What is a Multiscale Problem in Molecular Dynamics?

In this work, we make an attempt to answer the question of what a multiscale problem is in Molecular Dynamics (MD), or, more in general, in Molecular Simulation (MS). By introducing the criterion of separability of scales, we identify three major (reference) categories of multiscale problems and discuss their corresponding computational strategies by making explicit examples of applications.

[1]  Luigi Delle Site,et al.  Adsorption of alanine on a Ni(111) surface: A multiscale modeling oriented density functional study , 2006 .

[2]  Kurt Kremer,et al.  Dual-scale modeling of benzene adsorption onto Ni(111) and Au(111) surfaces in explicit water. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

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

[4]  Kurt Kremer,et al.  Adhesion of Polycarbonate Blends on a Nickel Surface , 2005 .

[5]  L Delle Site,et al.  Polymers near metal surfaces: selective adsorption and global conformations. , 2002, Physical review letters.

[6]  A. Laio,et al.  QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water. , 2003, Chemphyschem : a European journal of chemical physics and physical chemistry.

[7]  L Delle Site,et al.  Comment on "Adaptive multiscale molecular dynamics of macromolecular fluids". , 2011, Physical review letters.

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

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

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

[11]  L. Ghiringhelli,et al.  Phenylalanine near inorganic surfaces: conformational statistics vs specific chemistry. , 2008, Journal of the American Chemical Society.

[12]  Kurt Kremer,et al.  Kirkwood-Buff Analysis of Liquid Mixtures in an Open Boundary Simulation. , 2012, Journal of chemical theory and computation.

[13]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[14]  Gerhard Hummer,et al.  Pore opening and closing of a pentameric ligand-gated ion channel , 2010, Proceedings of the National Academy of Sciences.

[15]  Efthimios Kaxiras,et al.  From Electrons to Finite Elements: A Concurrent Multiscale Approach for Metals , 2005, cond-mat/0506006.

[16]  Pep Español,et al.  Hamiltonian adaptive resolution simulation for molecular liquids. , 2012, Physical review letters.

[17]  L Delle Site,et al.  Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir. , 2011, Physical review letters.

[18]  Luigi Delle Site,et al.  Interaction of Hydrated Amino Acids with Metal Surfaces: A Multiscale Modeling Description , 2007 .

[19]  Kurt Kremer,et al.  Derivation of coarse grained models for multiscale simulation of liquid crystalline phase transitions. , 2012, The journal of physical chemistry. B.

[20]  H. Berendsen.  Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics , 2007 .

[21]  Kurt Kremer,et al.  Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[22]  Pep Español,et al.  Monte carlo adaptive resolution simulation of multicomponent molecular liquids. , 2013, Physical review letters.

[23]  Bernd Ensing,et al.  Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. , 2010, Physical chemistry chemical physics : PCCP.

[24]  Kurt Kremer,et al.  Multiscale modeling of polymers on a surface: From ab initio density functional calculations of molecular adsorption to large-scale properties , 2005 .

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

[26]  J. C. de Almeida,et al.  Concluding Remarks , 2015, Clinical practice and epidemiology in mental health : CP & EMH.

[27]  K. Kremer,et al.  Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals. , 2007, Journal of chemical theory and computation.

[28]  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.

[29]  L Delle Site,et al.  Quantum locality and equilibrium properties in low-temperature parahydrogen: a multiscale simulation study. , 2012, The Journal of chemical physics.

[30]  Christoph Junghans,et al.  A reference implementation of the adaptive resolution scheme in ESPResSo , 2010, Comput. Phys. Commun..

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

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

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

[34]  Kurt Kremer,et al.  BPA-PC on a Ni111 surface: the interplay between adsorption energy and conformational entropy for different chain-end modifications. , 2004, Journal of the American Chemical Society.

[35]  Gregory A Voth,et al.  Mixed Resolution Modeling of Interactions in Condensed-Phase Systems. , 2009, Journal of chemical theory and computation.

[36]  K. Kremer,et al.  Multiscale modelling of mesoscopic phenomena triggered by quantum events: light-driven azo-materials and beyond. , 2011, Physical chemistry chemical physics : PCCP.

[37]  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.

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

[39]  N. Doltsinis,et al.  Azobenzene photoswitches in bulk materials. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[40]  Berk Hess,et al.  Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties. , 2008, Journal of the American Chemical Society.

[41]  Christof Schütte,et al.  Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. , 2012, Journal of chemical theory and computation.

[42]  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.

[43]  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 .

[44]  Kurt Kremer,et al.  Classical simulations from the atomistic to the mesoscale and back: coarse graining an liquid crystal. , 2008, Soft matter.

[45]  Gerhard Hummer,et al.  Gating transition of pentameric ligand-gated ion channels. , 2009, Biophysical journal.

[46]  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.

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

[48]  K Kremer,et al.  Specific interaction of polymers with surface defects: structure formation of polycarbonate on nickel , 2005 .

[49]  Donald G Truhlar,et al.  Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations. , 2008, Journal of chemical theory and computation.

[50]  Carsten Hartmann,et al.  Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique , 2013, 1301.4802.

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

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

[53]  Tomiki Ikeda,et al.  Optical Switching and Image Storage by Means of Azobenzene Liquid-Crystal Films , 1995, Science.