Modeling and simulation
The Research Program RP3 is guaranteed by the Nanostructure Physics Group (http://nano.osu.cz), which is a part of the Department of Physics at the Faculty of Science, University of Ostrava. This group focuses on a promising direction in fundamental research within the field of electronic structure theory and computer modeling of molecular complexes and (nano)materials at the atomic scale. Computational methods are applied to molecules, clusters, solids, surfaces, and nanomaterials, with a focus on predicting their structural, electronic, optical, adsorption properties, and their interactions. Complex systems and phenomena such as transition metals, their oxides, non-covalent interactions, physisorption, nuclear delocalization effects in strongly quantum systems, or excitonic effects in nanostructures are successfully described.
Within RP3 of the LERCO project, we plan to develop selected computational methods (main activity 1, see below). A part of the research will be dedicated to the study of interactions (main activity 2, see below), and a completely new research direction focused on molecular modeling (computational molecular physics – molecular simulations using force fields; main activity 3) will emerge, primarily serving as support for experimental research in other research programs.
Productive and computationally demanding calculations (e.g., quantum Monte Carlo) are performed on supercomputers in computing centers in the Czech Republic and abroad. Simultaneously, the workplace has its own computing cluster used for less demanding calculations and method tuning. As part of the LERCO project, we plan to revitalize the computing cluster into a more modern and powerful system, which will be utilized during its implementation.
Main Activity 1: Methodology Development
RP3 is focused on applications such as computer modeling of the electronic structure of complex nano-systems or molecular modeling of mesoscopic bio-systems with resolution at the atomic scale, using computational methods in chemical physics. Within the project, we plan to develop selected computational methods, both very accurate and computationally demanding methods for reference calculations, as well as approximate, computationally less demanding methods with favorable scaling suitable for large systems.
Concerning the reference computational methods, we plan conceptual and algorithmic development of stochastic reference methods (quantum Monte Carlo) for an accurate description of complex systems where many-body electron correlation effects play a role. Within the LERCO project, the developed methods will focus primarily on the reference description of non-covalent interactions in biomolecules and chemical reactions in the field of environmental chemistry.
Regarding the less demanding and approximate computational methods with favorable scaling of computational complexity, we plan to search for suitable parameterizations and computational protocols suitable for describing large systems with acceptable accuracy. Examples could include selecting suitable quantum-mechanical effective DFT methods for a specific problem using reference calculations on small representative systems or parameterizing tight-binding methods and embedded models (multiscale modeling). Within the LERCO project, approximate methods will be particularly utilized in studying chemical reactions and interactions on selected material surfaces or nanoparticles in the field of environmental chemistry and in studying interactions in biologically relevant systems.
Main Activity 2: Computer Modeling of Complex Systems at the Atomic Scale
The goal of Main Activity 2 is to utilize computer modeling for the independent research of complex systems at the atomic scale and as support for experimental research in other research programs. The independent research will be focused on three categories.
The study of interactions in bio/macromolecules and nanostructures will focus on describing the energetics of non-covalent interactions, which play a crucial role in processes such as interactions between drugs and biomolecules or pollutant-surface interactions.
Another research area will focus on describing chemical reactions crucial for biology, environmental chemistry, and biochemistry. For instance, this could involve reactions of metallic nanoparticles with pollutants, aiming to study the degradation processes of pollutant molecules and identifying nanoparticles effective for this purpose.
The last research area will be dedicated to (photo)catalysis of important reactions on (nano)materials and (bio)complexes, for example, modeling water splitting on surfaces with d-elements, potentially replacing expensive metals currently used for this purpose. Electrochemical water splitting to obtain hydrogen as a renewable and sustainable energy source is currently limited and awaits the discovery of a "cheap" material that could enable the reaction to be performed on an industrial scale.
Main Activity 3: Molecular Modeling
The aim of Main Activity 3 is to establish a new group dedicated to computational molecular modeling. This group will focus on describing biologically relevant systems, and the created simulations will gradually complement and support experimental research, especially in molecular biology, biophysics, or biochemistry. Unlike Main Activities 1 and 2, Main Activity 3 will be starting continuously throughout the project.
The scientific work of the molecular modeling team will be based on modeling mesoscopic systems using computational molecular physics methods at the atomic scale, such as molecular simulations using force fields employing molecular dynamics methods (or Monte Carlo methods) and their application in describing biologically relevant systems, alternatively biomaterials, and nanostructures.
Collaboration with other Research Programs
Due to the strong interdisciplinary connection, the Research Program 3 team will collaborate on certain specific activities with other research teams of the LERCO project. Primarily, this collaboration will support ongoing experimental research in the field of molecular biology (Research Program 1) and the modeling of interactions involving adsorbents with target molecules, as well as in biological systems (Research Program 2).
