相关论文: Small ionic radii limit time step in Martini 3 mol…

Global and local linear gyrokinetic simulations of 42 pedestal equilibria from three DIII-D discharges are used to investigate pedestal stability and its impact on pedestal structure and confinement. Microtearing modes (MTMs) and kinetic…

The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…

We devise a new 1D atomistic scale model of vicinal growth based on Cellular Automaton. In it the step motion is realized by executing the automaton rule prescribing how adatoms incorporate into the vicinal crystal. Time increases after…

Water scarcity is a reality in our world, and scenarios predicted by leading scientists in this area indicate that it will worsen in the next decades. However, new technologies based in low-cost seawater desalination can prevent the worst…

We present a concurrent Monte Carlo (MC) - molecular dynamics (MD) approach to modeling of matter response to excitation of its electronic system. The two methods are combined on-the-fly at each time step in one code, TREKIS-4. The MC model…

Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is limited by the slow relaxation time of…

We report a high energy-resolution neutron backscattering study, combined with in-situ diffraction, to investigate slow molecular motions on nanosecond time scales in the fluid phase of phospholipid bilayers of…

In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its…

From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…

Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…

For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate…

To a large extent, the stiffness of the bidomain and monodomain models depends on the choice of the ionic model, which varies in terms of complexity and realism. In this paper, we compare and analyze a variety of time-stepping methods:…

In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong…

We study three different time integration methods for a dynamic pore network model for immiscible two-phase flow in porous media. Considered are two explicit methods, the forward Euler and midpoint methods, and a new semi-implicit method…

Internal coordinate molecular dynamics (ICMD) is an efficient method for studying biopolymers, but it is readily applicable only to molecules with tree topologies, that is with no internal flexible rings. Common examples violating this…

We have developed a coarse-grained (CG) model of a polymer-clay system consisting of organically modified montmorillonite nanoclay as the nanoparticle in accordance with the MARTINI forcefield. We have used mechanical properties and…

Bosonic exchange symmetry leads to fascinating quantum phenomena, from exciton condensation in quantum materials to the superfluidity of liquid Helium-4. Unfortunately, path integral molecular dynamics (PIMD) simulations of bosons are…

In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…

The presence and the properties of lipid bilayer nanometer-scale domains might be important for understanding the membranes of living cells. We used molecular dynamics (MD) simulations to investigate perturbations of a small patch of…

We report an accessible and robust tool for evaluating the effects of Coulomb collisions on a test particle in a plasma that obeys Maxwell-J\"uttner statistics. The implementation is based on the Beliaev-Budker collision integral which…