Related papers: Concurrent coupling of atomistic simulation and me…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
A simulation model is presented, comprising elastic spheres with a short range attraction. Besides conservative forces, radial- and shear friction, and radial noise are added. The model can be used to simulate colloids, granular solids and…
One of the key choices for numerical models of geophysical fluids is how parametrisations of physical processes interact with the numerical methods that handle the resolved flow, known in the atmospheric community as the dynamical core. As…
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…
Accurate and efficient flow models for hydrocarbons are important in the development of enhanced geotechnical engineering for energy source recovery and carbon capture & storage in low-porosity, low-permeability rock formations. This work…
We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
We provide a basic method of Smoothed Particle Hydrodynamics (SPH) to simulate liquid droplet with surface tension in three dimensions. Liquid droplet is a simple case for surface tension modeling. Surface tension works only on fluid…
A previously-developed hybrid particle-continuum method [J. B. Bell, A. Garcia and S. A. Williams, SIAM Multiscale Modeling and Simulation, 6:1256-1280, 2008] is generalized to dense fluids and two and three dimensional flows. The scheme…
We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
The accuracy and stability of implicit CFD codes are frequently impaired by the decoupling between variables, which can ultimately lead to numerical divergence. Coupled solvers, which solve all the governing equations simultaneously, have…
Even though the Dissipative Particle Dynamics (DPD) has shown its worth in a variety of research areas, it has been rarely used for polymer dynamics, particularly in dilute and semi-dilute conditions and under imposed flow fields. For such…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
Mixed-quantum classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional…