Methods for multiscale modeling of membranes

Multiscale modeling is a recent approach to simulating molecular systems, such as membranes and liposomes, in which different levels of detail are combined. By using distinct models, it is often possible to speed up or enrich the sampling of a given system. Examples are the use in molecular dynamics simulations of both coarse-grained and fine-grained representations, either simultaneously or alternating in time or space domains. Another possible example is the combination of Monte Carlo and molecular dynamics simulations. This chapter reviews the existing proposed methods of multiscale modeling and simulation and also presents new insights into this fascinating new trend.

[1]  Kurt Kremer,et al.  Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations , 2006 .

[2]  Noam Bernstein,et al.  Spanning the continuum to quantum length scales in a dynamic simulation of brittle fracture , 1998 .

[3]  Florian Müller-Plathe,et al.  Mapping atomistic simulations to mesoscopic models: a systematic coarse-graining procedure for vinyl polymer chains. , 2005, The journal of physical chemistry. B.

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

[5]  Gregory A Voth,et al.  Probing the molecular-scale lipid bilayer response to shear flow using nonequilibrium molecular dynamics. , 2005, The journal of physical chemistry. B.

[6]  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.

[7]  Sidney Yip,et al.  Coupling continuum to molecular-dynamics simulation: Reflecting particle method and the field estimator , 1998 .

[8]  Nicolae Goga,et al.  New Multiscale Heat Transfer Techniques , 2011 .

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

[10]  Lydia E Kavraki,et al.  From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes , 2007, Proteins.

[11]  Gregory A Voth,et al.  Reconstructing atomistic detail for coarse-grained models with resolution exchange. , 2008, The Journal of chemical physics.

[12]  Berni J. Alder.  Highly discretized dynamics , 1997 .

[13]  Rafael Delgado-Buscalioni,et al.  Hybrid molecular-continuum fluid models: implementation within a general coupling framework , 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[14]  J. Q. Broughton,et al.  Concurrent Coupling of Length Scales in Solid State Systems , 2000 .

[15]  Alejandro L. Garcia,et al.  Adaptive Mesh and Algorithm Refinement Using Direct Simulation Monte Carlo , 1999 .

[16]  Wilfred F van Gunsteren,et al.  Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. , 2006, The Journal of chemical physics.

[17]  Aldo Frezzotti,et al.  A particle scheme for the numerical solution of the Enskog equation , 1997 .

[18]  Jorn Eggers,et al.  New Algorithms for Application in the Direct Simulation Monte Carlo Method , 2008 .

[19]  D Hash,et al.  A hybrid DSMC/Navier-Stokes solver , 1995 .

[20]  D. C. Wadsworth,et al.  One-dimensional hybrid continuum/particle simulation approach for rarefied hypersonic flows , 1990 .

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

[22]  Kurt Kremer,et al.  Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate. , 2006, Soft matter.

[23]  A. A. van Steenhoven,et al.  Molecular Dynamics and Monte Carlo Simulations for Heat Transfer in Micro-and Nanochannels , .

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

[25]  Wolfgang Banzhaf,et al.  Artificial ChemistriesA Review , 2001, Artificial Life.

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

[27]  David B. Goldstein,et al.  Hybrid Euler/Direct Simulation Monte Carlo Calculation of Unsteady Slit Flow , 2000 .

[28]  Wilfred F. van Gunsteren,et al.  GROMOS Force Field , 2002 .

[29]  Nicolae Goga,et al.  New Gromacs Implementations for Multiscaling Space MD , 2009 .

[30]  Aldo Frezzotti,et al.  Monte Carlo simulation of the heat flow in a dense hard sphere gas , 1999 .

[31]  H. Berendsen.  Simulating the Physical World , 2004 .

[32]  Eirik Grude Flekkøy,et al.  Hybrid model for combined particle and continuum dynamics , 2000 .

[33]  Hassan Hassan,et al.  A decoupled DSMC/Navier-Stokes analysis of a transitional flow experiment , 1996 .

[34]  O'Connell,et al.  Molecular dynamics-continuum hybrid computations: A tool for studying complex fluid flows. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[35]  Patrick Le Tallec,et al.  Coupling Boltzmann and Navier-Stokes Equations by Half Fluxes , 1997 .

[36]  Klaus Schulten,et al.  Disassembly of nanodiscs with cholate. , 2007, Nano letters.

[37]  Alessandra Villa,et al.  Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation. , 2009, Physical chemistry chemical physics : PCCP.

[38]  S. Harvey,et al.  The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition , 1998, J. Comput. Chem..

[39]  Andrzej J. Rzepiela,et al.  Reconstruction of atomistic details from coarse‐grained structures , 2010, J. Comput. Chem..

[40]  Timothy S. Carpenter,et al.  Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. , 2008, Biophysical journal.

[41]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[42]  A. Patera,et al.  Heterogeneous Atomistic-Continuum Representations for Dense Fluid Systems , 1997 .

[43]  O. Aktas,et al.  A Combined Continuum/DSMC Technique for Multiscale Analysis of Microfluidic Filters , 2002 .

[44]  Moulay D. Tidriri,et al.  Coupling Boltzmann and Navier-Stokes Equations by Friction , 1996 .

[45]  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.

[46]  Edward Lyman,et al.  Resolution Exchange Simulation with Incremental Coarsening. , 2006, Journal of chemical theory and computation.

[47]  Siewert J Marrink,et al.  Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. , 2011, Physical chemistry chemical physics : PCCP.

[48]  A. J. Markvoort,et al.  Molecular dynamics study of the influence of wall-gas interactions on heat flow in nanochannels. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[49]  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.

[50]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[51]  Paj Peter Hilbers,et al.  Hybrid method coupling molecular dynamics and Monte Carlo simulations to study the properties of gases in microchannels and nanochannels. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[52]  Marek Cieplak,et al.  Proteins in a shear flow. , 2007, The Journal of chemical physics.

[53]  N. Hadjiconstantinou.  Regular Article: Hybrid Atomistic–Continuum Formulations and the Moving Contact-Line Problem , 1999 .