TY - GEN A1 - Kharma, Sami A1 - Wies, Tobias A1 - Schintke, Florian T1 - Comprehensive Plugin-Based Monitoring of Nexflow Workflow Executions T2 - SCA/HPC Asia 2026 Y1 - 2026 UR - https://www.sc-asia.org/2026/data/poster/post140.pdf ER - TY - GEN A1 - Ramaki, Niaz Mohammad A1 - Schintke, Florian T1 - Ensuring Reproducibility in Stream Processing with Blockchain Technologies T2 - 2025 11th International Conference on Computer and Communications (ICCC) Y1 - 2025 U6 - https://doi.org/10.1109/ICCC68654.2025.11437772 SP - 1383 EP - 1391 PB - IEEE ER - TY - CHAP A1 - Schelten, Niklas A1 - Christgau, Steffen A1 - Hutzler, Merit A1 - Kreowsky, Philipp A1 - De Lucia, Marco A1 - Schnor, Bettina A1 - Signer, Hannes A1 - Spazier, Johannes A1 - Stabernack, Benno A1 - Yahdzhyiev, Serhii T1 - Using FPGA-based Network-Attached Accelerators for Energy-Efficient AI Training in HPC Datacenters T2 - 2026 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) N2 - FPGA-based Network-Attached Accelerators offer a disaggregated alternative to closely-coupled FPGAs or GPUs, but their adoption is very limited due to missing hardware/software frameworks. However, the usability and energy-efficiency of FPGAs for HPC use-cases has been demonstrated previously. Yet, the support by HPC infrastructure for those devices is lacking behind other accelerators. This paper addresses this shortcoming and demonstrates a full-stack approach that seamlessly integrates Network-Attached Accelerators in HPC datacenters and allows flexible and scalable usage of FPGAs. The presented work includes the according framework, integration steps and a show-case application from the geoscience domain. We evaluate our approach by comparing the training of a Physics-Informed Neural Network on the NAA against two GPU implementations. The NAA reduces total energy consumption by about 50% and 17% compared to the Keras and CUDA implementation, respectively. These results demonstrate that FPGA-based NAAs can be successfully integrated into HPC environments and are a viable path toward more energy-efficient AI training. Y1 - 2026 ER - TY - CHAP A1 - Schelten, Niklas A1 - Christgau, Steffen A1 - Schulte, Anton A1 - Schnor, Bettina A1 - Signer, Hannes A1 - Stabernack, Benno T1 - A Flexible Open-Source Framework for FPGA-based Network-Attached Accelerators using SpinalHDL T2 - Architecture of Computing Systems - 39th International Conference, ARCS 2026, Mainz, Germany, March 24-26, 2026, Proceedings. N2 - Domain-specific accelerators are increasingly vital in heterogeneous computing systems, driven by the demand for higher computational capacity and especially energy efficiency. Network-attached FPGAs promise a scalable and flexible alternative to closely coupled FPGAs for integrating accelerators into computing environments. While the advantages of specialized hardware implementations are apparent, traditional hardware development and integration remain time-consuming and complex. We present an open-source framework which combines a hardware shell with supporting software libraries, which enables fast development and deployment of FPGA-based network-attached accelerators. In contrast to traditional approaches using VHDL or Verilog, we leverage generative programming with SpinalHDL, providing a flexible hardware description with multi-level abstractions. This work eases the integration of accelerators into existing network infrastructures and simplifies adaptation to different FPGAs, eliminating complex and lengthy top-level hardware descriptions. Y1 - 2026 ER - TY - JOUR A1 - Raya-Moreno, Martí A1 - Dasch, Noah Alexy A1 - Farahani, Nasrin A1 - Gonzalez Oliva, Ignacio A1 - Gulans, Andris A1 - Hossain, Manoar A1 - Kleine, Hannah A1 - Kuban, Martin A1 - Lubeck, Sven A1 - Maurer, Benedikt A1 - Pavone, Pasquale A1 - Peschel, Fabian A1 - Popova-Gorelova, Daria A1 - Qiao, Lu A1 - Richter, Elias A1 - Rigamonti, Santiago A1 - Rodrigues Pelá, Ronaldo A1 - Sinha, Kshitij A1 - Speckhard, Daniel T. A1 - Tillack, Sebastian A1 - Tumakov, Dmitry A1 - Hong, Seokhyun A1 - Uzulis, Janis A1 - Voiculescu, Mara A1 - Vona, Cecilia A1 - Yang, Mao A1 - Draxl, Claudia T1 - An exciting approach to theoretical spectroscopy Y1 - 2026 ER - TY - JOUR A1 - Qiao, Lu A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - First-principles approach to ultrafast pump-probe spectroscopy in solids Y1 - 2026 ER - TY - JOUR A1 - Hölter, Arne A1 - Lemke, Mathias A1 - Weinzierl, Stefan A1 - Stein, Lewin T1 - Non-Reflecting Characteristic Boundary Conditions for Adjoint Time-Domain Acoustic Simulations JF - Journal of Theoretical and Computational Acoustics N2 - Accurate acoustic simulations in the free field require non-reflective boundary conditions to suppress spurious reflections at the computational domain boundaries. Although several characteristic-based formulations for direct (forward) simulations have been proposed in recent decades, the adjoint formulations of such characteristic-based boundary conditions (CBCs) have received limited atten- tion in the literature and lack a comprehensive analysis. This paper presents the derivation and evaluation of adjoint CBCs complementing the existing direct CBCs. Both the forward and adjoint CBCs are applied to the (nonlinear) Euler equations and linear acoustic equations in time-domain simulations. In this manner, the CBCs are investigated and subsequently compared to assess their respective accuracy and consistency. The CBCs were implemented using both a single-point and a zonal approach, with the former optionally combined with a sponge layer. Both approaches yielded comparable results in direct and adjoint simulations, while the zonal CBC exhibited improved ac- curacy at lower frequencies. Across the evaluated frequency range of approximately 350 – 5600 Hz, spurious reflections were attenuated by up to −70dB in both forward and adjoint cases, demon- strating the effectiveness and consistency of the proposed boundary treatment. Y1 - 2025 ER - TY - JOUR A1 - Clausecker, Robert A1 - Lemire, Daniel A1 - Schintke, Florian T1 - Faster Positional‐Population Counts for AVX2, AVX‐512, and ASIMD JF - Concurrency and Computation: Practice and Experience Y1 - 2025 U6 - https://doi.org/10.1002/cpe.70435 SN - 1532-0626 VL - 37 IS - 27-28 PB - Wiley ER - TY - JOUR A1 - Krishnadas, Anirudh A1 - Moshi, Maryam A1 - Quintana, Ramon Alain Miranda A1 - Fournier, Rene T1 - Geometric Features and a Neural Network Classifier for Detecting Melting-Like Transitions in Clusters. JF - AIP Publications - The Journal of Chemical Physics N2 - Melting-like transitions in clusters are normally identified by a peak in the heat capacity curve C(T ) at T = Tc. Computing C(T ) requires costly simulations with millions of steps. We discuss four easily calculated functions of temperature that help detect and characterize melting-like transitions. The first, f1 (or WU ), is the width of the potential energy distribution which shows an abrupt increase near Tc. The other three are statistics of the ordered set of N(N − 1)/2 interatomic distances rij: (i) f2 is a measure of dissimilarity to the lowest energy configuration, or global minimum; (ii) f3 is the effective number of rij’s found in a small interval centered around (r1 + r2)/2 where r1, r2 are the positions of the first two peaks in the pair distribution function; and (iii) f4 is a measure of non-uniformity in the distribution of the ri j’s. Numerical tests with empirical potentials that model three types of bonding (van der Waals, covalent, and metallic) show that f1, f2, f3, and f4 produce estimates for the middle of the melting region in general agreement with Tc. An Artificial Neural Network (ANN) classifier that takes, as inputs, f2, f3, and many variants of f4, is used to calculate the solid fraction FS(T) and find the solid-liquid coexistence region between freezing and melting temperatures, [Tf , Tm]. Inflection points in f3(T ) and FS(T ) are very sensitive indicators of phase transitions. Estimates of Tc obtained from them converge one to three orders of magnitude faster, in simulation time, than those obtained with C(T ). Y1 - 2025 ER - TY - JOUR A1 - Krishnadas, Anirudh A1 - Charron, Nicolas A1 - Fournier, Rene T1 - Melting Transitions in Small Aluminum Clusters Simulated with Energies Approaching DFT Accuracy. JF - ACS Publications- Journal of Chemical Theory and Computation N2 - We describe a computational framework for modelling melting-like transitions in atomic clusters that combines first-principles energy calculations, global optimization, and machine-learned interatomic potentials. A diverse set of configurations is generated by global optimization, and energies are calculated by Density Functional Theory. The energies are fitted to an accuracy of 10 meV/atom or better with an Allegro E(3)-equivariant neural network potential. The model allows efficient parallel tempering Monte Carlo simulations with near DFT-level accuracy. This methodology was validated by simulating Na_20 and comparing it to earlier experimental and computational results. We used it to study melting-like transitions in Al_n+ clusters (n=9 to 16), and Al_n and Al_n^- (n=12, 13,14). The simulated heat capacity of these clusters, in particular Al_16+, are in qualitative agreement with experiments. The melting point of Al_n+ clusters with n=11-16 are well above the bulk melting point (934 K). The closed-shell Al_13- species has an exceptionally high melting point, close to 2100 K. Y1 - 2025 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 - 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 - 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 - THES A1 - el Bahnasawy, Henry T1 - Konzeption und Entwicklung einer Plattform zur geographisch verteilten Bereitstellung von latenzkritischen Anwendungen Y1 - 2025 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 - 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 - 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 - 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 - 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 - 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 - 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 - Ji, Hongchen A1 - Anita, Ragyanszki A1 - Fournier, Rene T1 - Computational Study of the Reactions of CH2 with HCNO and HNCO JF - Canadian Journal of Chemistry N2 - We present a computational approach for screening reaction mechanisms with machine learning estimates of energy barriers. A comprehensive screening of thousands of reactions identified the CH2 reactions with HCNO and HNCO as possible sources of relatively complex organic molecules in space. We report detailed reaction mechanisms, including TS, intermediate, and product energies, calculated with density functional theory and coupled cluster theory. Singlet CH2, located 9 kcal/mol above the triplet ground state, reacts with HCNO or HNCO without a barrier, producing four prod11 ucts: CH2NCHO, N-methyleneformamide, the thermodynamically favored product; NHCHCHO, imine acetaldehyde; NHCHOCH; and (CH2OC)NH, oxiran-2-ylazanide. The lowest energy pathway for CH2 + HCNO, involving a triplet-to-singlet crossing, has a barrier of 8 kcal/mol and leads to N -methyleneformamide, imine acetaldehyde, and NHCHOCH. The reaction of triplet CH2 with HNCO has a lowest energy pathway with a barrier of 11 kcal/mol, yielding CH2(CO)NH. Y1 - 2025 U6 - https://doi.org/10.1139/cjc-2024-0203 VL - 103 IS - 7 SP - 386 EP - 395 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 - 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 - 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 - 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 - Höfling, Felix A1 - Straube, Arthur T1 - Langevin equations and a geometric integration scheme for the overdamped limit of rotational Brownian motion of axisymmetric particles JF - Physical Review Research N2 - The translational motion of anisotropic or self-propelled colloidal particles is closely linked with the particle’s orientation and its rotational Brownian motion. In the overdamped limit, the stochastic evolution of the orientation vector follows a diffusion process on the unit sphere and is characterized by an orientation-dependent (“multiplicative”) noise. As a consequence, the corresponding Langevin equation attains different forms depending on whether Itō’s or Stratonovich’s stochastic calculus is used. We clarify that both forms are equivalent and derive them in a top-down approach from a geometric construction of Brownian motion on the unit sphere, based on infinitesimal random rotations. Our approach suggests further a geometric integration scheme for rotational Brownian motion, which preserves the normalization constraint of the orientation vector exactly. We show that a simple implementation of the scheme, using Gaussian random rotations, converges weakly at order 1 of the integration time step, and we outline an advanced variant of the scheme that is weakly exact for an arbitrarily large time step. Due to a favorable prefactor of the discretization error, already the Gaussian scheme allows for integration time steps that are one order of magnitude larger compared to a commonly used algorithm for rotational Brownian dynamics simulations based on projection on the constraining manifold. For torques originating from constant external fields, we prove by virtue of the Fokker-Planck equation that the constructed diffusion process satisfies detailed balance and converges to the correct equilibrium distribution. The analysis is restricted to time-homogeneous rotational Brownian motion (i.e., a single rotational diffusion constant), which is relevant for axisymmetric particles and also chemically anisotropic spheres, such as self-propelled Janus particles. Y1 - 2025 U6 - https://doi.org/10.1103/wzdn-29p4 VL - 7 SP - 043034 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 - 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 - GEN A1 - Schintke, Florian A1 - Greve, Nico A1 - de Cuveland, Jan ED - Friese, Volker ED - Gasik, Piotr ED - Selyuzhenkov, Ilya T1 - Recent Flesnet developments and work in progress T2 - CBM Progress Report 2023 Y1 - 2024 U6 - https://doi.org/10.15120/GSI-2024-00765 SP - 132 PB - GSI Helmholtzzentrum für Schwerionenforschung GmbH ER - TY - JOUR A1 - Fritsch, Daniel A1 - Schorr, Susan T1 - Disorder induced band gap lowering in kesterite type Cu2ZnSnSe4 and Ag2ZnSnSe4: a first-principles and special quasirandom structures investigation JF - Journal of Physics: Condensed Matter N2 - Abstract Quaternary chalcogenides, i.e. Cu2ZnSnS4, crystallising in the kesterite crystal structure have already been demonstrated as potential building blocks of thin film solar cells, containing only abundant elements and exhibiting power conversion efficiencies of about 14.9% so far. However, due to the potential presence of several structurally similar polymorphs, the unequivocal identification of their ground state crystal structures required the application of more elaborate neutron diffraction experiments. One particular complication arose from the later identified Cu–Zn disorder, present in virtually all thin film samples. Subsequently, it has been shown experimentally that this unavoidable Cu–Zn disorder leads to a band gap lowering in the respective samples. Additional theoretical investigations, mostly based on Monte-Carlo methods, tried to understand the atomistic origin of this disorder induced band gap lowering. Here, we present theoretical results from first-principles calculations based on density functional theory for the disorder induced band gap lowering in kesterite Cu2ZnSnSe4 and Ag2ZnSnSe4, where the Cu–Zn and Ag–Zn disorder is modelled via a supercell approach and special quasirandom structures. Results of subsequent analyses of structural, electronic, and optical properties are discussed with respect to available experimental results, and will provide additional insight and knowledge towards the atomistic origin of the observed disorder induced band gap lowering in kesterite type materials. Y1 - 2024 U6 - https://doi.org/10.1088/1361-648X/ad52de SN - 0953-8984 VL - 36 IS - 37 PB - IOP Publishing ER - TY - CHAP A1 - Attree, Nicholas A1 - Gutiérrez, Pedro A1 - Groussin, Olivier A1 - Bürger, Johanna A1 - Keller, Horst Uwe A1 - Kramer, Tobias A1 - Lasagni Manghi, Riccardo A1 - Läuter, Matthias A1 - Lemos, Pablo A1 - Markkanen, Johannes A1 - Marschall, Raphael A1 - Schuckart, Christian T1 - The Results of ISSI Team #547: Understanding the Activity of Comets Through 67P's Dynamics T2 - EPSC Abstracts N2 - Understanding cometary activity gives us an insight into the materials properties, and therefore formation and evolution processes of these relatively pristine protoplanetary objects. We will present the results of an International Space Science Institute project to investigate the phenomenon through the effects of the outgassing activity on the orbit and spin-state of comet 67P/Churymov-Gerasimenko, e.g. its non-gravitational dynamics. This International Team gathered experts in orbital dynamics and trajectory reconstruction together with thermophysical modellers and comet observationalists, in order to compare the available extractions of 67P’s non-gravitational acceleration (NGA) from its trajectory. The team then fitted a combination of the NGA, the non-gravitational torque (NGT), and the total water-outgassing rate with a thermophysical activity model. The results of this model will be presented. In particular, it was found that: non-gravitational forces and torques are driven by water sublimation from the nucleus; thermal inertia and self-heating have only minor effects; spatially uniform activity cannot explain 67P's non-gravitational dynamics; spatially uniform momentum transfer cannot explain 67P's non-gravitational dynamics; and different terrain types have different instantaneous responses to insolation. The implications of these findings for the modelling of cometary material and the variety of surface types seen on 67P will be discussed. Y1 - 2024 U6 - https://doi.org/10.5194/epsc2024-82 VL - 17 ER - TY - JOUR A1 - Attree, Nicholas A1 - Gutiérrez, Pedro A1 - Groussin, Olivier A1 - Bürger, Johanna A1 - Keller, Horst Uwe A1 - Kramer, Tobias A1 - LASAGNI MANGHI, RICCARDO A1 - Läuter, Matthias A1 - Lemos, Pablo A1 - Markkanen, Johannes A1 - Marschall, Raphael A1 - Schuckart, Christian T1 - Varying water activity and momentum transfer on comet 67P/Churyumov-Gerasimenko from its non-gravitational forces and torques JF - Astronomy and Astrophysics N2 - Aims. We investigate the ability of a simultaneous fitting of comet 67P/Churyumov-Gerasimenko’s non-gravitational forces, torques, and total water-outgassing rate, as observed by Rosetta, to constrain complex thermophysical models of cometary material. Methods. We extend the previous work of fitting geographically defined surface outgassing models to the Rosetta observations by testing the effects of a more detailed geomorphological mapping, the resolution of the shape-model used, self-heating by neighbouring facets on the shape-model, thermal inertia in the outgassing solution, and the variation in the momentum coupling between the gas and the nucleus. We also directly compare the non-gravitational acceleration curves available in the literature. Results. We correct an error in the calculation of pole-orientation in the previous paper. We find that, under the assumptions of the model, non-gravitational forces and torques are driven by water sublimation from the nucleus, thermal inertia and self-heating have only minor effects, spatially uniform activity cannot explain 67P’s non-gravitational dynamics, spatially uniform momentum transfer cannot explain 67P’s non-gravitational dynamics, and different terrain types have different instantaneous responses to insolation. Conclusions. Consolidated terrain facing south on 67P/Churyumov-Gerasimenko has a high outgassing flux, a steep response to insolation, and a large gas momentum transfer coefficient. Instead, that facing north behaves differently, producing little to no water outgassing, and with a lower momentum transfer efficiency. Dusty terrain also has a lower outgassing rate and momentum transfer efficiency, and either depletes its volatile component or is buried in fall-back as the comet approaches the Sun. Momentum transfer appears correlated with insolation, likely due to an increased enhancement in the gas temperature as the dust it flows through is heated. Y1 - 2024 U6 - https://doi.org/10.1051/0004-6361/202450728 VL - 690 SP - A82 ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Benchmarking the rotating jet model of cometary activity with the trajectory of comet 67P/Churyumov-Gerasimenko T2 - EPSC Abstracts N2 - An important tool to assess the composition and the spatial origin of cometary material is the analysis of its trajectory reflecting gravitational acceleration due to solar system bodies complemented by non-gravitational accelerations (NGA). Y1 - 2024 U6 - https://doi.org/10.5194/epsc2024-207 VL - 17 ER - TY - JOUR A1 - Witzke, Joel A1 - Lößer, Ansgar A1 - Bountris, Vasilis A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - Low-level I/O Monitoring for Scientific Workflows JF - CoRR Y1 - 2024 U6 - https://doi.org/10.48550/ARXIV.2408.00411 VL - abs/2408.00411 SP - 1 EP - 10 ER - TY - CHAP A1 - Witzke, Joel A1 - Lößer, Ansgar A1 - Bountris, Vasilis A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - I/O of Scientific Workflows Monitored in Detail T2 - 20th IEEE International Conference on e-Science, e-Science 2024, Osaka, Japan, September 16-20, 2024 Y1 - 2024 U6 - https://doi.org/10.1109/E-SCIENCE62913.2024.10678728 N1 - Best Poster Award SP - 1 EP - 2 ER - 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 - JOUR A1 - Raharinirina, Nomenjanahary Alexia A1 - Sunkara, Vikram A1 - von Kleist, Max A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Multi-Input data ASsembly for joint Analysis (MIASA): A framework for the joint analysis of disjoint sets of variables JF - PLOS ONE Y1 - 2024 U6 - https://doi.org/10.1371/journal.pone.0302425 VL - 19 IS - 5 PB - Public Library of Science ER - TY - JOUR A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - Speeding up all-electron real-time TDDFT demonstrated by the exciting package JF - Comput. Phys. Commun. Y1 - 2024 U6 - https://doi.org/10.1016/j.cpc.2024.109292 VL - 304 SP - 109292 ER - TY - JOUR A1 - Schintke, Florian A1 - Belhajjame, Khalid A1 - De Mecquenem, Ninon A1 - Frantz, David A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Missier, Paolo A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel T. A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity constraints for data analysis workflows JF - Future Generation Computer Systems Y1 - 2024 U6 - https://doi.org/10.1016/j.future.2024.03.037 VL - 157 SP - 82 EP - 97 ER - TY - JOUR A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - A Microphysical Thermal Model for the Lunar Regolith: Investigating the Latitudinal Dependence of Regolith Properties JF - Journal of Geophysical Research: Planets N2 - The microphysical structure of the lunar regolith provides information on the geologic history of the Moon. We used remote sensing measurements of thermal emission and a thermophysical model to determine the microphysical properties of the lunar regolith. We expand upon previous investigations by developing a microphysical thermal model, which more directly simulates regolith properties, such as grain size and volume filling factor. The modeled temperatures are matched with surface temperatures measured by the Diviner Lunar Radiometer Experiment on board the Lunar Reconnaissance Orbiter. The maria and highlands are investigated separately and characterized in the model by a difference in albedo and grain density. We find similar regolith temperatures for both terrains, which can be well described by similar volume filling factor profiles and mean grain sizes obtained from returned Apollo samples. We also investigate a significantly lower thermal conductivity for highlands, which formally also gives a very good solution, but in a parameter range that is well outside the Apollo data. We then study the latitudinal dependence of regolith properties up to ±80° latitude. When assuming constant regolith properties, we find that a variation of the solar incidence-dependent albedo can reduce the initially observed latitudinal gradient between model and Diviner measurements significantly. A better match between measurements and model can be achieved by a variation in intrinsic regolith properties with a decrease in bulk density with increasing latitude. We find that a variation in grain size alone cannot explain the Diviner measurements at higher latitudes. Y1 - 2024 U6 - https://doi.org/10.1029/2023JE008152 VL - 129 IS - 3 ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Non-gravitational acceleration and torque on comet 67P/Churyumov-Gerasimenko T2 - Bulletin of the AAS N2 - From August 2014 to September 2016, the ESA operated the Rosetta spacecraft mission alongside with comet 67P/Churyumov-Gerasimenko (67P). The mission provided valuable long-term data on the comet’s nucleus, including its volume, mass, tensor of inertia, spatial position of the orbital trajectory, and rotational state. Y1 - 2023 UR - https://baas.aas.org/pub/2023n8i218p02 VL - 55 IS - 8 ER - TY - JOUR A1 - Majewski, Maciej A1 - Pérez, Adrià A1 - Thölke, Philipp A1 - Doerr, Stefan A1 - Charron, Nicholas A1 - Giorgino, Toni A1 - Husic, Brooke A1 - Clementi, Cecilia A1 - Noé, Frank A1 - De Fabritiis, Gianni T1 - Machine learning coarse-grained potentials of protein thermodynamics JF - Nature Communications N2 - A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics. Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-41343-1 VL - 14 ER - TY - CHAP A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - Investigating the Latitudinal Dependence of Lunar Regolith Properties Using LRO/Diviner Data and a Microphysical Thermal Model T2 - Bulletin of the AAS N2 - Regolith is formed through weathering of the local rock by meteorite bombardment, space weathering (Pieters & Noble, 2016) and thermal erosion (Delbo et al., 2014). In the case of the Moon, the space weathering effects and diurnal temperature variations are reduced towards the poles. The aim of this study is to investigate whether the lunar regolith properties derived from the comparison of regolith temperatures measured by the Diviner radiometer (Paige et al., 2010) on board the Lunar Reconnaissance Orbiter (LRO) with simulated temperatures derived from a microphysical thermal model show a latitudinal dependence. The developed microphysical thermal model expands upon previous models by more directly simulating regolith properties, such as grain radius and volume filling factor. Y1 - 2023 UR - https://baas.aas.org/pub/2023n8i207p02 VL - 55 IS - 8 ER - TY - JOUR A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Templeton, Clark A1 - Musil, Félix A1 - Bonneau, Klara A1 - Pasos-Trejo, Aldo A1 - Chen, Yaoyi A1 - Kelkar, Atharva A1 - Noé, Frank A1 - Clementi, Cecilia T1 - Machine learned coarse-grained protein force-fields: Are we there yet? JF - Current Opinion in Structural Biology N2 - The successful recent application of machine learning methods to scientific problems includes the learning of flexible and accurate atomic-level force-fields for materials and biomolecules from quantum chemical data. In parallel, the machine learning of force-fields at coarser resolutions is rapidly gaining relevance as an efficient way to represent the higher-body interactions needed in coarse-grained force-fields to compensate for the omitted degrees of freedom. Coarse-grained models are important for the study of systems at time and length scales exceeding those of atomistic simulations. However, the development of transferable coarse-grained models via machine learning still presents significant challenges. Here, we discuss recent developments in this field and current efforts to address the remaining challenges. Y1 - 2023 U6 - https://doi.org/10.1016/j.sbi.2023.102533 VL - 79 ER - TY - JOUR A1 - Krämer, Andreas A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Chen, Yaoyi A1 - Clementi, Cecilia A1 - Noé, Frank T1 - Statistically optimal force aggregation for coarse-graining molecular dynamics JF - The Journal of Physical Chemistry Letters N2 - Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used methodology for learning bottom-up CG force fields maps forces from all-atom molecular dynamics to the CG representation and matches them with a CG force field on average. We show that there is flexibility in how to map all-atom forces to the CG representation and that the most commonly used mapping methods are statistically inefficient and potentially even incorrect in the presence of constraints in the all-atom simulation. We define an optimization statement for force mappings and demonstrate that substantially improved CG force fields can be learned from the same simulation data when using optimized force maps. The method is demonstrated on the miniproteins chignolin and tryptophan cage and published as open-source code. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpclett.3c00444 VL - 14 IS - 17 SP - 3970 EP - 3979 ER - TY - JOUR A1 - Koyanagi, Gregory K. A1 - Lambo, Ricardo Lewis A1 - Ragyanszki, Anita A1 - Fournier, Rene A. A1 - Horbatsch, Marko W. A1 - Hessels, Eric A. T1 - Accurate calculation of the interaction of a barium monofluoride molecule with an argon atom: A step towards using matrix isolation of BaF for determining the electron electric dipole moment JF - Journal of Molecular Spectroscopy Y1 - 2023 U6 - https://doi.org/10.1016/j.jms.2023.111736 VL - 391 SP - 111736 ER - TY - JOUR A1 - Lambo, Ricardo Lewis A1 - Koyanagi, Gregory K. A1 - Ragyanszki, Anita A1 - Horbatsch, Marko A1 - Fournier, Rene A1 - Hessels, Eric A. T1 - Calculation of the local environment of a barium monofluoride molecule in an argon matrix: a step towards using matrix-isolated BaF for determining the electron electric dipole moment JF - Molecular Physics Y1 - 2023 U6 - https://doi.org/10.1080/00268976.2023.2198044 VL - 121 IS - 6 ER - TY - CHAP A1 - Witzke, Joel A1 - Schintke, Florian A1 - Lößer, Ansgar A1 - Scheuermann, Björn T1 - Proactive Resource Management to Optimize Distributed Workflow Executions T2 - IEEE International Conference on Big Data, BigData 2023, Sorrento, Italy, December 15-18, 2023 Y1 - 2023 U6 - https://doi.org/10.1109/BigData59044.2023.10386493 SP - 6305 EP - 6307 PB - IEEE ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Hsiao, Ching-Lien A1 - Hultman, Lars A1 - Birch, Jens A1 - Gueorguiev, Gueorgui Kostov T1 - Electronic and optical properties of core-shell InAlN nanorods: a comparative study via LDA, LDA-1/2, mBJ, HSE06, G0W0 and BSE methods JF - Physical Chemistry Chemical Physics Y1 - 2024 U6 - https://doi.org/10.1039/D3CP05295H VL - 26 SP - 7504 EP - 7514 PB - Royal Society of Chemistry ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Vona, Cecilia A1 - Lubeck, Sven A1 - Alex, Ben A1 - Gonzalez Oliva, Ignacio A1 - Draxl, Claudia T1 - Critical assessment of G0W0 calculations for 2D materials: the example of monolayer MoS2 JF - npj Comput. Mater. Y1 - 2024 U6 - https://doi.org/10.1038/s41524-024-01253-2 VL - 10 SP - 77 ER - TY - CHAP A1 - Clausecker, Robert A1 - Kaiser, Benjamin T1 - Sliding Tile Puzzles T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 SP - 57 ER - TY - JOUR A1 - Charron, Nicholas A1 - Musil, Félix A1 - Guljas, Andrea A1 - Chen, Yaoyi A1 - Bonneau, Klara A1 - Pasos-Trejo, Aldo A1 - Jacopo, Venturin A1 - Daria, Gusew A1 - Zaporozhets, Iryna A1 - Krämer, Andreas A1 - Templeton, Clark A1 - Atharva, Kelkar A1 - Durumeric, Aleksander A1 - Olsson, Simon A1 - Pérez, Adrià A1 - Majewski, Maciej A1 - Husic, Brooke A1 - Patel, Ankit A1 - De Fabritiis, Gianni A1 - Noé, Frank A1 - Clementi, Cecilia T1 - Navigating protein landscapes with a machine-learned transferable coarse-grained model JF - Nature Chemistry N2 - The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar prediction performance has been a long-standing challenge. By combining recent deep learning methods with a large and diverse training set of all-atom protein simulations, we here develop a bottom-up CG force field with chemical transferability, which can be used for extrapolative molecular dynamics on new sequences not used during model parametrization. We demonstrate that the model successfully predicts folded structures, intermediates, metastable folded and unfolded basins, and the fluctuations of intrinsically disordered proteins while it is several orders of magnitude faster than an all-atom model. This showcases the feasibility of a universal and computationally efficient machine-learned CG model for proteins. Y1 - 2025 U6 - https://doi.org/10.1038/s41557-025-01874-0 VL - 17 SP - 1284 EP - 1292 ER - TY - JOUR A1 - Policht, Veronica R. A1 - Mittenzwey, Henry A1 - Dogadov, Oleg A1 - Katzer, Manuel A1 - Villa, Andrea A1 - Li, Qiuyang A1 - Kaiser, Benjamin A1 - Ross, Aaron M. A1 - Scotognella, Francesco A1 - Zhu, Xiaoyang A1 - Knorr, Andreas A1 - Selig, Malte A1 - Cerullo, Giulio A1 - Dal Conte, Stefano T1 - Time-domain observation of interlayer exciton formation and thermalization in a MoSe2/WSe2 heterostructure JF - Nature Communications N2 - Vertical heterostructures of transition metal dichalcogenides (TMDs) host interlayer excitons with electrons and holes residing in different layers. With respect to their intralayer counterparts, interlayer excitons feature longer lifetimes and diffusion lengths, paving the way for room temperature excitonic optoelectronic devices. The interlayer exciton formation process and its underlying physical mechanisms are largely unexplored. Here we use ultrafast transient absorption spectroscopy with a broadband white-light probe to simultaneously resolve interlayer charge transfer and interlayer exciton formation dynamics in a MoSe2/WSe2 heterostructure. We observe an interlayer exciton formation timescale nearly an order of magnitude (~1 ps) longer than the interlayer charge transfer time (~100 fs). Microscopic calculations attribute this relative delay to an interplay of a phonon-assisted interlayer exciton cascade and thermalization, and excitonic wave-function overlap. Our results may explain the efficient photocurrent generation observed in optoelectronic devices based on TMD heterostructures, as the interlayer excitons are able to dissociate during thermalization. Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-42915-x VL - 14 SP - 1 EP - 9 PB - Springer Nature ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert A1 - Mavroskoufis, Michael T1 - Prioritised Unit Propagation by Partitioning the Watch Lists T2 - Proceedings of the 14th International Workshop on Pragmatics of SAT co-located with the 26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023) N2 - Conflict Driven Clause Learning (CDCL) SAT solvers spend most of their execution time iterating through clauses in unit propagation. Efficient implementations of unit propagation mostly rely on the two watched literals (TWL) scheme, a specialised data structure watching two literals per clause to prevent as many clause lookups as possible. In this paper, we present Priority Propagation (PriPro)—a minimally invasive method to adapt unit propagation in existing SAT solvers. With PriPro the traditional TWL scheme is partitioned to allow for rearranging the order in which clauses are examined. This is used to achieve a prioritisation of certain clauses. Using PriPro in combination with a dynamic heuristic to prioritise resolvents from recent conflicts, the effectiveness of unit propagation can be increased. In the state-of-the-art CDCL SAT solver CaDiCaL modified to use PriPro, we obtained a 5–10 % speedup on the SAT Competition 2021 benchmark set in a fair comparison with the unmodified CaDiCaL. Y1 - 2023 UR - https://ceur-ws.org/Vol-3545/paper2.pdf VL - 3545 SP - 14 EP - 34 PB - CEUR Workshop Proceedings ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Structure of liquid–vapor interfaces: perspectives from liquid state theory, large-scale simulations, and potential grazing-incidence X-ray diffraction JF - The Journal of Chemical Physics N2 - Grazing-incidence X-ray diffraction (GIXRD) is a scattering technique which allows one to characterize the structure of fluid interfaces down to the molecular scale, including the measurement of the surface tension and of the interface roughness. However, the corresponding standard data analysis at non-zero wave numbers has been criticized as to be inconclusive because the scattering intensity is polluted by the unavoidable scattering from the bulk. Here we overcome this ambiguity by proposing a physically consistent model of the bulk contribution which is based on a minimal set of assumptions of experimental relevance. To this end, we derive an explicit integral expression for the background scattering, which can be determined numerically from the static structure factors of the coexisting bulk phases as independent input. Concerning the interpretation of GIXRD data inferred from computer simulations, we account also for the finite sizes of the bulk phases, which are unavoidable in simulations. The corresponding leading-order correction beyond the dominant contribution to the scattered intensity is revealed by asymptotic analysis, which is characterized by the competition between the linear system size and the X-ray penetration depth in the case of simulations. Specifically, we have calculated the expected GIXRD intensity for scattering at the planar liquid--vapor interface of Lennard-Jones fluids with truncated pair interactions via extensive, high-precision simulations. The reported data cover interfacial and bulk properties of fluid states along the whole liquid--vapor coexistence line. A sensitivity analysis demonstrates the robustness of our findings concerning the detailed definition of the mean interface position. We conclude that previous claims of an enhanced surface tension at mesoscopic scales are amenable to unambiguous tests via scattering experiments. Y1 - 2024 U6 - https://doi.org/10.1063/5.0186955 VL - 160 SP - 104107 ER - TY - CHAP A1 - Christgau, Steffen A1 - Everingham, Dylan A1 - Mikolajczak, Florian A1 - Schelten, Niklas A1 - Schnor, Bettina A1 - Schroetter, Max A1 - Stabernack, Benno A1 - Steinert, Fritjof T1 - Enabling Communication with FPGA-based Network-attached Accelerators for HPC Workloads T2 - Proceedings of the SC'23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis, SC-W 2023, Denver, CO, USA, November 12-17, 2023 N2 - The use of stand-alone, network-coupled Field Programmable Gate Array (FPGA) accelerators is intended to significantly increase the energy efficiency of HPC applications and thus also of HPC data centers. A loose coupling between the nodes of the HPC data center and the FPGAs is established through the high-speed network of the data center. This allows greater flexibility in combining different nodes and accelerators. Both the resulting energy savings and the increased flexibility through the network connection, enable the economical use of FPGAs. This work presents a communication stack to integrate the so-called Network-attached Accelerator (NAA) into the HPC data center. A low-level Remote Direct Memory Access (RDMA) Application Programming Interface (API) and a high-level Remote Procedure Call (RPC) API is designed on top of the RDMA over Converged Ethernet v2 (RoCEv2) communication stack. The experimental results over 100 Gbps RoCEv2 show that our design and implementation deliver performance close to the theoretical maximum. Y1 - 2023 U6 - https://doi.org/10.1145/3624062.3624540 SP - 530 EP - 538 PB - ACM ER - TY - JOUR A1 - Ji, Hongchen A1 - Ragyanszki, Anita A1 - Fournier, Rene A. T1 - Machine learning estimation of reaction energy barriers JF - Computational and Theoretical Chemistry N2 - We describe a machine learning approach to approximate reaction energy barriers (E), requiring as input only estimates of geometry and energies of reactants and products. Using the dataset of Grambow, Pattanaik, and Green [Sci. Data 7 (1 3 7) (2020)] for reactions involving seven or fewer non-hydrogen atoms, 300 reaction features are computed, and an estimate of E is obtained by fitting a Kernel Ridge Regression (KRR) model with Laplacian kernel to a subset of Density Functional Theory reaction barriers. Our main interest is small energy barriers with the goal of modeling reactions in the interstellar medium and circumstellar envelope. We omitted reactions with E > 40 kcal mol−1 to obtain a subset of 5,276 reactions for 5-fold cross-validation. For this set, the KRR model predicts E with a mean absolute error of 4.13 kcal mol−1 and a root-mean square error of 6.02 kcal mol−1. Y1 - 2023 U6 - https://doi.org/10.1016/j.comptc.2023.114332 VL - 1229 SP - 114332 ER - TY - JOUR A1 - Juhasz, Anett A1 - Serra, Uneri Haymana A1 - Lakatos, Csilla A1 - Vadkerti, Bence A1 - Ragyanszki, Anita A1 - Farkas, Odon A1 - Keki, Sandor A1 - Nagy, Lajos T1 - The kinetics of uncatalyzed and catalyzed urethane forming reactions of aliphatic diisocyanates with butan-1-ol JF - New J. Chem. N2 - The kinetics of the urethane forming reactions of hexamethylene diisocyanate (HDI), 4,4′-dicyclohexyl-methane-diisocyanate (HMDI) and isophorone diisocyanate (IPDI) with butan-1-ol were systematically studied by electrospray ionization mass spectrometry (ESI-MS) in the off-line mode. The reactions were performed in toluene solution in the temperature range of 50–80 °C and perdeuterated butan-1-ol was used for quenching the reaction. The butan-1-ol was employed in high excess to diisocyanates to obtain pseudo first-order rate coefficients. For rendering the kinetics, a simple A → B → C consecutive model was applied and found to adequately describe the observed kinetic behaviors. The corresponding rate coefficients were determined and reactivities of the diisocyanates were found to decrease in the order HDI > IPDI > HMDI. Furthermore, it was observed that the second isocyanate group in HDI, due to the ring formation by intramolecular hydrogen bonds, reacted faster with butan-1-ol after the first isocyanate moiety had reacted. The formation of hydrogen bonding rings was also confirmed by DFT calculations. However, the reactivity of the second isocyanate moiety (after the first one has reacted) did not change significantly in the case of HMDI. From the temperature dependences the apparent activation parameters such as the pre-exponential factors and activation energies were determined. In addition, the reactions were also studied at 80 °C in the presence of tin(II)-2-ethylhexanoate at different concentrations and a mechanism was proposed for the catalytic process. Y1 - 2023 U6 - https://doi.org/10.1039/d3nj02747c VL - 47 SP - 16096 EP - 16107 ER - TY - JOUR A1 - Schintke, Florian A1 - De Mecquenem, Ninon A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity Constraints for Data Analysis Workflows JF - arXiv Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2305.08409 SP - 1 EP - 28 ER - TY - JOUR A1 - Gholami, Masoud A1 - Schintke, Florian T1 - CAWL: A Cache-aware Write Performance Model of Linux Systems JF - arXiv Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2306.05701 SP - 1 EP - 22 ER - TY - JOUR A1 - Clausecker, Robert A1 - Lemire, Daniel T1 - Transcoding unicode characters with AVX-512 instructions JF - Software: Practice and Experience N2 - Intel includes in its recent processors a powerful set of instructions capable of processing 512-bit registers with a single instruction (AVX-512). Some of these instructions have no equivalent in earlier instruction sets. We leverage these instructions to efficiently transcode strings between the most common formats: UTF-8 and UTF-16. With our novel algorithms, we are often twice as fast as the previous best solutions. For example, we transcode Chinese text from UTF-8 to UTF-16 at more than 5 GiB s−1 using fewer than 2 CPU instructions per character. To ensure reproducibility, we make our software freely available as an open-source library. Our library is part of the popular Node.js JavaScript runtime. Y1 - 2023 U6 - https://doi.org/10.1002/spe.3261 VL - 53 IS - 12 SP - 2430 EP - 2462 PB - John Wiley & Sons Ltd. 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 - 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 - CHAP A1 - Fürst, Steffen A1 - Rakow, Christian T1 - Parallelization of large-scale agent-based epidemiological simulations T2 - Proceedings of the 34th European Modeling & Simulation Symposium N2 - Agent-based epidemiological models have been applied widely successfully during the SARS-CoV-2 pandemic and assisted policymakers in assessing the effectiveness of intervention strategies. The computational complexity of agent-based models is still challenging, and therefore it is important to utilize modern multi-core systems as good as possible. In this paper, we are presenting our work on parallelizing the epidemiological simulation model MATSim Episim. Episim combines a large-scale person-centric human mobility model with a mechanistic model of infection and a person-centric disease progression model. In general, the parallelization of agent-based models with an inherent sequential structure — in the case of epidemiological models, the temporal order of the individual movements of the agents — is challenging. Especially when the underlying social network is irregular and dynamic, they require frequent communication between the processing elements. In Episim, however, we were able to take advantage of the fact that people are not contagious on the same day they become infected, and therefore immediate health synchronization is not required. By parallelizing some of the most computationally intensive submodels, we are now able to run MATSim Episim simulations up to eight times faster than the serial version. This makes it feasible to increase the number of agents, e.g. to run simulations for the whole of Germany instead of just Berlin as before. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.46354/i3m.2022.emss.008 ER - TY - CHAP A1 - Brook, Glenn A1 - Fuller, Douglas A1 - Swinburne, John A1 - Christgau, Steffen A1 - Läuter, Matthias A1 - Rodrigues Pelá, Ronaldo A1 - Lewin, Stein A1 - Christian, Tuma A1 - Steinke, Thomas T1 - An Early Scalability Study of Omni-Path Express N2 - This work provides a brief description of Omni-Path Express and the current status of its development, stability, and performance. Basic benchmarks that highlight the gains of OPX over PSM2 are provided, and the results of an initial performance and scalability study of several applications are presented. Y1 - 2022 UR - https://www.ixpug.org/events/isc22-ixpug-workshop U6 - https://doi.org/10.13140/RG.2.2.21353.57442 CY - Hamburg ER - TY - CHAP A1 - Lößer, Angar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis T2 - 2022 IEEE International Conference on Big Data, Posters Y1 - 2022 ER - TY - CHAP A1 - Bader, Jonathan A1 - Witzke, Joel A1 - Becker, Soeren A1 - Lößer, Ansgar A1 - Lehmann, Fabian A1 - Doehler, Leon A1 - Vu, Anh Duc A1 - Kao, Odej T1 - Towards Advanced Monitoring for Scientific Workflows T2 - 2022 IEEE International Conference on Big Data, 11th Workshop on Scalable Cloud Data Management Y1 - 2022 ER - TY - JOUR A1 - Lößer, Angar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis JF - arXiv Y1 - 2022 U6 - https://doi.org/10.48550/arXiv.2209.05358 SP - 1 EP - 20 ER - TY - GEN A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles N2 - Our theoretical study concerns an urea-urease-based pH oscillator confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the limit cycle, which controls the dynamics for giant vesicles and dominates the strongly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, amenable to analytic treatments, and show that the accuracy of predictions, including the period of oscillations, is highly sensitive to the choice of the reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The accurate description of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms. T3 - ZIB-Report - 22-21 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88179 SN - 1438-0064 ER - TY - CHAP A1 - Bürger, Johanna A1 - Gundlach, Bastian A1 - Blum, Jürgen A1 - Hayne, Paul A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Lunar regolith properties derived from LRO/Diviner data and thermophysical modelling T2 - Europlanet Science Congress N2 - The Moon as our nearest celestial object is one of the most important bodies for space resource exploration and planetary science. However, knowledge of the physical properties of the lunar regolith is required for the exploitation of lunar resources and for understanding the Moon's geologic history. This knowledge comes mainly from Apollo in-situ experiments and returned samples, but the global distribution of these properties is still poorly understood. Remote sensing measurements offer the opportunity to derive properties of unsampled areas with the help of models. In our study, a microphysical thermal model for the lunar regolith was developed and the simulated surface temperatures were compared with thermal emission measurements from the Diviner radiometer on board the Lunar Reconnaissance Orbiter (LRO) to derive regolith properties. This work expands upon previous investigations of lunar regolith properties using Diviner data, by more directly simulating physical properties such as particle size and porosity. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-92 SP - EPSC2022-92 ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - The near nucleus gas and dust environment around comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - The Rosetta mission to comet 67P/C-G provided a detailed view of the near nucleus environment of an active Jupiter family comet. The continuous monitoring of the gas pressure with the ROSINA experiment at the location of the Rosetta spacecraft in combination with the images of the dust environment acquired by the OSIRIS cameras allows one to test different hypotheses about the origin of the dust and gas emissions. In addition the orbital elements and the rotation axis and spin rate of the nucleus are affected by the gas release. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-281 SP - EPSC2022-281 ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Determination of the ice composition near the surface of comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - During the apparition of comet 67P/Churyumov-Gerasimenko (67P/C-G) solar irradiation causes varying rates for sublimation of volatile species from the cometary nucleus. Because sublimation processes take place close to the cometary surface, the relative abundance of volatiles in the coma and the ice composition are related to each other. To quantify this relation we assume a model for the expansion of a collisionless gas from the surface into the surrounding space. We use an inverse model approach to relate the in situ measurements of gas densities from the two Rosetta instruments COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) at the positions of the spacecraft to the locations of surface gas emissions during the Rosetta mission 2014-2016. We assume the temporally integrated gas emissions to be representative for the ice composition close to the surface. Our analysis shows characteristic differences in the ice compositions between both hemispheres of 67P/C-G. In particular CO2 ice has a reduced abundance on the northern hemisphere. In contrast to the hemispherical differences, the two lobes do not show significant differences in terms of their ice composition. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-826 SP - EPSC2022-826 ER - TY - CHAP A1 - Christgau, Steffen A1 - Knaust, Marius A1 - Steinke, Thomas T1 - A First Step towards Support for MPI Partitioned Communication on SYCL-programmed FPGAs T2 - IEEE/ACM International Workshop on Heterogeneous High-performance Reconfigurable Computing, H2RC@SC 2022, Dallas, TX, USA, November 13-18, 2022 N2 - Version 4.0 of the Message Passing Interface standard introduced the concept of Partitioned Communication which adds support for multiple contributions to a communication buffer. Although initially targeted at multithreaded MPI applications, Partitioned Communication currently receives attraction in the context of accelerators, especially GPUs. In this publication it is demonstrated that this communication concept can also be implemented for SYCL-programmed FPGAs. This includes a discussion of the design space and the presentation of a prototypical implementation. Experimental results show that a lightweight implementation on top of an existing MPI library is possible. In addition, the presented approach also reveals issues in both the SYCL and the MPI standard which need to be addresses for improved support of the intended communication style. Y1 - 2022 U6 - https://doi.org/10.1109/H2RC56700.2022.00007 SP - 9 EP - 17 PB - IEEE ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian T1 - Large-Scale Performance of the Data-Flow Scheduler (DFS) and FLESnet JF - CBM Progress Report 2021 Y1 - 2022 U6 - https://doi.org/10.15120/GSI-2022-00599 SP - 170 EP - 171 ER - TY - JOUR A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - Ehrenfest dynamics implemented in the all-electron package exciting JF - Electron. Struct. N2 - Ehrenfest dynamics combined with real-time time-dependent density functional theory has proven to be a reliable tool to study non-adiabatic molecular dynamics with a reasonable computational cost. Among other possibilities, it allows for assessing in real time electronic excitations generated by ultra-fast laser pulses, as e.g., in pump–probe spectroscopy, and their coupling to the nuclear vibrations even beyond the linear regime. In this work, we present its implementation in the all-electron full-potential package exciting. Three cases are presented as examples: diamond and cubic boron nitride (BN) relaxed after an initial lattice distortion, and cubic BN exposed to a laser pulse. Comparison with the Octopus code exhibits good agreement. Y1 - 2022 U6 - https://doi.org/10.1088/2516-1075/ac7afc VL - 4 SP - 037001 ER - TY - JOUR A1 - Gholami, Masoud A1 - Schintke, Florian T1 - IOSIG: Declarative I/O-Stream Properties Using Pragmas JF - Datenbank-Spektrum Y1 - 2022 U6 - https://doi.org/10.1007/s13222-022-00419-w VL - 22 IS - 2 SP - 109 EP - 119 PB - Springer Berlin Heidelberg ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Modelling the inner coma of comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - Based on about 1 million of pressure measurements around comet 67P/Churyumov-Gerasimenko we reconstruct the gas emission across the entire nucleus. Dust particles are seeded in the gas model and the resulting dust distribution follows a daily pattern which agrees with observations if a uniform dust release across the entire sunlit surface is assumed. Y1 - 2018 VL - 12 SP - EPSC2018-115-1 PB - Europlanet Science Congress ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Gas production of comet 67P/Churyumov-Gerasimenko reconstructed from DFMS/COPS data T2 - Europlanet Science Congress N2 - We reconstruct the temporal evolution of surface emissions for the four major gas species H2O, CO2, CO, and O2 emitted during the 2015 apparition of comet 67P/Churyumov-Gerasimenko (67P/C-G). Measurements from the Double Focusing Mass Spectrometer (DFMS) of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the COmet Pressure Sensor (COPS) are used to determine the gas sources on the surface with an inverse gas model for the entire coma. For all species, peak production rates and integrated production rates per orbit are evaluated separately for the northern and the southern hemisphere. Complemented with the total mass production, this allows us to estimate the dust-to-gas ratio of the emitted material. Y1 - 2018 VL - 12 SP - EPSC2018-515-1 PB - Europlanet Science Congress ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Matching the activity of comet 67P/Churyumov-Gerasimenko with long-term ground-based astrometry T2 - Europlanet Science Congress N2 - 50 years of astrometric data for comet 67P/C-G (orbital period about 6.45 years) provides a unique opportunity to benchmark non-gravitational acceleration models to the in situ measurements of the volatile release performed from the Rosetta rendezvous mission (2014-2016). Taken together, the Earth-bound and in-situ data yields lower fit errors and serves as a test-case for our ability to deduce thermophysical quantities of cometary nuclei from the Earth-bound observations. Y1 - 2021 U6 - https://doi.org/10.5194/epsc2021-337 VL - 15 SP - EPSC2021-337 PB - Europlanet Science Congress ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - The ice composition close to the surface of comet 67P/Churyumov-Gerasimenko JF - ACS Earth and Space Chemistry N2 - The relation between ice composition in the nucleus of comet 67P/Churyumov-Gerasimenko on the one hand and relative abundances of volatiles in the coma on the other hand is important for the interpretation of density measurements in the environment of the cometary nucleus. For the 2015 apparition, in situ measurements from the two ROSINA (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) sensors COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) determined gas densities at the spacecraft position for the 14 gas species H2O, CO2, CO, H2S, O2, C2H6, CH3OH, H2CO, CH4, NH3, HCN, C2H5OH, OCS, and CS2. We derive the spatial distribution of the gas emissions on the complex shape of the nucleus separately for 50 subintervals of the two-year mission time. The most active patches of gas emission are identified on the surface. We retrieve the relation between solar irradiation and observed emissions from these patches. The emission rates are compared to a minimal thermophysical model to infer the surface active fraction of H2O and CO2. We obtain characteristic differences in the ice composition close to the surface between the two hemispheres with a reduced abundance of CO2 ice on the northern hemisphere (locations with positive latitude). We do not see significant differences for the ice composition on the two lobes of 67P/C-G. Y1 - 2022 U6 - https://doi.org/10.1021/acsearthspacechem.1c00378 VL - 6 IS - 5 SP - 1189 EP - 1203 ER - TY - CHAP A1 - Knaust, Marius A1 - Seiler, Enrico A1 - Reinert, Knut A1 - Steinke, Thomas T1 - Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA T2 - FPGA '22: Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays N2 - Next-Generation Sequencing technologies generate a vast and exponentially increasing amount of sequence data. The Interleaved Bloom Filter (IBF) is a novel indexing data structure which is state-of-the-art for distributing approximate queries with an in-memory data structure. With it, a main task of sequence analysis pipelines, (approximately) searching large reference data sets for sequencing reads or short sequence patterns like genes, can be significantly accelerated. To meet performance and energy-efficiency requirements, we chose a co-design approach of the IBF data structure on the FPGA platform. Further, our OpenCL-based implementation allows a seamless integration into the widely used SeqAn C++ library for biological sequence analysis. Our algorithmic design and optimization strategy takes advantage of FPGA-specific features like shift register and the parallelization potential of many bitwise operations. We designed a well-chosen schema to partition data across the different memory domains on the FPGA platform using the Shared Virtual Memory concept. We can demonstrate significant improvements in energy efficiency of up to 19x and in performance of up to 5.6x, respectively, compared to a well-tuned, multithreaded CPU reference. Y1 - 2022 U6 - https://doi.org/10.1145/3490422.3502366 SP - 180 EP - 189 ER - TY - JOUR A1 - Mokhtari, Zahra A1 - Patterson, Robert I. A. A1 - Höfling, Felix T1 - Spontaneous trail formation in populations of auto-chemotactic walkers JF - New Journal of Physics Y1 - 2022 U6 - https://doi.org/10.1088/1367-2630/ac43ec VL - 24 SP - 013012 ER - TY - JOUR A1 - Gholami, Abbas A1 - Höfling, Felix A1 - Klein, Rupert A1 - Delle Site, Luigi T1 - Thermodynamic relations at the coupling boundary in adaptive resolution simulations for open systems JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000303 VL - 4 SP - 2000303 ER - TY - JOUR A1 - Klein, Rupert A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix A1 - Delle Site, Luigi T1 - Nonequilibrium induced by reservoirs: Physico-mathematical model and numerical tests JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202100071 VL - 4 SP - 2100071 ER - TY - JOUR A1 - Pathania, Yogyata A1 - Chakraborty, Dipanjan A1 - Höfling, Felix T1 - Continuous demixing transition of binary liquids: finite-size scaling from the analysis of sub-systems JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000235 VL - 4 SP - 2000235 ER - TY - JOUR A1 - Frömberg, Daniela A1 - Höfling, Felix T1 - Generalized master equation for first-passage problems in partitioned spaces JF - Journal of Physics A: Mathematical and Theoretical Y1 - 2021 U6 - https://doi.org/10.1088/1751-8121/abf2ec VL - 54 SP - 215601 ER - TY - GEN A1 - Lemke, Mathias A1 - Stein, Lewin A1 - Hölter, Arne A1 - Weinzierl, Stefan T1 - Adjungierten-basierte Synthese und Bestimmung optimaler Treiberfunktionen von Lautsprechern mit komplexer Richtcharakteristik N2 - Die Bestimmung optimaler Treiberfunktionen von Lautsprechern mit frequenzabhängiger Richtcharakteristik ist ein schlecht gestelltes Optimierungsproblem. Zu dessen Lösung haben die Autoren in vorangegangenen Beiträgen eine adjungierten-basierte Methode zur Optimierung von Lautsprecher-Arrays im Zeitbereich vorgestellt [5, 6, 8]. Diese ermöglicht unter anderem die Berücksichtigung von Berandungen und Umgebungseffekten wie Wind, war jedoch bisher auf monopol-artige Quellen beschränkt. Um diese Einschränkung zu beheben, haben die Autoren einen adjungierten-basierten Zeitbereichsansatz mit Finiten-Differenzen (FDTD) zur Synthese komplexer synthetischer Schallquellen durch diskrete, gitter-basierte Monopole vorgestellt [4, 9]. In diesem Beitrag demonstrieren die Autoren die entsprechende Modellierung eines realen Zweiwege-Monitors (A). Zudem wird gezeigt, wie sich die Vielzahl der zur Synthese verwendeten Monopole in eine Lautsprecher-Treiberfunktion überführen lassen (B). Y1 - 2021 SN - 978-3-939296-18-8 U6 - https://doi.org/https://doi.org/10.14279/depositonce-12515 PB - Deutsche Gesellschaft für Akustik e.V. ER - TY - JOUR A1 - Leser, Ulf A1 - Hilbrich, Marcus A1 - Draxl, Claudia A1 - Eisert, Peter A1 - Grunske, Lars A1 - Hostert, Patrick A1 - Kainmüller, Dagmar A1 - Kao, Odej A1 - Kehr, Birte A1 - Kehrer, Timo A1 - Koch, Christoph A1 - Markl, Volker A1 - Meyerhenke, Henning A1 - Rabl, Tilmann A1 - Reinefeld, Alexander A1 - Reinert, Knut A1 - Ritter, Kerstin A1 - Scheuermann, Björn A1 - Schintke, Florian A1 - Schweikardt, Nicole A1 - Weidlich, Matthias T1 - The Collaborative Research Center FONDA JF - Datenbank-Spektrum Y1 - 2021 U6 - https://doi.org/10.1007/s13222-021-00397-5 VL - 21 IS - 3 SP - 255 EP - 260 ER - TY - GEN A1 - Mokhtari, Zahra A1 - Patterson, Robert I. A. A1 - Höfling, Felix T1 - Spontaneous trail formation in populations of auto-chemotactic walkers N2 - We study the formation of trails in populations of self-propelled agents that make oriented deposits of pheromones and also sense such deposits to which they then respond with gradual changes of their direction of motion. Based on extensive off-lattice computer simulations aiming at the scale of insects, e.g., ants, we identify a number of emerging stationary patterns and obtain qualitatively the non-equilibrium \add{state} diagram of the model, spanned by the strength of the agent--pheromone interaction and the number density of the population. In particular, we demonstrate the spontaneous formation of persistent, macroscopic trails, and highlight some behaviour that is consistent with a dynamic phase transition. This includes a characterisation of the mass of system-spanning trails as a potential order parameter. We also propose a dynamic model for a few macroscopic observables, including the sub-population size of trail-following agents, which captures the early phase of trail formation. T3 - ZIB-Report - 21-36 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84466 SN - 1438-0064 ER - TY - JOUR A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - Höfling, Felix T1 - Stochastic pH oscillations in a model of the urea–urease reaction confined to lipid vesicles JF - J. Phys. Chem. Lett. N2 - The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We numerically study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the recovery of the pH level and yielding a constant supply of urea molecules. For microscopically small vesicles, the discreteness of the number of molecules requires a stochastic treatment of the reaction dynamics. Our analysis shows that intrinsic noise induces a significant statistical variation of the oscillation period, which increases as the vesicles become smaller. The mean period, however, is found to be remarkably robust for vesicle sizes down to approximately 200 nm, but the periodicity of the rhythm is gradually destroyed for smaller vesicles. The observed oscillations are explained as a canard-like limit cycle that differs from the wide class of conventional feedback oscillators. Y1 - 2021 U6 - https://doi.org/10.1021/acs.jpclett.1c03016 VL - 12 SP - 9888 EP - 9893 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 - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert T1 - CleanMaple T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 SP - 24 ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert T1 - CleanMaple_PriPro, CaDiCaL_PriPro and CaDiCaL_PriPro_no_bin T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 N1 - CaDiCaL_PriPro won the Special Innovation Price at the SAT Competition 2021 SP - 25 ER - TY - CHAP A1 - Baumann, Tobias A1 - Noack, Matthias A1 - Steinke, Thomas T1 - Performance Evaluation and Improvements of the PoCL Open-Source OpenCL Implementation on Intel CPUs T2 - IWOCL'21: International Workshop on OpenCL N2 - The Portable Computing Language (PoCL) is a vendor independent open-source OpenCL implementation that aims to support a variety of compute devices in a single platform. Evaluating PoCL versus the Intel OpenCL implementation reveals significant performance drawbacks of PoCL on Intel CPUs – which run 92 % of the TOP500 list. Using a selection of benchmarks, we identify and analyse performance issues in PoCL with a focus on scheduling and vectorisation. We propose a new CPU device-driver based on Intel Threading Building Blocks (TBB), and evaluate LLVM with respect to automatic compiler vectorisation across work-items in PoCL. Using the TBB driver, it is possible to narrow the gap to Intel OpenCL and even outperform it by a factor of up to 1.3× in our proxy application benchmark with a manual vectorisation strategy. Y1 - 2021 U6 - https://doi.org/10.1145/3456669.3456698 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 - Salem, Farouk A1 - Schintke, Florian T1 - Load balancing mechanism for FLESnet JF - CBM Progress Report 2020 Y1 - 2021 U6 - https://doi.org/10.15120/GSI-2021-00421 SP - 156 EP - 157 ER - TY - CHAP A1 - Thostrup, Lasse A1 - Skrzypczak, Jan A1 - Jasny, Matthias A1 - Ziegler, Tobias A1 - Binnig, Carsten T1 - DFI: The Data Flow Interface for High-Speed Networks T2 - SIGMOD '21: International Conference on Management of Data Y1 - 2021 U6 - https://doi.org/10.1145/3448016.3452816 SP - 1825 EP - 1837 PB - ACM ER - TY - CHAP A1 - Gholami, Masoud A1 - Schintke, Florian T1 - Combining XOR and Partner Checkpointing for Resilient Multilevel Checkpoint/Restart T2 - 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS) Y1 - 2021 U6 - https://doi.org/10.1109/IPDPS49936.2021.00036 SP - 277 EP - 288 ER - TY - JOUR A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix A1 - Klein, Rupert A1 - Delle Site, Luigi T1 - Theory and simulation of open systems out of equilibrium JF - The Journal of Chemical Physics N2 - We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations. Y1 - 2020 U6 - https://doi.org/10.1063/5.0014065 VL - 153 SP - 101102 ER -