JUNIOR STAR projects - The Czech Science Foundation (GACR)

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.”