Calculation of absolute binding affinities of phosphopeptides to 14‐3‐3 proteinCall: 2nd External Access Competition
Researcher: Jozef Hritz
14-3-3 proteins, found in all eukaryotic cells, are known to be important in cell-cycle regulation, apoptosis, and regulation of gene expression. They are also associated with oncogenic and neuro-degenerative amyloid diseases. The main aim of the project is to calculate the binding affinity between the 14-3‐3 protein and its selected target phospho-peptides. Experimental production of many phosphorylated proteins binding to 14-3‐3 in sufficient amounts for experimental binding affinity measurements is almost impossible. Once the approach is validated for PKCe and C-RAF kinase peptides by their comparison with the experimental data, the approach can be used almost for any of 850 known binding partners important particularly in neurobiochemistry and neurodegenerative diseases.
Air quality modelling in fine resolutionCall: 2nd External Access Competition
Researcher: Jaroslav Resler
Air quality is an important factor affecting health and life quality of a large part of the population. It is well known that transportation is an important source of air pollution, especially in large cities. Model simulations are an essential tool for the quantification of the impact of transportation on air quality; they serve as an aid for policy making and planning of transportation solutions. The main objective is to perform a pilot simulation of the air quality in very high resolution using Eulerian chemical transport model. Chemical transport model CMAQ (US EPA, USA) will be configured on matching domains and the main focus will be on the fine resolution domain and on the influence of the urban model. We expect to obtain new insights to dependence of air quality on emission sources and to a role of transportation and its impact on pollutant concentrations.
Blood flow simulation in a patient specific geometryCall: 2nd External Access Competition
Researcher: Jaroslav Hron
The motivation for this work is the question whether mathematical modeling can be of direct help in medical decision when encountering certain situations in cardiovascular system, specifically an aneurysm. Aneurysm is a specific local expansion of the blood vessel wall and its rupture can lead to a fatal situation. With increasing popularity of computer tomography and magnetic resonance imaging an aneurysm is often diagnosed as byproduct and raises a question if one can identify some indicators suggesting a chance of its rupture. The geometry for each case is unique and demands accurate computation. Proper understanding of blood rheology and connected chemical reactions, like coagulation process, and interactions with the vessel walls can be factors with significant importance. Identifying which of these parts plays important role in such decision will require great amount of computations which are considerably demanding on computational resources.
Modeling and shape optimization of periodic nanostructuresCall: 3rd Internal Access Competition
Researcher: Lukáš Halagačka
This project is focused on modelling and optimization of novel plasmonic and photonic periodic structures. Light propagation in the complex structures is hardly described using simple models and, therefore, advanced numerical modeling is needed. The main goal of the project is to use our own parallel code based on Rigorous Coupled Wave Analysis (RCWA) to model optical and magneto-optical properties of nanostructures, optimize geometric parameters to increase the figure-of-merit function in experimental data fitting procedure. Design of 1D periodic magnetoplasmonic devices founds possible application as a unidirectional optical filter. Such a type of device can be useful in further increasing of speed of optical telecommunications, for holographic applications and the solar cell structures.
Support for Exa2ct projectCall: 3rd Internal Access Competition
Researcher: David Horák
Today, only around one percent of codes support 10k+ cores, whereas machines with more than 200k cores are already available. EXA2CT Project aims to development of new algorithms and optimization of the existing ones to reach the scalability on future exascale supercomputers. As the communication among computational cores is the bottleneck in this time, an attention will be paid to rearrangement of known scalable algorithms based on avoiding or hiding the communication in the first phase of the project.
BEM4ICall: 3rd Internal Access Competition
Researcher: Michal Merta
Boundary element methods (BEM) are used for modelling physical phenomena by partial differential equations. Compared to volume discretization methods, such as finite element methods, BEM introduces unknowns only on the boundary, which is advantageous in case of unbounded computational domains, e.g. in electromagnetic scattering problems, or shape optimization. However if we want to use BEM to solve large real life problems, it is necessary to parallelize the computation on a supercomputer ANSELM.
Pure and doped water clusters - non zero pressure Monte Carlo simulationsCall: 3rd Internal Access Competition
Researcher: Aleš Vítek
This project is focused on the modeling of thermodynamics and structural properties of finite molecular systems – pure and doped water clusters under non-zero temperatures and pressures. Main attention will be focused on selected system sizes up to 50 molecules. The goal of this project is theoretical prediction of properties of this water - admixture complexes under different thermodynamic condition (broad interval of pressures and temperatures) and study of local structure in the admixture molecule vicinity. Our attention will be focused on these sizes of clusters, which create cage structures and may wrap the admixture atom or molecule. Results of this basic research may by interesting for understanding of behavior, stability and properties of very important crystalline hydrates, where bulk limit of water molecules at non-zero pressure can create a crystal structure with cages occupied by (usually hydrophobic) admixture particles, rare gases, CO2 and methane molecules. Methane and carbon dioxide hydrates are of general interest of many physical and chemical scientists now because of storage of this greenhouse gases or in the case of methane, as a possible source of energy for the future.
Lowdimensional magnetic systemsCall: 2nd Internal Access Competition
Researcher: Dominik Legut
One- and two-dimensional magnetically frustrated systems are suitable candidates for advancement of the current technology based on giant magnetic resistance (GMR) or tunnelling magnetic resistance (TMR). Both these methods are commercialized for read/write heads of the hard-drives, as, sensors for acceleration and for bearings detecting small magnetic fields. This research lies in mimic of the multilayered systems by using compounds that exhibit one- or two-dimensional magnetic ordering. These materials show high magnetic frustration, i.e. magnetic moment orientation. Using firstprinciples (ab initio) calculations, we are able to determine the level of frustration and the strength of magnetic interactions, which enables us to precisely determine the magnetic structure in these low-dimensional systems.
MatSol library - development, testing and support libraries developmentCall: 2nd Internal Access Competition
Researcher: Oldřich Vlach
The MatSol library, developed by IT4I researchers for computing problems from the field of mechanics, is written in MatLab, which enables quick code development. Implementation and debugging is more time consuming in C or FORTRAN. The MatSol library will therefore be used to test new algorithms so that it can be determined whether the given algorithm is suitable for implementation in a more difficult language, or whether it has to be modified.
Modeling of elementary processes in cold rare-gas plasmasCall: 2nd Internal Access Competition
Researcher: René Kalus
Low-temperature plasma with a rare-gas carrier medium seem to be a promising tool for medical applications. For example, it has been shown recently that low-temperature plasmas are very effective in surface sterilization, wounds healing, or even malignant cell inactivation. The main aim of this project is elementary collision processes modelling, particularly collisions of plasma particles and and their interaction with electromagnetic radiation. The results of this microscopic modelling will provide input for subsequent studies of plasma at the macroscopic level and optimization of its generators (it will be carried on in cooperation with Paul Sabatier University in Toulouse, France). Improvement of our knowledge can be thus expected not only in the field of basic research but also in the development of new technologies based on that research.
Axially and radially cooled GCS brake discs
Brake discs with internal cooling (or vented discs) are currently the most efficient braking system and are widely used in the automotive industry. Compared to drum brakes, they are much lighter and their cooling system is more efficient. On the other hand, they are more expensive and prone to malfunctions caused by dirt. The research focuses on optimizing air flow in the brake disc and the diffuser while taking account of the disc’s strength and material fatigue. Mathematical simulations on the supercomputer will significantly help in designing the geometry of the disc and the diffuser, as they will provide improved visualization of airflow, heat radiation, convection and conduction in the prototype. This will allow for minimizing disk deformations resulting from high temperatures and pressure. The GCS brake system may mark the same progress in braking technology as did the change from unvented to vented discs, because the authors assume that GCS reinforces the benefits of vented discs while minimising their drawbacks.
Testing codes for computational fluid dynamics
The main objective of this project is to test the scalability of freely available and commercial codes focusing on Computational Fluid Dynamics (CFD). Given the substantial demands of this type of calculation on computing time, the use of supercomputers in CFD is very important. Understanding the behaviour of the algorithms used within available libraries is crucial to the future efficient use of the small cluster in CFD calculations. The results will be processed into a freely accessible database covering typical fluid dynamics tasks and will be used for future collaboration with IT4Innovations’ external partners.
Thermal expansion of materials for Generation IV reactors
Generation IV fast nuclear reactors rely on melted alkali salts for cooling, which are also used for distributing nuclear fuel e.g. in the form of uranium carbide particles. This method provides much better heat transfer and allows for higher operating temperatures and, in turn, improves primary cycle efficiency. Possible materials for this use include the aforementioned uranium carbide compounds that have high melting points of about 2500 K. However, some of these compounds exhibit very unusual dimensional changes as temperatures increase. The main objective of this research is to understand this behaviour and to map the phase transformations of these compounds using first-principle (ab initio) calculations, i.e. procedures based on quantum mechanics.
Performance and scalability test of a hydrological model with remote execution
As a service, HPC (High Performance Computing) is a new area of hydrological modelling, which is of great benefit to end users such as flood warning committees and fire departments, but also the general public. These users need to get the results of hydrological simulations in real time so that they can use them to make informed decisions in emergency situations. The tests of this architecture will help assess and improve its scalability, identify possible shortcomings and improve its overall efficiency, thereby ensuring quick responses to the requirements of its users.
Enzymatic reaction mechanisms investigated by Car-Parinello ab initio dynamics
Carbohydrates play a critical role in many biological processes. On cell surfaces, they often take the form of highly branched glycoconjugates. The synthesis of such glycoconjugates involves many enzymes. Disruption of these enzyme activities can lead to life-threatening pathological conditions such as diabetes, Alzheimer’s disease and cancer. The study aims to investigate the reaction mechanisms of these enzymes at the atomic level, which may aid e.g. in drug development.
Simulations of particle acceleration by short ultra-intense laser pulses
The spatial and financial requirements of current particle accelerators considerably complicate their use in medicine, for example in cancer treatment. The main objective of this research is to understand how particle acceleration by high-intensity lasers operates. This research may contribute significantly to the development of future high-quality and less expensive sources of protons and X-rays from accelerated electron beams. These can be used for imaging very small structures on the order of nanometres (e.g. biological samples) and also for researching matter in astrophysics.
In silico drug design
Computer aided drug development has garnered a lot of attention due to its advantages, which include speed, low costs and the ability to select appropriate components for synthesis and subsequent biological screening. The aim of this project is to identify novel ligands that bind with therapeutically relevant proteins. Over the long term, the team has been researching components that are active in the treatment of cancer and acquired immunodeficiency syndrome (AIDS).
FLOCON – A Project by the Aerospace Research and Test Establishment
The FloCon project is aimed at affecting the boundary layer on the wings of modern commercial aircraft through blowing. The objective is to improve aerodynamic performance and reduce environmental impacts. CFD models for simulating modern 3D active flow control technologies will be prepared, tested and validated and subsequently implemented into the aerodynamic optimization loop.