 2D chiral species are managed using magnetic substrates that stabilize chiral chemical analogues of van der Waals heterostructures. Finally, the power of chemical–electrochemical control is released by applying experimental protocols in ultra-high vacuum conditions. The research strategy resonates with the current technology flagships in the European Union. Project outcomes have great potential for exploitation in nanoelectronics, quantum information, and artificial intelligence.

Aims

The project seeks to achieve electrochemical and chiral manipulation of excitons and superradiance in platforms based on ultraclean 2D lattices and chiral molecules to create multiple types of intrinsic chirality, such as geometric and Berry phase-induced chirality.

Observance Reconsidered: Uses and Abuses of the Reform (Individuals, Institutions, Society)

Doc. Antonín Kalous, Ph.D. | Univerzita Palackého v Olomouci - Filozofická fakulta

Abstract

The fifteenth century in Europe is regarded as a period of reform responding to a critical situation in the Church. Reform ideas spread from urbanised Italy (in form of popular piety, religious orders) to other parts of Europe, where they were confronted with similar local efforts. In central European context, this confrontation is best exemplified by John of Capistrano, the Observants and their diffusion in the region on the one hand, and by Jan Hus and the HussiteUtraquist tradition on the other. The project emphasizes the contrasts and parallels between the Catholic reform and that of the nascent stage of the European Reformation. In the Bohemian Lands and surrounding regions such a task needs to start with editions and analyses of unpublished sources. This work provides basis for interpretative studies, which will focus on urban communities and the reception and reflection of reform in local contexts. Based on previously unpublished material, the project will illuminate the manifold, often conflicting developments leading to the early modern division in Western Christendom.

Aims

“The project will:
a) make accessible important texts related to social and religious developments in Italy and Central Europe,
b) evaluate local and central sources of reform,
c) analyse the origins of social acceptance of the reform in the 15th and 16th centuries from a new perspective.”

Inferentialism naturalized: norms, meanings and reasons in the natural world

prof. RNDr. Jaroslav Peregrin, CSc. | Univerzita Hradec Králové - Filozofická fakulta

Abstract

The doctrine of inferentialism, based on the idea that meaningfulness is a matter of rules of inference, was first presented in Robert Brandom`s book “Making it explicit” in 1994. Since then, inferentialists (ourselves included) have further developed the logical and semantic dimensions of this view, making it into one of the most discussed philosophical doctrines of the twenty-first century. However, inferentialism is usually conceived of as a purely philosophical doctrine that provides a new perspective on uniquely human rational and expressive capacities, but which does not intersect with what science tells us about us as (hyper)social creatures with a natural, cultural and developmental history. We find this a missed opportunity and our project aims to bridge this crevasse by drawing on the current scientific research on cooperation, conventions, norms, language and reasoning to explain the ontogeny and phylogeny of the inferential rules that constitute meaning. This project will thereby build a naturalistic foundation for inferentialism.

Aims

The aim of the project is to produce a thoroughly naturalized version of inferentialism, which would result from a confrontation of the ideas tabled by the philosophy of inferentialism with the cutting-edge empirical research on cooperation, conventions, norms, language or reasoning.

Uncovering of missing genetic components and new chemical regulators of juvenile hormone signaling

prof. RNDr. Marek Jindra, CSc. | Biologické centrum AV ČR, v.v.i.

Abstract

Juvenile hormone (JH) is a sesquiterpenoid unique and vital to insects, many of which have immense economic (pollinators, pests) and health (disease vectors) impact on humanity. Despite progress incited by our discovery of the intracellular JH receptor (JHR), understanding of JH action remains incomplete. Means of controlling insect development are limited by lack of JHR antagonists or adequately selective agonists. To discover such compounds, we team up with a national infrastructure CZ-OPENSCREEN and utilize JHR to devise cell-based, highthroughput chemical screens. Parallel RNAi screens built on this platform are to identify missing players in JH signaling, such as a hypothetical cell-membrane JH receptor. These systems approaches are complemented by genetics in the Drosophila model and supported by international collaboration with leading experts. Besides fundamental knowledge on the endocrine regulation of development, the project should yield new chemistry for research and for potential use in insect growth regulation. It will also create background for a future ERC proposal.

Aims

Discover chemical antagonists and selective agonists of the juvenile hormone (JH) receptor as new research tools and insect growth regulators. Find unknown genes that effect cell membrane-initiated and nuclear branches of JH signaling during development. Establish grounds for a future ERC project.

In vivo mammalian RNAi revival

prof. Mgr. Petr Svoboda, Ph.D. | Ústav molekulární genetiky AV ČR, v.v.i.

Abstract

RNA interference (RNAi) is an ancestral antiviral innate immunity pathway abandoned during vertebrate evolution. The project seeks to understand how RNAi could be restored in vivo without significant negative effects and if augmented RNAi could provide broad antiviral defense. The project stems from ERC project D-FENs and will lay foundations for another ERC project aiming on converting knowledge of canonical RNAi and its constraints into a safe antiviral system deployable into infected cells. The research plan has three parts: 1) Analysis of effects of augmented RNAi in vivo. Using our mouse models, we will a) estimate genetically-induced RNAi pathway activity in different tissues and cell types, b) assess detrimental effects of RNAi in cells, organs and the whole mouse, and c) analyze competition, cooperativity & redundancy between RNAi and mammalian antiviral innate immunity. 2) Mechanistic understanding of RNAi activation. This part will clarifying the molecular mechanism behind the phenomenon of augmented RNAi. 3) Evaluation of strategies for augmenting RNAi for therapeutic use.

Aims

“To understand
1) how RNA interference, an ancestral antiviral innate immunity pathway lost during vertebrate evolution, could be safely restored in mammals in vivo without major negative effects,
2) what’s its functional range for antiviral defense,
3) how could it be used in antiviral therapy.”

Holistic exposure and effect potential assessment of complex chemical mixtures in the aquatic environment

doc. Mgr. Roman Grabic, Ph.D. | Jihočeská univerzita v Českých Budějovicích - Fakulta rybářství a ochrany vod

Abstract

The project will develop a conceptual framework for risk assessment of chemical mixtures and improve understanding of the cumulative risk from regulated and emerging bioactive chemicals present in surface waters. The methodology will combine innovative methods for exposure characterization using passive sampling, with bioanalytical tools for identifying its potential effects. A newly developed battery of high-throughput bioassays will address crucial mixture effects on endocrine disruption and (neuro)development, and focus also on relevant but little explored mechanisms of action including disruption of thyroid hormone signalling. Combination of high-throughput target and nontarget analyses using advanced high-resolution mass spectrometry together with fractionation and pull-down approaches will enable to characterize complex pollution scenarios and identify responsible effect drivers. The predictability of the bioanalytical responses towards real environmental situation will be assessed by investigation of in situ chemical impacts on exposed fish and invertebrates.

Aims

The project will provide a conceptual framework for risk assessment of complex mixtures of organic chemicals and for the identification of major effect drivers in surface waters by integrating innovative passive sampling, comprehensive instrumental analysis and bioanalytical tools.

Electrochemical Synthesis of Porphene

prof. RNDr. Josef Michl, CSc. | Ústav organické chemie a biochemie AV ČR, v.v.i.

Abstract

Porphene, a two-dimensional polymer with fourfold symmetry, has recently been prepared in our laboratory as large (up to 0.1 mm) double sheets by coupling Zn-porphyrin on water surface using a chemical oxidant. Its structure is analogous to that of graphene, but contains fused porphyrin rings instead of benzene rings (from grazing incidence X-ray diffraction). The ability of the porphyrin macrocycle to bind various metal cations carrying two, one, or no additional ligands implies that porphene is not a single polymer but a family of two-dimensional polymers with an identical fully conjugated pi-electron system, yet with tunable properties. We shall investigate the mechanism of porphene formation and try to replace the chemical oxidant with two-dimensional anodic oxidation in an effort to maximize the size of single crystalline domains within the sheets. Thereafter, attention will be paid to exfoliation of the bilayer and determination of fundamental spectroscopic, structural, chemical, electrical, and mechanical properties of porphene bilayers and monolayers.

Aims

Develop a new method of porphene synthesis that promises large single crystalline domains, prepare and characterize it.

Biogenesis and evolution of telomerase in plants

prof. RNDr. Jiří Fajkus, CSc. | Masarykova univerzita - Středoevropský technologický institut

Abstract

Telomere biology belongs to hot research topics due to its attractive links to cell ageing and immortality, genome stability, and pathogenesis of severe human diseases including cancer. Our research in plants contributed to this field, among other things, with the observations of: i) reversible regulation of telomerase activity and its coupling with cell proliferation; ii) evolutionary changes in plant telomere DNAs. Mechanisms underlying these phenomena, however, have not been known. The answer is presumably hidden in the most important telomere factor – the telomerase. Recently we identified templating telomerase RNA subunits across land plant phylogeny, which not only explains the observed evolutionary switches between diverse telomere repeats but allows us – in association with known catalytic telomerase subunits and other associated proteins – to address a problem of telomerase biogenesis in plants. Using a multidisciplinary approach, we aim to characterise distinct steps in telomerase assembly, with the focus on the presumed scaffolding role of telomerase RNA in this process.

Aims

“1. To elucidate transcriptional control of genes coding for plant telomerase RNA subunits (TRs).
2. To identify and examine structural motifs in TRs and their functions.
3. To clarify roles of other factors involved in telomerase biogenesis.
4. To characterise a process of evolutionary TR changes.”

Novel Functionalized (Bio)polymers Based on DNA Display of Small Molecules

prof. Ing. Michal Hocek, CSc., DSc. | Ústav organické chemie a biochemie AV ČR, v.v.i.

Abstract

The project aims at development of chemical and enzymatic synthesis of sequence-specific hyper-functionalized monodispersed polymers based on DNA or RNA scaffold containing all 4 (or even 6) modified bases. We will design and synthesize the nucleos(t)ide monomers, develop the chemical and polymerase synthesis of modified oligonucleotides and libraries of sequences and study their folding and assembly. They will be used for selection of aptamers against selected undruggable proteins. The aptamers will be further optimized and we will study their biological activity.

Aims

“(i) Development of chemical and enzymatic synthesis of hypermodified polymers based on DNA or RNA oligonucleotides with 4 or 6 modified bases, study of folding and assembly.
(ii) Synthesis of libraries of sequences, selection of aptamers against target proteins and study of biological activity.”

SubTHz on-chip devices for controlling protein nanomachines

Ing. Michal Cifra, Ph.D. | Ústav fotoniky a elektroniky AV ČR, v.v.i.

Abstract

Proteins are highly evolved natural nanomachines with a great nanotechnological potential. To be employed in nanotechnology to perform various tasks, their function needs to be controlled, what is typically done via chemical modifications. However, such methods are resource demanding and cumbersome. Here we take on a grand challenge of modulating protein function by coupling subTHz pulses to protein subTHz vibration modes, which govern protein function. To that end, we will design, fabricate and test unique subTHz on-chip devices employing advanced electromagnetic concepts to intensify wave-protein interaction and to monitor the effect of pulses on the tasks performed by proteins nanomachines using ultrafast super-resolution microscopy. The project will generate advanced electromagnetic tools and devices enabling subTHz-based control of protein nanomachine ensembles. We expect ground-breaking impact in nanotechnology based on new possibilities in the engineering of electromagnetic wave-matter nanoscale interaction.

Aims

“1.Develop microfluidic chip devices for subTHz spectroscopy and for subTHz pulse modulation of protein nanomachines function
2.Build subTHz spectroscopy and pulse systems integrated to advanced microscopies
3.Model and experimentally test subTHz spectra and subTHz control of protein nanomachines”

EXPRO 2019

Intertwined biogenesis of photosystems I and II: born together to work together

Prof. RNDr. Josef Komenda, DSc. | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

The key molecular machines of oxygenic photosynthesis are Photosystem I a II (PSI a PSII), complicated membrane complexes containing a number of proteins and cofactors. The way photosystems are built in the cell is still poorly understood. In a current model PSII is formed by a combination of modules consisting of a large chlorophyll-protein associated with small subunits and pigments under guidance of many auxiliary proteins. PSI biogenesis is expected to use distinct machinery and its early phase remains unclear. However, recent data indicate that biogenesis of both photosystems is tightly intertwined and performed by common cellular machinery integrating chlorophyll biosynthesis. To solve the organization of this cellular factory, its location and photoprotection, we employ the cyanobacterium Synechocystis 6803 and a number of its mutants. We use a variety of physiological, biophysical and biochemical methods including isolation and 2D analysis of protein complexes combined with protein and chlorophyll radiolabeling, mass spectrometry and confocal and cryo-electron microscopy

Aims

To verify hypothesis about intertwined biogenesis of both photosystems and elaborate its model. In connection with this to elucidate early phases of Photosystem I biogenesis, determine structure, location and photoprotection of the PSI/PSII biogenesis centre and role of auxiliary factors in it.

EVOLUTION AND POST-EMPLACEMENT HISTORY OF CARBONATITES: IMPLICATIONS FOR THE MOBILITY AND CONCENTRATION OF CRITICAL METALS

Doc. Jindřich Kynický, Ph.D. | BIC Brno spol. s.r.o.

Abstract

Carbonatites are rare igneous, carbonate-rich rocks derived from the Earth’s upper mantle. They are important because of their associated rare-metal mineralization. Rare metals, such as REE, Nb, Ta, Zr, Th and U, are initially concentrated early in the evolution of carbonatitic magma to form primary mineralization. The behavior of these metals during deformation and metasomatic processes (a series of textural, chemical and mineralogical changes of REE mineralization) is one significant aspect of carbonatite petrogenesis that has direct implications for the economic potential of these rocks. A significant number of carbonatites were emplaced in tectonically active settings, where they were subjected to metamorphism and underwent a series of changes affecting the distribution of REE, Nb and other rare metals in the host rock. This project challenges us to study evolution of carbonatites in order to better understand the factors that controls late-stage element fractionation effects of subsolidus processes on redistribution of rare metals.

Aims

The aim of the project isn to understand what are subsolidus processes, redistribution of rare metals and to develop a globally applicable metallogenetic model, or set of simplifying models for carbonatites in different geotectonic possitions.

Macroecology of plant invasions: global synthesis across habitats (SynHab)

prof. RNDr. Petr Pyšek, CSc. | Botanický ústav AV ČR, v. v. i.

Abstract

Studies on determinants of regional variation in numbers of naturalized plants largely overlook one key factor, which is the type of habitat that is invaded. This is because at global scale there is, despite intensive research, still lack of rigorous data on habitat affinities of alien species, both in their native and invaded ranges. SynHab will collect such data and provide so far the most robust generalizations of patterns and macroecological determinants of invasions worldwide, by employing habitat affinities together with a wide range of interacting factors – environmental, climatic, and socioeconomic, as well as biologically relevant species traits, residence times, pathways and propagule pressure. To yield a more detailed understanding of the mechanisms that are at play at finer scale, this big picture will be supplemented by zooming in on plant invasions in different types of natural habitats in protected areas. This will inform us about filtering from regional pools of alien plants into habitats with different position along the disturbance and propagule pressure continuum.

Aims

To evaluate, based on newly built global databases of habitat affiliations of naturalized plants and of invasions in protected areas, the factors determining regional diversity in plant invasions. To find out the role played by habitats interacting with a wide range of other relevant factors.

Fototrofní Gemmatimonadetes (PhotoGemm+)

Mgr. Michal Koblížek, Ph.D. | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

Four years ago we discovered a new phototrophic bacterium belonging to understudied phylum Gemmatimonadetes. Genetic analysis suggested, that this organism acquired photosynthesis via horizontal gene transfer of the complete photosynthesis gene cluster from purple bacteria (phylum Proteobacteria). This is the only known example of horizontal transfer of the complete package of photosynthetic genes among very distant organisms. The main scientific questions of this project are: 1) what are the necessary prerequisities on the side of the receiving organism for the successful transfer of photosynthesis between distant bacterial groups, 2) how much the photosynthetic apparatus changed during the evolution in Gemmatimonadetes from its original proteobacterial design, 3) how is photosynthesis integrated into its metabolism and regulation. To address these questions we propose a multidisciplinary project integrating classical microbiology, genomics, biochemistry, molecular biology and state-of-the art biophysical methods.

Aims

The aim of the project is to obtain a detailed cryoEM structure of photosynthetic complexes in Gemmatimonadetes. Characterize how the PS complexes are integrated into their membrane system. Describe how photosynthesis is integrated into their metabolism, and how they regulate the gene expression.

Homotopy and Homology Methods and Tools Related to Mathematical Physics

prof. Ing. Branislav Jurčo, DSc. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

This is a project in pure Mathematics driven by needs of Mathematical Physics and leading to applications on both sides. Homology and Homotopy are the key concepts allowing to handle extremely complicated algebraic structures unavoidable in algebraic topology, global analysis and geometry, and related fields in modern mathematical physics. We shall develop and extend essential tools including homotopical algebra for generalized operads, minimal models for quantum homotopy algebras, constructions of the category of loop homotopy algebras and their generalizations, quantization of higher Chern-Simons theories, study of T-duality, representations of Chekanov-Eliashberg algebras, constructions of generalized (co)homology theory for spaces with symmetries, BGG resolutions for singular infinitesimal character, description of higher symmetries for invariant operators, and description of curved versions of Juhl’s branching operators using ideas of semi-holonomic jet spaces. Although seemingly diverse, all these goals share a lot of motivation and potential applications.

Aims

We aim at innovative bridging of our expected topological and algebraic results with new emerging areas and applications in Mathematical Physics. At the same time, the advanced algebraic techniques and structures will lead to unexpected results in geometric analysis. Both aims are strongly related.

Ferroelectric skyrmions

Ing. Jiří Hlinka, Ph.D. | Fyzikální ústav AV ČR, v.v.i.

Abstract

Domain walls in ferroelectrics are naturally formed 2D solitons with a defined, nm-thick polarization profile stable over macroscopic lateral dimensions. Strong coupling of the polarization gradient with strain drastically changes the material properties within the domain wall thickness. Increasing attention is paid to these mobile interfaces because the characterization tools have recently reached the desired nanoscale resolution, needed to uncover the rich spectrum of new phenomena expected there. We are convinced that some ferroelectrics can also host 1D analogues of domain walls, i.e. spontaneously formed ferroelectric line solitons, similar to the recently experimentally confirmed Bogdanov-Yablonskitype magnetic skyrmion lines. We wish to extend the explorations also to these interesting topological objects and to pave a path to the experimental discovery of the ferroelectric skyrmion phases, analogous to the vortex states in superconductors and skyrmion phases of chiral magnets.

Aims

1. Provide phenomenological analysis of ferroelectric skyrmion host material requirements 2. Search for plausible skyrmion hosts using databases of crystalline structures and atomistic modeling 3. Investigate properties of selected real materials, susceptible to show ferroelectric skyrmions

Centre for European Vegetation Syntheses (CEVS)

Prof. RNDr. Milan Chytrý, Ph.D. | Masarykova univerzita - Přírodovědecká fakulta

Abstract

Fine-resolution continental-scale syntheses of vegetation and habitat diversity are a new research agenda that opened once our team created a fundament of European data infrastructure: European Vegetation Archive (EVA), an integrated database of 1.5 million vegetation plots. There is a high demand for such studies in macroecological and biogeographical research, but also in applications, especially in international decision making and planning of nature conservation. The aim of this project is to establish a European centre for vegetation syntheses with an extensive network of international collaborators. This centre will (1) further develop the research infrastructure including specialized analytical software, standardized data flows and databases of vegetation-plots, vegetation types and species; (2) prepare synthetic European studies of habitat and vegetation typology, their species, phylogenetic and functional diversity, and the levels of invasion by alien species; (3) provide the results obtained to the public via an online portal.

Aims

“(1) Establishing an international centre for European vegetation syntheses.
(2) Further developing analytical and data infrastructure for such syntheses.
(3) Synthesize diversity of European vegetation and habitats at multiple levels.
(4) Provide the results to the public via an online database.”

From Performativity to Institutionalization: Handling Conflict in the Late Middle Ages (Strategies, Agents, Communication)

Mgr. Pavel Soukup, Ph.D. | Filosofický ústav AV ČR, v.v.i.

Abstract

This project aims to comprehensively research the conflicts in Central Europe during the long fifteenth century. In three thematic strands, it approaches (1) religious and ideological controversies, (2) conflicts surrounding members of the Luxembourg dynasty, and (3) social tensions and disputes. The peculiar situation in the Czech Lands after the Compactata treaty of 1436, which officially ended the Hussite wars, is understood as an ‘institutionalized conflict’. Despite the stabilized situation which allowed the evolution of an Estate system, neither party (Catholic nor Hussite) could accept the correctness of the other’s faith without jeopardizing their own legitimacy. Seen as intertwined issues, the strategies of conflict management employed by individual actors, the communicative and performative aspects of controversies, and the evolution of institutions in a divided society will render a more adequate and nuanced image of the Late Middle Ages in Central Europe as a contentious period.

Aims

“1) to research late medieval conflicts from the perspective of both religious and political history
2) to clarify how conflicts affected social organization and its normative frameworks
3) to find out how actors used disputes as instruments of legitimation and what communication strategies they employed”

AQUAPARA-OMICS: Aquatic parasitism meets biomics - addressing key biological questions using novel datasets and modern analytical tools

prof. RNDr. Tomáš Scholz, CSc. | Biologické centrum AV ČR, v.v.i.

Abstract

Parasitism is one of the most successful lifestyles of living organisms. Despite the majority of parasites being aquatic, at least during part of their life cycle, comprehensive molecular datasets for them are still scarce. AQUAPARA-OMICS aims to explore the uncharted biodiversity of greatly undersampled groups of aquatic parasites such as the Myxozoa and Dicyemida, and monitor selected human and fish pathogens, by eDNA metabarcoding. Production of new genomic and transcriptomic datasets of basal neodermates, parasitic cnidarians and dicyemids will allow us to unveil their parasitic origin, evolutionary history and characterize unique and shared genomic traits. AQUAPARA-OMICS further aims to explore key genes and molecular mechanisms involved in parasite development, replication, survival strategies and host immune responses. This includes basic research related to the functional characterisation of candidate molecules for future studies on new therapies and vaccine developments, which are urgently required for emerging aquatic pathogens.

Aims

The principal goal of the project is to address some of the key questions related to evolutionary and functional aspects of parasitism, biodiversity and host-parasite interactions in the aquatic realm using different -omic approaches and complementary methodologies.

Molecular and functional analysis of casein kinase 1 biology

prof. Mgr. Vítězslav Bryja, Ph.D. | Masarykova univerzita - Přírodovědecká fakulta

Abstract

The aim of this project is to fill several major gaps in our understanding of casein kinase 1 (CK1) mediated cellular functions. CK1 acts as a component of several developmental pathways such as Wnt, Hedgehog or Yap/Taz that are important drivers of tumorigenesis. In this grant proposal we want to understand how CK1 gets activated and mediates the Wnt signalling pathway, a key signalling machinery dependent on CK1. Further, we will identify unique protein targets of individual CK1 isoforms in developmental signalling pathways, and analyse the biological consequences of the selective inhibition of CK1 isoforms in the context of chronic lymphocytic leukemia (CLL), a disease with the proven sensitivity to CK1 inhibition. We will take advantage of the state-of-the-art integrated structural biology, RNA Sequencing and global proteomic analyses in combination with standard cell physiology techniques. This work will provide mechanistic insight into the role of CK1 isoforms and will pave the avenue for the use of isoform-specific CK1 inhibitors in the treatment of cancer.

Aims

“(i) describe mechanistically the CK1 action in the Wnt signalling pathway
(ii) identify unique and non-redundant functions of individual CK1 isoforms in the developmental signalling pathways
(iii) analyse the biological consequences of the selective inhibition of CK1 isoforms in the context of CLL”

Relation between structure and function of carotenoids: New pathways to answer unresolved questions

prof. RNDr. Tomáš Polívka, Ph.D. | Jihočeská univerzita v Českých Budějovicích - Přírodovědecká fakulta

Abstract

The project aims to disclose the relation between structure and function of carotenoids by means of the methods of time-resolved spectroscopies extending from femtosecond to microsecond time scales. To find answers to the yet-unresolved questions of carotenoid photophysics, we propose to study excited-state properties of carotenoids both in solution and in proteins under conditions of excess energy that will be delivered either by exciting higher carotenoid energy states by UV radiation, or by working under elevated temperatures. Data obtained under these, so far unexplored, conditions will be compared with those measured at lower temperatures or after excitation of lower excited states. The ultrafast experiments will be carried out not only in the standard pump-probe regime, but also in advanced experimental schemes such as multipulse (pump-dump-probe) or two-photon excitation ultrafast spectroscopy. We plan to explore the influence of specific functional groups of carotenoids and their role in tuning the light-harvesting and/or photoprotective actions in biological systems.

Aims

to elucidate the influence of specific functional groups on photophysics of carotenoids; to find how the carotenoid structure relates to the function in biological systems; to reveal specific carotenoid-protein interactions allowing switching between light-harvesting and photoprotective functions

DyMoDiF - Dynamic Models for the Digital Finance

Prof. Wolfgang Karl Haerdle, Ph.D. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

The recent availability of large digital finance datasets brings new challenges to quantitative finance. Many of the classical financial econometric or optimization models become inappropriate or intractable when applied to digital finance data. Vast quantities of information available in every moment require improvement of the classical methodology, in order to understand correctly the information hidden in the data, as well as to model and predict any dynamic behavior. The project will contribute to the debate, and propose new methodologies, which will take the high-frequency structure of the data as the advantage and turn the ”curse of dimensionality” into ”blessing of dimensionality’’. In particular, new models for the dynamic risk measuring, optimal decision making and advanced asset pricing will be developed, analyzed and implemented. These models will help to better understand and explain the complex changes in financial world induced by upcoming digital age.

Aims

The goal of the project is to develop, analyze and implement new dynamic econometric and optimization models for risk measuring, asset pricing and optimal decision making for digital finance data in order to explain the complex changes in financial world induced by upcoming digital age.

Old Myths, New Fact: Czech Lands in the Centre of 15th-century Music Developments

doc. PhDr. Hana Vlhová-Wörner, Ph.D. | Masarykův ústav a Archiv AV ČR, v.v.i.

Abstract

Modern formation of the Czech identity is based, among other things, on reflection of the Hussite period, in which music took the role of the main medium for communication of new ideas. Surveys on 15th-century music, its repertory character and relationship to the European development is marked, from the 19th-century, by deliberate manipulation of historical facts and intentional dogmas about its esthetic value. This also affected descriptions of early music in Bohemia in a broader European context that is built on an insufficient, or even erroneous, understanding of a specific Central European development. General historical surveys refer to the Czech lands with terms such as “discontinuity”, “isolation”, “simplification”, or “delay”, when historical sources clearly indicate the opposite. The “myth” about the exclusive role of the Hussite tradition crucially influenced 19th- and 20th-century music composition, where pieces reflecting Hussite legacy, including those that quote erroneous reconstruction of Hussite tunes, were used to evoke Czech national feelings.

Aims

To evaluate historical repertory and put it into a European context; propose a new view on exceptional cultural phenomenon in the academic community; correct erroneous ideas about 15th-century music development in Bohemia, regarding ongoing debates on common European cultural legacy and integrity

Testing mechanisms that maintain high species diversity in food webs by experimental manipulation of trophic cascades in a tropical rainforest

Prof. RNDr. Vojtěch Novotný, CSc. | Biologické centrum AV ČR, v.v.i.

Abstract

This project aims to explain ecological and evolutionary mechanisms allowing the existence of highly complex food webs in tropical rainforests, a long-standing conundrum of tropical ecology. It is an experimental test of the Janzen-Connell hypothesis postulating that top-down effects by herbivores and/or pathogens maintain high plant diversity as they lead to negatively densitydependent population dynamics favouring rare plant species. We hypothesize that pathogens and herbivores shared among closely related plant species lead to apparent competition among plants that strengthens the Janzen-Connell effects, while the impact of predators on herbivores can drive vegetation dynamics in the opposite direction, reducing the positive impact of herbivores on plant diversity. We examine these tri-trophic effects in phylogenetic context, exploring evolutionary scenarios of anti-herbivore defence by rainforest plants. The study will take place in Papua New Guinea. It will contribute to indigenous rainforest conservation and engage local paraecologists and students.

Aims

The aim is to explain mechanisms allowing coexistence of high numbers of species in tropical forest food webs. It is an experimental test of the Janzen-Connell hypothesis that plant diversity is maintained by pathogens and herbivores, extended here to the effects of predators and competitors.

Modelling the future: Understanding the impact of technology on adolescent’s well-being

prof. PhDr. David Šmahel, Ph.D. | Masarykova univerzita - Fakulta sociálních studií

Abstract

Although impacts of technology usage on well-being have been examined from the onset of Internet development, the existing research lacks consistency and complexity in capturing diverse dimensions of well-being. Further, the advancing technological development creates a need for models enabling the prediction of future technology impacts based on comprehension of the general principles related to technology’s effects. Acknowledging these gaps, this project will develop a complex integrative theory depicting the short- and long- term impacts of technology usage on adolescents’ physical, psychological, and social well-being. We will integrate theories from diverse fields, notably media studies, psychology, and health. The theory development will be based on empirical data from (1) existing research, (2) 3-wave longitudinal study, (3) series of experimental studies, and (4) intense data collections with the support of innovative research tools. The project will develop prospective models that will help to understand and predict future impacts of technology on well-being.

Aims

The project aims to develop a complex evidence-based theory depicting the impacts of technology usage on physical, psychological, and social wellbeing of adolescents aged 11 to 18. Innovative research methods based on the software using artificial intelligence will be developed.

Principal mechanisms of peripheral continental growth during supercontinent cycle

prof. RNDr. Karel Schulmann, CSc. | Česká geologická služba

Abstract

The growth of eastern Pangea involves three contrasting orogenic cycles: 1) Baikalian cycle (570-540 Ma) consists of accretion of peri-Rodinian continental, Mirovoi and Panthalassan oceanic fragments to the Siberian margin followed by extensional HT reworking, the growth of magmatic arc, giant accretionary wedge and intraoceanic basin. 2) Altai cycle is typified by crustal thickening followed by syn-extensional melting of the accretionary wedge (420-380 Ma) and the opening of Mongol-Okhotsk ocean. Cycle terminates by the growth of migmatites domes (370-340 Ma), thrusting of intraoceanic ophiolites and relamination of molten material beneath oceanic crust. 3) Paleotethysian cycle (300-220 Ma) is represented by oroclinal buckling of the hybrid oceanic lithosphere. The Baikalian cycle is related to advances and retreats of Panthalassa ocean. Altai cycle results from dynamically advancing and retreating subduction of young and hot Rheic type ocean beneath Pacific one. This hot, weak and hybrid lithospheric segment was shortened and incorporated into Pangea supercontinent.

Aims

“1) Characterize orogenic cycles using a multidisciplinary approach.
2) Understand and model mechanisms of formation of hybrid oceanic lithosphere resulting from subduction of a hot interior ocean.
3) Proposing a mechanistic model of incorporation of this lithosphere into the Pangea supercontinent.”

Concerted toxin action in Bordetella pertussis virulence

prof. Ing. Peter Šebo, CSc. | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

Under this proposal we shall test the hypothesis that by concerted action of its protein toxins, the whooping cough agent Bordetella pertussis compromises the barrier function of airway epithelia in the initial catarrhal phase of the infection. A set of specifically mutated B. pertussis strains will be used for intranasal infections in germ-free and airway microbiota-deficient mice and for in vitro infections of polarized airway epithelial cell layers, corroborating the results by defined toxin treatment. This will enable us to test if penetration of the adenylate cyclase toxin (ACT) through the basal side of airway epithelial cells, through ACT-produced cAMP intoxication, upregulates epithelial mucus secretion, opens CFTR chloride channels and provokes loss of tight junction integrity and paracellular fluid leakage, thus eliciting the initial pertussis phase coryza and enabling spread of the pathogen by sneezing and coughing. Using a comprehensive set of cell biology approaches we will then decipher the molecular mechanism of this ‘nasal diarrhea’ phase of pertussis.

Aims

The aim of the project is to decipher the mechanism by which the virulence factors of Bordetella pertussis compromise the barrier function of airway epithelia and provoke the initial catarrhal phase of the whooping cough disease that is characterized by massive mucus secretion and fluid leakage.

Efficient approximation algorithms and circuit complexity

prof. Mgr. Michal Koucký, Ph.D. | Univerzita Karlova - Matematicko-fyzikální fakulta

Abstract

The goal of this project is to understand the role of approximation in fine-grained and parameterized complexity and create solid foundations for these areas by developing lower bound techniques capable of addressing the key unproven assumptions under-pinning these areas. We will focus on several central problems: Edit Distance, Integer Programming, Satisfiability and study their approximation and parameterized algorithms with the aim of designing the best possible algorithms. Additionally we will focus on several methods of proving complexity lower bounds.

Aims

The goal of the project is to design faster and optimal algorithms for several key problems in fine-grained and parametrized complexity, and develop new lower bound methods capable of proving their optimality.

ADORable catalysts

prof. Ing. Jiří Čejka, DrSc. | Univerzita Karlova - Přírodovědecká fakulta

Abstract

Zeolites are an important class of solids that are key heterogeneous catalysts in many industrial processes and they are also used widely in ion-exchange, adsorption/separation and medical applications. In recent years, the applicant’s group has developed a new strategy to synthesize zeolites termed Assembly-Disassembly-Organization-Reassembly (ADOR). In a substantial body of preliminary work, the ADOR protocol has been used to synthesize 10 new zeolites, not yet prepared using traditional solvothermal methods. These studies were reported in several papers published at high-impact chemistry journals (Angewandte Chemie, JACS and Nature Chemistry). This project proposal focuses on the synthesis of new zeolites using the ADOR protocol and going beyond to prepare various modified ADOR materials for catalytic applications. We aim to further develop the ADOR method to prepare ‘unfeasible’ materials, particularly for important catalytic processes. Ultimately, the project aims to deliver a considerable new set of materials with adjustable active sites for acid and redox catalyzed reactions.

Aims

The first goal of the project is to use the ADOR methodology to target zeolites and related catalysts being difficult to synthesize – the so-called ‘unfeasible’ materials. The second goal is to utilize these novel zeolites as catalysts for important organic reactions to control their performance.

Terahertz and neuromorphic memories based on antiferromagnets

prof. Tomáš Jungwirth, Ph.D. | Fyzikální ústav AV ČR, v.v.i.

Abstract

Spintronic memories combine non-volatility with speed and are expected to complement conventional microelectronics as universal energy-efficient memories beyond the International Technology Roadmap of Semiconductors. The aim of the TERANEU project is to scientifically underpin future development of spintronic computer memories with speeds extended from the gigahertz to the terahertz range and the operation extended from the digital to the neuromorphic mode. The enabling materials are antiferromagnets and the research plan spans from fundamental exploration of topological phenomena and dynamics in these complex magnets, to imaging of magnetic textures, and designing artificial neural networks for realistic internet of things applications. The project builds on our recent discovery of electrical switching of an antiferromagnet by a relativistic spintronic effect, demonstration of a proof-of-concept antiferromagnetic memory with analogue characteristics compatible with common microelectronics, and initial experimental verification of writing by picosecond electrical-current pulses.

Aims

We will scientifically underpin future development of spintronic computer memories based on antiferromagnets with speeds extended from the gigahertz to the terahertz range and the operation extended from the digital to the neuromorphic mode.

Cytoskeletal mechanics of the growth cone steering

RNDr. Zdeněk Lánský, Ph.D. | Biotechnologický ústav AV ČR, v.v.i.

Abstract

Neuronal pathfinding is a foundational developmental process. Mechanical forces driving the pathfinding are generated in the growth cone, a distinct structure at the tip of neuronal axons. The progression of the growth cone is propelled by actin dynamics, while the direction of growth is governed by microtubules, implying that crosstalk between microtubules and actin filaments is essential for the growth cone steering. Although vital, this crosstalk and its impact on the steering is not understood. Here, we will elucidate the steering by focusing on the proteins that couple actin filaments and microtubules. These crosslinkers constitute the hubs of cytoskeletal activity, coupling the driving force to directionality. We will employ live cell imaging, in vitro reconstitutions, together with microsurgical and single molecule perturbations and mathematical modeling. We will provide mechanistic explanation of the actin-microtubule crosstalk enabling neuronal pathfinding – the fundament required for the development of diagnostic or therapeutic tools addressing neurodevelopmental disorders.

Aims

Identify the roles of actin-microtubule crosslinkers in the growth cone steering. Estimate how forces generated by the crosslinkers regulate the steering. Explain the mechanisms that crosslinkers employ to generate forces. Generate quantitative model of the cytoskeletal mechanics of the steering.

Control of electronic properties of metal-containing molecules through their noncovalent interactions with solvents, ligands and 2D nanosystems

prof. Ing. Pavel Hobza, DrSc., FRSC | Ústav organické chemie a biochemie AV ČR, v.v.i.

Abstract

The project aims to develop new materials to control structural and electronic properties of metal-containing molecules via i) noncovalent physisorption onto 2D nanostructures, e.g. graphene (gr) or heteroatom (N,B, or S)-doped gr, ii) via dissolving them in various solvents, and finally, iii) via their coordination with various ligands. Each step or their combination will allow for a rational design of molecular systems with tailored properties for new applications. The use of 2D-surfaces, solvents and various ligands as “noncovalent tuners” of electronic, magnetic, and optical properties of small molecules is an unexplored alternative to existing strategies to manipulate physicochemical characteristics of molecules by strong external stimuli, e.g. covalent bonding, temperature, pressure, or UV radiation. A combined computational and experimental approach will be used to explore nature of the spin crossover processes upon interaction with 2D nanosystems, solvents and various ligands.

Aims

“Control of structural and electronic properties of metal-containing molecules via
i) noncovalent physisorption onto 2D nanostructures, e.g. graphene or N, B, or S-doped graphene,
ii) via dissolving them in various solvents and
iii) via their coordination with various ligands.”

Neural Representations in Multi-modal and Multi-lingual Modeling

Doc. Ing. Lukáš Burget, Ph.D. | Vysoké učení technické v Brně - Fakulta informačních technologií

Abstract

The NEUREM3 project encompasses basic research in speech processing (SP) and natural language processing (NLP) with accent on multi-linguality and multi-modality (speech and text processing with the support of visual information). Current deep machine learning methods are based on continuous vector representations that are created by the neural networks (NN) themselves during the training. Although empirically, the results of NNs are often excellent, our knowledge and understanding of such representations is insufficient. NEUREM3 has the ambition to fill this gap and to study neural representations for speech and text units of different scopes (from phonemes and letters to whole spoken and written documents) and representations acquired both for isolated tasks and multi-task setups. NEUREM3 will also improve NN architectures and training techniques, so that they can be trained on incomplete or incoherent data.

Aims

Systematic study of neural structures for speech and text modeling in multi-modal and multilingual settings. Addressing hierarchy of neural representations, human interpretability, and training under realistic conditions of non-ideal and incoherent data.

The chemistry in two dimensions - beyond graphene

prof. Ing. Zdeněk Sofer, Ph.D. | Vysoká škola chemicko-technologická v Praze - Fakulta chemické technologie

Abstract

The single element layered materials beyond graphene attract huge attention in last years, but their chemistry and possibilities of chemical modifications remain, up to date, almost unknown. The project will focus on the synthesis, exfoliation and chemical modification of layered elements beyond graphene (silicene, germanene, phosphorene, arsenene and antimonene). Compared to graphene, these materials exhibit non-zero bandgap in the single layer form. The synthesis strategies will explore „top-down“ approach based on exfoliation methods as well as „bottom-up“ methods based on molecular beam epitaxy of monolayers. The chemical modification will be investigated using radical, nucleophilic and electrophilic reactions. The properties and reactivity of derivatives will be studied in detail. The non-covalent derivatization will be investigated in order to improve environmental stability of exfoliated materials. The chemistry performed on the surfaces of crystals will provide information about derivatization on an atomic scale using combination of microscopic and spectroscopic methods.

Aims

“1) Synthesis of silicene, germanene and layered pnictogens by “top-down” and “bottom-up” approaches.
2) Exploration of further modification of synthesized materials.
3) Non-covalent surface functionalization for stability improvement.
4) Characterization of the modified materials.”

2D Nanomaterials Electrochemistry

prof. RNDr. Martin Pumera, Ph.D. | Vysoké učení technické v Brně - Středoevropský technologický institut

Abstract

The overall aim of this project is to develop fundamental understating of the electrochemistry of the layered and 2D materials. These materials include monoelemental materials, such as layered pnictogens (black phosphorus, layered arsenic, antimony and bismuth); binary materials such as layered transition metal dichalcogenides, MXenes, and ternary materials such as metal phosphorus chalcogenides and and their monolayer (2D) counterparts. We will find the answers to profound basic electrochemical questions regarding layered and 2D materials, such as: A) What is the edge vs. basal plane electroactivity? What are general underlying rules? B) What is the influence of crystal structures on the electroactivity? Why? C) What is the size confinement effect on electrocatalysis? D) What is the influence of atomic composition variation of the materials on the electrochemistry? E) What is the role of heteroatom dopants, impurities and vacancies in the lattice of 2D materials on their electrochemistry and electrocatalysis? F) What is the influence of materials curvature on electrochemistry?

Aims

We will find the answers to profound basic electrochemical questions regarding layered and 2D materials. PI will apply for ERC-ADG and receive this grant (PI received ERC-StG) Group will be English spoken with all 5 postdocs from overseas institutions. Group will publish 50 papers in top journals.

Operational Images and Visual Culture: Media Archaeological Investigations

Prof. Jussi Parikka, Ph.D. | Akademie múzických umění v Praze - Filmová a televizní fakulta

Abstract

The project approaches contemporary visual cultures through the notion of the operational image. It expands the scope of the concept from its roots in artistic engagement with military imaging to encompass the new sorts and applications of automated visual systems embedded in everyday life and focuses on their cultural and social implications. While the aim of the project is to produce a rich set of research findings, methodological insights and theoretical positions that pertain to contemporary visual media, it articulates such current themes in relation to a longer history of visual culture through the perspective of media archaeology. Expected results include 1 single-author monograph, 2 joint authored books, 1 edited book including contributions by the team members and other international scholars, 20 articles in prestigious international journals, 5 international conferences, and an ERC grant proposal.

Aims

Establishing a research team led by an outstanding internationally recognized scholar to enhance the excellence and competitiveness of Czech research in the national priority area Social and Cultural Challenges.

Frontiers in Energy Efficiency Economics and Modelling - FE3M

Prof. Anna Alberini, Ph.D. | Univerzita Karlova - Centrum pro otázky životního prostředí

Abstract

This research aims at pushing the frontiers of research on energy economics and modelling. We examine the causes of the energy efficiency gap, focusing on adoption and substitution of energy durables by households, and investigate to what extent consumers are willing to provide some flexibility to the energy system through demand response. We use both revealed and stated preferences, investigating their validity where appropriate. Standard bottom-up and topdown modelling tools are enriched to better represent household behaviour. We focus on the uptake and use of energy efficient technologies, the welfare effects associated with environmental burden and the health externalities that energy production and energy use cause. We develop several hybrid models utilizing Agent Based Modelling, Energy System Optimisation, Computable General Equilibrium, Environmentally-Extended Multi-Regional InputOutput, and Impact Pathway Analysis, integrated in a comprehensive modelling tool.

Aims

Improving economic modelling of consumers’ preferences and behaviour related to new energy efficient technologies and flexible demand, energy system and transport modelling informed by behavioural parameters, and combining bottom up and top down approaches to develop a hybrid model.

Concert of lipids, ions, and proteins in cell membrane dynamics and function

prof. Martin Hof, Dr.rer.nat., DSc. | Ústav fyzikální chemie J. Heyrovského AV ČR, v.v.i.

Abstract

In a traditional view of cellular processes at membranes, proteins are central in determining biological functions, with membranes and ions providing a flexible scaffold and chemical environment. To understand the more interwoven picture of reality, we will use fluorescence techniques and molecular simulations on model membranes to unravel how the interplay between membranes with complex lipid compositions and topologies together with specific ions control signalling proteins and dynamics of membrane processes. We will i) establish the role of membrane domain boundaries in localization of proteins and their intermolecular interactions, ii) elucidate how the crosstalk between Ca2+, calmodulin, and lipid membranes regulates signalling proteins, and iii) determine mechanisms modulating calcium-induced membrane fusion which hold similarities with a yet systematically unexplored action of fusogenic peptides. The overall aim is to establish a novel understanding of the tight crosstalk between lipids, ions, and proteins in membrane processes such as cell signalling and membrane trafficking.

Aims

To determine what drives proteins accumulation at domain boundaries and its intermolecular consequences. To elucidate mechanisms of calcium-calmodulin-regulation of signalling proteins. To find the mechanism of passive membrane fusion and the common denominator of calcium and peptide induced fusion.

Genocide, Postwar Migration and Social Mobility: Entangled Experiences of Roma and Jews

Mgr. Kateřina Čapková, Ph.D. | Ústav pro soudobé dějiny AV ČR, v.v.i.

Abstract

Engaging with debates in Holocaust and genocide studies and social anthropology of marginality, the project approaches the histories of Jewish and Romani communities on the territory of the pre-war Czechoslovakia in comparative perspective. Nazi genocidal policies altered the culture, social makeup, religious outlook, and geography of both victim groups, creating a rupture that fundamentally influenced the subsequent geographic and social mobility of both groups. Only an interdisciplinary approach—bringing together sociology, anthropology and history—can help us create an integrated account of Romani and Jewish experiences in twentieth and twenty-first century Central Europe. A team of multidisciplinary scholars with expertise in Jewish and Romani studies will focus on Jewish and Romani entangled experiences during the war, its aftermath and its current resonances. Tangible results: 6 books (editions of documents, collective volumes, and individual book projects); 3 articles with impact; 11 articles in Scopus; 2 conferences; 2 international workshops; database of ego-documents.

Aims

The aim of the project is to analyze the genocide, the (forced) migration, and the social mobility of Roma and Jews side by side in selected local contexts on the territories which belonged to pre-war Czechoslovakia from 1938 to present by applying historical and anthropological research methods.

Compositional and orbital mapping of meteoroid sources in the Solar System

RNDr. Jiří Borovička, CSc. | Astronomický ústav AV ČR, v.v.i.

Abstract

The project is devoted to studies of various types of small bodies in the Solar System by means of observation of bright meteors. We have built a network of Digital Autonomous Fireball Observatories spread over Czech and Slovak territories and part of Austria. Spectral versions of the observatories have been installed only in the Czech Republic so far. We propose to install one spectral observatory in Slovakia and one in Germany. From our data, including supplementary video records, we can derive precise trajectories, orbits, and light curves of fireballs caused by centimeter to meter-sized meteoroids and study physical properties of meteoroids. Spectral data available for bright fireballs can be used to derive chemical composition of meteoroids. By combining physical, chemical and orbital data we will map various asteroidal and cometary sources of meteoroids and meteorites in the Solar System. Possible differences in Mg/Fe ratios in various comets will be evaluated. Parent bodies of Geminids and Taurids will be studied in detail. Orbits of some minor meteor showers will be improved.

Aims

Combine data on physical, chemical and orbital properties of large meteoroids to obtain information about location and nature of various sources of meteoroids and meteorites. Infer the nature of parent bodies of Taurid and Geminid meteoroid streams. Characterize chemically distinct meteoroids.

Non-periodic pattern-forming metamaterials: Modular design and fabrication

prof. Ing. Jan Zeman, Ph.D. | České vysoké učení technické v Praze - Fakulta stavební

Abstract

Mechanical metamaterials are the most convincing example of a bottom-up paradigm for the design of engineering materials, in which unprecedented macroscopic properties emerge from the collective response of carefully architectured microstructures. The major bottleneck in currently used metamaterials that exhibit reversible pattern formation is a microstructure periodicity. This project explores the framework of non-periodic tilings, in which material microstructures arise from a compatible assembly of a handful of jigsaw puzzle-like material modules. Successful application requires (i) new generalized continuum theories for understanding the emergent behavior of metamaterials with non-uniform microstructures, (ii) novel algorithms for the simultaneous optimum design of tiles and their assemblies, (iii) validation studies performed on optimized assemblies, and (iv) investigation of mechanisms for targeted self-assembly based on passive interface interactions. The merits of non-periodic modular design will be illustrated with two proof-of-concept demonstrators

Aims

The principal objective is to develop a novel approach to the design and optimization of mechanical metamaterials based on the concept of Wang tilings and metaperiodicity, and to validate our approach by manufacturing two proof-of-concept demonstrators.

The robotic nano-pharmacist: Next-generation manufacturing processes for personalised therapeutic agents

prof. Ing. František Štěpánek, Ph.D. | Vysoká škola chemicko-technologická v Praze - Fakulta chemicko-inženýrská

Abstract

The current methodologies of drug product and process design are based on the principle of formulating a single active ingredient into a dosage form whose parameters are based on population averages. On the other hand, personalised medicine requires the ability to design and manufacture customised pills with an adjustable, patient-specific content of a larger number of active ingredients. The aim of this project is to lay down the scientific and engineering fundamentals of future manufacturing processes that will enable the industrial manufacture of personalised medicines. We will investigate encapsulation methods of active ingredients to prevent their undesired interactions, methods of particle-level dissolution control, methods of integrating unit operations and automating the whole manufacturing process, and mathematical models enabling accurate prediction of in vitro and in vivo behaviour of a specific formulation.

Aims

“1. Research of manufacturing processes for personalised medicines
2. Dissolution control at the particle level
3. Combination of several actives into a single carrier
4. Research of biorelevant in vitro dissolution methods
5. Research of simulation methods for the prediction of in vivo behaviour”

STRUCTURAL BIOLOGY – NEXT GENERATION: from isolated molecules to cells, from cells to tissues.

Mgr. Lukáš Trantírek, Ph.D. | Masarykova univerzita - Středoevropský technologický institut

Abstract

Our comprehension of biological mechanisms as well as our capacity to exploit this knowledge for devising of novel bio-materials, molecular devices and/or effective therapeutics, critically depends on a detail knowledge of fundamental principles that governs structure, stability and interactions of biomolecules in living cells. Historically, for methodological reasons, biological processes are either investigated at low resolution in biologically relevant systems (organisms, tissues) or at high-resolution on biomolecules isolated from their native cellular environment. Although recent methodological developments have allowed gaining high-resolution insight into structure and interactions of biomolecules in intact cells, this insight remains limited to prokaryotic organisms and mammalian cells either cryogenically frozen or living cells cultured in asynchronous populations. Influence of natively fluctuating composition of intracellular environment, as a result of propagation of the cell cycle or organization of cells into tissues, on biomolecules’ structure/function remains elusive.

Aims

The project aims at establishing and applications of a novel in-cell NMR based approach for characterization of DNA/RNA and their complexes with ligands/proteins in: A] cells in specific stage of the cell-cycle, B] 3D cell cultures, and C] in cell cultures emulating mammalian tissues (organoids).

Structural study of enterovirus replication in situ

Mgr. Pavel Plevka, Ph.D. | Masarykova univerzita - Středoevropský technologický institut

Abstract

Viruses from the genus Enterovirus, including coxsackieviruses and rhinoviruses, cause billions of infections every year. However, no anti-enterovirus treatments are available. We aim to structurally characterize enterovirus replication in situ to enable the identification of macromolecular interactions that could be targeted by therapeutics. We will use focused ion beam milling and cryo-electron tomography to determine: (1) how enteroviruses deliver their genomes into the cell cytoplasm; (2) whether enterovirus replication “factories” in infected cells contain the multi-subunit complexes of RNA-polymerases that were observed in vitro; and (3) whether enterovirus capsids assemble around genomes or if the genomes are packaged into capsids. To facilitate the cryo-electron tomography studies we will develop: (1) patterned grids to enable automation of the focused ion beam milling of cell sections; and (2) a method to embed macromolecules in rod-shaped vitreous ice to allow the recording of more complete tomographic data than is possible with currently used slab-shaped samples

Aims

“1. In situ cryo-electron tomography of enterovirus replication.
2. Development of patterned electron microscopy grids to facilitate focused ion beam milling of cell sections.
3. Highresolution study of enterovirus genome delivery.
4. Use of nanotubes to record cryo-electron tomography data.”

Global and transcript-specific analysis of translational control in disease.

Dr. rer. nat. Leoš Valášek, DSc. | Mikrobiologický ústav AV ČR, v.v.i.

Abstract

Regulation of gene expression lies at the heart of all life. Among others, it can be achieved on the level of translation of genetic information from mRNA into protein. Evidence for the importance of proper translational control is overwhelming, as even a small disturbance in timing or fidelity of translation of specific mRNAs causes or accompanies many human diseases. Hence it is not surprising that genes encoding translation factors are frequently amplified or dysregulated in cancer. One example is the multitasking, multisubunit eIF3. To elucidate its involvement in oncogenesis, we will investigate all translatome changes in cells where eIF3 levels were manipulated on a transcriptome-wide scale by the 80S ribosome profiling. We will also develop and apply variants of ribosome profiling to 1) monitor changes of 40S subunit footprints in the 5’ UTR and around start/stop codons, and to 2) follow dynamics of selected translation factors transcriptome-wide in yeasts and mammals. Finally, we will study mechanics of ATF4 translation control under various stresses and the eIF3 role in it.

Aims

“a) Translation efficiency and ribosome distribution analysis in human cells with altered eIF3 expression.
b) Mammalian TCP-seq development and its application.
c) Yeast and mammalian IP-TCP-seq development to measure eIFs dynamics.
d) Mechanics of ATF4 translation control and the role of eIF3 in it.”