Multiscale modeling of liquids and open MD

Multiscale modelling of liquids with molecular specificity

Hybrid-MD: coupling Molecular Dynamics with Fluctuating Hydrodynamics . 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.

HybridMD Sound waves can travel through an openMD box without spurious reflection

Publications

R. Delgado-Buscalioni Modelling the mesoscale with molecular specifity, Phys. Rev. Lett.97, 134501 (2006)

G. De Fabritiis, R. Delgado-Buscalioni and P. Coveney, Modelling the mesoscale with molecular specifity, Phys. Rev. Lett.97, 134501 (2006)

R .Delgado-Buscalioni and G. De Fabritiis, Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids, Phys. Rev. E 76, 036709 (2007)

R. Delgado-Buscalioni, P.V. Coveney and G. De Fabritiis, Towards multiscale modelling of complex liquids using hybrid particle-continuum schemes, Proceedings of the Institution of Mechanical Engineers, Part C, Journal of Mechanical Engineering Science, in press, (2007)

R. Delgado-Buscalioni and P. V. Coveney Continuum-particle hybrid coupling for mass, momentum and energy transfers in unsteady fluid flow, Phys. Rev. E, 67, 046704 (2003)

Rafael Delgado-Buscalioni, Peter V. Coveney, Graham D. Riley and Rupert Ford, Hybrid molecular-continuum fluid models: implementation within a general coupling framework, Phil. Trans. Roy. Soc. London A, 363 (1833), 1975-1985 (2005)

R. Delgado-Buscalioni, E. G. Flekkoy and P. V. Coveney , Fluctuations and continuity in particle-continuum hybrid simulations of unsteady flows based on flux-exchange, Europhysics Letters, 69, 959 (2005)

R. Delgado-Buscalioni and P. V. Coveney, Hybrid particle-continuum fluid dynamics, Phil. Trans. R. Soc. London 362, 1369 (2004)

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

Co-worker: Gianni De Fabritiis

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.
Keywords: particle insertion, flux boundary conditions, grand canonical ensemble, chemical potential evaluation

Publications

E. G. Flekkoy, R. Delgado-Buscalioni and P.V. Coveney , Flux boundary conditions in particle simulations, Phys. Rev. E, 72, 026703 (2005)

G. De Fabritiis, R. Delgado-Buscalioni and P.V. Coveney , Energy controlled insertion of polar molecules in dense fluids, J. Chem. Phys.121, 12139 (2004)

R. Delgado-Buscalioni and P. V. Coveney, USHER: an algorithm for particle insertion in dense liquids, J. Chem. Phys, 119, 978 (2003)

R. Delgado-Buscalioni, G. De Fabritiis and P. V. Coveney , Determination of the chemical potential using energy-biased sampling, J. Chem. Phys., 123, 054105 (2005)

Adaptive Resolution: AdResS - hybridMD

AdReSs-HybridMD A coarse-grained (DPD) layer interfaces the molecular and continuum descriptions alowing for an open molecular system

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.

NEW Hamiltonian Adaptive Resolution: H-AdResS

Co-workers:
Matej Praprotnik
Kurt Kremer

Publications

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

R. Delgado-Buscalioni, K. Kremer and M. Praprotnik, Coupling atomistic and continuum hydrodynamics through a mesoscopic model: Application to liquid water, J. Chem. Phys. 131, 244107 (2009)

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

Some talks and seminars

Multiscale modelling: hybrid MD

Hybrid MD (APS Meeting 2008)

Multiscale link: from DPD to fluctuating hydrodynamics (CECAM Workshop on DPD, July 2008)

The onion project (CECAM Workshop, Oct 2008)

Development and Analysis of Multiscale Methods; IMA, Univ. Minnesota, Minneapolis, Nov 2008
VIDEO OF THE PRESENTATION

Tools in multiscale modelling. Talk at the workshop: "Numerical analysis of multiscale computations" Banff Interantional Research Station, Alberta, Canada, Dec. 2009

Sound-soft matter interaction at different scales, ETH workshop, Ittingen. Oct. 2010.