@article{CharronMusilGuljasetal.2025, author = {Charron, Nicholas and Musil, F{\´e}lix and Guljas, Andrea and Chen, Yaoyi and Bonneau, Klara and Pasos-Trejo, Aldo and Jacopo, Venturin and Daria, Gusew and Zaporozhets, Iryna and Kr{\"a}mer, Andreas and Templeton, Clark and Atharva, Kelkar and Durumeric, Aleksander and Olsson, Simon and P{\´e}rez, Adri{\`a} and Majewski, Maciej and Husic, Brooke and Patel, Ankit and De Fabritiis, Gianni and No{\´e}, Frank and Clementi, Cecilia}, title = {Navigating protein landscapes with a machine-learned transferable coarse-grained model}, volume = {17}, journal = {Nature Chemistry}, arxiv = {http://arxiv.org/abs/2310.18278}, doi = {10.1038/s41557-025-01874-0}, pages = {1284 -- 1292}, year = {2025}, abstract = {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.}, language = {en} } @article{KrishnadasCharronFournier2025, author = {Krishnadas, Anirudh and Charron, Nicolas and Fournier, Rene}, title = {Melting Transitions in Small Aluminum Clusters Simulated with Energies Approaching DFT Accuracy.}, journal = {ACS Publications- Journal of Chemical Theory and Computation}, year = {2025}, abstract = {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.}, language = {en} } @article{KrishnadasMoshiQuintanaetal.2025, author = {Krishnadas, Anirudh and Moshi, Maryam and Quintana, Ramon Alain Miranda and Fournier, Rene}, title = {Geometric Features and a Neural Network Classifier for Detecting Melting-Like Transitions in Clusters.}, journal = {AIP Publications - The Journal of Chemical Physics}, year = {2025}, abstract = {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 ).}, language = {en} } @article{ClauseckerLemireSchintke2025, author = {Clausecker, Robert and Lemire, Daniel and Schintke, Florian}, title = {Faster Positional-Population Counts for AVX2, AVX-512, and ASIMD}, volume = {37}, journal = {Concurrency and Computation: Practice and Experience}, number = {27-28}, publisher = {Wiley}, issn = {1532-0626}, doi = {10.1002/cpe.70435}, year = {2025}, language = {en} } @article{HoelterLemkeWeinzierletal.2025, author = {H{\"o}lter, Arne and Lemke, Mathias and Weinzierl, Stefan and Stein, Lewin}, title = {Non-Reflecting Characteristic Boundary Conditions for Adjoint Time-Domain Acoustic Simulations}, journal = {Journal of Theoretical and Computational Acoustics}, year = {2025}, abstract = {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.}, language = {en} } @article{HoeflingStraube2025, author = {H{\"o}fling, Felix and Straube, Arthur}, title = {Langevin equations and a geometric integration scheme for the overdamped limit of rotational Brownian motion of axisymmetric particles}, volume = {7}, journal = {Physical Review Research}, arxiv = {http://arxiv.org/abs/2403.04501}, doi = {10.1103/wzdn-29p4}, pages = {043034}, year = {2025}, abstract = {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.}, language = {en} } @article{MarcelliBottinelliMontandonEbrahimiViandetal.2025, author = {Marcelli, Giorgia and Bottinelli Montandon, Tecla and Ebrahimi Viand, Roya and H{\"o}fling, Felix}, title = {Fluid flow inside slit-shaped nanopores: the role of surface morphology at the molecular scale}, volume = {162}, journal = {The Journal of Chemical Physics}, arxiv = {http://arxiv.org/abs/2411.04882}, doi = {10.1063/5.0246573}, pages = {104101}, year = {2025}, abstract = {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.}, language = {en} } @article{ZhongHoeflingJohn2025, author = {Zhong, Xin and H{\"o}fling, Felix and John, Timm}, title = {Hydrogen diffusion in garnet: insights from atomistic simulations}, volume = {26}, journal = {Geochemistry Geophysics Geosystems}, arxiv = {http://arxiv.org/abs/2410.07724}, doi = {10.1029/2024GC011951}, pages = {e2024GC011951}, year = {2025}, abstract = {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.}, language = {en} } @inproceedings{ChristgauDylanLuebkeetal.2025, author = {Christgau, Steffen and Dylan, Everingham and L{\"u}bke, Max and De Lucia, Marco and Puhan, Danny and Schelten, Niklas and Schnor, Bettina and Signer, Hannes and Spazier, Johannes and Stabernack, Benno and Steinert, Fritjof and Yahdzhyiev, Serhii}, title = {On the Usability and Energy Efficiency of High-Level Synthesis for FPGA-based Network-Attached Accelerators}, booktitle = {2025 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)}, doi = {10.1109/IPDPSW66978.2025.00139}, pages = {886 -- 895}, year = {2025}, abstract = {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.}, language = {en} } @article{LaeuterKramer2025, author = {L{\"a}uter, Matthias and Kramer, Tobias}, title = {Rotation dynamics and torque efficiency of cometary nuclei}, volume = {699}, journal = {Astronomy \& Astrophysics}, arxiv = {http://arxiv.org/abs/2507.06036}, doi = {10.1051/0004-6361/202553845}, pages = {A75}, year = {2025}, abstract = {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.}, language = {en} } @misc{elBahnasawy2025, type = {Master Thesis}, author = {el Bahnasawy, Henry}, title = {Konzeption und Entwicklung einer Plattform zur geographisch verteilten Bereitstellung von latenzkritischen Anwendungen}, pages = {102}, year = {2025}, language = {de} } @article{RossiQiaoDykstraetal.2025, author = {Rossi, Thomas and Qiao, Lu and Dykstra, Conner P. and Rodrigues Pel{\´a}, Ronaldo and Gnewkow, Richard and Wallick, Rachel F. and Burke, John H. and Nicholas, Erin and March, Anne-Marie and Doumy, Gilles and Buchholz, D. Bruce and Deparis, Christiane and Zu{\~n}iga-P{\´e}rez, Jesus and Weise, Michael and Ellmer, Klaus and Fondell, Mattis and Draxl, Claudia and van der Veen, Renske}, title = {Dynamic control of X-ray core-exciton resonances by Coulomb screening in photoexcited semiconductors}, volume = {6}, journal = {Communications Materials}, arxiv = {http://arxiv.org/abs/2412.01945}, doi = {10.1038/s43246-025-00909-w}, pages = {191}, year = {2025}, language = {en} } @article{HawthorneRaulinoRodriguesPelaetal.2025, author = {Hawthorne, Felipe and Raulino, Paulo R. E. and Rodrigues Pel{\´a}, Ronaldo and Woellner, Cristiano F.}, title = {Efficient and Accurate Machine Learning Interatomic Potential for Graphene: Capturing Stress-Strain and Vibrational Properties}, volume = {129}, journal = {The Journal of Physical Chemistry C}, arxiv = {http://arxiv.org/abs/2505.12140}, doi = {10.1021/acs.jpcc.5c03470}, pages = {16319 -- 16326}, year = {2025}, language = {en} } @inproceedings{LoesserWitzkeSchintkeetal.2025, author = {L{\"o}ßer, Ansgar and Witzke, Joel and Schintke, Florian and Scheuermann, Bj{\"o}rn}, title = {BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis}, booktitle = {Proceedings of the 16th ACM/SPEC International Conference on Performance Engineering (ICPE 2025)}, publisher = {Association for Computing Machinery}, doi = {10.1145/3676151.3719382}, url = {http://nbn-resolving.de/https://doi.org/10.1145/3676151.3719382}, pages = {11 -- 18}, year = {2025}, language = {en} } @article{GroussinJordaAttreeetal.2025, author = {Groussin, Olivier and Jorda, L. and Attree, N. and Birch, S.P.D. and B{\"u}rger, Johanna and Guti{\´e}rrez, Pedro and Jindal, Abhinav S. and Keller, H.U. and Kramer, Tobias and Lasagni Manghi, Riccardo and L{\"a}uter, Matthias and Markkanen, J. and Marschall, R. and Schuckart, C.}, title = {Thermal environment and erosion of comet 67P/Churyumov-Gerasimenko}, volume = {694}, journal = {Astronomy and Astrophysics}, doi = {10.1051/0004-6361/202452260}, pages = {A21}, year = {2025}, abstract = {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.}, language = {en} } @inproceedings{LoesserSchlechtSchintkeetal.2025, author = {L{\"o}ßer, Ansgar and Schlecht, Max and Schintke, Florian and Witzke, Joel and Weidlich, Matthias and Scheuermann, Bj{\"o}rn}, title = {Fast Min-ϵ Segmented Regression using Constant-Time Segment Merging}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, pages = {40312 -- 40327}, year = {2025}, language = {en} } @article{AgarwalGreveReinefeldetal.2025, author = {Agarwal, A. and Greve, Nico and Reinefeld, Alexander and Schintke, Florian and et al.,}, title = {Performance of the prototype Silicon Tracking System of the CBM experiment tested with heavy-ion beams at SIS18}, volume = {1082}, journal = {Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment}, publisher = {Elsevier BV}, issn = {0168-9002}, arxiv = {http://arxiv.org/abs/2505.20517}, doi = {10.1016/j.nima.2025.171059}, pages = {171059}, year = {2025}, language = {en} } @article{JiAnitaFournier2025, author = {Ji, Hongchen and Anita, Ragyanszki and Fournier, Rene}, title = {Computational Study of the Reactions of CH2 with HCNO and HNCO}, volume = {103}, journal = {Canadian Journal of Chemistry}, number = {7}, doi = {10.1139/cjc-2024-0203}, pages = {386 -- 395}, year = {2025}, abstract = {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.}, language = {en} } @misc{RamakiSchintke2025, author = {Ramaki, Niaz Mohammad and Schintke, Florian}, title = {Ensuring Reproducibility in Stream Processing with Blockchain Technologies}, journal = {2025 11th International Conference on Computer and Communications (ICCC)}, publisher = {IEEE}, doi = {10.1109/ICCC68654.2025.11437772}, pages = {1383 -- 1391}, year = {2025}, language = {en} }