Related papers: Force probe simulations using an adaptive resoluti…
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…
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…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
Active Plasma Resonance Spectroscopy (APRS) is a well-established plasma diagnostic method: a radio frequency signal is coupled into the plasma via a probe or antenna, excites it to oscillate, and the response is evaluated through a…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
FFT-based solvers are increasingly used by many researcher groups interested in modelling the mechanical behavior associated to a heterogeneous microstructure. A development is reported here that concerns the viscoelastic behavior of…
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…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh…
Atomic force microscopy (AFM) is one of the most promising methods for investigating the structure of materials at the micro and nanoscale levels, as well as their local physical-mechanical properties. The experimental data obtained with…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
A non-linear system governed by multi-spatial and multi-temporal physics scales cannot be fully understood with a single diagnostic, as each provides only a partial view, leading to information loss. Combining multiple diagnostics may also…