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Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Interfacial fluctuations in a two-phase binary fluid mixture reveal signatures of underlying physical processes that occur within each phase and on a range of spatial and temporal scales. In this study, we investigate a model binary fluid…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
The conformational and dynamical properties of active self-propelled filaments/polymers are investigated in the presence of hydrodynamic interactions by both, Brownian dynamics simulations and analytical theory. Numerically, a discrete…
Brownian motion is essential for describing diffusion in systems ranging from simple to complex liquids. Unlike simple liquids, which consist of only a solvent, complex liquids, such as colloidal suspensions or the cytoplasm of a cell, are…
Thermophoresis is an effective method to drive the motion of nanoparticles in fluids. The transport of nanoparticles in polymer networks has significant fundamental and applied importance in biology and medicine, and can be described as…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
Discrete particle simulation, a combined approach of computational fluid dynamics and discrete methods such as DEM (Discrete Element Method), DSMC (Direct Simulation Monte Carlo), SPH (Smoothed Particle Hydrodynamics), PIC…
We develop a new algorithm for the Brownian dynamics of soft matter systems that evolves time by spatially correlated Monte Carlo moves. The algorithm uses vector wavelets as its basic moves and produces hydrodynamics in the low Reynolds…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
The Eulerian-Lagrangian approach based on Large-Eddy Simulation (LES) is one of the most promising and viable numerical tools to study turbulent dispersed flows when the computational cost of Direct Numerical Simulation (DNS) becomes too…
Lagrangian particle methods based on detailed atomic and molecular models are powerful computational tools for studying the dynamics of microscale and nanoscale systems. However, the maximum time step is limited by the smallest oscillation…
Direct numerical simulations (DNS) of microscale fluid-structure interactions (mFSI) in multicomponent multiphase flows pose many challenges, including the thermodynamic consistency of multiphysics couplings, tracking of moving interfaces,…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…