Topics

Multiscale modelling: molecular/continuum hybrids

Fluctuating hydrodynamics

Polymer dynamics

Capillary waves

Coarse graining with proper dynamics

Some talks in pdf

Multiscale modelling

HybridMD: coupling molecular dynamics with fluctuating hydrodynamics

Multiscale modelling of liquids with molecular specificity

The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the full molecular nature of the system where it is of interest and coarse-graining it elsewhere. This is made possible by coupling molecular dynamics with a mesoscopic description of realistic liquids based on Landau's fluctuating hydrodynamics. We show that our scheme correctly couples hydrodynamics and that fluctuations, at both the molecular and continuum levels, are thermodynamically consistent. Hybrid simulations of sound waves in bulk water and reflected by a lipid monolayer are presented as illustrations of the scheme.

Modelling the mesoscale with molecular specificity, Phys. Rev. Lett. 97, 134501 (2006). pdf file

Co-worker: Gianni De Fabritiis
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Open MD: molecular dynamics for open systems:

One of the requisities of the hybrid particle-continuum models is that the molecular system has to be open . In other words, mass, momentum and energy have to be transfered from and to the MD domain to the outside world. As an important byproduct, HybridMD provides a route to perform molecular simulations in the grand canonical ensemble, preserving the correct dynamical properties at the MD domain. Note that previous simulations in the GC ensemble were either MonteCarlo (dynamics are not solved), or do disrupt the dynamics of the MD domain by brute force particle insertion. The present algorithm only affects a small particle buffer at the MD borders, where the particle exchange takes place and external pressure is imposed. In fact, just like in a real confined system.

Triple scale modelling: AdResS - hybridMD

In this work we construct a triple-scale simulation scheme for molecular liquids which concurrently couples: atomistic, coarse-grained and continuum descriptions of the liquid. The presented multiscale approach covers the length-scales ranging from the micro- to macro-scale and it is based on a combination of two dual-scale models: the particle-based Adaptive Resolution Scheme (AdResS) , which couples the atomic and mesoscopic scales, and the hybrid continuum-molecular dynamics scheme (HybridMD) . The combined AdResS-HybridMD scheme sorts out the problem of large molecule insertion in hybrid particle-continuum simulations of molecular liquids. The combined model is shown to correctly describe the hydrodynamics within a hybrid particle-continuum framework. The presented approach opens up the possibility to perform efficient grand-canonical molecular dynamics simulations of liquids composed by relatively large molecules.

R. Delgado-Buscalioni, K. Kremer and M. Praprotnik, Concurrent triple-scale simulation for molecular liquids J. Chem. Phys. 128 114110 (2008).

Co-workers: Matej Praprotnik , Kurt Kremer

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Fluctuating hydrodynamics

Fluctuating hydrodynamics for realistic liquid models

A good representation of mesoscopic fluids is required to complement molecular simulations at larger scales. However, computational models providing accurate and efficient description of hydrodynamics at the nanoscale are scarce, possibly because of the stochastic character of the underlaying flucutating hydrodynamics (FH) equations. Here, we derive a simple finite volume discretization over a regular grid of the compressible isothermal fluctuating hydrodynamics equations in the Eulerian reference system. We describe realistic fluids, such as argon at arbitrary densities and water (TIP3P model) at ambient conditions (T=300 K). To that end, molecular dynamics simulations are used to derive the required fluid properties: transport coefficients and pressure equation of state. The equilibrium state of the model is shown to be thermodynamically consistent and shown to correctly reproduce linear hydrodynamics (relaxation of sound and shear modes). We also consider non-equilibrium states involving diffusion and convection, in cavities with either slip or no-slip boundary conditions.
Co-workers: Mar Serrano (UNED) , Gianni De Fabritiis
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Open boundary conditions for fluctuating hydrodynamics

Co-workers: Anne Dejoan (CIEMAT)

Polymer dynamics

Dynamics of a single polymer under shear flow: cyclic dynamics

video

The long-time dynamics of a single end-tethered chain under shear flow are studied using molecular and Brownian dynamics simulations of a flexible polymer. As observed in previous experiments with tethered DNA [Phys. Rev. Lett. 84, 4769 (2000)], under a flow sheared at constant rate the chain performs a cyclic motion. But contrary to what it has been previously suggested, a well defined characteristic period exists and, it is clearly revealed in the cross-spectra of the chain extension along flow and gradient directions. The main cycling time scales like the convective time needed by the flow to stretch the polymer, being about ten times the longest relaxation time of the chain in flow. This coherent recursive motion introduces long memory in the fluid and suggests resonance effects under periodic external forcing.

R. Delgado-Buscalioni, Cyclic dynamics of a tethered polymer under shear flow, Phys. Rev. Lett. 96, 088303 (2006)

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