7th Users' Conference of IT4Innovations

30 Oct 2023, 10:00 → 31 Oct 2023, 14:00 Europe/Prague

atrium (IT4Innovations)

7^th Users' Conference of IT4Innovations will take place on 30 and 31 October 2023. All of our users, as well as research and project partners from various organisations, research institutions, and industry, are welcome to attend the Conference.

The submission of contributions deadline is 10 September 2023.

Registration is open until 24 October 2023.

Attendees will discover more about our future upgrade plans, listen to talks given by our prominent users, and can engage in discussions during the Users' Council meeting and a poster session.

Contribution types: Users' talks/Posters

Users' talks

Selected talks by our prominent users will be presented at scheduled times during the whole conference. Each talk is expected to take max. 20 mins (with discussion included).

Posters

Please note that the required poster size is A1 portrait orientation. 

The poster session will take place on 30 October during lunch and dinner.

Conference Programme

How to get to Ostrava and Accommodation tips

Presentations Branislav Jansik Presentation Poster Session Programme

Monday, 30 October

10:00 → 11:00 Registration and networking

11:00 → 11:30 Welcome and IT4Innovations news

11:30 → 12:00 Keynote I

11:30 The first CACHE challenge: searching for hit molecules in ultra-large chemical databases

The CACHE initiative (Critical Assessment of Computational Hit-finding Experiments) was created to improve and accelerate development of approaches for primary hit finding. The first competition involved 25 leading groups in computational chemistry and chemoinformatics from all over the world to find promising hit molecules for the WD40 repeat (WDR) domain of leucine-rich repeat kinase 2 (LRRK2) which is the most commonly mutated gene in familial Parkinson's Disease. The goal was to find hits among compound supplied by the Enamine company which maintains the database of about 2.5 million of synthesized compounds and a Enamine REAL Space which includes more than 10 billion of virtually enumerated synthetically accessible molecules. The 3D structure of the protein was resolved recently, however, no highly active hits were known for this protein that created an additional challenge.
We developed and used a multi-step pipeline to enable fast searching of potential hits in a database of billions of molecules. It included de novo generation of query molecules, similarity searching in a large database, a consensus scoring approach incorporated molecular docking and calculation of binding free energy by MM-GBSA, etc. After the first stage of the CACHE challenge we identified 8 experimentally confirmed hits, which brought us to top 5 teams. These hits were further optimized during the second stage. The final outcomes of the challenge must be released in September. In the talk we will describe challenges and opportunities in mining of ultra-large chemical libraries and the lessons we learned.

The work was supported by the Ministry of Education, Youth and Sports of the Czech Republic through INTER_EXCELLENCE II grant LUAUS23262 and the e-INFRA CZ (ID:90254) and projects ELIXIR-CZ (LM2023055) and CZ-OPENSCREEN (LM2023052). We also acknowledge the contributions from the project ENOCH (CZ.02.1.01/0.0/0.0/16_019/0000868).

Speaker: Pavel Polishchuk (IMTM, Palacky University)

12:00 → 13:00 Users' Talks I

12:00 Extramedullary multiple myeloma: insights into pathogenesis and tumor microenvironment using whole exome, RNA and single-cell sequencing

Our study represents the most comprehensive next-generation sequencing analysis of extramedullary multiple myeloma (EMM) tumor cells to date, uncovering key molecular features and describing the tumor microenvironment. We found the co-occurrence of 1q21 gain/amplification and MAPK pathway mutations in 79% of EMM samples, suggesting these are crucial mutational events in EMM development. Additionally, we demonstrated that patients with mutated KRAS and 1q gain/amp at the time of diagnosis display significantly higher risk of EMM development (HR=2.1, p=0.008) using large coMMpass dataset (N=1039). Next, we observed a downregulation of vital molecules for EMM cell homing – CXCR4, enhanced cell proliferation and predominant production of light chains compared to heavy chains. We revealed decreased expression of therapeutic targets such as CD38, SLAMF7, GPCR5D and FCRH5 as well as reduced expression of HLA-B/C molecules, potentially explaining lower efficacy of immunotherapy in EMM. On the other hand, we identified significantly up-regulated EZH2 and CD70 as potential future therapeutic options. For the first time we report on EMM's tumor microenvironment, revealing CD8+ T cells and NK cells as predominant immune effector cells using single cell sequencing. Finally, this is the first longitudinal study in EMM ever performed catching the molecular changes since the time of diagnosis.

Speaker: David Žihala (Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic; Department of Hematooncology , University Hospital Ostrava, Ostrava, Czech Republic)

12:20 Quantum chemistry and machine learning for computer-aided drug design

Accurate estimation of protein–ligand binding affinity is the cornerstone of computer-aided drug design. We have developed a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semi-empirical quantum-mechanical computational methods. SQM2.20 incorporates the latest methodological advances while remaining computationally efficient even for systems with thousands of atoms (with computation time ~ 30 minutes at one core). [preprint: https://doi.org/10.26434/chemrxiv-2023-zh03k ]

To validate the SQM2.20 scoring function rigorously, we have compiled a benchmark dataset consisting of high-resolution crystal structures and reliable experimental affinities for ten diverse protein targets, the PL-REX data set.

Comparative assessments demonstrate that SQM2.20 outperforms other scoring methods and reaches a level of accuracy similar to much more costly DFT calculations. In the PL-REX dataset, it achieves excellent correlation with experimental data (average R2 = 0.69) and exhibits consistent performance across all targets.

To address the remaining limitations of the SQM methods while keeping our physics-based approach independent of prior data on protein-ligand interactions, we are developing a Δ-ML approach which brings all the calculations in the scoring protocol close to the accuracy of DFT. Our results show that it is possible to achieve excellent results not attainable by either uncorrected SQm calculations or pure ML approach without the SQM component.

Speaker: Jan Řezáč (UOCHB AV ČR)

12:40 Atomistic simulations of ancient ribosomes and their parts

Ribosome is particularly famous as a key player in protein synthesis. This large biomolecular complex of ribosomal RNA and ribosomal proteins catalyses peptide bond formation in all known cells. Within a so-called accretion model it is believed that during evolution, ribosome grew in size and chemical complexity. Hence, the central parts of the ribosome are molecular fossils that suggest how the peptide bonds were formed billions years ago before the first life emerged. Recently, a catalytic activity of two ancient ribosomes - much smaller than the modern ribosome - was demonstrated. We have used all-atom molecular dynamics simulations to address the structural stability of the ancient ribosomes. The simulations show that the fragments of ribosomal proteins stabilize the catalytic center of the ancient ribosome, thus may be responsible for the increase of ribosome efficiency.

Speaker: Michal H. Kolar (University of Chemistry and Technology)

13:00 → 14:00 Lunch & Poster Session

14:00 → 15:00 Users' Talks II

14:00 Interactions of Ionizable and Cell Membrane Lipids

Lipid-based drug delivery systems, such as lipid nanoparticles (LNPs), are a promising branch of current medical research. The most notable recent example of such LNP-based molecular delivery are the novel COVID-19 vaccines, where a LNP containing engineered ionizable lipids (ILs) carries an mRNA molecule into the human body. Delivering of short-interfering or messenger RNA into cells is also a very versatile strategy how to silence precisely defined genes or prepare personalised anti-cancer vaccines.

To deliver its cargo into the cell’s cytoplasm, the LNP must first cross the outer cellular membrane. There are several proposed mechanisms of this process, however, the exact nature of the LNP-membrane dynamics has so far gained only limited attention as it is challenging to study experimentally. In contrast, molecular dynamics simulations can provide an insight into complex structures with atomic and femtosecond resolution. In this project we use molecular dynamics to visualize and describe the interactions of the ionizable and membrane lipids, to help understand the fine details of a LNP entering the cell on a molecular level.

We simulated LNPs (in charged and uncharged form of the IL) both on the atomic level (to describe the physical-chemical details of the interaction with biological membrane) and in the coarse-grained resolution to evaluate larger-scale dynamics of LNP-membrane fusion, mimicking a possible endocytosis mechanism.

On the atomic level, the ionizable lipids do not significantly disrupt the membrane structure, however, in the uncharged form they make the centre of the bilayer more hydrophilic. On the coarse-grained level, LNPs induced a change in membrane phase increasing its curvature significantly. Such rapid changes in endosomal membrane stability can explain the mechanism of RNA release. The understanding of LNP behaviour inside cells will be another step towards efficient in-silico design of LNP composition.

Speaker: Dr Petra Čechová (Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc: Olomouc, CZ)

14:20 Biocompatibility of carbon nanomaterials from an in-silico perspective

Carbon nanomaterials have revolutionized the field of biomedicine, offering opportunities for their diverse applications. Their unique tunable physicochemical, optical, mechanical and electronic properties make them ideal candidates for a wide range of biomedical applications. Carbon nanomaterials, including carbon nanotubes, graphene, and carbon dots, have shown remarkable promise in areas such as drug delivery, tissue engineering, biosensing, and imaging. However, to harness their full potential and ensure their safe and efficient use, it is crucial to gain a comprehensive understanding of their interactions with biomaterials at the molecular level. For this, experimental techniques yet lack the required atomistic resolution and therefore we can rely on molecular dynamics simulations, which can provide valuable insights into the underlying mechanisms governing the biocompatibility of carbon nanomaterials.
Here we focus on the modeling of interactions of carbon dots (CDs) and graphene derivatives with biomolecules. We investigated the interactions of CDs with nucleic acids and identified preferential modes of interaction between CDs and various nucleic acid shapes. Further, we focused on understanding of the behaviour of graphene derivatives on larger scales and their interactions with complex lipid membranes in coarse-grained resolution. Through these simulations, we elucidated the nature of interactions between graphene derivatives and lipid membranes, providing insights into graphene-membrane interactions and the effect of graphene on membrane lipid organization.
The simulations of bio-nano interface bring new challenges in their setup, as they require mutually compatible force fields for both bio- and nanomaterials. We present here a complex approach to simulations of the bio-nano interface in multiscale resolution, necessary for capturing the required level of details. These simulations can be a start of in-silico studies on nanotoxicity of the nanomaterials or used for targeted design increasing their biocompatibility.

Speaker: Markéta Paloncýová (Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc)

14:40 Benchmark of time-dependent density functional theory simulations on a variety of European CPU-based supercomputers

With the advent of super-computing, first-principle simulations became essential for the generation of contemporary knowledge, notably in condensed matter (1), but also in more applied fields, e.g., where the development of applications is based on the usage of intense laser radiation on solid materials (2–5).

Although numerous open source scientific codes are nowadays available, mastering these can require a long-term investment, making them not directly available to a wide range of users. In addition, long-term access to super-computing centers for research purposes remains challenging in the context of the current energy crisis, making benchmarking actions time-demanding in comparison to nowadays scientific production requirements. As a result, a benchmark of versatile and experimentally validated simulation techniques acquired along years of research experience can be of high value.

In this work, the data generated using time-dependent density functional theory (TDDFT) using the Octopus code (1) on a variety of European supercomputers was benchmarked by reusing production runs that were validated both on established theories (2) and on dedicated experiments (6). From the ~2,000 available simulations, the run-average of the time needed per iteration was acquired on a variety of 10 European super-computing facilities, counting among them some that were listed in the Top 500 world chart (top500.org).

By correlating the time measurements with specifications of the employed libraries, processors, compiler chains and their parameters, the results demonstrate the modularity of the employed code and suggest guidelines for researchers, developers and machine providers in view of offering a wider usage of the TDDFT in near future.

This work was supported by the European Regional Development Fund and the state budget of the Czech Republic (project BIATRI: CZ.02.1.01/0.0/0.0/15 003/0000445, project HiLASE CoE: No. CZ.02.1.01/0.0/0.0/15 006/0000674). Computational support was provided by the Ministry of Education, Youth and Sports of the Czech Republic through the e-INFRA CZ (ID:90140). The numerical results of this research have been partially achieved using the DECI resource Navigator based in Portugal at University of Cambria with support from the PRACE aisbl, and ELI Beamlines for the extra computational support (Eclipse HPC cluster).

References
1. N. Tancogne-Dejean et al., J Chem Phys. 152, 124119 (2020).
2. T. J.-Y. Derrien et al., Phys. Rev. B. 104, L241201 (2021).
3. I. Gnilitskyi et al., Sci. Rep. 7, 8485 (2017).
4. I. Gnilitskyi, L. Orazi, T. J.-Y. Derrien, N. M. Bulgakova, T. Mocek, Method of ultrafast laser writing of highly-regular periodic structures on metallic materials (2016), (available at https://patentscope.wipo.int/search/en/detail.jsf?docId=WO18010707).
5. T. J.-Y. Derrien, Y. Levy, N. M. Bulgakova, in Ultrafast Laser Nanostructuring: The Pursuit of Extreme Scales (Springer, 2022; https://link.springer.com/book/9783031147517), vol. 239 of Springer Series in Optical Sciences.
6. P. Suthar, F. Trojánek, P. Malý, T. J.-Y. Derrien, M. Kozák, Commun. Phys. 5, 288 (2022).

Speaker: Dr Thibault J.-Y. Derrien (HiLASE Centre - Institute of Physics)

15:00 → 16:00 Users' Council

16:00 → 16:30 Coffee break

16:30 → 17:00 Keynote II

16:30 Cinematic Visualization of Large Scientific Data Sets

The talk is focused on scientific visualization. High-fidelity scientific simulations utilize HPC infrastructures and generate terabytes to petabytes of data. To properly analyze and explore such data fast post-processing and visualization are fundamental.

Two approaches, which are developed to provide a workflow for high-quality cinematic visualization of large scientific data sets, will be presented. Both utilize IT4Innovations infrastructure to ensure data pre-processing and rendering. Blender software is used to create final visualizations. In this way, numerous features such as lights, materials, cameras, and others can be conveniently set up. Moreover, we have developed a modified version of Blender path-tracing-based renderer, which allows the distribution of the computation among cluster resources and thus provides high-quality as well as fast rendering.

The first approach is focused on visualization using a path-tracing volume rendering technique. A scalable workflow for processing and visualization of unstructured data will be described. This approach uses our internal MESIO library for data set loading and processing. The second approach integrates Vistle into Blender. Vistle is an open-source tool for scientific data reading and processing. Blender serves as a user interface with further rendering capability while Vistle runs in the background and can utilize HPC resources for data processing before the visualization.

Speaker: Marketa Faltynkova

17:00 → 18:20 Users' Talks III

17:00 Karolina system energy efficiency optimization

In 2022, IT4Innovations was forced to temporarily turn off operated HPC systems because electricity prices increased enormously. Since then, the price has stayed high, and to avoid a potential next outage due to budget shortage, we investigated possible improvements to the Karolina system's energy efficiency. The behavior of accommodated CPUs and GPUs when executing workloads of a wide range of arithmetic intensities and instruction sets was analyzed in various hardware configurations to identify high power savings settings with limited impact on the performance of users' applications.

The talk will present the methodology used to identify the hardware configurations, power savings gain, and statistical evaluation of the impact of reduced resources on users' jobs.

Speaker: Ondřej Vysocký (IT4Innovations)

17:20 A first principles study of structural and optoelectronic properties and photocatalytic performance of GeC- MX2 (M = Mo and W; X= S and Se) van der Waals heterostructures

Heterostructured two-dimensional (2D) material, particularly van der Waals heterostructures (vdW)[1], are promising photocatalysts because of their adjustable optoelectronic properties such as efficient carrier separation[2] and type-II band alignment[3]. The layers of vdW heterostructures are assembled in a highly regulated sequence thus providing a platform for creating novel materials and novel peculiarities in nanoelectronics. In this work, we used density functional theory to investigate the optoelectronic and photocatalytic properties of novel GeC-MX2 vdW heterostructures for photocatalysis applications. AIMD simulations show that the GeC-MX2 heterostructures are thermally stable. The optical absorption spectrum indicates that these heterostructures have a considerable optical absorption in the visible range. The type-II band alignment in GeC-MoS2 and GeC-WS2 enables the photogenerated electron-hole pairs to be separated continuously. The electrons transfer from GeC to MX2 monolayer leads to a built-in electric field at the interface. This induced electric field is essential for preventing the recombination of the photogenerated charges. Moreover, the band-edge locations suggest that GeC-MX2 heterostructures can be used as water-splitting photocatalysts. Therefore, we expect that the optoelectronic properties of these novel GeC-MX2 heterostructures will find practical utilization in future photocatalysis applications.

The present research has been published (Phys. Chem. Chem. Phys. 25. 11169, 2023) and received support from the project “Novel nanostructures for Engineering Applications” No. CZ.02.1.01/0.0.0.0/16_026/0008396, and e-INFRA CZ (ID: 90140)

References
[1] A. K. Geim and I. V. Grigorieva, Nature, 2013, 499, 419–425.
[2] Y. Bai, Q. Zhang, N. Xu, K. Deng and E. Kan, J. Phys. Chem. C, 2018, 122, 15892–15902.
[3] Z. Zhang, Q. Qian, B. Li and K. J. Chen, ACS Appl. Mater. Interfaces, 2018, 10, 17419–17426.

Speaker: Tahir wahab (Czech Technical University in Prague)

17:40 Employing supercomputers to determine the local structure of framework and extra-framework species and to subsequently evaluate their NMR parameters for comparison with experiments

Zeolites are crystalline microporous aluminosilicates widely used as molecular sieves and catalysts in industrial chemical processes. Extra–framework cations compensate the negative charge of the microporous aluminosilicate frameworks [Sin-mAlmO2n]m- made of corner–sharing TO4 tetrahedra (T = Si, Al-). Furthermore, also electron-pair acceptor Al framework Lewis sites are often present in zeolite catalysts. The Al framework Lewis sites were suggested to correspond to Al centers tricoordinated to the zeolite framework. A typical feature of many silicon-rich zeolites is a high number of crystallographically distinguishable T sites. Since the cationic species bind to the AlO4-tetrahedra, the crystallographic position of aluminum in zeolite frameworks governs the location of the active sites, which in turn affects the catalytic activity and selectivity.
We present our results regarding the structures and NMR parameters of extra–framework Li+[1] and Na+[2] cations in the zeolites of the ferrierite structure as well as the Al framework Lewis sites in the beta zeolite.[3]
Periodic DFT calculations including extensive molecular dynamics conformational sampling of all possible Li+ and Na+ sites for all the possible distinguishable Al(T) sites were performed employing the cp2k program. The B3LYP 7Li and 23Na NMR parameters were evaluated utilizing the Gaussian program and seven coordination shell clusters and compared with our experiments. We reveal the siting of Li+ and Na+ balancing framework Al atoms located in all the distinguishable framework T sites of ferrierite.
Extensive periodic DFT calculations including molecular dynamics employing the VASP program were carried out for our plausible models of the Al framework Lewis sites in the beta zeolite. Afterwards, B3LYP 27Al NMR parameters were evaluated utilizing the Gaussian program and seven coordination shell clusters and compared with our experiments. We show the most likely structure of the Al framework Lewis sites in the beta zeolite.

References
(1) Klein, P.; Dedecek, J.; Thomas, H. M.; Whittleton, S. R.; Pashkova, V.; Brus, J.; Kobera, L.; Sklenak, S. NMR crystallography of monovalent cations in inorganic matrixes: Li+ siting and the local structure of Li+ sites in ferrierites. Chem. Commun. 2015, 51, 8962-8965.
(2) Klein, P.; Dedecek, J.; Thomas, H. M.; Whittleton, S. R.; Klimes, J.; Brus, J.; Kobera, L.; Bryce, D. L.; Sklenak, S. NMR crystallography of monovalent cations in inorganic matrices: Na+ siting and the local structure of Na+ sites in ferrierites. J. Phys. Chem. C 2022, 126, 10686-10702.
(3) Kobera, L.; Dedecek, J.; Klein, P.; Tabor, E.; Brus, J.; Fishchuk, A. V.; Sklenak, S. Formation and local structure of framework Al Lewis sites in beta zeolites. J. Chem. Phys. 2022, 156, 104702.

Speaker: Dr Stepan Sklenak (J. Heyrovsky Institute of Physical Chemistry)

18:00 Generating coupled cluster code for modern distributed memory tensor software

The goal of this project is to design a set of software tools for elegant development of relativistic coupled clusters methods.

Figure 1: The workflow scheme of the tenpi toolchain includes a code generator, intermediate optimizer and a unified interface towards tensor libraries. Fig. from [3].

Modern computer architectures are composed of heterogeneous processing and memory hierarchies. Data movement cost often dominates the cost of computation and only a fraction of peak CPU/GPU power is used. Despite this, most software still uses programming systems lacking any reasoning about the placement and movement of data.

Unlike BLAS for matrix operations, there is no unified tensor interface/library used by the community.
Available distributed memory libraries used for chemical applications are not adapted to heterogeneous architectures.
The tenpi toolchain addresses this problem.

Motto: “Separate science from the computational platform.”

The first application of the tenpi toolchain is on molecular properties as part of the HAMP-vQED project [4].
Studies so far indicate that QED-effects (electron self-energy and vacuum polarization) reduce relativistic effects by about 1%. However, such investigations have been limited to valence properties, since there are currently no reliable tools for general molecules to study the core region, where QED-effects are generated [2].

[2] P. Pyykko, J. F. Stanton, Chemical Reviews 112 (2012) 1.
[3] https://starpu.gitlabpages.inria.fr, visited 2.6.2023
[4] A. Sunaga, M. Salman and Trond Saue, J. Chem. Phys. 157 (2022) 164101.

Speaker: Jan Brandejs (Laboratoire de Chimie et Physique Quantiques, CNRS)

18:20 → 21:00 Conference Dinner and Poster Session

Tuesday, 31 October

09:00 → 09:30 Keynote III

09:00 Plasma shutter for laser-driven ion acceleration and spiral pulse generation

The plasma shutter is a thin solid foil (or series of them) placed in front of the main target irradiated by high intense laser. It can mitigate the prepulse [1, 2] and also shape the main pulse, resulting in the generation of a steep-rising front [3] and local intensity increase [4] of the pulse. We study the application of the shutter for ion acceleration via 3D PIC simulations assuming Si3N4 plasma shutter, ultrathin silver target and a PW-class laser [5]. The application of shutter results in the increase of maximal ion energy for both linear and circular polarizations. It also significantly reduces the beam divergence for the linear polarization. In the case of circular polarization, the transmitted laser pulse obtains a spiral-like intensity profile (Fig. 1-a). The structure is transferred into the electron density profile of the shutter and the main target behind it (Fig. 1-b).

The use of a double-shutter is studied via a combination of 2D PIC and hydrodynamic simulations assuming the laser pulse accompanied by a sub-ns prepulse. We present a prototype of the double-shutter and the design of the whole shutter-target setup [5]. The generated steep-front has also positive effect on different scenario with low-Z double-layer targets [6]. The 3D shutter simulation is also represented via an interactive Virtual Reality visualization [6].

References
[1] S.A. Reed, T. Matsuoka, S. Bulanov, et al. Appl. Phys. Lett., 94, 201117 (2009).
[2] W.Q. Wei, X.H. Yuan, Y. Fang, et al. Phys. Plasmas, 24, 113111 (2017).
[3] V.A. Vshivkov N.M. Naumova, F. Pegoraro, et al., Phys. Plasmas, 5, 2727 (1998).
[4] M. Jirka, O. Klimo and M. Matys, Phys. Rev. Res., 3, 033175 (2021).
[5] M. Matys, S.V. Bulanov, M. Kucharik, et al. New J. Phys., 24, 113046, (2022).
[6] M. Matys, J. Psikal, K. Nishihara, et al., Photonics, 10, 61, (2023).

Speaker: Dr Martin Matys (ELI Beamlines)

09:30 → 10:50 Users' Talks IV

09:30 Numerical Simulations at Karolina for Advancing Research at ELI NP

The Extreme Light Infrastructure Nuclear Physics (ELI NP) facility in Magurele, Romania, runs the currently most powerful laser in the world, capable to deliver two 10 PW pulses each minute. It stands at the forefront of cutting-edge research in laser-driven particle acceleration and high-energy nuclear physics. In pursuit of advancing our understanding of these fields, our simulation group relies heavily on advanced numerical simulations conducted at IT4I’s Karolina. We present and overview of the pivotal role of numerical simulations in supporting and enhancing research at ELI NP, with a focus on three critical areas:
1. Ion Acceleration: Record ion energy from the laser plasma accelerator should be announced soon by ELI NP. Besides, we will present simulations supporting medical applications, particularly in carbon therapy.
2. Ultrabright Gamma Sources: The generation of ultrabright gamma sources is a key research area at ELI NP, with implications for fundamental nuclear physics and medical imaging. By leveraging Karolina's computational power, we can model the complex physics involved in gamma source generation and optimize experimental conditions for maximum efficiency.
3. Electron Acceleration (LWFA): ELI NP employs Laser Wakefield Acceleration (LWFA) as a groundbreaking technique for electron acceleration. In particular, we will discuss its application as a bremsstrahlung x-ray source from a derived few-cycle 100 TW laser pulse.
The synergy between cutting-edge experiments at ELI NP and the computational capabilities of Karolina empowers us to push the boundaries of knowledge in nuclear physics, laser-driven particle acceleration, and astrophysics. The simulations not only validate experimental designs but also open doors to new possibilities and applications in fundamental research, industry, and medicine.

Speaker: Vojtěch Horný (Extreme Light Infrastructure - Nuclear Physics)

09:50 Testing the accuracy of random-phase approximation for molecular solids

There is a range of quantum mechanical methods that can be used to calculate binding energies of molecular clusters or between molecules and surfaces. The individual approaches then differ in computational cost they require and accuracy they can provide. We will discuss the random-phase approximation (RPA), which is a method that, in terms of accuracy and computational demands, sits between advanced coupled clusters (CC) techniques and less demanding density functional theory (DFT) approximations. For RPA we obtained binding energies of several molecular solids and of methane in water clathrate cage. To analyse the accuracy of RPA we do not only consider the binding energy of the whole cluster or solid but also break it down using many-body expansion (MBE). In this way we obtain a large set of molecular dimers, trimers, and tetramers for which we obtain reference CC binding energies as well as energies for RPA and other schemes. The results show that RPA dimer binding energies significantly depend on the distance between molecules in dimer. Errors are large for small separations but very low for large separations. For the non-additive energies of trimers we identified two problems: first, the RPA energies have much larger dependence on the basis-set size compared to CC values and, second, they partly inherit the often large errors that DFT methods exhibit. We discuss several ways that we identified that can be used to reduce these issues.

Speaker: Jiri Klimes (Faculty of Mathematics and Physics, Charles University)

10:10 Quantum mechanical insights into the optical properties of carbon dots

Carbon dots (CDs) are photoluminescent nanomaterials with a broad application potential including nanosensors, cellular bioimaging, and optoelectronics. Besides the bright photoluminescence (PL), they manifest high (photo)stability, low toxicity, biocompatibility, and high structural variability. CDs can be described as two-domain structures containing a graphitic-like or amorphous carbon core and a surrounding shell which may also contain other light elements such as oxygen and nitrogen, included as local dopants and/or functional groups. In addition, molecular fluorophores as remnants of reaction precursors can be attached and/or embedded in CDs. The origins of the PL of CDs featuring both excitation-dependent and excitation-independent components are still under intense debate, mostly due to the complex structure and the variability of the PL centers of CDs [1,2]. In our recent works [3-5], we used classical MD simulations and QM methods to describe the structural features and absorption/emission characteristics of CDs providing useful insights into the dynamics, structural organization and interplay of PL centers of CDs in solution.

[1] M. Langer et al., Appl. Mat. Today 22, 100924 (2021).
[2] F. Mocci et al., Chem. Rev. 122, 13709 (2022).
[3] F. Siddique et al., J. Phys. Chem. C 124, 14327 (2020).
[4] M. Langer et al., J. Phys. Chem. C 125, 12140 (2021).
[5] M. Langer et al., Nanoscale 15, 4022 (2023).

Speaker: Miroslav Medveď (RCPTM, CATRIN, Palacky University Olomouc, Czech Republic)

10:30 MoS2 crystallization via Reactive Molecular Dynamics Simulations

Molybdenum disulfide, $MoS_2$, is a layered material from transition metals dichalcogenide (TMD) family[1]. Applications of TMDs range from tribological coatings[2,3] to electronics[4], optics[5] and catalysis[6].

TMD films are commonly prepared as an amorphous material. Tribological applications rely on a natural tendency of TMDs to crystallize during sliding. Catalysis applications might benefit from creating specific defects[7-10]. Electronics applications might require achieving very high crystallinity in tricky conditions, e.g. $MoS_2$ on polymer film for flexible stretchable photodetectors[11].

Several computational studies were recently dedicated to $MoS_2$ crystallization, employing ab initio methods[12,13] and reactive molecular dynamics with REBO[14] and ReaxFF[15,16] empirical potentials. However, ab initio methods are computationally expensive, while classical MD methods strongly depend on the quality of the force field.

We recently developed a ReaxFF force field for the Mo-S-(C-O) system[17,18]. This parameterization, unlike others, matches DFT energies in a wide range of configurations and reproduces crystallization of $MoS_2$ in melt-quench simulations[17] and during simulated sliding[18] at reasonable temperatures and pressures.

In this study we apply our ReaxFF to exploring crystallization of $MoS_2$. We study the kinetics and mechanism of crystallization depending on setup, temperature, load, density, sliding, stoichiometry, impurities. Our goal is to provide valuable insights that would enable a more intelligent approach to material design for a wide variety of applications.

References
[1] A. R. Lansdown, Ed., Chapter 1 History. Elsevier, 1999. doi: https://doi.org/10.1016/S0167-8922(99)80004-2.
[2] M. R. Vazirisereshk et al, Lubricants, vol. 7, no. 7, 2019, doi: 10.3390/LUBRICANTS7070057.
[3] T. Vitu et al, Wear, vol. 480–481, Sep. 2021, doi: 10.1016/j.wear.2021.203939.
[4] R. H. Kim et al, Nanoscale, vol. 11, no. 28, pp. 13260–13268, 2019, doi: 10.1039/c9nr02173f.
[5] M. Timpel et al, Npj 2D Mater. Appl., vol. 5, no. 1, Art. no. 1, Jul. 2021, doi: 10.1038/s41699-021-00244-x.
[6] G. Pacholik et al, J. Phys. Appl. Phys., vol. 54, no. 32, 2021, doi: 10.1088/1361-6463/ac006f.
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Speaker: Ilia Ponomarev (Czech Technical University in Prague)

10:50 → 11:00 Coffee break

11:00 → 12:00 User's Talks V

11:00 Interatomic interactions in the vicinity of lattice defects in intermetallics

Thermodynamic stability of metallic materials and their many properties are strongly affected by presence of defects in crystal lattices. An analysis of changes in interatomic bonding induced by defects is required to reveal the exact nature of defect-related phenomena. Ab initio atomistic simulations based on density functional theory are an ideal tool for such task. Information about “bond stiffness” for a particular pair of atoms can be obtained from phonon calculations by projections of the force constants on the unit vector along each bonding direction. A deeper insight into mutual chemical interaction between individual atoms can by provided by the analysis of crystal orbital Hamilton population (COHP). In the present work, we analyze the first- and second-nearest-neighbor interactions in (i) the vicinity of Sn substitutional impurity in Mg$_{2}$Ge intermetallic with antifluorite structure and (ii) Σ5(210) grain boundaries (GBs) in Ni$_{3}$Si intermetallic with Cu$_{3}$Au structure. In addition, we also analyze the effect of Al impurity segregated in Ni$_{3}$Si GB.
The bond stiffness of bonds between the Sn impurity atom and its first nearest neighbors, i.e. Sn-Mg bonds, is significantly higher than bond stiffness of Mg-Ge bonds in bulk Mg$_{2}$Ge. This increase corresponds very well to the reported higher heat capacity of Mg$_{2}$Sn compare to Mg$_{2}$Ge. The studied Ni$_{3}$Si GB variant containing both Ni and Si atoms at the interface is shown to be unstable with respect to a shear deformation. The COHP and bond stiffness analysis reveal that this instability originates in a weak interaction far from the GB interface between the Ni atoms in the 3rd plane and the atoms in the 4th, 5th, 6th plane. However, this bond weakening is a consequence of a very strong interaction between the Si atoms in the GB plane and Ni atoms in the 3rd plane of the GB interface. The described bond weakening was not observed in stable GB variant containing two Ni atoms at the interface and when Si atom at the interface is replaced by Al.

Speaker: Martin Zelený (Faculty of Mechanical Engineering, Brno University of Technology)

11:20 Magneto-elastic properties calculation via computational high-throughput approach

Magnetostriction is a physical phenomenon in which the process of magnetization induces a change in shape or dimension of a magnetic material. Nowadays, materials with large magnetostriction are used in many electromagnetic microdevices as actuators and sensors. By contrast, magnetic materials with extremely low magnetostriction are required in applications such as for electric transformers. Magneto-elasticity is also interesting and related phenomena, the change of the exchange upon the various tensile or compressive loadings or an inverse as the external magnetic field can induces sample shape and lenght change. Here, we determine in a number of examples materials from simple bcc Fe, to those of lower symmetry like YCo where by using MAELAS (in house developed code, see www.md-esg.eu/software [1-3]) anisotropic magnetostriction coefficients, magnetoelastic constants, and isotropic volume exchange striction in an automated way by employing accurate DFT calculations. The behavior of the magneticrystalline anisotropy energy and magnetostrictive coefficients under general external magnetic field could be visualized as a relative length change using our MAELASviewer tool[4]. To verify accuracy and our approach in general we present a number of examples of each crystal symmetry class with calculated magnetostriction and magnetoelastic constants and compare them with recorded data. Particularly, we shed a light on the origin of the magnetostriction of tetragonal phase of FePt.[5]

References:
1. P. Nieves, S. Arapan, SH. Zhang, A. Kadzielawa, RF. Zhang, D. Legut, MAELAS: MAgneto-ELAStic properties calculation via computational high-throughput approach, Comp. Phys. Comm. 264, 107964 (2021), doi:10.1016/j.cpc.2021.107964
2. P. Nieves, S. Arapan, SH. Zhang, A. Kadzielawa, RF. Zhang, D. Legut, MAELAS 2.0: A new version of a computer program for the calculation of magneto-elastic properties, Comp. Phys. Comm. 271, 108197 (2022), doi:10.1016/j.cpc.2021.108197
3. P. Nieves, S. Arapan, SH. Zhang, A. Kadzielawa, RF. Zhang, D. Legut, Automated calculations of exchange magnetostriction, Comp. Mater. Sci 224, 112158 (2023), doi:10.1016/j.commatsci.2023.112158
4. P. Nieves, MAELASviewer: An Online Tool to Visualize Magnetostriction et al., Sensors, 20 6436 (2020), doi:10.3390/s20226436
5. D. Legut, T. Das, P. Nieves, Origin of Larger Magnetostriction and Anisotropy Energy in L1$_0$-FePt, Int. J. Eng. Sci. (under review)

Speaker: Dominik Legut (IT4I)

11:40 Structural Tuning of Band Gap in Doped Diamonds

Diamond-based compounds own a large band gap about the Fermi level making them ideal candidate materials to build nanoengineered devices with wide applicability in nanophotonics, optomechanics, photovoltaics and electronics. However, the band gap must be suitably tuned for each target application.

With this aim, we performed quantum mechanical simulations of diamond-based materials doped with a variety of doping atoms in different concentrations.[1] Subsequently, we expanded the study by considering cluster defects formed by dopants and carbon vacancies in different geometric configurations; such an expansion allowed us to focus on coupled structural-electronic features even in more detail. Furthermore, we were able to investigate more intriguing electronic structures with a variety of opto-electronic applications such as intermediate band photovoltaics or lasers. We conducted extensive electronic and geometric analysis on the ground state geometries, using geometric and electronic features such as interatomic distances, orbital polarizations, bond covalencies and Hirshfeld charges. We show that the specific charge distributions at the dopant atomic site govern the size of the band gap; in order to tune the gap and the band structure in general, we propose how to choose the suitable dopant atomic types, their concentration, geometric configuration and how to impose convenient axial strains on the structures. Furthermore, we suggest different routes of acting on the lattice parameters to switch the character of the band gap from indirect to direct.

The results of our investigation constitute guidelines for further use in experimental and technical fields and can be promptly applied to the design of new semiconducting materials. Furthermore, as our theoretical results are general, they can be applied to the study of optical and electronic materials irrespective of their chemical composition and atomic topology.

This work has been supported by the project “Center for Advanced Photovoltaics” [grant number CZ.02.1.01/0.0/0.0/15_003/0000464]; the Grant Agency of the Czech Technical University in Prague [grant number SGS22/166/OHK3/3T/13]; and by the Ministry of Education, Youth and Sports of the Czech Republic through the e-INFRA CZ [grant number ID: 90140].

References
[1] A. Cammarata, M. Kaintz and T. Polcar, Diam. Relat. Mater., 2022, 128, 109237.

Speaker: Matúš Kaintz (Czech Technical University in Prague)

12:00 → 13:00 Lunch