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Granular materials are heterogenous grains in contact, which are ubiquitous in many scientific and engineering applications such as chemical engineering, fluid mechanics, geomechanics, pharmaceutics, and so on. Granular materials pose a…
Recent advances in (scanning) transmission electron microscopy have enabled routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
The coarse-graining approach to deriving the quantum Markovian master equation is revisited, with close attention given to the underlying approximations. It is further argued that the time interval over which the coarse-graining is…
Brownian dynamics of colloidal particles on complex surfaces has found important applications in diverse physical, chemical and biological processes. However, current Brownian dynamics simulation algorithms mostly work for relatively simple…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the…
Coarse-Graining (CG) models are low resolution approximation of high resolution models, such as all-atomic (AA) models. An effective CG model is expected to reproduce equilibrium values of sufficient physical quantities of its AA model,…
Automated analyses of the outcome of a simulation have been an important part of atomistic modeling since the early days, addressing the need of linking the behavior of individual atoms and the collective properties that are usually the…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Coarse-grained (CG) models are often parametrized to reproduce one-dimensional structural correlation functions of an atomically-detailed model along the degrees of freedom governing each interaction potential. While cross correlations…
Mesoscale simulations of woven composites using parameterized analytical geometries offer a way to connect constituent material properties and their geometric arrangement to effective composite properties and performance. However, the…
We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a quasi-equilibrium approximation of the particle distribution function, the model closely captures important analytical properties of the…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
This study presents a coarse-grained molecular dynamics simulation model to investigate the process of oxidative aging in polymers. The chemical aging effect is attributed to the auto-oxidation mechanism, which is initiated by radicals,…
A challenging topic in materials engineering is the development of numerical models that can accurately predict material properties with atomistic accuracy, matching the scale and level of detail achieved by experiments. In this regard,…