TY - JOUR A1 - Roy, Sutapa A1 - Höfling, Felix T1 - Critical surface adsorption of confined binary liquids with locally conserved mass and composition JF - Molecular Physics N2 - Close to a solid surface, the properties of a fluid deviate significantly from their bulk values. In this context, we study the surface adsorption profiles of a symmetric binary liquid confined to a slit pore by means of molecular dynamics simulations; the latter naturally entails that mass and concentration are locally conserved. Near a bulk consolute point, where the liquid exhibits a demixing transition with the local concentration as the order parameter, we determine the order parameter profiles and characterise the relevant critical scaling behaviour, in the regime of strong surface attraction, for a range of pore widths and temperatures. The obtained order parameter profiles decay monotonically near the surfaces, also in the presence of a pronounced layering in the number density. Overall, our results agree qualitatively with recent theoretical predictions from a mesoscopic field-theoretical approach for the canonical ensemble. Y1 - 2024 U6 - https://doi.org/10.1080/00268976.2024.2391998 VL - 122 IS - 21-22 SP - e2391998 ER - TY - THES A1 - Jami, Masoud T1 - Optimizing Checkpoint/Restart and Input/Output for Large Scale Applications Y1 - 2024 UR - https://doi.org/10.18452/29985 U6 - https://doi.org/10.18452/29985 PB - Humboldt-Universität zu Belin ER - TY - JOUR A1 - Marcelli, Giorgia A1 - Bottinelli Montandon, Tecla A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix T1 - Fluid flow inside slit-shaped nanopores: the role of surface morphology at the molecular scale JF - The Journal of Chemical Physics N2 - Non-equilibrium molecular dynamics (NEMD) simulations of fluid flow have highlighted the peculiarities of nanoscale flows compared to classical fluid mechanics; in particular, boundary conditions can deviate from the no-slip behavior at macroscopic scales. For fluid flow in slit-shaped nanopores, we demonstrate that surface morphology provides an efficient control on the slip length, which approaches zero when matching the molecular structures of the pore wall and the fluid. Using boundary-driven, energy-conserving NEMD simulations with a pump-like driving mechanism, we examine two types of pore walls—mimicking a crystalline and an amorphous material—that exhibit markedly different surface resistances to flow. The resulting flow velocity profiles are consistent with Poiseuille theory for incompressible, Newtonian fluids when adjusted for surface slip. For the two pores, we observe partial slip and no-slip behavior, respectively. The hydrodynamic permeability corroborates that the simulated flows are in the Darcy regime. However, the confinement of the fluid gives rise to an effective viscosity below its bulk value; wide pores exhibit a crossover between boundary and bulk-like flows. In addition, the thermal isolation of the flow causes a linear increase in fluid temperature along the flow, which we relate to strong viscous dissipation and heat convection, utilizing conservation laws of fluid mechanics. Noting that the investigated fluid model does not form droplets, our findings challenge the universality of previously reported correlations between slippage, solvophobicity, and a depletion zone. Furthermore, they underscore the need for molecular-scale modeling to accurately capture the fluid dynamics near boundaries and in nanoporous materials, where macroscopic models may not be applicable. Y1 - 2025 U6 - https://doi.org/10.1063/5.0246573 VL - 162 SP - 104101 ER - TY - JOUR A1 - Zhong, Xin A1 - Höfling, Felix A1 - John, Timm T1 - Hydrogen diffusion in garnet: insights from atomistic simulations JF - Geochemistry Geophysics Geosystems N2 - Garnet has been widely used to decipher the pressure-temperature-time history of rocks, but its physical properties such as elasticity and diffusion are strongly affected by trace amounts of hydrogen. Experimental measurements of H diffusion in garnet are limited to room pressure. We use atomistic simulations to study H diffusion in perfect and defective garnet lattices, focusing on protonation defects at the Si and Mg sites, which are shown to be energetically favored. Transient trapping of H renders ab-initio simulations of H diffusion computationally challenging, which is overcome with machine learning techniques by training a deep neural network that encodes the interatomic potential. Our results from such deep potential molecular dynamics (DeePMD) simulations show high mobility of hydrogen in defect-free garnet lattices, whereas H diffusivity is significantly diminished in defective lattices. Tracer simulations focusing on H alone highlight the vital role of atomic vibrations of heavier atoms like Mg on the release of H atoms. Two regimes of H diffusion are identified: a diffuser-dominated regime at high hydrogen content with low activation energies due to saturation of vacancies by hydrogen, and a vacancy-dominated regime at low hydrogen content with high activation energies due to trapping of H atoms at vacancy sites. These regimes account for experimental observations, such as a H-concentration dependent diffusivity and the discrepancy in activation energy between deprotonation and D-H exchange experiments. This study underpins the crucial role of vacancies in H diffusion and demonstrates the utility of machine-learned interatomic potentials in studying kinetic processes in the Earth's interior. Y1 - 2025 U6 - https://doi.org/10.1029/2024GC011951 VL - 26 SP - e2024GC011951 ER - TY - JOUR A1 - Caruso, Fabio A1 - Sentef, Michael A1 - Attaccalite, Claudio A1 - Bonitz, Michael A1 - Draxl, Claudia A1 - De Giovannini, Umberto A1 - Eckstein, Martin A1 - Ernstorfer, Ralph A1 - Fechner, Michael A1 - Grüning, Myrta A1 - Hübener, Hannes A1 - Joost, Jan-Philip A1 - Juraschek, Dominik A1 - Karrasch, Christoph A1 - Marvin Kennes, Dante A1 - Latini, Simone A1 - Lu, I-Te A1 - Neufeld, Ofer A1 - Perfetto, Enrico A1 - Rettig, Laurenz A1 - Rodrigues Pelá, Ronaldo A1 - Rubio, Angel A1 - Rudzinski, Joseph A1 - Ruggenthaler, Michael A1 - Sangalli, Davide A1 - Schüler, Michael A1 - Shallcross, Samuel A1 - Sharma, Sangeeta A1 - Stefanucci, Gianluca A1 - Werner, Philipp T1 - The 2025 Roadmap to Ultrafast Dynamics: Frontiers of Theoretical and Computational Modelling JF - J. Phys. Mater. Y1 - 2026 U6 - https://doi.org/10.1088/2515-7639/ae1165 VL - 9 IS - 1 ER - TY - GEN A1 - Ragyanszki, Anita A1 - Ji, Hongchen A1 - Fournier, Rene T1 - Understanding the Origins of Life - A Machine learning approach to estimate reaction mechanisms of biotic precursors T2 - Perspectives and challenges of future HPC installations for atomistic and molecular simulations N2 - Life as we know it is the result of billions of years of evolution; yet, understanding how the very first organisms came into existence is a challenge that has yet to be solved. One theory states that components of the first biotic molecules may not have formed on Earth. Rather, they may have initially formed in the interstellar medium (ISM) and been transported to Earth, as supported by recorded instances of organic molecules detected in space. The ISM, with its low temperatures and specific collision processes, allows for molecular stability and the formation of biotic precursors that would otherwise be unlikely in Earth's prebiotic conditions. Understanding how these molecules formed in the ISM may be the key to determining how life began. The goal of this research is to develop a new model for solving astrobiophysical problems by studying the formation mechanisms of biomolecules found in the ISM. Although such pathways have been studied individually, there has not yet been a comprehensive method to understand all the formation reactions that can occur in ISM. Several quantum chemical and numerical methods are available for finding transition states (TS) and energy barriers (E) of chemical reactions but are time-consuming and can hardly be applied to systems with more than a few atoms. Our main interest is to develop a a machine learning approach to approximate TS, and E, requiring as input only estimates of geometry and energies of reactants and products. Using a complete dataset 300 reaction features are computed, and an estimate of E is obtained by fitting a Kernel Ridge Regression (KRR) model with Laplacian kernel, and a fully connected Artificial Neural Network (ANN) to estimate reaction energy barriers. Y1 - 2024 ER - TY - GEN A1 - Ragyanszki, Anita A1 - Ji, Hongchen A1 - Fournier, Rene T1 - Understanding the Origins of Life – A Machine learning approach to estimate reaction mechanisms of biotic precursors T2 - SIMPLAIX N2 - Understanding the Origins of Life - A Machine learning approach to estimate reaction mechanisms of biotic precursors. Life as we know it is the result of billions of years of evolution; however, understanding how the very first organisms came into existence is a challenge that has yet to be solved. One theory states that components of these molecules may have formed in the interstellar medium (ISM) and been transported to Earth. The ISM, with its specific conditions, allows for molecular stability and the formation of biotic precursors that would otherwise be unlikely in Earth's prebiotic conditions. Understanding how these molecules formed in the ISM may be the key to determining how life began. The goal of this research is to develop a model for solving astrobiophysical problems by studying the formation mechanisms of biomolecules found in the ISM. Although such pathways have been studied individually, there has not yet been a comprehensive method to understand the complete reactions mechanisms. Several QM methods are available for finding transition states (TS) and energy barriers (E) of chemical reactions but are time-consuming and can hardly be applied to more complex systems. Our interest is to develop a machine learning approach to approximate TS, and E, requiring as input only estimates of geometry and energies of reactants and products. Y1 - 2024 ER - TY - CHAP A1 - Christgau, Steffen A1 - Dylan, Everingham A1 - Lübke, Max A1 - De Lucia, Marco A1 - Puhan, Danny A1 - Schelten, Niklas A1 - Schnor, Bettina A1 - Signer, Hannes A1 - Spazier, Johannes A1 - Stabernack, Benno A1 - Steinert, Fritjof A1 - Yahdzhyiev, Serhii T1 - On the Usability and Energy Efficiency of High-Level Synthesis for FPGA-based Network-Attached Accelerators T2 - 2025 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) N2 - Heterogeneity in high performance computing systems is one of the most promising approaches towards more energy-efficient computing on one hand and satisfying the raising demand of global computation capacity on the other hand. Besides the well-known key components like CPUs and GPGPUs are domain-specific accelerators like TPUs, FPGAs well known for their energy efficiency. This is especially true for highly specialized use cases. Network-attached accelerators promise more scalability and flexibility for FPGA usage in HPC environments. Easy and efficient programming of those accelerators is, however, still an open issue. Based on a framework for such accelerators which enables decoupling of FPGAs from their host system, we present a workflow using High-Level Synthesis (HLS) to offload application kernels to them. We evaluate this approach against a conventional Hardware Description Language (HDL) based workflow. In addition, we introduce the energy measurement tool EMA and assess the energy efficiency of both HLS and HDL design. Y1 - 2025 U6 - https://doi.org/10.1109/IPDPSW66978.2025.00139 SP - 886 EP - 895 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Rotation dynamics and torque efficiency of cometary nuclei JF - Astronomy & Astrophysics N2 - The dynamics of a rigid cometary nucleus is described by the evolutions of its center-of-mass and of its rotation state. Solar irradiation that reaches the surface of a cometary nucleus causes the sublimation of volatiles that form the coma around the nucleus. The sublimation process transfers linear momentum and rotational angular momentum from the nucleus to the surrounding space, and thus affects the dynamics via nongravitational forces and nongravitational torques. With the exception of close approaches to planets, these torques exert the dominant influence on the rotation states of cometary nuclei. The Rosetta mission 2014-2016 accompanying comet 67P/Churyumov-Gerasimenko provides the longest continuous observational data to track its rotation state. In particular, the data set encompasses the direction of the angular velocity, denoted by ω, and the angular frequency |ω|over a time period of approximately 700 days. The observed change of the rotation state is not explained by a low heat conductivity thermophysical model in combination with a homogeneous surface ice coverage of comet 67P. Spatially and/or temporally varying weights for effective active fraction with respect to a prescribed set of surface regions provide a potential solution to this problem. Here, we present a methodology for classifying the surface based on vectorial efficiency of the torque. On any cometary surface without geometric symmetry, the methodology highlights the decomposition into eight characteristic regions that encode the signs of torque efficiency with respect to all vector components. This decomposition is divided into two subsets of four regions each of which is located in one of both hemispheric regions. We analyze in detail rotation states close to lowest energy and different thermophysical models, and we discuss how the uncertainties of observations affect the model parameters. We study the occurrence of these regions for an oblate ellipsoid, a nearprolate ellipsoid, a bilobed shape, and a shape model analogous to that of comet 67P. The sensitivity analysis for comet 67P indicates that the observations constrain only one of the eight weights uniquely. The other directions are poorly constrained and show the limitation of the rotational data to determine the regional activity on comet 67P. Y1 - 2025 U6 - https://doi.org/10.1051/0004-6361/202553845 VL - 699 SP - A75 ER - TY - THES A1 - el Bahnasawy, Henry T1 - Konzeption und Entwicklung einer Plattform zur geographisch verteilten Bereitstellung von latenzkritischen Anwendungen Y1 - 2025 ER - TY - JOUR A1 - Rossi, Thomas A1 - Qiao, Lu A1 - Dykstra, Conner P. A1 - Rodrigues Pelá, Ronaldo A1 - Gnewkow, Richard A1 - Wallick, Rachel F. A1 - Burke, John H. A1 - Nicholas, Erin A1 - March, Anne-Marie A1 - Doumy, Gilles A1 - Buchholz, D. Bruce A1 - Deparis, Christiane A1 - Zuñiga-Pérez, Jesus A1 - Weise, Michael A1 - Ellmer, Klaus A1 - Fondell, Mattis A1 - Draxl, Claudia A1 - van der Veen, Renske T1 - Dynamic control of X-ray core-exciton resonances by Coulomb screening in photoexcited semiconductors JF - Communications Materials Y1 - 2025 U6 - https://doi.org/10.1038/s43246-025-00909-w VL - 6 SP - 191 ER - TY - JOUR A1 - Hawthorne, Felipe A1 - Raulino, Paulo R. E. A1 - Rodrigues Pelá, Ronaldo A1 - Woellner, Cristiano F. T1 - Efficient and Accurate Machine Learning Interatomic Potential for Graphene: Capturing Stress–Strain and Vibrational Properties JF - The Journal of Physical Chemistry C Y1 - 2025 U6 - https://doi.org/10.1021/acs.jpcc.5c03470 VL - 129 SP - 16319 EP - 16326 ER - TY - JOUR A1 - Clausecker, Robert A1 - Lemire, Daniel A1 - Schintke, Florian T1 - Faster Positional-Population Counts for AVX2, AVX-512, and ASIMD JF - CoRR Y1 - 2024 U6 - https://doi.org/10.48550/arXiv.2412.16370 VL - abs/2412.16370 SP - 1 EP - 23 ER - TY - CHAP A1 - Lößer, Ansgar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis T2 - Proceedings of the 16th ACM/SPEC International Conference on Performance Engineering (ICPE 2025) Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?https://doi.org/10.1145/3676151.3719382 SP - 11 EP - 18 PB - Association for Computing Machinery ER - TY - JOUR A1 - Ji, Hongchen A1 - Ragyanszki, Anita A1 - Fournier, Rene T1 - A Machine Learning and Quantum Chemistry Approach for Identifying Prebiotic Molecules in the Interstellar Medium JF - Physical Chemistry Chemical Physics N2 - The discovery of molecules in the interstellar medium (ISM) plays a key role in understanding prebiotic chemistry. Relatively few (∼250) molecules have been confirmed in the ISM, and detecting additional species is crucial for expanding our knowledge of astrochemical processes. We present a strategy for predicting possible prebiotic molecules in the ISM that combines machine learning and high-accuracy quantum chemistry calculations. Using a reaction dataset of over 153,000 possible combinations of known interstellar molecules, we applied a machine learning model to estimate reaction energy barriers and identify those with low or zero barriers that are most likely to occur in the ISM. From this screening process, 24 molecules were identified, five of which have already been observed in interstellar space. For the remaining 19 molecules, we conducted density functional theory (DFT) and coupled cluster theory calculations to determine the most stable conformers, spectroscopic parameters, and predict their detectability through spectroscopy. We present data to guide future observational searches for new interstellar species, contributing to the ongoing exploration of complex organic molecules in space and their potential role in prebiotic chemistry. Y1 - 2024 ER - TY - JOUR A1 - Rozsa, Zsofia Borbala A1 - Ragyanszki, Anita A1 - Viskolcz, Bela A1 - Szori, Milan T1 - Chemical space of the singlet C4H8O2 species. A systematic theoretical analysis on their structural and thermochemical properties JF - Computational and Theoretical Chemistry N2 - The goal of this study was to explore and define the thermodynamic properties of one of the subspaces of ‘chemical space’ using a mixture of graph theory and theoretical chemistry tools. Therefore, all possible mo- lecular structures with C4H8O2 stoichiometry were generated, considering constitutional isomers and molecular complexes. The thermodynamic properties of the obtained isomers have been obtained by G3MP2B3 protocol. The classification of the obtained isomers was simplified by using thermodynamic maps, which is an effective method for the comparison of thermodynamic stability for entities of complex molecular systems. Modern computational methods can be used to understand larger systems, which has made it possible to characterize a chemical subspace not only by selecting individual entities, but also as a whole. With this pro- cedure one can catch a glimpse into the diversity of a molecular system and predict further uses of newly discovered molecules or design molecules with predefined properties. Y1 - 2023 U6 - https://doi.org/10.1016/j.comptc.2023.114162 VL - 1225 SP - 114162 ER - TY - JOUR A1 - Ragyanszki, Anita A1 - Fiser, Bela A1 - Lee-Ruff, Edward A1 - Liebman, Joel F. T1 - Strained Small Nitrogen Heterocycles-Azabicyclobutanes and Azirines JF - ChemistrySelect N2 - Small ring nitrogen heterocycles, azabicyclobutanes and azirines, were investigated by computational methods in order to address the discrepancy between their regioisomers 1- and 2-azabicyclobutane and 1H- and 2H-azirines. Both 1-azabicyclobutane and 2H-azirine are well known synthetic starting points to larger nitrogen heterocycles whereas 2-azabicyclobutane and 1H-azirine and their derivatives have yet to be reported as isolable compounds. Calculated parameters such as structure, base strength (proton affinities), NICS values and enthalpies of formation from which strain energies are derived are reported. The destabilization of the less stable regioisomers is attributed to homoantiaromaticity in 2-azabicyclobutane and antiaromaticity in 1H-azirine. Two stereoisomers exist for 2-azabicyclobutane with the endo- stereoisomer being more stable. This phenomenon is indicative of the hydrogen bond acceptor properties of the neighboring cyclpropane and the π-bond character of the central bond in 2-azabicyclobutane. Y1 - 2023 U6 - https://doi.org/10.1002/slct.202301405 VL - 8 IS - 26 ER - TY - JOUR A1 - Groussin, Olivier A1 - Jorda, L. A1 - Attree, N. A1 - Birch, S.P.D. A1 - Bürger, Johanna A1 - Gutiérrez, Pedro A1 - Jindal, Abhinav S. A1 - Keller, H.U. A1 - Kramer, Tobias A1 - Lasagni Manghi, Riccardo A1 - Läuter, Matthias A1 - Markkanen, J. A1 - Marschall, R. A1 - Schuckart, C. T1 - Thermal environment and erosion of comet 67P/Churyumov-Gerasimenko JF - Astronomy and Astrophysics N2 - Aims. This paper focuses on how insolation affects the nucleus of comet 67P/Churyumov-Gerasimenko over its current orbit. We aim to better understand the thermal environment of the nucleus, in particular its surface temperature variations, erosion, relationship with topography, and how insolation affects the interior temperature for the location of volatile species (H2O and CO2). Methods. We have developed two thermal models to calculate the surface and subsurface temperatures of 67P over its 6.45-year orbit. The first model, with high resolution (300 000 facets), calculates surface temperatures, taking shadows and self-heating into account but ignoring thermal conductivity. The second model, with lower resolution (10 000 facets), includes thermal conductivity to estimate temperatures down to ∼3 m below the surface. Results. The thermal environment of 67P is strongly influenced by its large obliquity (52◦), which causes significant seasonal effects and polar nights. The northern hemisphere is the coldest region, with temperatures of 210–300 K. H2O is found in the first few centimetres, while CO2 is found deeper (∼2 m) except during polar night around perihelion, when CO2 accumulates near the surface. Cliffs erode 3–5 times faster than plains, forming terraces. The equatorial region receives maximum solar energy (8.5×109 J m−2 per orbit), with maximum surface temperatures of 300–350 K. On the plains, H2O is found in the first few centimetres, while CO2 is found deeper (∼2 m) and never accumulates near the surface. In the southern hemisphere, a brief intense perihelion heating raises temperatures to 350–400 K, which is followed by a 5-year polar night when surface temperatures drop to 55 K. Here H2O remains in the first few centimetres, while CO2 accumulates shallowly during polar night, enriching the region. Erosion is maximal in the southern hemisphere and concentrated on the plains, which explains the observed overall flatness of this hemisphere compared to the northern one. Over one orbit, the total energy from self-heating is 17% of the total energy budget, and 34% for thermal conduction. Our study contributes to a better understanding of the surface changes observed on 67P. Y1 - 2025 U6 - https://doi.org/10.1051/0004-6361/202452260 VL - 694 SP - A21 ER - TY - CHAP A1 - Lößer, Ansgar A1 - Schlecht, Max A1 - Schintke, Florian A1 - Witzke, Joel A1 - Weidlich, Matthias A1 - Scheuermann, Björn T1 - Fast Min-ϵ Segmented Regression using Constant-Time Segment Merging T2 - Proceedings of the 42nd International Conference on Machine Learning Y1 - 2025 UR - https://proceedings.mlr.press/v267/losser25a.html VL - 267 SP - 40312 EP - 40327 ER - TY - JOUR A1 - Agarwal, A. A1 - Greve, Nico A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - et al., T1 - Performance of the prototype Silicon Tracking System of the CBM experiment tested with heavy-ion beams at SIS18 JF - Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment Y1 - 2025 U6 - https://doi.org/10.1016/j.nima.2025.171059 SN - 0168-9002 N1 - This paper has 343 authors. For the complete list of authors use the DOI, please. VL - 1082 SP - 171059 PB - Elsevier BV ER - TY - CHAP A1 - Clausecker, Robert A1 - Schintke, Florian T1 - A Measure of Quality for IDA* Heuristics T2 - Proceedings of the Fourteenth International Symposium on Combinatorial Search (SoCS 2021) Y1 - 2021 N1 - Best SoCS21 paper award SP - 55 EP - 63 ER - TY - JOUR A1 - Alhaddad, Samer A1 - Förstner, Jens A1 - Groth, Stefan A1 - Grünewald, Daniel A1 - Grynko, Yevgen A1 - Hannig, Frank A1 - Kenter, Tobias A1 - Pfreundt, F.J. A1 - Plessl, Christian A1 - Schotte, Merlind A1 - Steinke, Thomas A1 - Teich, J. A1 - Weiser, Martin A1 - Wende, Florian T1 - The HighPerMeshes Framework for Numerical Algorithms on Unstructured Grids JF - Concurrency and Computation: Practice and Experience N2 - Solving PDEs on unstructured grids is a cornerstone of engineering and scientific computing. Heterogeneous parallel platforms, including CPUs, GPUs, and FPGAs, enable energy-efficient and computationally demanding simulations. In this article, we introduce the HPM C++-embedded DSL that bridges the abstraction gap between the mathematical formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different programming models on the other hand. Thus, the HPM DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HPM DSL, and demonstrate its usage with three examples. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters, is presented. A code generator and a matching back end allow the acceleration of HPM code with GPUs. Finally, the achievable performance and scalability are demonstrated for different example problems. Y1 - 2022 U6 - https://doi.org/10.1002/cpe.6616 VL - 34 IS - 14 ER -