Adaptive Brownian Dynamics

Sammüller, Florian; Schmidt, Matthias

doi:10.1063/5.0062396

Cited by 22 publications

(19 citation statements)

References 78 publications

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“…In the Brownian dynamics regime, momentum is not conserved 72 ; particles comprising the system feel a random force and a drag force, or friction, relative to a constant background (eq. ( 21 )), and thus their motions become Brownian 72 , 74 .…”

Section: Methodsmentioning

confidence: 99%

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

2023

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Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.

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Section: Methodsmentioning

confidence: 99%

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

2023

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“…We choose a fixed timestep ∆t. (See [64] for adaptive Brownian dynamics for soft potentials.) At the beginning of a simulation step, the particle velocities are randomised according to the Maxwell distribution.…”

Section: Brownian Dynamicsmentioning

confidence: 99%

Dynamic decay and superadiabatic forces in the van Hove dynamics of bulk hard sphere fluids

2022

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We study the dynamical decay of the van Hove function of Brownian hard spheres using event-driven Brownian dynamics simulations and dynamic test particle theory. Relevant decays mechanisms include deconfinement of the self particle, decay of correlation shells, and shell drift. Comparison to results for the Lennard-Jones system indicates the generality of these mechanisms for dense overdamped liquids. We use dynamical density functional theory on the basis of the Rosenfeld functional with self interaction correction. Superadiabatic forces are analysed using a recent power functional approximation. The power functional yields a modified Einstein long-time self diffusion coefficient in good agreement with simulation data.

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“…Several fast simulation algorithms have been developed in the past to tackle the hard-sphere interactions in Brownian dynamics simulations [30][31][32][33][34]. When we refer to simulation results in the following, we always used the algorithm given by Scala et al [31].…”

Section: Defect-mediated Transportmentioning

confidence: 99%

Collective excitations in jammed states: ultrafast defect propagation and finite-size scaling

et al. 2022

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In crowded systems, particle currents can be mediated by propagating collective excitations which are generated as rare events, are localized and have a finite lifetime. The theoretical description of such excitations is hampered by the problem of identifying complex many-particle transition states, calculation of their free energies, and the evaluation of propagation mechanisms and velocities. Here we show that these problems can be tackled for a highly jammed system of hard spheres in a periodic potential. We derive generation rates of collective excitations, their anomalously high velocities, explain the occurrence of an apparent jamming transition and its strong dependence on the system size. The particle currents follow a scaling behavior, where for small systems the current is proportional to the generation rate and for large systems given by the geometric mean of the generation rate and velocity. Our theoretical approach is widely applicable to dense nonequilibrium systems in confined geometries. It provides new perspectives for studying dynamics of collective excitations in experiments.

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Adaptive Brownian Dynamics

Cited by 22 publications

References 78 publications

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

Dynamic decay and superadiabatic forces in the van Hove dynamics of bulk hard sphere fluids

Collective excitations in jammed states: ultrafast defect propagation and finite-size scaling

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