NEW
Hamiltonian Adaptive Resolution: H-AdResS
Raffaello Potestio, Sebastian Fritsch, Pep Español, Rafael Delgado-Buscalioni, Kurt Kremer, Ralf Everaers, and Davide Donadio
Hamiltonian Adaptive Resolution Simulation for Molecular Liquids,
Physical Review Letters 110, 108301 (2013)
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.
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
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
Raffaello Potestio, Sebastian Fritsch, Pep Español, Rafael Delgado-Buscalioni, Kurt Kremer, Ralf Everaers, and Davide Donadio
Hamiltonian Adaptive Resolution Simulation for Molecular Liquids,
Physical Review Letters 110, 108301 (2013)
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)
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.