Statistical Physics Problems in Adaptive Resolution Computer Simulations of Complex Fluids

Simulating complex fluids or in general complex molecular systems requires approaches covering decades of time and length scales. This usually cannot be achieved within one simulation model. Over the years many different methods and models have been developed ranging from rather generic models, representing most efficiently the universal statistical mechanical properties of e.g. polymers, to all atom models and even quantum mechanical treatments. While these allow for scientifically very important studies in their own right, only a combination and close link between models of different levels allows for a truly quantitative description of materials and processes. In the present contribution we discuss an adaptive resolution approach where different levels of detail are treated within one simulation and the molecules are free to diffuse between different regions in space, where the molecules interact with different interaction potentials.

[1]  Matej Praprotnik,et al.  Multiscale simulation of soft matter: from scale bridging to adaptive resolution. , 2008, Annual review of physical chemistry.

[2]  Alan K. Soper,et al.  Empirical potential Monte Carlo simulation of fluid structure , 1996 .

[3]  Matej Praprotnik,et al.  Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[4]  T F Nonnenmacher,et al.  Fractional integral and differential equations for a class of Levy-type probability densities , 1990 .

[5]  Matej Praprotnik,et al.  Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water. , 2009, The Journal of chemical physics.

[6]  Florian Müller-Plathe,et al.  Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.

[7]  W G Noid,et al.  Generalized Yvon-Born-Green theory for molecular systems. , 2009, Physical review letters.

[8]  Matej Praprotnik,et al.  Adaptive resolution simulation of liquid water , 2007 .

[9]  Matej Praprotnik,et al.  Modeling diffusive dynamics in adaptive resolution simulation of liquid water. , 2007, The Journal of chemical physics.

[10]  Simón Poblete Thermodynamic concepts in adaptive resolution simulations , 2010 .

[11]  P. Español,et al.  Statistical Mechanics of Dissipative Particle Dynamics. , 1995 .

[12]  R. Hilfer Applications Of Fractional Calculus In Physics , 2000 .

[13]  Dusanka Janezic,et al.  Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators. , 2005, Journal of Chemical Physics.

[14]  Matej Praprotnik,et al.  Coupling different levels of resolution in molecular simulations. , 2009, The Journal of chemical physics.

[15]  Kurt Kremer,et al.  Multiscale simulation of soft matter systems. , 2010, Faraday discussions.

[16]  K. Kremer,et al.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.

[17]  Kurt Kremer,et al.  Simulation of Polymer Melts. II. From Coarse-Grained Models Back to Atomistic Description , 1998 .

[18]  Cecilia Clementi,et al.  Communication: On the locality of hydrogen bond networks at hydrophobic interfaces. , 2010, The Journal of chemical physics.

[19]  Luigi Delle Site Some fundamental problems for an energy-conserving adaptive-resolution molecular dynamics scheme. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[20]  Alessandra Villa,et al.  Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model. , 2009, Physical chemistry chemical physics : PCCP.

[21]  G. Voth Coarse-Graining of Condensed Phase and Biomolecular Systems , 2008 .

[22]  Matej Praprotnik,et al.  Concurrent triple-scale simulation of molecular liquids. , 2008, The Journal of chemical physics.

[23]  Gregory A Voth,et al.  Multiscale coarse graining of liquid-state systems. , 2005, The Journal of chemical physics.

[24]  William George Noid,et al.  Extended ensemble approach for deriving transferable coarse-grained potentials , 2009 .

[25]  Kurt Kremer,et al.  Bridging the Gap Between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives , 2000 .

[26]  Gregory A Voth,et al.  Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. , 2004, The Journal of chemical physics.

[27]  Mehdi Dalir,et al.  Applications of Fractional Calculus , 2010 .

[28]  Matej Praprotnik,et al.  FAST TRACK COMMUNICATION: Fractional dimensions of phase space variables: a tool for varying the degrees of freedom of a system in a multiscale treatment , 2007 .

[29]  L Delle Site,et al.  Adaptive resolution simulation of liquid para-hydrogen: testing the robustness of the quantum-classical adaptive coupling. , 2011, Physical chemistry chemical physics : PCCP.

[30]  Matej Praprotnik,et al.  Adaptive molecular resolution via a continuous change of the phase space dimensionality. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[31]  Matej Praprotnik,et al.  A macromolecule in a solvent: adaptive resolution molecular dynamics simulation. , 2007, The Journal of chemical physics.

[32]  Alessandra Villa,et al.  Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water. , 2010, Journal of chemical theory and computation.

[33]  M. Naber,et al.  Fractional differential forms , 2001, math-ph/0301013.

[34]  Vasily E Tarasov Fractional systems and fractional Bogoliubov hierarchy equations. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[35]  G De Fabritiis,et al.  Multiscale modeling of liquids with molecular specificity. , 2006, Physical review letters.

[36]  A. Lyubartsev,et al.  Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[37]  K. Kremer,et al.  Dissipative particle dynamics: a useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[38]  Matej Praprotnik,et al.  Simulation approaches to soft matter: Generic statistical properties vs. chemical details , 2008, Comput. Phys. Commun..

[39]  Vasily E Tarasov Fractional generalization of Liouville equations. , 2004, Chaos.

[40]  Kurt Kremer,et al.  Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations , 2008 .

[41]  Dirk Reith,et al.  Deriving effective mesoscale potentials from atomistic simulations , 2002, J. Comput. Chem..

[42]  J. Q. Broughton,et al.  Concurrent coupling of length scales: Methodology and application , 1999 .

[43]  Matej Praprotnik,et al.  Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat. , 2007, Soft matter.

[44]  Cracks and crazes: on calculating the macroscopic fracture energy of glassy polymers from molecular simulations. , 2001, Physical review letters.

[45]  L Delle Site,et al.  Classical to path-integral adaptive resolution in molecular simulation: towards a smooth quantum-classical coupling. , 2010, Physical review letters.

[46]  Kurt Kremer,et al.  Simulation of polymer melts. I. Coarse‐graining procedure for polycarbonates , 1998 .

[47]  Bernd Ensing,et al.  Adaptive multiscale molecular dynamics of macromolecular fluids. , 2010, Physical review letters.

[48]  Michele Parrinello,et al.  Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics. , 2007, Journal of chemical theory and computation.

[49]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

[50]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[51]  Sabine H. L. Klapp,et al.  Why are effective potentials 'soft'? , 2004 .

[52]  A. Mark,et al.  Coarse grained model for semiquantitative lipid simulations , 2004 .

[53]  R. L. Henderson A uniqueness theorem for fluid pair correlation functions , 1974 .

[54]  J. Koelman,et al.  Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics , 1992 .