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Although the dynamics of colloids in the vicinity of a solid interface has been widely characterized in the past, experimental studies of Brownian diffusion close to an air-water interface are rare and limited to particle-interface gap…
We develop a path-integral dynamics method for water that resembles centroid molecular dynamics (CMD), except that the centroids are averages of curvilinear, rather than cartesian, bead coordinates. The curvilinear coordinates are used…
In this paper, we present a multiple-time-step integration algorithm (MTSA) for particle collisions in particle-resolved simulations. Since the time step required for resolving a collision process is much smaller than that for a fluid flow,…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
The crystal nucleation from liquid in most cases is too rare to be accessed within the limited timescales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal…
We have investigated the slow dynamics of ultrasoft particles in crystalline cluster phases, where point particles interact through the generalized exponential potential u(r) = \epsilon \exp[-(r/\sigma)^n], focusing on the cluster fcc phase…
Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence,…
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…
The Verlet method is still widely used to integrate the equations of motion in ab initio molecular dynamics simulations. We show that the stability limit of the Verlet method may be significantly increased by setting an upper limit on the…
During our previous modeling using all-atom molecular dynamics, we have identified several foldamers whose nanoscale behavior resembles that of classic bistable machines, namely the Euler archs and Duffing oscillators. However, time…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
Molecular dynamics simulations are performed to study the lithium jumps in LiPO3 glass. In particular, we calculate higher-order correlation functions that probe the positions of single lithium ions at several times. Three-time correlation…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
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…
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on…
Simulations of SiC crystal growth using molecular dynamics (MD) have become popular in recent years. They, however, simulate very fast deposition rates, to reduce computational costs. Therefore, they are more akin to surface sputtering,…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
Using molecular dynamics simulations we study the slow dynamics of a colloidal fluid annealed within a matrix of obstacles quenched from an equilibrated colloidal fluid. We choose all particles to be of the same size and to interact as hard…
Magnetic reconnection in laboratory, space and astrophysical plasmas is often invoked to explain explosive energy release and particle acceleration. However, the timescales involved in classical models within the macroscopic MHD regime are…
We performed large-scale molecular dynamics simulations based on a machine-learning force field (MLFF) to investigate the Li-ion transport mechanism in cation-disordered Li$_3$TiCl$_6$ cathode at six different temperatures, ranging from…