相关论文: Pychastic: Precise Brownian Dynamics using Taylor-…
The immersed boundary method (IB) is an elegant way to fully couple the motion of a fluid and deformations of an immersed elastic structure. In that vein, the IB2d software allows for expedited explorations of fluid-structure interaction…
Dissipative Particle Dynamics (DPD) is a popular simulation model for investigating hydrodynamic behavior of systems with non-negligible equilibrium thermal fluctuations. DPD employs soft core repulsive interactions between the system…
A framework for performant Brownian Dynamics (BD) many-body simulations with adaptive timestepping is presented. Contrary to the Euler-Maruyama scheme in common non-adaptive BD, we employ an embedded Heun-Euler integrator for the…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Physical systems can often be described via a continuous-time dynamical system. In practice, the true system is often unknown and has to be learned from measurement data. Since data is typically collected in discrete time, e.g. by sensors,…
Current research efforts in aeroelasticity aim at including higher fidelity aerodynamic results into the simulation frameworks. In the present effort, the Python--based Fluid--Structure Interaction framework of the well known SU2 code has…
Robotics demands simulation that can reason about the diversity of real-world physical interactions, from rigid to deformable objects and fluids. Current simulators address this by stitching together multiple subsolvers for different…
We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense…
Fluctuating hydrodynamics based techniques have been developed in recent years for the simulation of Brownian motion of particles. These mesoscale simulation tools are viable approaches for problems where molecular dynamics simulations may…
An open-source, Python-based Temporal Analysis of Products (TAP) reactor simulation and processing program is introduced. TAPsolver utilizes algorithmic differentiation for the calculation of highly accurate derivatives, which are used to…
Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the…
Brownian motion near soft surfaces is a situation widely encountered in nanoscale and biological physics. However, a complete theoretical description is lacking to date. Here, we theoretically investigate the dynamics of a two-dimensional…
Data assimilation techniques are often confronted with challenges handling complex high dimensional physical systems, because high precision simulation in complex high dimensional physical systems is computationally expensive and the exact…
Stokesian Dynamics (SD) is a powerful computational framework for simulating the motion of particles in a viscous Newtonian fluid under Stokes-flow conditions. Traditional SD implementations can be computationally expensive as they rely on…
Two specialized algorithms for the numerical integration of the equations of motion of a Brownian walker obeying detailed balance are introduced. The algorithms become symplectic in the appropriate limits, and reproduce the equilibrium…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
TBPLaS is an open-source software package for the accurate simulation of physical systems with arbitrary geometry and dimensionality utilizing the tight-binding (TB) theory. It has an intuitive object-oriented Python application interface…
The aim of this note is to propose a novel numerical scheme for drift-less one dimensional stochastic differential equations of It\^o's type driven by standard Brownian motion. Our approximation method is equivalent to the well known…
We investigate the computational performance of various numerical methods for the integration of the equations of motion and the variational equations for some typical classical many-body models of condensed matter physics: the…
Standard algorithms for the numerical integration of the Langevin equation require that interactions are slowly varying during to the integration timestep. This in not the case for hard-body systems, where there is no clearcut between the…