Related papers: Multisecond ligand dissociation dynamics from atom…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust,…
In conventional fluid mechanics, the chemical composition and thermodynamic state of a fluid-solid interface are not considered when establishing velocity-field boundary conditions. As a consequence, fluid simulations are usually not able…
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…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics…
In this paper we have investigated, through computer simulations, dislocation nucleation and dislocation dynamics in a heterostructure system with the lattice-mismatch interface, i.e. a system with internal strain. In particular, we have…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Complex systems are often characterized by the interplay of multiple interconnected dynamical processes operating across a range of temporal scales. This phenomenon is widespread in both biological and artificial scenarios, making it…
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
Metastable condensed matter typically fluctuates about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of…
The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids, to the micrometers and beyond millisecond for cellular signalling processes. While…
Motivated by the decade-long debate over the issue of criticality supposedly observed in nuclear multifragmentation, we propose a dynamical lattice model to simulate the phenomenon. Its Ising Hamiltonian mimics a short range attractive…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component…
The adsorption of single colloidal microparticles (0.5--1 $\mu$m radius) at a water-oil interface has been recently studied experimentally using digital holographic microscopy [Kaz \textit{et al., Nat. Mater.}, 2012, \textbf{11}, 138--142].…