ACCURACY LIMITS OF QUANTUM MONTE CARLO IN WEAK-INTERACTION LIMIT III

Call: 18th Open Access Grant Competition
Researcher: Dr Matúš Dubecký

Institution: University of Ostrava
Field: Material Sciences

 

More than 4 million core hours were awarded to Matúš Dubecký for his research focused on determining the accuracy limits of the Fixed-node diffusion Monte Carlo (FNDMC) method for noncovalent interactions. Noncovalent interactions play a key role in many research areas such as material science and drug design. The team led by Matúš Dubecký will conduct a benchmark study as a follow up to their previous research and application of the FNDMC method, for example, in 2D materials, the properties of which are affected by noncovalent interactions of molecules, and 1D conductors on their surfaces. The objective of this project is to determine, by means of a supercomputer, the accuracy limits of the FNDMC method, which is currently frequently used as a quantum reference method for large noncovalent systems. Apart from gaining a physical insight into the FNDMC method and design of potential improvements, the results will lead to better accuracy control and more rational application of this method not only for large systems.



ACCURACY AND PRECISION FOR EXTENDED SYSTEMS IV

Call: 18th Open Access Grant Competition
Researcher: Dr Jiří Klimeš

Institution: Charles University in Prague
Field: Material Sciences

 

 

More than 2.8 million core hours of the IT4Innovations computational resources were awarded to a team led by Jiří Klimeš for a project focused on precision and accuracy of binding energies calculations in crystals, especially those bound by non-covalent interactions. These materials, such as methane clathrates at the bottom of the sea, pharmaceuticals crystals, and layered systems such as graphite to name but few. One of their peculiar properties is polymorphism – the ability of a crystalline material to adopt different crystal structures, even under same conditions. One of the objectives of this project is to use a supercomputer to develop a method that would allow a reliable description of the stability of different polymorphs or different crystalline phases of materials. It is a basic research project aiming at both gaining deeper understanding of the accuracy limits of the currently used methods and development of higher precision methods applicable in future material simulations. The research team led by Jiří Klimeš would also like to integrate developed scripts for preparation and analysis of calculation into “packages” used for automated working procedures. This all is expected to ensure that the methods for accurate calculations of binding energies can be used by other research groups as well as increase reproducibility of such results.



FROM ANTIPHASE BOUNDARIES TO NEW RARE-EARTH-FREE MAGNETS

Call: 17th Open Access Grant Competition
Researcher: Prof. Mojmír Šob

Institution: CEITEC
Field: Material Sciences


The research team led by Prof. Mojmír Šob from CEITEC was awarded more than 8 million core hours for the project focused on analysis of antiphase (AP) boundaries on magnetic properties of intermetallic compounds and their thermodynamic as well as mechanical stability. This information is essential for successful development of new magnetic materials. The project aims at Fe-Al alloys, the magnetic properties of which can be improved by AP boundaries by up to dozens of per cents according to the latest experiments. The awarded computational resources will be used by the research team to study the properties of conventional (rare-earth-free) Fe-Al-based magnets and to understand the relevant physical mechanisms, the knowledge of which is essential to improve the properties of these magnetic materials.



NEURAL NETWORK POTENTIALS FOR IN SILICO DESIGN OF ZEOLITES

Call: 17th Open Access Grant Competition
Researcher: Dr Lukáš Grajciar

Institution: Charles University in Prague
Field: Material Sciences


 

Lukáš Grajciar was awarded more than 2 million core hours for implementing his project focused on the in silico design of new catalysts, such as zeolites. Zeolites have great potential in the area of developing green technologies because they are the most important industrial catalysts used primarily in crude oil processing and petrochemistry. Lukáš Grajciar along with his colleagues Andreas Erlebach, Christopher J. Heard, and Petr Nachtigall use the awarded computational resources for simulations using deep neural network-based force fields for screening large databases of candidate structures and their modelling under operating conditions with unprecedented accuracy. The project results shall provide deeper insight into the structure and stability of existing and hypothetical zeolites, which have not yet been synthesized, and improve the catalytic properties of zeolites in general.



MOLECULAR AND MESOSCOPIC SIMULATIONS OF AQUEOUS SOLUTIONS IN INHOMOGENEOUS ENVIRONMENTS

Call: 16th Open Access Grant Competition
Researcher: Dr Barbora Planková

Institution: Czech Academy of Sciences
Field: Material Sciences

 

Barbora Planková from the Institute of Chemical Process Fundamentals of the Czech Academy of Sciences was awarded more than 1 million core hours for molecular and mesoscopic simulations of aqueous solutions in non-homogenous environments. Aqueous solutions are omnipresent in nature, industrial processes, and daily life. Understanding their behavior in inhomogeneous environments (nanopores, self-assembled systems) is important in many key applications such as medicine and enviromental protection. Together with her colleagues, Karel Šindelka and Martin Lísal, Planková will use the supercomputer in three research areas. The first one is graphene-aqueous electrolyte interfaces. Graphene is also called the miracle material of the 21st century. Graphene membranes, for example, could be used in water desalination or its cleaning. First of all, however, it is important to understand the elementary molecular processes, which will be studied by the project author using the supercomputer. The second research area is focused on ionic surfactants used, for example, in fabric conditioners. Part of the allocated computational resources will be used to study of the behaviour of these active substances and their interaction with soft surfaces – the key aspects of their functionality. The third research area focuses on solubilisation of small molecules in interpolyelectrolyte complexes, which can influence drug effectiveness and removal of pollutants.



HIGH-THROUGHPUT SCREENING OF METAL-ORGANIC FRAMEWORKS FOR CO2 SEPARATION FROM A POST-COMBUSTION GAS MIXTURE UNDER HUMID CONDITIONS

Call: 16th Open Access Grant Competition
Researcher: Dr Pezhman Zarabadi-Poor

Institution: CEITEC, Masaryk University
Field: Material Sciences

 

Dr. Pezhman Zarabdi-Poor from CEITEC was awarded more than 3 million core hours for identification of the best performing metal-organic frameworks that can separate CO2 from a post-combustion gas mixture using high-throughput systematic screening. The main anthropogenic source of CO2 emission is combustion of fossil fuels. Economic growth and industry development have continually been contributing to its concentration increase in the atmosphere, which leads to global warming of the Earth. One of the most efficient methods to avert this unwanted phenomenon and to maintain industrial development is Carbon Capture Sequestration (CCS). In this regard, metal-organic frameworks (MOFs) are considered attractive solid adsorbents that can efficiently be utilized for carbon capture from one of the main sources of CO2 emission, i.e. post-combustion gas (average content of CO2 is 15–16 %). The supercomputer and the computational resources in the amount of 3.3 million core hours will be used by Zarabdi-Poor to find best performing metal-organic frameworks, which will later be synthesized and experimentally verified in a laboratory. This research is part of the CMPSTORE project funded by the EU Horizon 2020 programme within the Marie Skłodowska-Curie action and co-funded by the South Moravian Region. The project is implemented within the research group of Prof. Radek Marek, and its active participant is Esmaiel Farajpour Bonab, a student of the Physical Chemistry PhD study programme.



IN SILICO DRUG DESIGN

Call: 14th Open Access Grant Competition
Researcher: Prof. Pavel Hobza

Institution: The Czech Academy of Sciences
Field: Material Sciences

The Principal Investigator of the project focused on development of in silico drug design methods is Pavel Hobza from the Czech Academy of Sciences. This is his ninth project involving the use of a supercomputer, which was awarded IT4Innovations computational resources. The objective of his research group’s work is to develop a reliable computing strategy for identification of new ligands, which bind to therapeutically relevant proteins such as HIV protease, cyclin-dependent kinases, and aldo-keto reductases. The team is currently focused on developing reliable protocols for the virtual screening of compound libraries, which may contain millions of chemical substances. For the project of virtual screening for drug discovery, the team of professor Hobza was awarded more than 6 million core hours this time.



EFFECTS OF BIOMECHANICAL PROPERTIES OF LIPID MEMBRANES

Call: 14th Open Access Grant Competition
Researcher: Prof. Pavel Jungwirth

Institution: The Czech Academy of Sciences
Field: Material Sciences

Prof. Pavel Jungwirth from the Institute of Organic Chemistry and Biochemistry of the CAS focuses on the research of macroscopic properties of lipid membranes. Aided by a supercomputer and molecular dynamics methods, he will perform a simulation of lipid bilayer behaviour. In plasma membranes, not only their chemical composition (e.g., types of the membrane-forming lipids) but also their shape will be investigated. The team of Prof. Jungwirth aims to detect the effects of the bilayer shape on membrane interactions. New findings about membrane shapes will open new opportunities for understanding the regulation of enzymes and other proteins in cells.



A MACHINE LEARNING APPROACH FOR THE DESCRIPTION OF ZEOLITES

Call: 14th Open Access Grant Competition
Researcher: Dr Miroslav Rubeš

Institution: Czech Academy of Sciences
Field: Material Sciences

The scientific domain with projects with the highest allocation of computational resources not only in our centre is material science. The project of Miroslav Rubeš from the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, which was awarded almost 2 million core hours, falls in this domain as well. It is focused on zeolites, which are used as detergents, catalysts, and adsorbents. In 2017, the value of the global zeolite market was about 30 billion US dollars. The objective of Miroslav Rubeš project is to use machine learning algorithms to create a model which enables deeper understanding of the phenomena occurring in zeolitic materials.



ACCURACY AND PRECISION FOR MOLECULAR SOLIDS - II

Call: 13th Open Access Grant Competition
Researcher: Dr Jiří Klimeš

Institution: Charles University
Field: Material Sciences

Dr Jiří Klimeš and his research team were awarded almost 2 million core hours for their development of materials simulation methods. His “Accuracy and precision for molecular solids – II project” applies quantum chemistry knowledge and approaches used for the description of solids, and received the prestigious start-up grant by European Research Council. In nature as well as industry molecular solids (molecular crystals) play an important role, for example, methane hydrate, also called Burning Ice, a potentially very important source of energy, carbon dioxide ice caps on Mars, and pharmaceuticals in pills. Some molecular crystals have peculiar yet important properties. An interesting example is polymorphism, which is the ability of a molecule of the same compound to exist in different structures under same conditions, and as such it may be crucial for effectiveness of drugs in the body. The objective of Dr Klimeš‘ project is to develop methods for reliable calculations of lattice energies in materials such as molecular crystals, which will help understand their properties. In this project, the Salomon supercomputer will be used for extracting the lattice energies of 13 selected molecular crystals.



OPTIMIZATION DESIGN OF FUNCTIONAL MATERIALS IN A NEW TYPE OF LITHIUM BASED BATTERY

Call: 12th Open Access Grant Competition
Researcher: Dr Dominik Legut

Institution: IT4Innovations
Field: Material Sciences

Our colleague Dr. Dominik Legut is involved in the research of lithium-based metal batteries. Unlike lithium-ion batteries, these batteries have higher energy density and are capable of storing ten times more energy. However, lithium anodes face many of the challenges associated with their lower charging efficiency, change of volume while charging/ discharging, and especially with dendritic growth. In 2017, Dr. Legut, together with his colleagues from the USA, China, and Singapore, published an article about protective films for lithium-based metal batteries in the Advanced Energy Materials journal with an impact factor of 16. Special protective two-dimensional films with a thickness of a few atoms are capable of preventing electrodes connecting (and the subsequent dangerous short-circuit), which can potentially occur as a result of dendritic growth on lithium-based anodes. This time, Dr. Legut was awarded 8 million core hours for his research of the optimal structure of lithium-based anodes. Together with other colleagues, he will aim at designing optimal materials for lithium-based anodes using prediction algorithms, chemical stability and mechanical properties calculations.



DEVELOPMENT OF RELATIVISTIC SPECTROSCOPY (RESPECT) COMPUTATIONAL CODE FOR STUDY OF HEAVY METAL ANTICANCER COMPLEXES

Call: 12th Open Access Grant Competition
Researcher: Dr Jan Vícha

Institution: Tomáš Baťa University in Zlín
Field: Material Sciences

 

One of the cancer medical treatment methods is chemotherapy. The most frequently used chemotherapeutics are platinum-based drugs. The key step for their further development is a more detailed study of their structure, properties, dynamics, and reaction mechanisms. The project of Dr. Jan Vícha from Tomáš Baťa University in Zlín carries on his previous research project, as well as the results of his project, which was awarded computational resources within our 9th Open Access Grant Competition. The objective of the new project, which has now been awarded 1,134,000 core hours, is to enhance prediction ability and the accuracy of computation of complex platinum-based alloys spectroscopic properties using the ReSpect program developed by the project partner organization - Arctic University of Norway. The newly modified code of the program will first be tested using magnetic resonance parameter computations of simple platinum chemotherapeutics, such as cisplatin and oxaliplatin in solution. The scope of the research activities will then be extended to simulations of new advanced carriers of platinum drugs, which is also the main topic of the Advanced Carriers for Platinum Drugs project supported by the Grant Agency of the Czech Republic, also implemented by Dr. Vícha. The allocated computational resources will be used in testing the modified code and for relativistic quantum chemical computations performed by the ReSpect program for prediction and analysis of magnetic resonance parameters for heavy metal complex compounds.



MOLECULAR SIMULATIONS OF TIN BASED MATERIALS FOR EUV LITHOGRAPHY

Call: 11th Open Access Grant Competition
Researcher: Prof. Petr Slavíček

Institution: The University of Chemistry and Technology Prague
Field: Material Sciences

 

How can focused high-energy radiation change a material? What particular changes will occur at a molecular level? The chemical changes of materials under the influence of high- -energy photons are studied by the team led by Prof. Petr Slavíček from the Laboratory of the Theoretical Photodynamics Research Group at the University of Chemistry and Technology in Prague. Their project titled Molecular simulations of tin based materials for EUV lithography has been awarded 1,082,000 core hours. The objective of this project is to describe molecular changes occurring in extreme ultraviolet (EUV) ionization of tin based organic compounds (particularly so-called Sn-O cages). These compounds may potentially be used as photoresist materials for EUV lithography, a new generation of lithography for nanometric dimensions applicable in effective production of new computer chips. The method is based on the changes of physical and chemical properties of photoresists (e.g. their solubility) after EUV radiation. By exposing specific areas of a material to the radiation, the dimension of the resulting structure can be up to 10 nm, which is the threshold limit dimension of today‘s commercial chips. Considerable computational intensity of molecular simulations of ionized Sn-O compounds is generated by the rich electron structure of tin. Simulation of a single trajectory taking half a picosecond requires almost a week to be computed using common processors. With its 76,896 cores (Intel Haswell processors and Intel Xeon Phi accelerators), our Salomon supercomputer will allow the researchers to perform extensive simulation, which would not be practically executable otherwise.



IN SILICO DRUG DESIGN

Call: 10th Open Access Grant Competition
Researcher: Prof. Pavel Hobza

Institution: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Field: Material Sciences

 

Prof. Pavel Hobza from the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences conducts research on computer-aided drug design. His project “In silico drug design” has been awarded 7,425,000 core hours within the 10th Open Access Competition. The allocated computational resources will be used for developing virtual screening methods for drugs. Used by the pharmaceutical industry, this approach is based on molecular modelling (docking and scoring) in order to identify suitable substances for designing new drugs. Due to its high computing performance requirements, the reliability of these methods has been low so far. Using the IT4Innovations supercomputers and employing exact quantum chemistry computations, the researchers from Prof. Hobza’s team are able to predict both the drug structure at the active site of proteins and their ability to bind, which determines their therapeutic effects. The recently published approach is currently used in collaboration with leading pharmaceutical companies.