A framework for performant Brownian Dynamics (BD) many-body simulations with adaptive timestepping is presented. Contrary to the Euler-Maruyama scheme in common non-adaptive BD, we employ an embedded Heun-Euler integrator propagation of overdamped coupled Langevin equations motion. This enables derivation a local error estimate and formulation criteria acceptance or rejection trial steps contro...

We report the implementation of an atomistic Brownian dynamics simulation of proteins. A protein was described by united-atom model with AMBER91 force field. The solvent was treated by distance-dependent dielectric/surface area model. The computation time of the Brownian dynamics and the calculated results on structure and dynamics of 28-mer ββα fold peptide with the implicit solvent model were...

Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular...

This paper serves as an introductory review of Brownian Dynamics (BD), Molecular Dynamics (MD), and Monte Carlo (MC) modeling techniques. These three simulation methods have proven to be exceptional investigative solutions for probing discrete molecular, ionic, and colloidal motions at their basic microscopic levels. The review offers a general study of the classical theories and algorithms tha...

The theory of Brownian dynamics is used to model permeation and the blocking of KcsA potassium channels by tetraethylammonium (TEA). A novel Brownian dynamics simulation algorithm is implemented that comprises two free energy profiles; one profile is seen by the potassium ions and the other by the TEA molecules whose shape is approximated by a sphere. Our simulations reveal that internally appl...