Hlavní řešitel: Fabien Jaulmes
Projekt: Computational modelling of fast ion orbits in tokamak plasmas
Alokace: 1 739 000 jádrohodin
Abstrakt: Nuclear fusion technology might enable us to generate energy without releasing large amounts of greenhouse gases into the atmosphere or leaving behind us long lived radioactive waste. Among the approaches to fusion, tokamak seems to be the most promising one. The concept involves the use of magnetic fields to confine plasma hot enough to sustain fusion within itself. Today, as a part of international project under the title ITER, a new tokamak is built in southern France. If successful, the device would be the first one of its kind to produce net energy. COMPASS is a small tokamak located in Prague, Czech Republic. It allows scientific investigation of various physics issues related to the operation of the future ITER. In particular this year, a new 80keV Neutral Beam Injection system is planned. The study and modelling of NBI-born particle behavior is of great relevance and might impact future design of the system and its integration in COMPASS, as well as in the planned upgrade of the machine in 2022 (COMPASS-Upgrade). We request here computational time for the modelling of the interaction of the fast particles with the background plasma. Our modelling tool, the EBdyna code with its new collisional features, has been benchmarked against the NUBEAM code on several test-cases.
Hlavní řešitel: Karel Sindelka
Projekt: Mesoscopic simulations of aqueous solutions in inhomogeneous environments
Alokace: 794 000 jádrohodin
Abstrakt: Aqueous solutions are omnipresent in nature, industrial processes and daily life. Understanding their behaviour in inhomogeneous environments (nanopores, self-assembled systems) is important in many key applications such as medicine or environmental protection. In this project, we focus on two aqueous solutions: surfactant adsorption on soft surfaces and solubilisation of small molecules into polymeric structures. We use mesoscopic simulations to provide the molecular-level insights into these water systems as well as to fill gaps in our understanding of the physical and chemical behaviour of these systems.
Hlavní řešitel: Olena Mokshyna
Projekt: Search for new anticancer compounds and investigation their mechanism of action
Alokace: 510 000 jádrohodin
Abstrakt: The development of novel anticancer agents is a long and complicated process, which involves an investigation of many potential targets for such therapies. In this project we are going to address several of such targets. Bystin is a compact protein involved in cell growths process. It was found that bystin is overexpressed in human cancer cells and promotes cell growth. Despite bystin being a promising target for anticancer drugs and drugs against blackfan anemia, no site of binding was previously identified. The only available crystal structures of bystin are those of pre-40S ribosomal subunit. No holo X-ray structures of bystin (i.e. bound to ligand) are available at the moment, and no ligands were previously described in literature. This project continues the study of bystin and its interaction with small molecule ligands. Our previous findings have shown that bystin has two primary shallow binding sites. For such binding sites identification of small molecules binding and explaining their activity is an extremely non-trivial task. We explored the mechanisms of binding of promising drug-like compounds studied in IMTM using a combination of docking methods and classical molecular dynamics. And we were able to establish stable binding poses for most of the ligands and distinguish two main groups of ligands with varying activity. This project aims to further explore bystin dynamics using enhanced sampling methods and perform free energy calculations of ligand-protein systems. We intend to employ a range of methods with emphasis on metadynamics simulations. This would allow to explore the ligands’ mechanism of actions in silico. The second target protein is CYP2w1 – one of the CYP450 kinases, which are the main metabolic proteins in human body. The uniqueness of CYP2w1 consists in the fact that it’s mostly expressed in tumor cells, not in healthy tissues. This feature makes CYP2w1 a potential target for selective anticancer agents. The potential drug would not only selectively bind to the metabolic site of the protein, but also turn to a cytotoxic compound, thus destroying a cancer cell, but not damaging the healthy tissues. At the moment, only a few such compounds are known. This project aims to perform big-scale (millions of compounds) virtual screening to select compounds with a similar mode of action for further experimental testing. Every part of this project will be conveyed in close collaboration with the experimental biologists.
Hlavní řešitel: Lukas Vojacek
Projekt: PaReTran5
Alokace: 241 000 jádrohodin
Abstrakt: During the past decade, one of the main topics in reactive transport modelling has been the ongoing global search for strategies of safe nuclear waste disposal (Parhurst and Wissmeier 2015, Cochepin et al. 2008, Montarnal et al. 2007). Reactive transport modelling can provide crucial information about the evolution of contaminant plumes over long time scales, and information about near-field processes, which are used to improve safety in the design of confining structures and containers (Parhurst and Wissmeier 2015). Globally, there are two commonly accepted disposal options – near surface disposal and deep geological disposal (WNA 2017). Near-surface disposal at ground level, or in caverns below ground level (at depths of tens meters) is implemented in many countries including the Czech Republic. The aim of the project is to improve the possibilities of a potential risk analysis of environmental contamination due to the long-term radioactive species spread around a deep radioactive waste repository. This aim will be made by integrating HPC infrastructure into the process of the reactive transport modelling. The solution is complicated by a low accuracy of known rock medium parameters values in large depths and in far future. The sensitivity analysis using numerical simulation computations is then very computationally consuming. Also, the individual reaction-transport simulations themselves are computationally consuming and their parallelization and using of HPC (High-Performance Computing) allow performing of the simulations in real size and available time.
Hlavní řešitel: Lukas Jeremias
Projekt: NMR and EPR Properties of Binuclear Paramagnetic Complexes
Alokace: 1 765 000 jádrohodin
Abstrakt: Nuclear magnetic resonance (NMR) spectroscopy is a widely employed method for characterizing the structures of new chemical compounds and biomolecular systems. However, this technique is generally less successful for open-shell molecules and metal complexes with unpaired electrons. Despite the difficulties (very unusual position of signals, signal broadening etc.), paramagnetic NMR (pNMR) spectroscopy is becoming very important in areas of research such as the structural characterization of paramagnetic metalloproteins, magnetic resonance imaging, or the development of molecular magnets. The interpretation of the experimentally obtained pNMR spectra rely mostly on DFT (Density-Functional Theory) calculations. For mononuclear complexes with one unpaired electron, the situation starts to be handled well especially for small molecules. The mononuclear complexes with more than one unpaired electron or complexes with more paramagnetic metal centers are still challenging for DFT calculations. The computational resources provided by IT4I infrastructure will be used for fully relativistic calculations of magnetic response properties of binuclear paramagnetic complexes.
Hlavní řešitel: Pablo Nieves
Projekt: Magneto-AELAS: Software for the high-throughput calculation of magnetostrictive coefficients
Alokace: 5 212 000 jádrohodin
Abstrakt: A magnetostrictive material is one which changes in dimension due to a change of state of magnetization. These materials are characterized by magnetostrictive coefficients (λ) derived from elastic and magneto-elastic constants. In many technical applications such as for electric transformers, motor shielding, and magnetic recording, magnetic materials with extremely small magnetostrictive coefficients are required. By contrast, materials with large magnetostrictive coefficients are needed for many applications in electromagnetic microdevices as actuators and sensors. The strongest magnetostriction was found in elementary Rare-Earth metal (under low temperature and high magnetic field) and in various compounds with Rare-Earth and transition metals. Despite the tremendous advances in modern electronic structure theory to study in materials science, magnetostriction has been rarely attacked until very recently, due to its intrinsic complexity mainly related to the spin-orbit coupling. Within current proposal, based on AELAS code for the calculation of elastic constants, we intend to extend this code by developing, testing and optimizing a code capable to perform accurate high-throughput calculation of magnetostrictive coefficients. In particular, we aim to apply this new tool to set a benchmark for cubic and hexagonal materials in order to improve and validate the methodology, as well as to quantify its scalability.
Hlavní řešitel: Jan Rezac
Projekt: Large-scale benchmarking of non-covalent interactions – London dispersion and sigma-hole bonds
Alokace: 2 418 000 jádrohodin
Abstrakt: To apply computational chemistry to real-world chemical problems, it is often necessary to work with large systems with thousands of atoms. This is especially true in the two currently most prominent research directions, in the applications of computational methods to biochemistry and to (nano)materials. This requires the use of approximate methods, often including empirical parameters. The development of such method then relies on accurate reference data that can be used for their parametrization and validation. Also, the emerging applications of machine learning to molecular systems require enormous amounts of data for their development. Here, we focus on non-covalent interactions, an effect of key importance in larger molecular systems. This proposal is a part of a larger project that aims to build a state-of-the-art database of accurate calculations that can serve this propose. First data sets covering hydrogen bonds had been already published [J. Řezáč, J. Chem Theory Comput. 2020], and made openly available at a dedicated website www.nciatlas.org. To complete the coverage of most common types of non-covalent interactions, I am developing two additional data sets covering London dispersion and sigma-hole bonds. Again, they will cover larger chemical space and their size is more than an order of magnitude larger than the current state of the art. This proposal covers benchmark calculations on the former, and building the model systems for the latter data set.
Hlavní řešitel: Lukas Kyvala
Projekt: Thermodynamics of actinium metal
Alokace: 272 000 jádrohodin
Abstrakt: Actinium (Ac), the first actinide element, is one of the radioactive products of thorium and uranium. Its concentration in nature is very low because of the very short half-life even at the most stable isotope (21.77 years). Due to very low concentration in nature and high radioactivity, only a few experiments on metal actinium were done and actinium remains as one of the least explored naturally occurring elements. Even the basic property as lattice constant has been subject of discussion for many years and its unusually small value has not been fully elucidated. Moreover, the relativistic effects can be significant due to the high proton number. In this proposal, we investigate not only the ground state of actinium metal at 0 K, but also thermodynamic properties for different phases at finite temperature. It is likely that phase transformations occurs as in the case of its isoelectronic element lanthanum. As actinium has started to be used in radiotherapy, we would like to analyze the physical properties (thermodynamics, electronic, mechanical) and its stability at finite temperatures and the effect of relativity on them.
Hlavní řešitel: Tomas Karasek
Projekt: Multilevel Monte Carlo hierarchy analysis for high Reynolds benchmark
Alokace: 385 000 jádrohodin
Abstrakt: The ExaQUte project aims at constructing a framework to enable Uncertainty Quantification and Optimization Under Uncertainties in complex engineering problems using computational simulations on Exascale systems. The stochastic problem of quantifying uncertainties will be tackled by a Multilevel Monte Carlo approach that allows using a high number of stochastic variables. Gradient-based optimization techniques will be extended to consider uncertainties by developing methods to compute stochastic sensitivities. The application chosen as a demonstrator focuses on wind engineering, which includes the quantification of uncertainties in the response of civil engineering structures to the wind action, and the shape optimization taking into account uncertainties related to wind loading, structural shape and material behavior.
Hlavní řešitel: Radim Uhlář
Projekt: Monte Carlo method application for explosive materials identification
Alokace: 182 000 jádrohodin v první periodě
Abstrakt: Neutron activation analysis (NAA) is one of the most sensitive analytical method for multi-element analysis of materials, as for some elements giving the sensitivity superior to those possible by any other analytical technique. One possible application of NAA is the detection of explosive materials, e.g. by measuring the isotopic ratios O/C and N/C enabling to distinguish hazardous materials from neutrals by the excitation of the nuclei of the material by neutrons and the subsequent measurement of gamma radiation and inelastically scattered neutrons accompanying these excitations. Several types of neutron sources are available up to present: primarily nuclear reactors, furthermore isotopic sources – (α, n) reaction or spontaneous fission, accelerators and compact neutron generators (NG) based on deuterium-deuterium (D-D), deuterium-tritium (D-T) or tritium-tritium (T-T) fusion reactions. In the Laboratory of Neutron Activation Analysis of VSB-TU Ostrava we operate the D-T neutron generator MP320 (Thermo Scientific Inc.) and it will be supplemented by a specialized large-scale NaI (Tl) spectrometer optimal for the measurement of gamma rays with energy typical for reactions of the explosive materials with the fast neutrons.
Hlavní řešitel: Martin Fajcik
Projekt: Unsupervised pre-training for statistical open-domain question answering
Alokace: 385 000 jádrohodin
Abstrakt: The main goal of this project is to build a scalable embedding index for document retrieval in open-domain question answering (Open-QA). Given a question, the role of the Open-QA system is to provide an answer to the given question. This often includes retrieval from the large collection of documents, as the Open-QA system seeks the document with the correct answer and its evidence from this external knowledge. Current methods of document retrieval in open-domain question answering are either mostly based on traditional information retrieval approaches (BM25, TF-IDF). Only recently, there has been a success in the field of neural information retrieval (ORQA, REALM). However, success comes with novel methods of unsupervised learning applied or the pre-training of large retrieval-based models. So far, this process requires tremendous computational resources. Therefore, we aim at lowering current computational requirements and improving neural document retrieval of pre-training by exploring new, less noisy unsupervised objectives.
Hlavní řešitel: Martin Zeleny
Projekt: Design of a new smart material with magnetic shape memory effect
Alokace: 4 159 000 jádrohodin v první periodě
Abstrakt: Abstract
Hlavní řešitel: Ladislav Foltyn
Projekt: Parallel-in-Time Combined with 3D Wire-Basket DDM
Alokace: 48 000 jádrohodin
Abstrakt: A parallel solution to boundary value problems for partial differential equations (PDEs) by means of domain decomposition methods (DDM) is nowadays well-established. Extensions towards time-dependent problems are much less understood and any progress in this direction is appreciated from both scientific and practical points of view. In this project, we propose to combine the Parareal method with spatial domain decomposition based on Schur complement technique in 3d. We rely on an MPI-C++ inhouse code of one of the investigators.
Hlavní řešitel: Martina Greplová Žáková
Projekt: Effects of advanced target designs on laser-accelerated ion beams parameters
Alokace: 308 000 jádrohodin
Abstrakt: Laser-driven proton/ion acceleretation is a field of big interest because of its implications in basic science, fast ignition, medicine (i.e. hadrontherapy), astrophysics, material science, non-destructive heritage testing and others. With the continuous development of laser technology, laser facilities delivering femtosecond pulses of ultra-high peak power of several PWs are being build, such as Extreme Light Infrastructure (ELI) in the Czech Republic. These laser installations will enable to accelerate ions to energies about several hundreds of MeV per nucleon, suitable for many applications, including hadrontherapy (ELIMAIA beamline [2]; HAPLS L3 laser (1 PW, <30 fs, 10 Hz)). On the other hand, not only maximum achieved energy have to be tuned and controlled when fulfilling the challenging requirements of wide range of foreseen applications. 3D PIC simulations presented in this project will help us to design suitable targets and understand the effect of target shape and density profile to control particle beam parameters. Mainly we will focus on decreasing the proton beam divergence and increasing maximum proton energy and number. Advanced designs of targets including microstructured plastic ones and cryogenic hydrogen expanded targets after laser prepulse (with possibly controlled density profile) will be used.
Hlavní řešitel: Michal Merta
Projekt: Development of parallel BEM-based solvers III
Alokace: 385 000 jádrohodin
Abstrakt: One can choose from several numerical methods for modelling natural phenomena occurring in the real world, let us mention, e.g., the finite element method or the finite volume method. The main features of the boundary element method (BEM) make it well suited for problems stated on unbounded domains (such as sound or electromagnetic wave scattering) or shape optimization problems. Within the previous projects, we have focused on optimization of BEM solvers for Haswell and Skylake microarchitecture and its acceleration using Intel Xeon Phi coprocessors which are installed at infrastructure of IT4Innovations National Supercomputing Center and also at development of solvers for time-dependent heat equation. The current project aims mainly at the optimization of the distributed memory parallelization of the time-dependent heat equation solver. The global space-time approach will lead to the possibility of parallelization both in space and time and will improve the scalability on current and future supercomputers. This is a continuation of the project Development of parallel BEM-based solvers.
Hlavní řešitel: Michael Komm
Projekt: Particle-in-cell simulations of the modified Katsumata probe
Alokace: 385 000 jádrohodin
Abstrakt: Reliable measurements of plasma parameters in tokamaks requires usage of well-understood diagnostics, which can acquire the desired measurements with sufficient accuracy as well as temporal and spatial resolution. One of the crucial parameters is the electron temperature in the edge of the plasma, which is needed to measure heat fluxes, which are deposited by plasma particles onto the plasma-facing components of the tokamak. Over the past decade, IPP has developed and employed the so-called “Ball-pen probe”, which in combination with Langmuir probes is capable of achieving such measurements, with temporal resolution of 1 μs. Recently, an improved design of such probe, so-called “Modified Katsumata probe”, has been developed. The advantage of this concept is that it does not require additional probes to obtain measurements of electron temperature, which simplifies the design and more importantly improves the capability to measure temperature fluctuations and the spatial resolution of the measurements. Within this project, we aim to optimise the design of the modified Katsumata probe by means of particle-in-cell simulations.
Hlavní řešitel: Nitin Wadnerkar
Projekt: Effect of Jahn-Teller deformation on catalytic activity in conducting perovskite surfaces
Alokace: 1 324 000 jádrohodin
Abstrakt: The understanding of ORR activity on perovskite oxide surfaces is essential for promising future fuel cell and metal-air batteries applications. The structural and electronic properties, and effect of orientation of orbitals and distortion with respect to ABO3 type oxide surfaces on Oxygen Reduction Reaction (ORR) will be closely examined by the state-of-art methodology.
Hlavní řešitel: Radek Halfar
Projekt: Investigation of biological systems using chaos theory II
Alokace: 8 000 jádrohodin
Abstrakt: The project is a continuation of long-term research dealing with the investigation of biological systems in terms of chaos theory, and its possibilities for detection and prediction of life-threatening conditions. This project is focused on the investigation of the propagation of the electrical signals in heart tissue. The effects of heterogeneous structures created by various diseases are investigated. For this purpose, the mathematical models of human cardiac tissue, modern techniques along with the state of the art tools are planned to apply.
Hlavní řešitel: Vladislav Pokorny
Projekt: Correlation effects in superconducting quantum dot junctions II
Alokace: 182 000 jádrohodin
Abstrakt: Conventional Josephson junctions are miniature devices in which two superconducting electrodes are separated by a weak link, usually an insulating barrier. These junctions had become a standard building blocks of various devices including rapid single flux quantum (RSFQ) electronics and qubits in quantum computing. If the insulating layer is replaced by a quantum dot, e.g. a carbon nanotube or semiconducting nanowire, we obtain a hybrid device in which various quantum mechanical phenomena as superconductivity, electron correlations and quantum tunneling can be separately tuned. Understanding the complex interplay of these phenomena is necessary step in developing a new generation of superconducting devices as quantum supercurrent transistors or monochromatic single-electron sources. Supercomputers are now a necessary tool for simulating the prospective superconducting devices, understanding the available experimental results and predicting their behavior.
Hlavní řešitel: Jan Krenek
Projekt: Extension of HPC platforms for executing scientific pipelines
Alokace: 96 000 jádrohodin
Abstrakt: The project is focused on the extension of HPC infrastructure capabilities for executing scientific tasks by specialized services. This extension will use an HPC-as-a-Service concept solution, special parallel programming models and domain-specific programming languages. The extension will be mainly focused on tasks in the field of transport modeling, machine learning, etc. One of the project objectives is the benchmarking of enhanced data compression algorithms. We developed modifications of compress/decompress algorithms for different types of datasets and we need to determine the suitability and loss ratio of these algorithms for the specific type of each dataset. These compress/decompress algorithms will be used in data transfer between Endpoint users and HPC job applications.
Hlavní řešitel: Lubica Valentova
Projekt: Rupture parameters of dynamic source models compatible with empirical ground motions
Alokace: 481 000 jádrohodin
Abstrakt: The main aim of the proposed project is to examine general properties of the earthquake source parameters that control the rupture process along with their variabilities using numerical simulations. For this purpose, we generate a large synthetic earthquake database that is based on simulations of physics-based earthquake rupture scenarios. For the numerical calculations, we employ our recently developed FD3D_TSN_PT code, which is based on random sampling optimization of the earthquake source parameters. However, not all simulated events correspond to the real earthquakes. Therefore, we apply selection criteria – only those simulations that generate strong ground motions agreeing with observations from a large number of real earthquakes are accepted into the database. The resulting events will exhibit various magnitudes and complexity. We will inspect their seismologically determinable parameters (e.g., rupture duration, size of the ruptured area, stress drop, energy budget) that may be compared with their real counterparts. Moreover, we will analyse also simulation parameters acting in the friction law on the fault, which trigger and control the rupture process and are not generally accessible for real events.
Hlavní řešitel: Jana Pavlikova Precechtelova
Projekt: Towards Reliable QM-Computed Chemical Shift Sequence Trends in Intrinsically Disordered Proteins
Alokace: 819 000 jádrohodin
Abstrakt: In the project, we perform calculations of nuclear magnetic resonance (NMR) chemical shifts (CSs) for a complete sequence of the human tyrosine hydroxylase (hTH1), an example of an intrinsically disordered protein (IDP). IDPs are involved in the regulation of molecular mechanisms that cause neurodegenerative diseases. For humans, the understanding the structure of proteins and their interactions with other biomolecules is essential. Due to the high flexibility of IDPs, their structural characterization by experimental techniques such as NMR spectroscopy is made more difficult. The problem can be substantially alleviated by the use of computational methods. In the proposed project, we employ structural ensembles generated by molecular dynamics (MD) simulations to obtain coordinates of protein fragments and their surroundings. The coordinates are then used for CS calculations building on methods of quantum mechanics (QM). The combination of MD and QM methods enables to reflect the flexibility of IDPs. Our objective is to carry out density functional theory calculations of CS sequence trends in IDPs and compare them with semiempirical predictions as well as experimental data. The calculations will employ (i) triple-zeta basis sets and (ii) statistical averaging of the computed CSs. The project contributes to the development of approaches for computer-aided structural characterization of IDPs.
Hlavní řešitel: Michal Krumnikl
Projekt: Fiji Bioimage Informatics on HPC – „Path to Exascale“
Alokace: 481 000 jádrohodin
Abstrakt: “Bioimage Informatics on HPC” allows IT4Innovations to be involved in research on a completely new topical area of big biological image data processing on HPC. This specific research is focused on parallelization of key steps in lightsheet microscopy data processing as well as analysis of big data generated from other microscopic modalities. Particularly, multi-dimensional microscopy acquisitions present one of the main primary data sources in modern biological sciences and deployment of HPC in these areas is a necessary condition for making biologically meaningful conclusions. This project is a continuation of the previous OPEN-17-47 call, solving particular VP3 subtasks of the Path to Exascale project. In the previous period, SPIM Workflow Manager was developed and published under Apache License. The project aims at further development and dissemination of HPC-aware plugins for the Fiji community. In this call we would like to specifically focus on utilization of a newly developed library for seamless parallel execution of SciJava plugins – SciJava Parallel and an automatic image segmentation and region labeling plugin – Labkit. As a new research topic we are starting to parallelize a simulator of artificial time-lapse images from developmental biology – EmbryoGen.
Hlavní řešitel: Karel Tuma
Projekt: 3D modeling of microstructure evolution during indentation-induced martensitic phase transformation in shape memory alloys
Alokace: 168 000 jádrohodin
Abstrakt: The important functional properties of Shape Memory Alloys (SMAs), notably shape-memory effect and pseudoelasticity, originate from the crystallographically reversible martensitic phase transformation between the parent phase (austenite) and the product phase (martensite). At the micro-scale, the martensitic transformation proceeds via the formation and evolution of complex martensite microstructures, which are accompanied by nucleation, propagation and annihilation of interfaces. In the pseudoelastic regime, which is of great importance due to numerous engineering and biomedical applications, the stress-induced martensitic microstructure developed in SMA vanishes upon unloading as a result of the reverse transformation. This concerns also the microstructure formed during indentation. Accordingly, modeling is seemingly the only way to analyze the microstructure during indentation, and the continuum modeling is the most suited technique for such complex problem. The phase-field method is an efficient computational tool for modeling the martensitic transformation and the related microstructure evolution. The essence of the phase-field modeling is in introducing a diffuse-interface approximation of the interphase boundaries and thus the direct tracking of interfaces is avoided. The main benefit of the diffuse-interface approach is that it leads to efficient computational schemes in which formation and evolution of microstructure can be modelled on a fixed computational mesh (or grid).
Hlavní řešitel: Petr Kovar
Projekt: Scheduling 2
Alokace: 19 000 jádrohodin
Abstrakt: Scheduling of round robin tournaments or incomplete tournaments can be described by a graph and its decomposition to so called 1-factors. Each 1-factor represents one round of the tournament. The goal is to schedule tournaments under certain restrictions, for example prescribed number of rounds/opponents, average strength of selected opponents, etc. This can be represented by various graph labelings. To give such labelings large graphs are constructed by inductive approach, while small cases have to be found or excluded by brute force. Here a supercomputer can help.
Hlavní řešitel: Rajko Cosic
Projekt: Comparison of the photoabsorption spectra of HeN+ clusters calculated via PIMC method using the diatomics-in-molecules potential with the accurate potential given by ab initio calculations represented by the artificial neural networks.
Alokace: 311 000 jádrohodin
Abstrakt: The aim of present project is to continue the work on potential energy surface (PES) evaluation via the artificial neural networks (ANNs) started within preceding projects (OPEN-16-21, OPEN-17-49). The main task of this project is to provide reliable PES representation for medium sized charged helium cluster, He10+, qualitatively comparable to the ab initio calculations and to use it in the path integral Monte Carlo simulations in order to obrain the photoabsorption spctra. One of the main problems is, due to the computational complexity of ab initio methods, the creation of a proper training set which has to be done in an adaptive, iterative, way.
Hlavní řešitel: Andrzej Kadzielawa
Projekt: Inhibition of corrosion with compounds based on imidazole
Alokace: 1 174 000 jádrohodin
Abstrakt: We investigate the inhibition of corrosion in the mild steel dipped in the solution of hydrochloric acid (HCl) by selected organic compounds based on imidazole: 1-C2nH2n+1-3-methylimidazolium hydrogensulphates, chlorides, and bromides, where n∊{2,3,4} (i.e., butyl, hexyl or octyl chain). To explain the experimental trends observed in polarization measurements that show the corrosion inhibition of the imidazole-based compounds, we study the charge transfer from Iron surface to the molecule using the ab-initio methods. We apply the Density Functional Theory to the artificial surface-vacuum-molecule-vacuum system. For this, we use the state-of-the-art computational approach, including the meta-GGA strongly-constrained and appropriately normed (SCAN) semilocal density functional to model the electronic properties of both free and bounded-to-surface molecules of 1-butyl-, 1-hexyl-, and 1-octyl-3-methylimizadolium bromide, chloride, and hydrogensulphate. From our calculations we extract the highest occupied molecular orbital (HOMO) – lowest unoccupied molecular orbital (LUMO) gap, hardness, electronegativity, and charge transfer of electrons from/to molecules-in-question.
Hlavní řešitel: Jan Zemen
Projekt: Modeling Magnetic Structures of Antiperovskite Nitrides Subject to Strain
Alokace: 1 651 000 jádrohodin
Abstrakt: We propose to explore the non-collinear magnetic structure of Mn-based antiperovskite nitrides and its dependence on chemical composition and lattice strain. The main aim of the project is to identify systems with triangular AFM structure which has been shown to host a range of effects typically expected only in ferromagnets such as the Anomalous Hall Effect (AHE), Magneto-optical Kerr Effect (MOKE), or Anomalous Nernst Effect (ANE). Several magnetic phases including non-collinear antiferromagnetic (AFM) structures have been detected in the family of Mn-based antiperovskite nitride alloys by neutron diffraction. We will calculate Magneto-optical (MO) spectra for the competing magnetic phases, taking into account their possible alignments with the lattice (magnetic anisotropy), which can be compared to experimental MOKE data despite the very small net magnetic moment. This work will build directly on the results and methodology of project OPEN-17-26, where we demonstrated that the magnetic ordering is highly sensitive to the chemical composition and lattice strain due to geometrically frustrated exchange interactions between neighbouring magnetic moments of three Mn atoms in the unit cell. The comparison to MOKE spectra measured in an expanding range of available samples will allow us to identify samples with the desirable triangular AFM structure and potential applications in non-volatile memory devices, sensors, and actuators or even in solid-state cooling devices.
Hlavní řešitel: Zdenek Futera
Projekt: Redox protein interactions with charged electrodes and their conductivites
Alokace: 991 000 jádrohodin
Abstrakt: Charge transfer processes in living organisms like photosynthesis, respiration cycle and many others are typically facilitated by redox proteins arranged into complex redox cascades. Often, transition metal cations are present in the structure of such proteins to provide suitable electronic states for efficient charge transfer while the protein matrix is believed to behave like an insulator. However, recent scanning tunneling microscopy (STM) measurements in vacuum as well as EC-STM experiments in solution, probing conductivity of single protein junctions, suggested ability of redox proteins to conduct electrons over long-range distances and with high efficiency even upon modifications of their metal sites. Naturally, these observations raised fundamental questions about importance of protein interaction with the metal electrode on its conductivity and effect of the present electric field on the protein structure. Here, we propose computational methodology based on non-equilibrium classical molecular dynamics (MD) and density function theory (DFT) calculations to predict the adsorption structure, determine its electronic states and explain the conductive properties of the proteins on metal electrodes. In the first stage of the project we are going to investigate electric field effects on amino-acid adsorption on gold surface as the reference data for the following MD simulations.
Hlavní řešitel: Sergiu Arapan
Projekt: Computational study of 2D materials as permeable multi-functional membranes
Alokace: 1 800 000 jádrohodin
Abstrakt: Membranes are fundamental components of a wide variety of physical, chemical, and biological systems, used in everything from cellular compartmentalization to mechanical pressure sensing. The defect-free graphene is considered to be completely impermeable to all gases and liquids. This makes it an ideal protective layer. For many applications, however, it is desirable to have a certain selectivity of the permeating agents, for example, size based criterion, which allows only small objects to penetrate the layer. Another type of selectivity could be based on chemical reactivity of different agents with the membrane. One way to make graphene sheet selective is to make nano-scale pores. Thus one can make use of the structure factor to control the size of the permeating objects. The great success of graphene, however, has boosted intensive search for other single-layer thick materials, like Si, Ge, and Sn atoms arranged in a honeycomb lattice. This new class of two-dimensional (2D) crystals, known as 2D-Xenes, becomes an emerging field of intensive research due to their remarkable electronic properties. 2D-Xenes have bonding configuration and properties close to but substantially different from graphene, which could make them important players in the field of nano-scale physics and technological applications. Within this project we aim to study via numerical methods the interaction of 2D-Xenes with various molecular systems and determine their role as multifunctional membranes.
Hlavní řešitel: Jiri Jaros
Projekt: Photoacoustic tomography of the breast III
Alokace: 385 000 jádrohodin
Abstrakt: Photoacoustic tomography (PAT) is a biomedical imaging modality based on the photoacoustic effect. In PAT, non-ionizing laser pulses are delivered into biological tissues. Some of the delivered energy will be absorbed and converted into heat, leading to transient thermoelastic expansion and thus wideband ultrasonic emission in the low MHz range. The generated ultrasonic waves are detected by ultrasonic transducers and then analyzed to produce images. Since the optical absorption is closely associated with physiological properties, such as hemoglobin concentration and oxygen saturation, the PAT is used to visualize vasculature inside tumors with a very high resolution. This simulation study is focused on the optimization and validation of the PAT software being developed as part of the H2020 project Pammoth on a set of breast phantoms. The resolution, accuracy, sharpness, motion and noise artifact, and the depth of penetration will be investigated and optimized. This study is the third phase of the model validation and moves us towards the deployment in a real PAT system for breast mammography.
Hlavní řešitel: Miroslav Voznak
Projekt: Population mobility data retrieval from mobile networks I
Alokace: 556 000 jádrohodin
Abstrakt: Enhanced awareness about the population mobility could improve the quality and the extent of the services provided by a public authorities and a private sector. We use our expertise in mobile networks signaling data processing to extract key performance indicators of population mobility at the level of all basic regional units in the Czech Republic. The results can be used for transport supply-demand management as well as regional planning. Next day delivery of outputs can serve as a base to understand the impacts of decisions that affect mobility in the territory. Examples of such impact on population mobility include COVID-19 restrictions (https://atlas-mobility.danse.tech/).
Hlavní řešitel: Jiri Brabec
Projekt: Theoretical study of polycyclic aromatic hydrocarbons at the DMRG level
Alokace: 2 166 000 jádrohodin
Abstrakt: Recent progress in ultra-high vacuum (UHV) on-surface chemistry and scanning probe microscopy with the unprecedented sub-molecular resolution enabling precise determination of molecular products opened new possibilities to synthesize and characterize molecular species not available via traditional solution chemistry. For example, a possibility to synthetize polycyclic aromatic hydrocarbons (PAH) possessing open shell electronic structure featuring magnetic properties. So far, however, room-temperature stable magnetic carbon nanostructures have only been theoretical constructs. For the first time, the researchers have now succeeded in producing such a structure in practice and showed that the theory does correspond to reality. The new possibilities of radical PAHs synthesis rise also challenges for precise theoretical modelling of their electronic and magnetic properties. This requires very accurate but computationally demanding techniques such as the density matrix renormalization group (DMRG) method, which are able to correctly describe their complex electronic structure ranging from biradical to polyradical character. For this purpose, we would like to employ the recently developed massively parallel DMRG code, MOLMPS. In particular, we will study the electronic and magnetic structure of PAHs such rhombene-derivates or acene-bridged polymers showing interesting magnetic properties, which have been recently prepared by means of UHV on-surface synthesis by our experimental partners.
Hlavní řešitel: Ctirad Cervinka
Projekt: Benchmarking Phase Change Enthalpies of Ionic Liquids from Polarizable Molecular Dynamics Simulations
Alokace: 1 797 000 jádrohodin
Abstrakt: Ionic liquids (ILs) are leaving the position of novel and astonishing compounds as they are becoming commercially available on a large scale and in a relatively high purity. Therefore, investigation of their thermodynamic properties, such as volatility and heats of vaporization or fusion, should be performed in a more concise way than in the times of first pioneering studies a decade or two ago. However, there are still principal hindrances (low volatility, high viscosity or difficult removal of trace amounts of water) impeding reliable experimental determinations of the given properties for ILs. On the other hand, molecular-dynamics (MD) computer simulations can help to fill gaps in data availability for newly synthesized compounds or species difficult or dangerous to handle. Quality of such theoretically calculated data depend in case of MD mostly on the underlying empirical force-field model describing molecular interactions at the atomic level. Recent development and implementation of polarizable force fields in MD simulations represents a major step forward in the computational methodology. Concurrently, broad employment of the polarizable models, being up to one order magnitude more demanding for the computing time compared to former non-polarizable MD, is getting possible only thanks to the steady increase of the computational resources available. Still, polarizable force fields cannot be proclaimed as the game-changers for the predictions of thermodynamic properties of ILs in terms of their accuracy and reliability before enough benchmark calculations validating the implemented computational models are carried out.
Hlavní řešitel: Pavel Praks
Projekt: Stochastic methods for optimisation of distribution networks in the energy sector
Alokace: 39 000 jádrohodin
Abstrakt: The electrical power consumption is gradually increasing over the years. In combination with the ageing of distribution grids and required integration of new uncontrolled sources (wind and solar systems), a higher emphasis is placed on power flow control and monitoring elements to ensure continued supply and required quality of the provided electrical energy for the society. However, the purchase price and the maintenance cost of the switching and monitoring devices is high, therefore discrete optimization must be employed to identify optimal placement and operating mode of the control devices. The stochastic approach is very robust but extremely time-consuming. Fortunately, the performance of stochastic methods can be accelerated by the parallel implementation on HPC systems. It is a pilot Open Access Call project for modelling and optimisation of Czech distribution networks using supercomputers of IT4innovations.
Hlavní řešitel: Jan Novotny
Projekt: Magnetic properties of open-shell supramolecular metallocomplexes by Respect program
Alokace: 2 721 000 jádrohodin
Abstrakt: Current strategies of cancer treatment utilizing coordination compounds of transition metals are limited by non-specific action of these drugs and side effects. The binding of metallodrugs to functionalized carriers is considered as a promising way to diminish this deficiency. To perform a rational design of supramolecular drug-carrier systems, NMR spectroscopy together with quantum-chemical calculations pose a unique tool for structure-dynamic determination. However, paramagnetic nature of Ru(III) metallodrugs disables to apply conventional methods of NMR and therefore predictions provided by accurate relativistic calculations can help to gain correct interpretations of experimental observations. In this project we will use computational resources provided by IT4I infrastructure to apply relativistic methodology1 for calculations of magnetic response properties in paramagnetic host-guest systems. Previously studied static systems with single unpaired electron will be extended by ensembles of geometries with explicit solvation shell. We are also planning to employ new protocols for characterization of complexes in higher spin state and analyze fundamental terms contributing to hyperfine shielding.
Hlavní řešitel: Michal Novotny
Projekt: High accuracy calculation of absorption spectra of small mercury clusters II
Alokace: 289 000 jádrohodin
Abstrakt: Mercury and its small molecular clusters are of high interest to the fundamental understanding of chemical bonding. An ab-initio approach is required to provide accurate data of its electronic structure, be it in the ground state or excited states. High accuracy methods such as CCSD(T) (coupled clusters with singles doubles and iterative triples) and EOM-CCSD (equation of motion coupled clusters) are applicable only to the smallest sizes of such clusters (2-5 atoms) and therefore a cheaper yet still accurate method needs to found to properly interpret experimental data as well as provide insight into the metallic transition of such clusters. Here we propose a quantum mechanical study to benchmark an appropriate DFT method as well as provide accurate absorption spectra of small mercury clusters.
Hlavní řešitel: Petr Kulhanek
Projekt: Quantum Mechanical Modeling of Mismatched DNA
Alokace: 532 000 jádrohodin
Abstrakt: DNA double helix is composed of two complementary strands, which are held together by Watson-Crick base pairing. Incorrect base-pairing can result in the development of inherited genetic diseases, cancer, and aging. Therefore, organisms developed several ways how to detect such errors and keep the integrity of genetic information. One of them is the mismatch repair pathway (MMR). In our previous studies, we tried to decipher how MMR can effectively detect mismatches. Our results were based on molecular mechanics (MM), which is a method used in computational studies of large biomolecular systems. However, its reliability to describe corrupted dsDNA poses many open questions due to its empiricism. In this project, we will employ quantum-chemical (QM) calculations to validate the performance of MM in the description of mismatched base pairs. The use of QM calculation, which are first principle methods, will not only provide information about the quality of MM calculations but also detailed information about individual interactions and their importance for mismatch recognition. Such data can give a new direction for designing chemical substances suitable in anti-cancer therapy targeting damaged DNA.
Hlavní řešitel: Jiri Klimes
Projekt: Accuracy and precision for extended systems V
Alokace: 2 515 000 jádrohodin
Abstrakt: Materials bound by non-covalent interactions are important both in nature and industries. From methane clathrates at the bottom of the sea, over pharmaceuticals in pills, to layered systems such as graphite. Many of them have also some peculiar properties. For example, even at the same conditions, many pharmaceuticals can exist in different crystal structures, called polymorphs. One of these polymorphs is the most stable, but the others are usually very close in energy. One of the long term goals of our project is to develop a theoretical modelling scheme that would allow a reliable description of the stability of the different polymorphs or different phases of materials in general. The problem is that to get the tiny energy differences between different phases, we need to use quantum mechanics. Solving the equations of quantum mechanics is only possible for simple systems and for extended systems we need to use approximations. To reach our goal we want to combine one of the most accurate schemes currently available for the treatment of extended systems with a method used to calculate reference quality binding energies of molecules. Moreover, we want to develop methods that will ensure that our results are very precise and thus reproducible. This will enable us to obtain highly reliable binding energies of extended systems.
Hlavní řešitel: Alberto Marmodoro
Projekt: SwitchAFM
Alokace: 1 117 000 jádrohodin
Abstrakt: Anti-ferromagnets (AFMs) have no macroscopic magnetic moment.. This is due to compensation of anti-parallel contributions. The field of antiferromagnetic spintronics studies these materials as possible venue for new, efficient information storage and processing technology. A crucial advantage of AFMs is their resilience against external perturbations, thanks to zero net magnetic moment to which a stray field may couple. Conversely, this feature has initially posed challenges for the practical manipulation and detection of the Néel vector, as a potential degree of freedom in which to encode and retrieve information. With the demonstration that electric currents can both produce and detect the desired switching behavior in the CuMnAs AFM, efforts to further characterize known-switchable AFM compounds; search for new ones and understand the underlying physical mechanisms have intensified. Ab initio electronic structure calculations will support this research line, exploring in particular the role of (i) punctual defects, like chemical substitutions or finite temperature fluctuations in atomic position or magnetization; or (ii) extended defects, like domain walls or surface/interfaces, in connection with transport properties and new experimental evidence of switching by means of intense laser pulses or high magnetic fields.
Hlavní řešitel: Mauricio Maldonado Dominguez
Projekt: Electron-Proton Transfer in Biomimetic Binuclear Transition-Metal Active Sites
Alokace: 1 163 000 jádrohodin
Abstrakt: We recently calibrated a methodology to accurately reproduce the experimental redox potentials and acidity constants of binuclear Fe2S2 clusters, related to the Rieske and mitoNEET proteins. The latter is of special interest since recent studies have begun shown its significance to human health and its relation to cancer and diabetes. The calibrated protocol serves as a cornerstone for the posterior investigation of Fe2S2-containing proteins. In the present stage of the project, we plan to apply the selected DFT-based methodology to reconcile the existing experimental information about mitoNEET proteins, namely, their reactivity and stability in solution at different pH values as a function of their redox state. These proteins are known to repair other iron-sulfur enzymes damaged by oxidative stress and have been highlighted as a key player in the iron-sulfur traffic between the mitochondria and the cytosol. Although this has been found directly related to several diseased, the mechanism of action of NEET protein is unknown. We are convinced that the present study will provide molecular details of the underlying mechanisms triggering cluster transfer in NEET proteins, paving the way for the elucidation of their function as pH-dependent redox sensors.
Hlavní řešitel: Yanjun Gu
Projekt: radiation damping effects in laser-plasma driven ion acceleration
Alokace: 924 000 jádrohodin
Abstrakt: In the recent decades, high power laser facilities have achieved great progress. The short pulse lasers with the power of TW and PW are available nowadays. Even larger laser facilities are being built, e.g. Extreme Light Infrastructure (ELI) in Prague, and the peak power is expected to reach 10PW. With such high power and intensity, the laser-plasma interactions are radiation and QED dominated. The radiation power and the emitted photons momentum become comparable to the emitting electron and should be significantly considered. Such phenomena could extend the horizon of laser physics from atomic and condensed-matter studies to plasma, nuclear, high energy physics, general relativity and cosmology, and even physics beyond the standard model. On the other hand, the laser driven ion acceleration are expected to be useful in many fields such as high energy density physics diagnostics, materials science and ion-beam tumor therapy. Several regimes for achieving the energetic proton bunches have been proposed and realized in experiments, including the target normal sheath acceleration (TNSA), collisionless electrostatic shock acceleration, breakout afterburner (BOA) acceleration, radiation pressure acceleration (RPA). The main goal of our research project is focused on the radiation damping effects in the laser-plasma interactions for ion acceleration. Our recent 2D simulations revealed the accelerated ion energies are significantly changed with the consideration of radiation reaction. As the leading electrons loss the energies via the Compton scattering, the gamma factor of the electrons and the effective mass changes. The process such as RPA can be extended and the higher energy ions can be expected. The process is highly beneficial to the fundamental particle physics since it can serve as a novel source for gamma-ray and heavy ions. It requires further investigations including 3D simulations to optimize the regime. It’s also important to activate more functions including ionization and recollision to fully describe and understand the process.
Hlavní řešitel: Ales Vitek
Projekt: Mercury clusters – thermodynamics
Alokace: 249 000 jádrohodin
Abstrakt: This project is focused on basic research. In our group MolDyn of ParLab, IT4Innovations, we investigate interesting properties of small mercury clusters. We have focused our attention on photoabsorption spectra of very small mercury clusters [1] and on the medium size clusters [2]. Photoabsorption spectra of mercury clusters can be easily experimentally measured. In our computations can be computed from configurations generated by Monte Carlo simulation. We computed photoabsorption spectra of mercury clusters in different temperatures and pressures. Now, we would like to compute thermodynamics properties in wide intervals of temperatures and pressures using Monte Carlo simulations. We would like to test, if theoretical modelling of such sub-nano systems can give results which can be experimentally verified. The goal of our computations will be to find, how are the thermodynamic properties changes with the increasing of particles from small clusters towards to the bulk limit.
Hlavní řešitel: Frantisek Karlicky
Projekt: Ab initio spectroscopy of two-dimensional binary semiconductors
Alokace: 2 141 000 jádrohodin v první periodě
Abstrakt: The goal of this project is accurate many-body approach to theoretical linear and non-linear optical properties of materials. Suggested methods allow analysis of temperature dependent excitons, their binding energies, spatial localization, and lifetimes. The methods will be applied to new group of semiconducting 2D materials (binary buckled group V materials), which are perspective for applications in (nano)electronics and photovoltaics. The materials will be investigated in detail including basic point defects and applied strain.
Hlavní řešitel: Prashant Dwivedi
Projekt: Atomistic design of Multilayered Amorphous/Crystalline nanostructures for modern surface engineering. (MAC)
Alokace: 3 883 000 jádrohodin
Abstrakt: New and improved mechanical, chemical and/or optical properties may be established by manipulating the design of the materials at the atomic level. In this sense, both surface structure and particle size are of great importance in the nanostructured material. Nanostructured materials are today and will continue to be well into the future, one of the highest-profile types of materials in science and engineering. Extensively varied potential applications include nuclear industry, aerospace, automobile, more efficient solar panels, drug delivery systems etc. Developing new theories, design protocols and models, as well as characterization methods, is important for understanding the possible structure-function relations. Nowadays, computer simulations are becoming more and more appealing as complementary tools to experimental research thanks to an increasing number of powerful techniques, adding valuable guidance for further inquiries and, also important, sometimes reducing costs of experimental studies. The strength of nanostructured material, when the external stress is applied, is mainly determined by dislocation confinement at interfaces. By tuning layer thicknesses, compositions (if we include alloys) and/or a combination of amorphous and crystalline layers there is plenty of room for improvement. The concept applies to almost all metals and offers a positive way of producing resistance-tunable alloys for highly demanding applications in engineering. We plan to study multilayered amorphous/crystalline metallic systems by means of classical molecular dynamics (MD). The goal of the project is to investigate the appearance of dislocations, their evolution, and interaction in the interfaces employing atomistic simulations and to validate our models against experimental results. The starting hypothesis is backed by our previous work. There, advanced theoretical design based in classical and ab initio simulations, resulted in a huge reinforcement of the Zr-Nb multilayered system with 10.8 GPa hardness, which is about 6 GPa higher than its homogeneous crystalline counterparts.
Hlavní řešitel: Jan Kuriplach
Projekt: Planar interfaces in materials: structure and atomic movement
Alokace: 385 000 jádrohodin
Abstrakt: Lithium iron phosphate (LFP) is an important Li-ion battery material with existing practical applications. Many aspects of Li function in this material are yet far from being understood. Relevant properties include Li ion interaction with planar and point defects which affect Li ion diffusion, which is the key process affecting Li-ion battery performance. Studying defect interactions with Li ions will unveil useful consequences for the operation and efficiency of Li-ion batteries based on LFP. Likewise, the complex concentrated alloy HfNbTaTiZr represents a prospective material for high temperature applications. The tendency to the short range order, discovered recently only, affects the microstructure. In particular, Nb+Ti-rich regions (bcc) separate in phase from Zr+Hf-rich regions (hcp) with Ti being roughly equally present in both phases. Investigating grain boundaries and bcc-hcp phase interfaces including the diffusion of atomic species around and through the interfaces will help to understand the microstructure of the studied alloy, which is the critical aspect to allow for the development of real applications.
Hlavní řešitel: Ivan Kolos
Projekt: Numerical modeling of load of structures in quasi-static effect of wind
Alokace: 96 000 jádrohodin
Abstrakt: The project is focused on numerical modeling of flow around objects in the atmospheric boundary layer. This issue is complicated mainly due to the atmospheric turbulence, which requires the use of advanced numerical models of the flow coupled with detailed computational mesh of the domain. This research will contribute to bigger efficiency in design of building structures.
Hlavní řešitel: Stepan Sklenak
Projekt: Periodic DFT studies of zeolite-based catalysts
Alokace: 732 000 jádrohodin
Abstrakt: Zeolite based catalysts are the most important industrial catalysts used mainly in petrochemistry (production of fuels, various hydrocarbons), and furthermore, for N2O decomposition and N2O selective catalytic reduction (SCR), for direct NO decomposition as well as for SCR of NOx using various reducing agents. In addition, zeolites are also employed as catalysts in synthesis of fine chemicals and as well as in the processing of biomass. Zeolites are also used as ion exchange agents (e.g. they replaced harmful phosphates in washing powder detergents). Zeolites are crystalline microporous aluminosilicates with a unique microporous nature, where the shape and size of a particular pore system exerts a steric influence on the reaction, controlling the access of reactants and products. Thus, zeolites are often said to act as shape-selective catalysts. Increasingly, attention has focused on fine-tuning the properties of zeolite catalysts in order to carry out very specific syntheses of high-value chemicals. Periodic DFT methods permit investigations of properties of zeolite-based catalysts which are needed for their fine-tuning. DFT calculations are complementary to experimental examinations and together they can provide more complex knowledge of the properties of the studied catalysts and the reactions they catalyze.
Hlavní řešitel: Santiago Alonso
Projekt: Catalytic properties of [Fe4S4]-dependent metalloenzymes (II)
Alokace: 530 000 jádrohodin
Abstrakt: [Fe4S4]-based radical S-adenosylmethionine (SAM) enzymes belongs to a huge superfamily with more than 100,000 members and carrying out more than 70 different radical-mediated reactions. In radical SAM enzymology, the preparatory stage of catalysis involves the activation of SAM through the reductive cleavage of the SAM C-S bond, which leads to the radical intermediate. Recently, the existence of another catalytically competent organometallic intermediate (so called Ω) was observed for several members of superfamily. However, the geometric and electronic structure of Ω remains unknown. Besides that, some other radical SAM enzymes are puzzling for their substrate promiscuity or for a different modus operandi of the 5’-deoxyadenosyl radical (activating C-H, N-H bonds). For these reasons, our goals are to investigate (i) a mechanism of interconversion between the radical and the organometallic intermediates and reveal the function of Ω, (ii) a mechanism of the C-H vs. N-H bond activation driven by the 5’-deoxyadenosyl radical and (iii) a mechanism of selective activation of substrate by the enzymatic radical intermediate. To accomplish these goals, we plan to use DFT-based methods and to apply the broken-symmetry strategy to find a proper electronic configuration for the proposed systems.
Hlavní řešitel: Dominik Legut
Projekt: Ultrastrong Graphene-Transition Metal Carbide and Nitride Heterostructures: a road to superhard materials
Alokace: 9 002 003 jádrohodin
Abstrakt: Superhard materials have always been an important research topic because of their fundamental importance in material science/physics and technological applications. Considering the extraordinary mechanical properties of 2D materials, it brings accordingly a scientific curiosity whether the strong 2D materials may form strong thin interface in the bulk materials. In combination with the strongest size of nanocrystallites, whether it may strengthen/harden the bulk materials to be superhard. In this project, taking graphene and several TM carbides/nitrides as prototypes, we will study the strengthening and toughening of TM carbides/nitrides by graphene layers via ab initio derived ideal strength and Peierls stress with several aims: 1) stability of different types of graphene-TM carbide/nitride heterostructure with different interface spacing and with different thickness of graphene layer; 2) ab initio derived ideal strength and Peierls stress of graphene-TM carbide/nitride heterostructure, and the corresponding mechanism, e.g., Friedel oscillations, electronic structure instabilities, etc. that are responsible for these upper limits of strength and stress.