Related papers: Effective potentials and electrostatic interaction…
A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…
It is demonstrated by molecular dynamics simulations that liquids interacting via the Buckingham potential are strongly correlating, i.e., have regions of their phase diagram where constant-volume equilibrium fluctuations in the virial and…
Gaining access to the cell interior is fundamental for many applications, such as electrical recording, drug and biomolecular delivery. A very promising technique consists of culturing cells on nano/micro pillars. The tight adhesion and…
Transient electric fields across cell bilayer membranes can lead to electroporation, as well as to cell fusion, and have been extensively studied. We find that transmembrane electric fields similar to those in cells can lead to a massive,…
We study the interaction of lipid bilayers with short chain alcohols using molecular dynamics on different length scales. We use detailed atomistic modeling and modeling on the length scale where an alcohol is just an amphiphilic dimer. Our…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
The central approximation made in classical molecular dynamics simulation of materials is the interatomic potential used to calculate the forces on the atoms. Great effort and ingenuity is required to construct viable functional forms and…
Accurate, yet computationally efficient energy functions are essential for state-of-the art molecular dynamics (MD) studies of condensed phase systems. Here, a generic workflow based on a combination of machine learning-based and empirical…
Non-equilibrium electrochemistry raises new challenges for atomistic simulation: we need to perform molecular dynamics for the nuclear degrees of freedom with an explicit description of the electrons, which in turn must be free to enter and…
In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…
We investigate the effect of an applied electric potential on the mechanics of a coarse grained POPC bilayer under tension. The size and duration of our simulations allow for a detailed and accurate study of the fluctuations. Effects on the…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
We introduce and test via molecular simulation a simple model for predicting the manner in which interparticle interactions and thermodynamic conditions impact the single-particle free-volume distributions of equilibrium fluids. The model…
We present a mathematical model of polymer bilayers that undergo large bending deformations when actuated by non-mechanical stimuli such as thermal effects. The simple model captures a large class of nonlinear bending effects and can be…
We consider a linear system that consists of a linear wave equation on a horizontal hypersurface and a parabolic equation in the half space below. The model describes longitudinal elastic waves in organic monolayers at the water-air…
We study the effects of chiral constituent molecules on the macroscopic shapes attained by lipid bilayer membranes. Such fluid membranes are beautiful examples of statistical ensembles of random shapes, sometimes coupled to in-plane order.…
Hybrid quantum mechanics / molecular mechanics (QM/MM) models successfully describe the properties of biological macromolecules. However, most QM/MM methodologies are constrained to unrealistic gas phase models, thus limiting their…