Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water

We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is robust against the details of the mesoscopic model owing to the conservation of linear momentum by the adaptive resolution forces. Our multiscale approach is designed for molecular simulations of open domains with relatively large molecules, either in the grand canonical ensemble or under non-equilibrium conditions.Comment: triple-scale simulation, molecular dynamics, continuum, wate

Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent

We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport information from the other two domains is exchanged. The exchange of information in the overlap region ensures that momentum, energy and mass are conserved. The validity of the hybrid code is demonstrated by studying a single polymer tethered to a hard wall immersed in explicit solvent and undergoing shear flow. In classical molecular dynamics simulation a great deal of computational time is devoted to simulating solvent molecules, although the solvent itself is of no direct interest. By contrast, the hybrid code simulates the polymer and surrounding solvent explicitly, whereas the solvent farther away from the polymer is modeled using a continuum description. In the hybrid simulations the MD domain is an open system whose number of particles is controlled to filter the perturbative density waves produced by the polymer motion.We compare conformational properties of the polymer in both simulations for various shear rates. In all cases polymer properties compare extremely well between the two simulation scenarios, thereby demonstrating that this hybrid method is a useful way to model a system with polymers and under nonzero flow conditions. There is also good agreement between the MD and hybrid schemes and experimental data on tethered DNA in flow. The computational cost of the hybrid protocol can be reduced to less than 6% of the cost of updating the MD forces, confirming the practical value of the method.Comment: 13 pages, 8 figure

Monte Carlo adaptive resolution simulation of multicomponent molecular liquids

Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The non-matching properties of high- and low-resolution models, however, lead to thermodynamic imbalances between the system's subdomains. Such inhomogeneities can be healed by appropriate compensation forces, whose calculation requires nontrivial iterative procedures. In this work we employ the recently developed Hamiltonian Adaptive Resolution Simulation method to perform Monte Carlo simulations of a binary mixture, and propose an efficient scheme, based on Kirkwood Thermodynamic Integration, to regulate the thermodynamic balance of multi-component systems

Hamiltonian adaptive resolution simulation for molecular liquids

Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well defined statistical ensembles can be generated making use of all standard Molecular Dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.Comment: 11 pages, 3 Figure

The Stokes-Einstein Relation at Moderate Schmidt Number

The Stokes-Einstein relation for the self-diffusion coefficient of a spherical particle suspended in an incompressible fluid is an asymptotic result in the limit of large Schmidt number, that is, when momentum diffuses much faster than the particle. When the Schmidt number is moderate, which happens in most particle methods for hydrodynamics, deviations from the Stokes-Einstein prediction are expected. We study these corrections computationally using a recently-developed minimally-resolved method for coupling particles to an incompressible fluctuating fluid in both two and three dimensions. We find that for moderate Schmidt numbers the diffusion coefficient is reduced relative to the Stokes-Einstein prediction by an amount inversely proportional to the Schmidt number in both two and three dimensions. We find, however, that the Einstein formula is obeyed at all Schmidt numbers, consistent with linear response theory. The numerical data is in good agreement with an approximate self-consistent theory, which can be used to estimate finite-Schmidt number corrections in a variety of methods. Our results indicate that the corrections to the Stokes-Einstein formula come primarily from the fact that the particle itself diffuses together with the momentum. Our study separates effects coming from corrections to no-slip hydrodynamics from those of finite separation of time scales, allowing for a better understanding of widely observed deviations from the Stokes-Einstein prediction in particle methods such as molecular dynamics.Comment: Submitte