Related papers: From Molecular Dynamics to Brownian Dynamics
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…
Molecular dynamics (MD) has served as a powerful tool for designing materials with reduced reliance on laboratory testing. However, the use of MD directly to treat the deformation and failure of materials at the mesoscale is still largely…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
Brownian motion is essential for describing diffusion in systems ranging from simple to complex liquids. Unlike simple liquids, which consist of only a solvent, complex liquids, such as colloidal suspensions or the cytoplasm of a cell, are…
We study quasi two-dimensional, monodisperse systems of active Brownian particles (ABPs) for a range of activities, stiffnesses, and densities. We develop a microscopic, analytical method for predicting the dense phase structure formed…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is…
Molecular dynamics (MD) simulations are a central tool in science and engineering enabling the study of dynamical behavior and the link between microscopic structure and macroscopic function. Their high computational cost, however, has…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The…
Stiff forces, which bind objects together or otherwise confine motion, are found widely in soft-matter systems - colloids with short range attractions, ligand-receptor contacts, particles in optical traps, fibres that resist stretching,…
We develop two-dimensional Brownian dynamics simulations to examine the motion of disks under thermal fluctuations and Hookean forces. Our simulations are designed to be experimental-like, since the experimental conditions define the…
Two-dimensional Molecular Dynamics simulations are used to model the free surface flow of spheres falling down an inclined chute. The interaction between the particles in our model is assumed to be subjected to the Hertzian contact force…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…