Related papers: Multisecond ligand dissociation dynamics from atom…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
Advanced thermostats for molecular dynamics are proposed on the base of the rigorous Langevin dynamics. Because the latter accounts for the subsystem-bath interactions in details, the bath anisotropy and nonuniformity are described via the…
Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information of the full…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
We present a stochastic phase-field model for multicomponent lipid bilayers that explicitly accounts for the quasi-two-dimensional hydrodynamic environment unique to a thin fluid membrane immersed in aqueous solution. Dynamics over a wide…
We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
In this work we study the diffusion mechanisms in lithium disilicate melt using molecular dynamics simulation, which has an edge over other simulation methods because it can track down actual atomic rearrangements in materials once a…
Molecular dynamic (MD) simulations are applied to investigate the dependency of the kinetic friction coefficient on the temperature at the nano-scale. The system is comprised of an aluminum spherical particle consisting of 32000 atoms in an…
Ultrafast chemical reactions are difficult to simulate because they involve entangled, many-body wavefunctions whose computational complexity grows rapidly with molecular size. In photochemistry, the breakdown of the Born-Oppenheimer…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
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,…
Understanding intrusion and extrusion in nanoporous materials is a challenging multiscale problem of utmost importance for applications ranging from energy storage and dissipation to water desalination and hydrophobic gating in ion…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
This paper is concerned with tuning friction and temperature in Langevin dynamics for fast sampling from the canonical ensemble. We show that near-optimal acceleration is achieved by choosing friction so that the local quadratic…