@article{DelleSiteKrekelerWhittakeretal.2019, author = {Delle Site, Luigi and Krekeler, Christian and Whittaker, John and Agarwal, Animesh and Klein, Rupert and H{\"o}fling, Felix}, title = {Molecular Dynamics of Open Systems: Construction of a Mean-Field Particle Reservoir}, volume = {2}, journal = {Advanced Theory and Simulations}, arxiv = {http://arxiv.org/abs/1902.07067}, doi = {10.1002/adts.201900014}, pages = {1900014}, year = {2019}, abstract = {The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed.}, language = {en} } @article{DibakFroehnerNoeetal.2019, author = {Dibak, Manuel and Fr{\"o}hner, Christoph and No{\´e}, Frank and H{\"o}fling, Felix}, title = {Diffusion-influenced reaction rates in the presence of pair interactions}, volume = {151}, journal = {The Journal of Chemical Physics}, arxiv = {http://arxiv.org/abs/1908.07764}, doi = {10.1063/1.5124728}, pages = {164105}, year = {2019}, abstract = {The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi's volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction-diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction-diffusion equation in the steady state and derive semi- analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions.}, language = {en} } @article{StraubeKowalikNetzetal.2020, author = {Straube, Arthur and Kowalik, Bartosz G. and Netz, Roland R. and H{\"o}fling, Felix}, title = {Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures}, volume = {3}, journal = {Commun. Phys.}, publisher = {Nature}, doi = {10.1038/s42005-020-0389-0}, pages = {126}, year = {2020}, abstract = {Friction in liquids arises from conservative forces between molecules and atoms. Although the hydrodynamics at the nanoscale is subject of intense research and despite the enormous interest in the non-Markovian dynamics of single molecules and solutes, the onset of friction from the atomistic scale so far could not be demonstrated. Here, we fill this gap based on frequency-resolved friction data from high-precision simulations of three prototypical liquids, including water. Combining with theory, we show that friction in liquids emerges abruptly at a characteristic frequency, beyond which viscous liquids appear as non-dissipative, elastic solids. Concomitantly, the molecules experience Brownian forces that display persistent correlations. A critical test of the generalised Stokes-Einstein relation, mapping the friction of single molecules to the visco-elastic response of the macroscopic sample, disproves the relation for Newtonian fluids, but substantiates it exemplarily for water and a moderately supercooled liquid. The employed approach is suitable to yield insights into vitrification mechanisms and the intriguing mechanical properties of soft materials.}, language = {en} } @misc{MokhtariPattersonHoefling2021, author = {Mokhtari, Zahra and Patterson, Robert I. A. and H{\"o}fling, Felix}, title = {Spontaneous trail formation in populations of auto-chemotactic walkers}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-84466}, year = {2021}, abstract = {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.}, language = {en} } @article{PathaniaChakrabortyHoefling2021, author = {Pathania, Yogyata and Chakraborty, Dipanjan and H{\"o}fling, Felix}, title = {Continuous demixing transition of binary liquids: finite-size scaling from the analysis of sub-systems}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202000235}, pages = {2000235}, year = {2021}, language = {en} } @article{FroembergHoefling2021, author = {Fr{\"o}mberg, Daniela and H{\"o}fling, Felix}, title = {Generalized master equation for first-passage problems in partitioned spaces}, volume = {54}, journal = {Journal of Physics A: Mathematical and Theoretical}, doi = {10.1088/1751-8121/abf2ec}, pages = {215601}, year = {2021}, language = {en} } @article{KleinEbrahimiViandHoeflingetal.2021, author = {Klein, Rupert and Ebrahimi Viand, Roya and H{\"o}fling, Felix and Delle Site, Luigi}, title = {Nonequilibrium induced by reservoirs: Physico-mathematical model and numerical tests}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202100071}, pages = {2100071}, year = {2021}, language = {en} } @article{GholamiHoeflingKleinetal.2021, author = {Gholami, Abbas and H{\"o}fling, Felix and Klein, Rupert and Delle Site, Luigi}, title = {Thermodynamic relations at the coupling boundary in adaptive resolution simulations for open systems}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202000303}, pages = {2000303}, year = {2021}, language = {en} } @article{MokhtariPattersonHoefling2022, author = {Mokhtari, Zahra and Patterson, Robert I. A. and H{\"o}fling, Felix}, title = {Spontaneous trail formation in populations of auto-chemotactic walkers}, volume = {24}, journal = {New Journal of Physics}, doi = {10.1088/1367-2630/ac43ec}, pages = {013012}, year = {2022}, language = {en} } @article{HoeflingDietrich2024, author = {H{\"o}fling, Felix and Dietrich, Siegfried}, title = {Structure of liquid-vapor interfaces: perspectives from liquid state theory, large-scale simulations, and potential grazing-incidence X-ray diffraction}, volume = {160}, journal = {The Journal of Chemical Physics}, arxiv = {http://arxiv.org/abs/2311.06425}, doi = {10.1063/5.0186955}, pages = {104107}, year = {2024}, abstract = {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.}, language = {en} } @inproceedings{SkoblinHoeflingChristgau2023, author = {Skoblin, Viktor and H{\"o}fling, Felix and Christgau, Steffen}, title = {Gaining Cross-Platform Parallelism for HAL's Molecular Dynamics Package using SYCL}, volume = {36}, booktitle = {29. PARS-Workshop 2023}, issn = {0177-0454}, arxiv = {http://arxiv.org/abs/2406.04210}, year = {2023}, abstract = {Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of HAL's MD package that has been successfully migrated from CUDA to SYCL. We describe the different strategies that we followed in the process of porting the code. Following these strategies, we achieved code portability across major GPU vendors. Depending on the actual kernels, both significant performance improvements and regressions are observed. As a side effect of the migration process, we obtained impressing speedups also for execution on CPUs.}, language = {en} }