@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} } @article{StraubeHoefling2024, author = {Straube, Arthur and H{\"o}fling, Felix}, title = {Memory effects in colloidal motion under confinement and driving}, volume = {57}, journal = {J. Phys. A: Math. Theor.}, publisher = {IOP Publishing}, issn = {1751-8113}, doi = {10.1088/1751-8121/ad5b2d}, pages = {295003}, year = {2024}, abstract = {The transport of individual particles in inhomogeneous environments is complex and exhibits non-Markovian responses. The latter may be quantified by a memory function within the framework of the linear generalised Langevin equation (GLE). Here, we exemplify the implications of steady driving on the memory function of a colloidal model system for Brownian motion in a corrugated potential landscape, specifically, for one-dimensional motion in a sinusoidal potential. To this end, we consider the overdamped limit of the GLE, which is facilitated by separating the memory function into a singular (Markovian) and a regular (non-Markovian) part. Relying on exact solutions for the investigated model, we show that the random force entering the GLE must display a bias far from equilibrium, which corroborates a recent general prediction. Based on data for the mean-square displacement (MSD) obtained from Brownian dynamics simulations, we estimate the memory function for different driving strengths and show that already moderate driving accelerates the decay of the memory function by several orders of magnitude in time. We find that the memory may persist on much longer timescales than expected from the convergence of the MSD to its long-time asymptote. Furthermore, the functional form of the memory function changes from a monotonic decay to a non-monotonic, damped oscillatory behaviour, which can be understood from a competition of confined motion and depinning. Our analysis of the simulation data further reveals a pronounced non-Gaussianity, which questions the Gaussian approximation of the random force entering the GLE.}, 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{RoyHoefling2024, author = {Roy, Sutapa and H{\"o}fling, Felix}, title = {Critical surface adsorption of confined binary liquids with locally conserved mass and composition}, volume = {122}, journal = {Molecular Physics}, number = {21-22}, doi = {10.1080/00268976.2024.2391998}, pages = {e2391998}, year = {2024}, abstract = {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.}, 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} } @article{StraubeHoefling2024, author = {Straube, Arthur and H{\"o}fling, Felix}, title = {Depinning transition of self-propelled particles}, volume = {110}, journal = {Physical Review E}, number = {6}, arxiv = {http://arxiv.org/abs/2306.09150}, doi = {10.1103/PhysRevE.110.L062601}, pages = {L062601}, year = {2024}, abstract = {For self-propelled particles in a corrugated potential landscape, we describe a discontinuous change of the classical depinning transition and a host of unique behaviors sensitive to the persistence of the propulsion direction. Exact and semianalytic results for active Brownian particles corroborate a creep regime with a superexponentially suppressed drift velocity upon lowering the force towards the threshold value. This unusual nonlinear response emerges from the competition of two critical scaling laws with exponents of 1/2 for rapidly reorienting particles and 𝑑/2 for particles with a persistent orientation; the latter case depends on the dimensionality 𝑑 of rotational motion and also includes run-and-tumble particles. Additionally, different giant diffusion phenomena occur in the two regimes. Our findings extend to random dynamics with bounded noise near a saddle-node bifurcation and have potential applications in various nonequilibrium problems, including arrested active matter and cell migration.}, language = {en} } @article{StraubeOliconMendezWinkelmannetal.2025, author = {Straube, Arthur and Olic{\´o}n M{\´e}ndez, Guillermo and Winkelmann, Stefanie and H{\"o}fling, Felix and Engel, Maximilian}, title = {Unfolding the geometric structure and multiple timescales of the urea-urease pH oscillator}, arxiv = {http://arxiv.org/abs/2508.07275}, year = {2025}, abstract = {We study a two-variable dynamical system modeling pH oscillations in the urea-urease reaction within giant lipid vesicles - a problem that intrinsically contains multiple, well-separated timescales. Building on an existing, deterministic formulation via ordinary differential equations, we resolve different orders of magnitude within a small parameter and analyze the system's limit cycle behavior using geometric singular perturbation theory (GSPT). By introducing two different coordinate scalings - each valid in a distinct region of the phase space - we resolve the local dynamics near critical fold points, using the extension of GSPT through such singular points due to Krupa and Szmolyan. This framework enables a geometric decomposition of the periodic orbits into slow and fast segments and yields closed-form estimates for the period of oscillation. In particular, we link the existence of such oscillations to an underlying biochemical asymmetry, namely, the differential transport across the vesicle membrane.}, language = {en} } @article{delRazoFroembergStraubeetal.2022, author = {del Razo, Mauricio and Fr{\"o}mberg, Daniela and Straube, Arthur and Sch{\"u}tte, Christof and H{\"o}fling, Felix and Winkelmann, Stefanie}, title = {A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations}, volume = {112}, journal = {Letters in Mathematical Physics}, number = {49}, arxiv = {http://arxiv.org/abs/arXiv:2109.13616}, doi = {10.1007/s11005-022-01539-w}, year = {2022}, language = {en} } @article{StraubeWinkelmannSchuetteetal.2021, author = {Straube, Arthur and Winkelmann, Stefanie and Sch{\"u}tte, Christof and H{\"o}fling, Felix}, title = {Stochastic pH oscillations in a model of the urea-urease reaction confined to lipid vesicles}, volume = {12}, journal = {J. Phys. Chem. Lett.}, doi = {10.1021/acs.jpclett.1c03016}, pages = {9888 -- 9893}, year = {2021}, abstract = {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.}, language = {en} }