Short directional X-rays have been extensively studied due to their high potential in many
applications such as high-quality phase-contrast imaging of biological samples and spectroscopy at
femtosecond timescale. Interaction of very intense laser pulses with plasma medium enables the
production of high energy photons in X- and gamma-ray range by several mechanisms, such as
betatron...
To understand how the conformational space of small peptide fragments determine the formation of protein three-dimensional structures is one of the important goals of modern biochemistry and structural biology. Achieving this goal will allow significant progress, for example, in the design of specific enzyme-based catalysts which would greatly simplify chemical synthesis in industry. Full...
Handling error states in C++ applications is managed by exceptions. In distributed applications, it is necessary to inform the other processes, that something wrong happened, and the application should either recover from the faulty state, or report the error and terminate gracefully. Unfortunately, the MPI standard does not provide any support for distributed error handling. This poster...
The magneto-hydrodynamic description is adopted in many disciplines, where the dynamics of magnetized fluids is investigated. It plays a vital role in plasma physics, where high-temperature plasma becomes highly electrically conductive. Its modelling is then essential for the applications like inertial and magnetic confinement fusion, laboratory astrophysics and many others. For this purpose,...
We performed a quantum-mechanical molecular-dynamics (MD) study of Fe$_{3}$Al with and without hydrogen atoms under conditions of uniaxial deformation up to the point of fracture. Addressing a long-lasting problem of hydrogen-induced brittleness of iron-aluminides under ambient conditions, we performed our density-functional-theory (DFT) MD simulations for T = 300 K (room temperature). Our MD...
In recent years, HPC workloads and communities have undergone substantial paradigm shifts. There is an increasing amount of users that want to leverage HPC clusters to execute many simple and embarrassingly parallel tasks as easily as possible. However, due to the limitations of traditional HPC job managers, these users must often resort to manual aggregation of tasks into a smaller number of...
The interaction of the oceanic tidal flows with the Earth's main magnetic field provides a powerful natural source of electromagnetic energy suitable for sub-oceanic upper-mantle electrical conductivity sounding. We have developed a new frequency-domain, spherical harmonic-finite element approach to the inverse problem of global electromagnetic (EM) induction. It is set up for an effective...
Complex scientific workflows describing challenging
real-world problems are composed of a lot of computational tasks
which require high performance computing or cloud facilities to
be computed in a sensible time. Most of such tasks are also
written as distributed parallel programs being able to run across
multiple compute nodes. The amount of requested resources
per task influences both...
Recent successes of deep-learning based approaches to the protein folding problem1,2 have greatly relied on the existence of large protein structural3 and genomic4 databases. However, since these deep-learning based approaches cannot predict structure exactly, and the sufficiently precise DFT-based methods are computationally too expensive,...
Realistic ultrasound simulations are becoming integral part of many novel medical procedures such as photoacoustic screening and non-invasive treatment planning. The common denominator of all these applications is the need for cheap and relatively large-scale ultrasound simulations with sufficient accuracy. Typical medical applications require full-wave simulations which take...
Non-uniform-timestep Distributed Pseudospectral Method allows different timestep sizes in different sub-domains of simulation. This requires special care when marching overlap regions forward in time. Overlap regions have to be evaluated at timesteps to match the neighbor's temporal discretization. This process involves the extrapolation of such values using a modified integration scheme. To...
Ultrafast intersystem crossing (ISC) in transition metal complexes represents a challenging process for both experimental and theoretical investigation. Two computational approaches have been employed to study the relaxation processes during the ISC of complex [Re(bpy)(CO)$_\rm3$Cl] (bpy = 2,2’-bipyridine) in explicit dimethylsulfoxide solvent. Several relaxation processes has been identified...
Evolutionary design has become a successful concept in the areas where a solution to a problem needs an exploration of extensive search spaces (i.e. the analytical approach is intractable or not known). It has been shown during recent years that innovative or still unknown solutions can be obtained automatically using proper evolutionary setups. Cellular automata represent a massively parallel...
The distributed computing of the ATLAS experiment at LHC is allowed to opportunistically use computing resources of the Czech national HPC center IT4Innovations. Two submission systems based on the ARC-CE are used. Those will be the main focus of this contribution including description of their structures, functionalities and requirements, comparison of their advantages and disadvantages, and...
Intrinsically disordered proteins (IDPs) are identified by polypeptide chains that do not have a stable single well-defined structure. They are responsible for the development of neurogenetic diseases such as Alzheimer and Parkinson. Structural characterization of IDPs has to be facilitated by both NMR experiment and computational techniques. The functionality of standard techniques such as...
Amorphous materials, such as amorphous alloys and metallic glasses (MGs) [1-4] are of current interest due to their peculiar internal structures and unusual properties [5-8] like high strength, excellent corrosion and wear resistance, localized deformation by shear banding and much higher hardness than crystalline alloys of comparable elastic modulus. Because glassy alloys do not exist in...
While the elastic properties of a composite microstructure are relatively straightforward in obtaining (e.g., using the resonance ultrasound spectroscopy), the features of a single grain are not directly measured. Here, we show our approach to determine these properties by employing large-scale ab-initio modeling techniques. Furthermore, we quantitatively reproduce the observed values of the...
A plasma shutter [1,2] is usually a thin solid foil that is placed in front of the main target in the laser-target interaction. The laser pulse with its prepulses then needs to burn through it which can improve the laser pulse contrast and its intensity profile. This includes the generation of a steep rising front [3] and intensity increase [4] . The new pulse shape can improve the consequent...
Modeling thermal properties of new materials using computational methods based on Quantum Mechanics usually provides us with a well-defined ground state of the system, but not its transitional temperatures. For obtaining these properties, we propose a generic and high-performance method for mapping an ab-initio system onto the Heisenberg model using our original code...
Proteins are the most ubiquitous biomolecules found in nature. Proteins are responsible for catalyzing reactions, transducing signals, structural properties, and much more. During their lives, proteins are found in various environments. It is not rare that proteins are found in enclosed spaces, such as pores, channels, and tunnels. For instance, in the first seconds of their existence,...
Molybdenum disulfide, MoS$_2$, is a layered material from transition metal dichalcogenide (TMD) family. Its range of applications includes tribological coatings, materials for electronics, and catalysis.
TMD thin films are often prepared via deposition processes, that originally yield an amorphous material[1]. Tribological applications mostly rely on the ability of MoS$_2$ to crystallize in...
Achieving lubrication at high temperatures and pressures, as well as in oxidative environment, is a challenging problem of modern tribology, relevant for a wide range of applications such as turbomachinery, machining tools and aerospace industry [1, 2]. A promising solution for the conditions of high temperatures/pressures and presence of oxygen is to use a hard and oxidation-resistant coating...
Using a first-principles approach we investigated an effect of oxygen as substitutional impurity on cohesion of three transition metal nitride multilayers. Namely, we studied AlN/VN, AlN/TiN and VN/TiN systems in a rock-salt structure (B1) with (0 0 1) interfaces. Preferred oxygen positions were determined with the help of calculations of free energy that also included vibrational entropy...
Caged hydrocarbons exhibit interesting properties, rendering these materials suitable candidates for a variety of uses. Their carbon skeleton usually experiences a large strain unlike other, chained hydrocarbons – this prompts discussion about their use as energy storage media, precursors for pharmaceuticals or explosives. Despite this, relevant thermodynamic data for these compounds is...
The Brønsted acidity of zeolites has been addressed numerous times as zeolite science progressed in last 50 years, however, the question of acidity of particular zeolitic framework was not yet resolved either theoretically or experimentally. The theoretical issues stems from the fact that electrostatic part of the total energy does not converge for charged cells without introducing...
Proteins are the most ubiquitous biomolecules found in nature. Proteins are responsible for catalyzing reactions, transducing signals, structural properties, and much more. During their lives, proteins are found in various environments. It is not rare that proteins are found in enclosed spaces, such as pores, channels, and tunnels. For instance, in the first seconds of their existence,...
