Bedőházi Zsolt[1,2] and Biricz András[1] (2023.02.13 - 05.15)

[1] ELTE Department of Complex Systems in Physics
[2] ELTE Doctoral School of Informatics

Abstract: The application of deep learning in gigapixel whole slide image analysis has shown promising results in terms of accuracy and efficiency compared to traditional image analysis techniques. Transformer based models as the current state-of-the-art algorithms are designed to identify and classify various structures and patterns within the tissue, providing insights into the underlying pathology and helping in the diagnosis and treatment of diseases. We are currently working on multiple projects in this field including breast cancer stage prediction [1] and colorectal cancer detection [2].

István Csabai, Ákos Gellért, Balázs Pál (2022.01.01 - 2022.03.30)

ELTE Department of Physics of Complex Systems

Publication: SARS-CoV-2 RBD deep mutational AlphaFold2 structures carry phenotypic information

Abstract: The COVID-19 epidemic created an extraordinary situation for the whole humanity, claiming millions of lives and causing a significant economic setback. At the same time, the international research community has rapidly generated an order of magnitude larger data set than ever before, which can contribute to understanding the evolution and dynamics of the epidemic, to its containment and to the prevention of similar pandemics. The GISAID and COVID-19 Data Portal databases contain millions of complete SARS-CoV-2 genomes. The genetic sequences can be obtained relatively easily and quickly thanks to modern genome sequencers, but it is very difficult to tell how rapidly a given variant will spread or how serious disease will it cause, solely based on the genetic sequences and the mutations. The genetic information is transcribed into proteins, and the spatial structure, charge distribution and interaction of the proteins with the host proteins determine the function of the virus, the so called phenotype. In summary, the genotype-phenotype problem is the estimation of the behaviour of a virus based on genetic information.

In the last year, the rapidly developing artificial intelligence approach has achieved a milestone that can significantly help genotype-phenotype research. Using the Alphafold2 method, the spatial structure of large proteins can be determined with sufficient accuracy in a reasonable time. The machine learning-based Alphafold2 method requires significant computational, mainly GPU, capacity.

We are collaborating with EMBL-EBI on the development of a SARS-CoV-2 genetic archive in the framework of a H2020 project. We aim to complement this with 3D structures of proteins of as many variants as possible and to use these structures to advance the genotype-phenotype question.

Andor Menczer (ELTE), Áron Vízkeleti (Wigner RCP), Mihály Máté (Wigner RCP) and Örs Legeza (Wigner RCP) - (2022.09.01 - 2022.11.30)

Abstract: Numerical simulation of quantum systems where strong interaction between atomic spins and itinerant electrons is present, and at the same time cannot be described with perturbative methods are in the focus of modern physics. These simulations are challenging because computational resources, in general, scale exponentially with system size. Developing algorithms to simulate these systems with polynomial complexity is one of the most heavily researched subjects today.

The density-matrix renormalization group (DMRG) algorithm is one such method, with the additional advantage that the underlying tensor algebra, in light of the conserved quantum numbers, can be broken up into millions of independent tasks. This makes this algorithm ideal for MPI and GPU based massive parallelization. Our research group have been researching the subject for two decades. A GPU based kernel application have been implemented recently thanks to Andor Menczer (ELTE graduate student). In this project we would like to test, and based on the results, optimize this application. At the same time, we would also like to apply it to two-dimensional electron systems, strongly correlated molecular clusters, and atomic nuclei.

The project involves Andor Menczer (ELTE), Áron Vízkeleti (WignerFK), Mihály Máté (WignerFK) and Örs Legeza (WignerFK). The source code was written in Matlab, and a standalone version was compiled using Matlab Compiler. We wish to carry out the testing, fine-tuning and application to large systems in steps. The GPU kernel was built using the Matlab Paralelization Toolbox, and CODA Coder. For the first step, we would like to ask for a three months long interval of access to one of the nodes (cluster 1, 2, 3, 4) that access NVIDIA graphics cards.

We plan to publish the simulation results in prestigious international journals, like the ones our previous work appeared in [1,2]

[1] The density matrix renormalization group algorithm on kilo-processor architectures: implementation and trade-offs, Csaba Nemes, Gergely Barcza, Zoltán Nagy, Örs Legeza, Péter Szolgay, Computer Physics Communications Volume 185, Issue 6, June 2014, Pages 1570-1581

[2] Massively parallel quantum chemical density matrix renormalization group method, Jiří Brabec, Jan Brandejs, Karol Kowalski, Sotiris Xantheas, Örs Legeza, Libor Veis, Computational Chemistry, https://doi.org/10.1002/jcc.26476

István Papp, Larissa Bravina, Mária Csete, Igor N. Mishustin, Dénes Molnár, Anton Motornenko, Leonid M. Satarov, Horst Stöcker, Daniel D. Strottman, András Szenes, Dávid Vass, Tamás S. Biró, László P. Csernai, Norbert Kroó (2022.01.01 - 2022.06.30)

Publication: Laser Wake Field Collider

Abstract: Inertial Confinement Fusion is a promising option to provide massive, clean, and affordable energy for humanity in the future. The present status of research and development is hindered by hydrodynamic instabilities occurring at the intense compression of the target fuel by energetic laser beams. NAno-Plasmonic, Laser Inertial Fusion Experiments (NAPLIFE) were proposed, as an improved way to achieve laser driven fusion. The improvement is the combination of two basic research discoveries:
(i) The possibility of detonations on space-time hyper-surfaces with time-like normal (i.e. simultaneous detonation in a whole volume)[1] and
(ii) to increase this volume to the whole target, by regulating the laser light absorption using nano-shells or nano-rods as antennas [2].
These principles can be realized in an in-line, one dimensional configuration, in the simplest way with two opposing laser beams as in particle colliders [3]. Such, opposing laser beam experiments were also performed recently. Here we study the consequences of the Laser Wake Field Acceleration (LWFA) if we experience it in a colliding laser beam set up. These studies can be applied to laser driven fusion, but also to other rapid phase transition, combustion, or ignition studies in other materials.

References:
[1] L. P. Csernai and D. D. Strottman, “Volume ignition via time-like detonation in pellet fusion,” Laser Part. Beams. 33 (2), 279--282 (2015).
[2] L. P. Csernai, N. Kroo, and I. Papp, “Radiation dominated implosion with nano--plasmonics,” Laser Part. Beams. 36 (2), 171--178 (2018).
[3] L.P Csernai, M. Csete, I.N. Mishustin, A. Motornenko, I. Papp, L.M. Starov, H. Stöcker, N. Kroó, "Radiation dominated implosion with flat target", Physics of Wave Phenomena, 2020, accepted for publication.

István Papp, Larissa Bravina, Mária Csete, Igor N. Mishustin, Dénes Molnár, Anton Motornenko, Leonid M. Satarov, Horst Stöcker, Daniel D. Strottman, András Szenes, Dávid Vass, Tamás S. Biró, László P. Csernai, Norbert Kroó (2022.07.01 - 2022.12.31)

Abstract: Our dependence on fossil fuels grew more and more in the last century and today we are urged to find alternative energy sources. Laser driven fusion is a promising option for clean and safe energy production. The most successful configuration up to now uses indirect drive, the thermal radiation coming from a cylindrical Hohlraum. After the target is compressed by the incoming light, it develops Rayleigh-Taylor instabilities. An ongoing activity at Wigner Research Centre’s Nanoplasmonic Laser Fusion National Laboratory (NAPLIFE) collaboration is aiming for improving the chances of fusion by high-power short laser pulses and target fabrication, combining recent discoveries in heavy-ion collisions and optics [1]. Our aim is studying in simulations the surface plasmonic effect of resonant gold nano-antennas in different monomer mediums. The monomer serves only experimental purposes, proving the effectiveness of the nanorods. The plasmonic effect is vital for the project, since it will be used to manipulate the target’s absorption properties. The different layers of monomers with different gold nanoparticle densities will be studied, taking into account the lifetime of plasmons using a kinetic plasma model for conducting electrons [2]. The results will be essencial for future experiments in ELI-ALPS Szeged laser facility.

[1] L.P Csernai, N. Kroo and I. Papp, Radiation dominated implosion with nanoplasmonics, Laser and Particle Beams, Volume 36, Issue 2, June 2018 , pp. 171-178

[2] I. Papp, L. Bravina, M. Csete, et al., Kinetic model evaluation of the resilience of plasmonic nanoantennas for laser-induced fusion, PRX Energy, Vol. 1, Iss. 2 (2022)

Ernő Dávid, Dávid El-Saig, Zoltán Lehóczky and Gergely Gábor Barnaföldi (2021.12.01 - 2022.08.31)

Wigner RCP and Lombiq Technologies Ltd. cooperation

Abstract: Hastlayer by Lombiq Technologies allows software developers of the .NET platform to utilize FPGAs as compute accelerators. It converts standard .NET constructs into equivalent hardware implementations, automatically enhancing the performance while lowering the power consumption of suitable algorithms. Developers keep writing .NET programs as usual, no hardware design knowledge is required.

Hastlayer needs dedicated firmware and software components for each supported hardware platforms. In collaboration with Wigner RC there are already several supported platforms (like Microsoft Catapult cards and the Xilinx Alveo FPGA card family). The aim of the next development phase is to enable Hastlayer support for embedded platforms like FPGA cards based on the Xilinx Zynq family members.

Wigner's task is to develop the necessary firmware framework to run the Hastlayer-generated hardware cores and if there is a need then customize the Linux operating system running on the embedded ARM CPU cores.

Marcell Stippinger, András Telcs (2022.01.01 - 2022.03.30)

Wigner Research Centre for Physics

Abstract: The aim of the project is to develop a framework in which causal connection between time series can be explored. The core concept of the project is the investigation of Markov properties of different conditioned time series. The core of the method is the collection of result of large amount of conditional independence tests. The results then lead to a simple conclusion via a simple decision tree.

Balázs Kacskovics (2016.09.01 - 21.05.31)

Supervisor: Mátyás Vasúth

Wigner Research Centre for Physics

Publication:The orbital evolution and gravitational waves of OJ 287 in the 4th post-Newtonian order

Abstract: Although gravitational waves have been detected in 2016 with GW150914, but there are still many exotic cases to discover, e.g. binaries with Zoom-Whirl orbits, Super Massive Black Holes, etc. To examine such cases the Wigner RCP Gravitational group developed a software called CBwaves , that we would like to upgrade with the fourth terms of the post-Newtonian formalism and with its Hamiltonian formalism. Also we would like to enchance the runime of our code using parallelism.

Dr. Papp Gábor (ELTE), Bíró Gábor (Wigner FK), Feiyi Liu (ELTE), Xiangna Chen (CCNU, Wuhan), Dudás Bence (ELTE), Misur Patricia (ELTE) (2021.06.01-08.31)

Abstract: One effective way to kill localized cancerous tumors that are not accessible by surgery is radiation treatment with a proton (or heavier ions as He or C, respectively). In the process, one treatment is usually sufficient compared to conventional radiation therapy, since the proton is very well focused, (with an accuracy of 1 mm, heavier ions with even greater accuracy). However, because the in matter penetration profiles of proton and gamma rays are different, CT tomography does not calibrate the proton beam and does not allow accurate device alignment, resulting in practice in treatment that is far less accurate than the theoretical limit. Greater accuracy can be achieved by proton tomography using a proton beam used for treatment at a higher energy. To detect particles passing through the patient, we developed a detector system based on ALPIDE chips and CERN technology in the framework of the international pCT collaboration (https://wiki.uib.no/pct/index.php/Main_Page). Because processing of the detector signals is a time-consuming process, we want to speed it up by using a neural network: the goal is to develop and train a neural network that can tell the direction and energy of protons leaving the body based on detector signals. By measuring these at several angles, a tomographic image of the examined area can be obtained and the data required for the treatment can be calculated.

Dávid Ernő, Ván Péter, Fenyvesi Edit (Wigner RCP); Tóth Gyula (BME); Szondy György (Creasis Ltd.) (2021.02.01-2021.03.31)

Abstract: In the recently modernized Eötvös balance measurements the readout of the torsion wire angle position is a camera photo. The position is determined by reading the scale numbers and the centre of the picture with Fourier transformation enhanced computation methods. Then we can achieve a precision under the hundredth of the scale units. During a normal registration period, there are two photos per second and sometimes recalculations of longer periods are necessary. Our purpose of using the computational capacity of the Wigner GPU lab is to perform these long computations. Now we would like to elaborate on a monthlong registration period that could take several weeks in our normal computers. Later on, we would like to use the calculation capacity in case of necessity.

Emese Forgács-Dajka (2020.10.12-2021.12.31)

Eötvös Loránd University

Abstract: Mean motion resonances (MMRs) play an important role in shaping the dynamics of the Solar system bodies. MMRs in the Solar system usually occur between a planet and small bodies, e.g. the members of the Hilda group of asteroids are in a 3:2, while the Trojan asteroids are in a 1:1 MMR with Jupiter. Based on the geometrical meaning of the resonance variable, an efficient method has been introduced and described in Forgács-Dajka, Sándor & Érdi (2018), by which mean motion resonances can be easily found without any a priori knowledge of them. The efficiency of this method - named FAIR - is clearly demonstrated by using some known members of different families of asteroids being in mean motion resonances with a planet. The Hungaria group is a family of asteroids in the main asteroid belt orbiting the Sun between the orbit of Mars and that of Jupiter. In this research we systematically apply the method FAIR to the Hungaria family objects to identify the dynamically relevant MMRs between them and Jupiter or Mars. Our investigation may help to find possible new subfamilies of the Hungaria group based on resonance, and besides, we examine whether there is any correlation between the physical properties and the dynamical parameters of asteroids.

Publication: Astronomy & Astrophysics, Volume 657, id.A135 DOI: 10.1051/0004-6361/202141719 arXiv: arXiv:2110.11745 Publisher link: https://www.aanda.org/articles/aa/pdf/2022/01/aa41719-21.pdf

Károly Kubicskó, Ödön Farkas (2020.06.01 - 2020.11.30)

Eötvös Loránd University, Department of Organic Chemistry

Abstract: The metabolism of biogenic N,N-dimethyltryptamine (DMT) starts with its enzymatic oxidation to indole-3-N,N-dimethylethaniminium cation (imDMT+) by monoamine oxidase (MAO). Following this reaction, a non-enzymatic hydrolysis occurs, yielding indole-3-acetaldehyde (IAL) and dimethylamine (DMA). In our in silico study, using a hybrid DFT method at the M06-2X/aug-cc-pVDZ level, we examined the necessity of explicit water molecules to accurately model the hydrolysis. Our calculations revealed that despite an implicit continuum solvent model, one or two explicit solvent molecules should be added to obtain meaningful activation barriers. Thus, we demonstrate that the hydrolysis can occur in a human cell without enzymatic assistance, paving the way for deeper understanding of DMT metabolism.

Publication: Quantum chemical study of the hydrolysis of oxidized endogenous psychedelic N,N-dimethyltryptamine

Ernő Dávid, Dávid El-Saig, Zoltán Lehóczky and Gergely Gábor Barnaföldi (2020.01.01 - 2020.11.30)

Wigner Research Centre for Physics and Lombiq Technologies Ltd. cooperation

Publication: Implementing Hastlayer support for Xilinx SoC Zynq FPGA family

Abstract: Hastlayer by Lombiq Technologies allows software developers of the .NET platform to utilize FPGAs as compute accelerators. It converts standard .NET constructs into equivalent hardware implementations, automatically enhancing the performance while lowering the power consumption of suitable algorithms. Developers keep writing .NET programs as usual, no hardware design knowledge is required.

Hastlayer needs to support FPGA boards specifically, and formerly it only supported one that was suitable for testing and creating proof of concepts, but not for high performance computing scenarios. The recently finished work in collaboration with Wigner RCP was about making it support high-performance FPGAs of the Microsoft Catapult platform. Wigner's task was to create the FPGA-side hardware framework that hosts the automatically generated hardware cores created by Hastlayer.

The current project is similar, but about making Hastlayer support all SDAccel-compatible Xilinx FPGAs. This will open up a wide range of possibilities for Hastlayer-accelerated applications by unlocking the large product line of high-performance SDAccel-compatible FPGAs running on premise, as well as in multiple public cloud computing providers.

Zoltán Zimborás, Dániel Nagy, András Németh, Gábor Németh (2020.05.22-2020.12.31)

Wigner Research Cetnre for Physics, Eötvös University Faculty of Science and Faculty of Informatics,Ericsson Research

Abstract: In recent years, both experimental quantum computers and quantum algorithms have been significantly improved. The advantage of quantum over classical computation is that if multiple qubits get entangled, the dimensionality of the Hilbert-space increases exponentially, and thus a quantum computer might be exponentially faster at solving certain problems than a classical one. Apart from this, the laws of quantum mechanics enable such computations and communication protocols, that are totally infeasible using classical computers. However, experimental quantum computers accessible at the moment contain only a few dozens of qubits, and those are quite noisy as well. Hence, when developing quantum algorithms, it is indispensable to use high performance classical computers to simulate these quantum algorithms in a reasonable time for a reasonable cost. Furthermore, an important research area is the investigation of hybrid quantum-classical algorithms, where the use of modern GPUs is necessary along with the quantum processors.

Forgács-Dajka Emese, Dobos László, Ballai István (2021.01.01-2021.09.30)

Eötvös Loránd Tudományegyetem, John Hopkins University és Sheffield University

Kivonat: A napaktivitás jelenségeinek megfigyelése nagy múltra tekint vissza, így lehetőségünk van hosszú időskálán történő vizsgálatok készítésére. Célunk a napfoltcsoportok területének időfejlődésének tanulmányozása egy 130 évet felölelő, különféle adatbázisokból álló, de konzisztens nagy mintában, a legmodernebb statisztikai módszerekkel. A gondosan leválogatott, de véletlenszerű minta esetében Bayes-modellt alkalmazunk, melynek segítségével a napfoltok teljes területére ferde normális függvényt illesztve meghatározzuk a folt növekedésének és bomlásának ütemét és az esetleges aszimmetriát. Ezen eljárás nagy előnye, hogy az olyan foltcsoportok esetén is megkaphatjuk a teljes élettartamra vonatkozó tulajdonságokat (pl. élettartam, fejlődési szakaszok különböző részei, mint felfutási, lefutási rész), melyekről nincsenek teljes adatsorok a megjelenéstől az eltűnésig. Ennek oka a megfigyelésben keresendő, azaz a Nap forgása miatt a foltcsoportok teljes életciklusa nem követhető végig minden esetben. Eredményeink robosztus módon alátámasztják azt a feltételezésünket, hogy a foltcsoportoknak két típusa van: (i) egy a megjelenést követően gyorsan kifejlődő, de lassabban lebomló, illetve (ii) egy lassabban felfutó, gyorsabban lecsengő. Emellett a modellparaméterek segítségével vizsgáltuk a napfoltcsoportok élettartamát, illetve az élettartam, maximális terület közötti összefüggéseket is.

Publikáció: Astronomy & Astrophysics, Volume 653, id.A50, 10 pp. DOI: 10.1051/0004-6361/202140731 arXiv: arXiv:2106.04917 Publisher link: https://www.aanda.org/articles/aa/pdf/2021/09/aa40731-21.pdf

József Kadlecsik (2019.12.01 - 2020.02.29)

Wigner RCP, SzHK

Publication: Laboratory study of water surface polygon vortices

Abstract: Although gravitational waves have been detected in 2016 with GW150914, but there are still many exotic cases to discover, e.g. binaries with Zoom-Whirl orbits, Super Massive Black Holes, etc. To examine such cases the Wigner RCP Gravitational group developed a software called CBwaves , that we would like to upgrade with the fourth terms of the post-Newtonian formalism and with its Hamiltonian formalism. Also we would like to enchance the runime of our code using parallelism.

David Legrady, Gabor Tolnai, Tamas Hajas, Előd Pázmán (2021.06.01 - 2022.04.30)

BME Institute of Nuclear Techniques

Publication: Full Core Pin-Level VVER-440 Simulation of a Rod Drop Experiment with the GPU-Based Monte Carlo Code GUARDYAN

Abstract: The GUARDYAN (GPU Assisted Reactor Dynamic Analysis, developed at BME Institute of Nuclear Techniques) Monte Carlo code directly follows the time evolution of the neutron field in a nuclear reactor. Contrary to the conventionally applied deterministic (i.e. non-Monte Carlo) or Monte-Carlo based techniques relying on quasistatic approximations modelling errors are minimal for GUARDYAN. For a fast evolving („hard”), localized transients even the magnitude of the modelling errors posed by conventional techniques can hardly be estimated, and experimental confirmation due to nuclear hazards is out of question. Therefore, simulations with GUARDYAN could be set as a gold standard for other computational methods. The project aims at the simulation of a rod ejection transient in a full-scale currently operational nuclear power plant type (VVER-440) using the code GUARDYAN.

Ernő Dávid, Dávid El-Saig and Zoltán Lehóczky (2019.08.31 - 2019.12.31)

Wigner RCP és Lombiq Technologies Ltd. cooperation

Abstract: Hastlayer by Lombiq Technologies allows software developers of the .NET platform to utilize FPGAs as compute accelerators. It converts standard .NET constructs into equivalent hardware implementations, automatically enhancing the performance while lowering the power consumption of suitable algorithms. Developers keep writing .NET programs as usual, no hardware design knowledge is required.

Hastlayer needs to support FPGA boards specifically, and formerly it only supported one that was suitable for testing and creating proof of concepts, but not for high performance computing scenarios. The work ongoing in collaboration with Wigner RCP is about making it support high-performance FPGAs of the Microsoft Catapult platform. Wigner's task is to create the FPGA-side hardware framework that hosts the automatically generated hardware cores created by Hastlayer.