Calculating diffusion coefficients from molecular dynamics simulations for foam extrusion modelling of polypropylene with CO₂, N₂ and ethanol

Calculating potentials of mean force from steered molecular dynamics simulations.

Steered molecular dynamics (SMD) permits efficient investigations of molecular processes by focusing on selected degrees of freedom. We explain how one can, in the framework of SMD, employ Jarzynski's equality (also known as the nonequilibrium work relation) to calculate potentials of mean force (PMF). We outline the theory that serves this purpose and connects nonequilibrium processes (such as...

Transport coefficients for granular media from molecular dynamics simulations.

Under many conditions, macroscopic grains flow like a fluid; kinetic theory predicts continuum equations of motion for this granular fluid. In order to test the theory, we perform event-driven molecular simulations of a two-dimensional gas of inelastic hard disks, driven by contact with a heat bath. Even for strong dissipation, high densities, and small numbers of particles, we find that contin...

Insights into channel dysfunction from modelling and molecular dynamics simulations

Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use...

Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations

Bayesian inference is used to obtain self-consistent estimates of free energies and position-dependent diffusion coefficients along complex reaction coordinates from molecular dynamics simulation trajectories. Effectively, exact solutions for the dynamics of a diffusive model are matched globally to the observed molecular dynamics data. The approach is first tested for a simple onedimensional d...

Diffusion in liquids from molecular dynamics simulations | QuantumWise 2017 Documentation