Related papers: Efficient Brownian Dynamics Simulation of Single D…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
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…
A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by Molecular Dynamics (MD) computer simulation and compared to results of Lattice Boltzmann (LB) simulations. By the…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
We have developed a simulation model to study the hydrodynamic flow fields around Brownian colloidal particles with an active surface patch. Hydrodynamics is introduced by modeling low-Reynolds-number fluid flows around a colloid using…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Slender bodies capable of spontaneous motion in the absence of external actuation in an otherwise quiescent fluid are common in biological, physical and technological contexts. The interplay between the spontaneous fluid flow, Brownian…
The paper presents a two-phase hydrodynamic model for the numerical simulation of collective motion in a thin layer of active colloids containing spherical microswimmers. The model accounts for three fundamental mechanisms governing the…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…
Experiments have recently shown the feasibility of utilising bacteria as micro-scale robotic devices, with special attention paid to the development of bacteria-driven micro-swimmers taking advantage of built-in actuation and sensing…
A novel approach to account for hard-body interactions in (overdamped) Brownian dynamics simulations is proposed for systems with non-vanishing force fields. The scheme exploits the analytically known transition probability for a Brownian…
We present a hybrid Brownian dynamics / Monte Carlo algorithm for simulating solutions of highly entangled semiflexible polymers or filaments. The algorithm combines a Brownian dynamics time-stepping approach with an efficient scheme for…
In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge…
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
Microswimmers play an important role in shaping the world around us. The squirmer is a simple model for microswimmer whose cilia oscillations on its spherical surface induce an effective slip velocity to propel itself. The rapid development…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
The last few years have witnessed an explosion of new numerical methods for filament hydrodynamics. Aside from their ubiquity in biology, physics, and engineering, filaments present unique challenges from an applied-mathematical point of…