Development of multiscale simulation methods

[1]  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.

[2]  R. Epand,et al.  Relationship of membrane curvature to the formation of pores by magainin 2. , 1998, Biochemistry.

[3]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

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

[5]  Julien Michel,et al.  Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. , 2008, The journal of physical chemistry. B.

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

[7]  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.

[8]  Huey W. Huang Molecular mechanism of antimicrobial peptides: the origin of cooperativity. , 2006, Biochimica et biophysica acta.

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

[10]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

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

[12]  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.

[13]  B. Bechinger,et al.  Zwitterionic phospholipids and sterols modulate antimicrobial peptide-induced membrane destabilization. , 2007, Biophysical journal.

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

[15]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

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

[17]  W G Noid,et al.  Recovering physical potentials from a model protein databank , 2010, Proceedings of the National Academy of Sciences.

[18]  Ű. Langel,et al.  Mechanism of the cell-penetrating peptide transportan 10 permeation of lipid bilayers. , 2007, Biophysical journal.

[19]  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.

[20]  R. Hancock Peptide antibiotics , 1997, The Lancet.

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

[22]  Jim Pfaendtner,et al.  A systematic methodology for defining coarse-grained sites in large biomolecules. , 2008, Biophysical journal.

[23]  Durba Sengupta,et al.  Toroidal pores formed by antimicrobial peptides show significant disorder. , 2008, Biochimica et biophysica acta.

[24]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

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

[26]  Gregoria Illya,et al.  Coarse-grained simulation studies of peptide-induced pore formation. , 2008, Biophysical journal.

[27]  W G Noid,et al.  Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration. , 2010, The Journal of chemical physics.

[28]  E. Vanden-Eijnden,et al.  Mori-Zwanzig formalism as a practical computational tool. , 2010, Faraday discussions.

[29]  H. Berendsen,et al.  A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field , 1998 .

[30]  Avisek Das,et al.  The multiscale coarse-graining method. V. Isothermal-isobaric ensemble. , 2010, The Journal of chemical physics.

[31]  Birgit Schiøtt,et al.  Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. , 2008, Biophysical journal.

[32]  P E Correa,et al.  The building of protein structures from alpha-carbon coordinates. , 1990, Proteins.

[33]  Wilfred F van Gunsteren,et al.  On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. , 2009, Physical chemistry chemical physics : PCCP.

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

[35]  Thomas Huber,et al.  G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. , 2007, Journal of the American Chemical Society.

[36]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[37]  L. Sarkisov,et al.  Spontaneous formation of a barrel-stave pore in a coarse-grained model of the synthetic LS3 peptide and a DPPC lipid bilayer. , 2009, The journal of physical chemistry. B.

[38]  J. Onuchic,et al.  Theory of Protein Folding This Review Comes from a Themed Issue on Folding and Binding Edited Basic Concepts Perfect Funnel Landscapes and Common Features of Folding Mechanisms , 2022 .

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

[40]  J. Schlitter Estimation of absolute and relative entropies of macromolecules using the covariance matrix , 1993 .

[41]  Christian Kandt,et al.  Computer simulation of antimicrobial peptides. , 2007, Current medicinal chemistry.

[42]  R. Larson,et al.  The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.

[43]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[44]  M. Zasloff Antimicrobial peptides of multicellular organisms , 2002, Nature.

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

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

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

[48]  Peter J Bond,et al.  Coarse-grained simulations of the membrane-active antimicrobial Peptide maculatin 1.1. , 2008, Biophysical journal.

[49]  R. Hancock,et al.  Cationic host defense (antimicrobial) peptides. , 2006, Current opinion in immunology.

[50]  Theodora Spyriouni,et al.  Coarse-Grained and Reverse-Mapped United-Atom Simulations of Long-Chain Atactic Polystyrene Melts: Structure, Thermodynamic Properties, Chain Conformation, and Entanglements , 2007 .

[51]  Wilfred F van Gunsteren,et al.  Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.

[52]  C. Dempsey The actions of melittin on membranes. , 1990, Biochimica et biophysica acta.

[53]  Siewert J Marrink,et al.  Cholesterol shows preference for the interior of polyunsaturated lipid membranes. , 2008, Journal of the American Chemical Society.

[54]  Ilpo Vattulainen,et al.  Multiscale modeling of emergent materials: biological and soft matter. , 2009, Physical chemistry chemical physics : PCCP.

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

[56]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

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

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

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

[60]  H. Berendsen,et al.  A LEAP-FROG ALGORITHM FOR STOCHASTIC DYNAMICS , 1988 .

[61]  H. C. Öttinger Systematic Coarse Graining: “Four Lessons and A Caveat” from Nonequilibrium Statistical Mechanics , 2007 .

[62]  Alex H. de Vries,et al.  Effects of bundling on the properties of the SPC water model , 2010 .

[63]  Wilfred F van Gunsteren,et al.  Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.

[64]  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.

[65]  Alan E. Mark,et al.  The GROMOS96 Manual and User Guide , 1996 .

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

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

[68]  A. Louis Beware of density dependent pair potentials , 2002, cond-mat/0205110.

[69]  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.

[70]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[71]  K. Brogden Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? , 2005, Nature Reviews Microbiology.

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

[73]  Chris Oostenbrink,et al.  A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..

[74]  Sergei Izvekov,et al.  The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials. , 2010, The Journal of chemical physics.

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

[76]  Gregory A. Voth,et al.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.

[77]  Siewert J. Marrink,et al.  Release of content through mechano-sensitive gates in pressurized liposomes , 2010, Proceedings of the National Academy of Sciences.

[78]  David Baker,et al.  Motif‐directed flexible backbone design of functional interactions , 2009, Protein science : a publication of the Protein Society.

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

[80]  D Peter Tieleman,et al.  Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop. , 2006, Journal of the American Chemical Society.

[81]  Siewert J. Marrink,et al.  Methodological issues in lipid bilayer simulations , 2003 .

[82]  B. Bechinger,et al.  Structure and Functions of Channel-Forming Peptides: Magainins, Cecropins, Melittin and Alamethicin , 1997, The Journal of Membrane Biology.

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

[84]  P. F. Almeida,et al.  A quantitative model for the all-or-none permeabilization of phospholipid vesicles by the antimicrobial peptide cecropin A. , 2008, Biophysical journal.

[85]  Siewert J Marrink,et al.  Martini Coarse-Grained Force Field: Extension to Carbohydrates. , 2009, Journal of chemical theory and computation.

[86]  Siewert J Marrink,et al.  Antimicrobial peptides in action. , 2006, Journal of the American Chemical Society.

[87]  Jt Johan Padding,et al.  Time and length scales of polymer melts studied by coarse-grained molecular dynamics simulations , 2002 .

[88]  Wilfred F. van Gunsteren,et al.  Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry , 1987, J. Comput. Aided Mol. Des..

[89]  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.

[90]  A. Laio,et al.  Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[91]  Durba Sengupta,et al.  Polarizable Water Model for the Coarse-Grained MARTINI Force Field , 2010, PLoS Comput. Biol..

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

[93]  Marilisa Neri,et al.  Coarse-grained model of proteins incorporating atomistic detail of the active site. , 2005, Physical review letters.

[94]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[95]  I. Vattulainen,et al.  Molecular mechanism for lipid flip-flops. , 2007, The journal of physical chemistry. B.

[96]  N. Fujii,et al.  An antimicrobial peptide, magainin 2, induced rapid flip-flop of phospholipids coupled with pore formation and peptide translocation. , 1996, Biochemistry.

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

[98]  O. Berger,et al.  Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. , 1997, Biophysical journal.

[99]  Martin Karplus,et al.  Molecular dynamics simulations with experimental restraints , 1991 .

[100]  Siewert J Marrink,et al.  Lipids on the move: simulations of membrane pores, domains, stalks and curves. , 2009, Biochimica et biophysica acta.

[101]  Ilpo Vattulainen,et al.  Conformational analysis of lipid molecules by self-organizing maps. , 2007, The Journal of chemical physics.

[102]  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.

[103]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[104]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[105]  E. Dufourc,et al.  Pore formation induced by an antimicrobial peptide: electrostatic effects. , 2008, Biophysical journal.

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

[107]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[108]  Shekhar Garde,et al.  Do Inverse Monte Carlo Algorithms Yield Thermodynamically Consistent Interaction Potentials , 2006 .

[109]  Nicolae Goga,et al.  Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. , 2010, Faraday discussions.

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

[111]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[112]  H. Berendsen,et al.  Efficient Algorithms for Langevin and DPD Dynamics. , 2012, Journal of chemical theory and computation.

[113]  Gregory A Voth,et al.  Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. , 2007, The Journal of chemical physics.

[114]  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.

[115]  B. Bechinger,et al.  Detergent-like actions of linear amphipathic cationic antimicrobial peptides. , 2006, Biochimica et biophysica acta.

[116]  Edward Lyman,et al.  Resolution exchange simulation. , 2005, Physical review letters.

[117]  William George Noid,et al.  A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials† , 2010 .

[118]  P. Axelsen A chaotic pore model of polypeptide antibiotic action. , 2008, Biophysical journal.

[119]  R. Larson,et al.  Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer. , 2008, The journal of physical chemistry. B.

[120]  Siewert J. Marrink,et al.  The molecular face of lipid rafts in model membranes , 2008, Proceedings of the National Academy of Sciences.

[121]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[122]  Cecilia Clementi,et al.  Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.

[123]  Wilfred F. van Gunsteren,et al.  A generalized reaction field method for molecular dynamics simulations , 1995 .

[124]  Kurt Kremer,et al.  Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back , 2009 .

[125]  Klaus Schulten,et al.  Four-scale description of membrane sculpting by BAR domains. , 2008, Biophysical journal.

[126]  M. Ortiz,et al.  Quasicontinuum analysis of defects in solids , 1996 .

[127]  S. White,et al.  Sizing membrane pores in lipid vesicles by leakage of co-encapsulated markers: pore formation by melittin. , 1997, Biophysical journal.

[128]  Y. Shai,et al.  Mode of action of membrane active antimicrobial peptides. , 2002, Biopolymers.

[129]  Robert E W Hancock,et al.  Rational Design of α-Helical Antimicrobial Peptides with Enhanced Activities and Specificity/Therapeutic Index* , 2005, Journal of Biological Chemistry.

[130]  Margaret E. Johnson,et al.  Representability problems for coarse-grained water potentials. , 2007, The Journal of chemical physics.

[131]  Kurt Kremer,et al.  Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? , 2009, The European physical journal. E, Soft matter.

[132]  K. Miyajima,et al.  Pore formation and translocation of melittin. , 1997, Biophysical journal.

[133]  Qiang Shi,et al.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. , 2006, The journal of physical chemistry. B.