Coarse-Grained Simulations of Macromolecules : From DNA to Nanocomposites

This review discusses multiscale modeling and simulations of macromolecules and macromolecular systems in the context of two specific examples. In the first, recent attempts to develop coarse-grained representations of DNA are reviewed, and a discussion of recent predictions of such models is presented, particularly in the context of DNA melting and rehybridization. The second example considers polymer nanocomposites; a review of recent simulations is presented, with an emphasis on the description of entanglements in such systems and new methods for the study of the segregation of nanoparticles that arises in copolymers, in which composition heterogeneity can be used to control nanoparticle position and develop an increased understanding of nanoparticle-polymer interactions.

[1]  Sanat K. Kumar,et al.  Lattice Monte Carlo Simulations of Chain Conformations in Polymer Nanocomposites , 2005 .

[2]  E. Sambriski,et al.  Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[3]  Alan M. Ferrenberg,et al.  New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.

[4]  U. Hansmann.  Parallel tempering algorithm for conformational studies of biological molecules , 1997, physics/9710041.

[5]  M. Graham,et al.  Multiple free energy minima in systems of confined tethered polymers—toward soft nanomechanical bistable elements , 2009 .

[6]  D. Landau,et al.  Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.

[7]  Sanat K. Kumar,et al.  Nanocomposites: structure, phase behavior, and properties. , 2010, Annual review of chemical and biomolecular engineering.

[8]  Anna C. Balazs,et al.  Nanoparticle Polymer Composites: Where Two Small Worlds Meet , 2006, Science.

[9]  D. Theodorou,et al.  A novel Monte Carlo scheme for the rapid equilibration of atomistic model polymer systems of precisely defined molecular architecture. , 2002, Physical review letters.

[10]  J. Ghosh,et al.  Simulations of glasses: multiscale modeling and density of states Monte-Carlo simulations , 2006 .

[11]  Marina Guenza,et al.  Theoretical models for bridging timescales in polymer dynamics , 2008 .

[12]  P. Nealey,et al.  Local mechanical properties of polymeric nanocomposites. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[13]  Bumjoon J. Kim,et al.  Hybrid particle-field simulations of polymer nanocomposites. , 2006, Physical review letters.

[14]  Juan J. de Pablo,et al.  Multiscale Modeling in Advanced Materials Research: Challenges, Novel Methods, and Emerging Applications , 2007 .

[15]  Masato Makino,et al.  Simulation of DNA motion in a microchannel using stochastic rotation dynamics. , 2007, The Journal of chemical physics.

[16]  Christopher J. Ellison,et al.  Mean-field models of structure and dispersion of polymer-nanoparticle mixtures , 2010 .

[17]  Martin Kröger,et al.  Projection from an atomistic chain contour to its primitive path , 2002 .

[18]  Xiang-Jun Lu,et al.  3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures , 2008, Nature Protocols.

[19]  Florian Müller-Plathe,et al.  Scale-Hopping in Computer Simulations of Polymers , 2002 .

[20]  M. Vacatello.  Molecular Arrangements in Polymer-Based Nanocomposites , 2002 .

[21]  Adrien Saladin,et al.  Insights on protein‐DNA recognition by coarse grain modelling , 2008, J. Comput. Chem..

[22]  Modeling Self-Assembly Processes Driven by Nonbonded Interactions in Soft Materials , 2008 .

[23]  N. Cozzarelli,et al.  DNA overwinds when stretched , 2006, Nature.

[24]  S. A. Baeurle.  Multiscale modeling of polymer materials using field-theoretic methodologies: a survey about recent developments , 2008 .

[25]  Anna C. Balazs,et al.  Block Copolymer-Directed Assembly of Nanoparticles: Forming Mesoscopically Ordered Hybrid Materials , 2002 .

[26]  K. Schweizer,et al.  Structure, scattering patterns and phase behavior of polymer nanocomposites with nonspherical fillers , 2010 .

[27]  Karen Drukker,et al.  A Model for Simulating Dynamics of DNA Denaturation , 2000 .

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

[29]  N. Go,et al.  Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. , 2009 .

[30]  J. Douglas,et al.  Model for reversible nanoparticle assembly in a polymer matrix. , 2008, The Journal of chemical physics.

[31]  P. Nealey,et al.  Theoretically informed coarse grain simulations of block copolymer melts: method and applications , 2009 .

[32]  Todd Emrick,et al.  Self-directed self-assembly of nanoparticle/copolymer mixtures , 2005, Nature.

[33]  B. Brooks,et al.  Multiscale methods for macromolecular simulations. , 2008, Current opinion in structural biology.

[34]  J. Weng,et al.  Atomic-scale interactions at the interface of biopolymer/hydroxyapatite , 2008, Biomedical materials.

[35]  Julien Dorier,et al.  DNA supercoiling inhibits DNA knotting , 2008, Nucleic acids research.

[36]  R Lavery,et al.  From atomic to mesoscopic descriptions of the internal dynamics of DNA. , 1999, Biophysical journal.

[37]  J J de Pablo,et al.  Simulation of phase transitions in fluids. , 1999, Annual review of physical chemistry.

[38]  Q. Zhang,et al.  Structure-related diffusion in poly(methyl methacrylate)/polyhedral oligomeric silsesquioxanes composites: A molecular dynamics simulation study , 2009 .

[39]  The Effect of Nanoparticle Shape on Polymer-Nanocomposite Rheology and Tensile Strength , 2007, cond-mat/0701607.

[40]  A. E. Likhtman.  Single-Chain Slip-Link Model of Entangled Polymers: Simultaneous Description of Neutron Spin-Echo, Rheology, and Diffusion , 2005 .

[41]  S. K. Sukumaran,et al.  Modeling Entangled Dynamics: Comparison between Stochastic Single-Chain and Multichain Models , 2009 .

[42]  Gregory N. Toepperwein,et al.  Entanglement network in nanoparticle reinforced polymers. , 2009, The Journal of chemical physics.

[43]  R. Larson,et al.  Concentration Dependence of Shear-Induced Polymer Migration in DNA Solutions near a Surface , 2007 .

[44]  Kurt Kremer,et al.  Rheology and Microscopic Topology of Entangled Polymeric Liquids , 2004, Science.

[45]  Jean-Louis Barrat,et al.  Molecular dynamics simulations of glassy polymers , 2010, 1002.2065.

[46]  Hejun Li,et al.  Atomistic and mesoscale interface simulation of graphite nanosheet/AgCl/polypyrrole composite , 2009 .

[47]  S. S. Sternstein,et al.  Reinforcement Mechanism of Nanofilled Polymer Melts As Elucidated by Nonlinear Viscoelastic Behavior , 2002 .

[48]  Christian Holm,et al.  Modeling the separation of macromolecules: A review of current computer simulation methods , 2009, Electrophoresis.

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

[50]  K. Schweizer,et al.  Molecular theories of polymer nanocomposites , 2010 .

[51]  E. Shaqfeh,et al.  The conformational dynamics of lambda-DNA in the anti-Brownian electrokinetic trap: Brownian dynamics and Monte Carlo simulation. , 2009, The Journal of chemical physics.

[52]  Juan J. de Pablo,et al.  Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides , 2011 .

[53]  Gregory N. Toepperwein,et al.  Dynamics of a Glassy Polymer Nanocomposite during Active Deformation , 2009 .

[54]  Doros N. Theodorou,et al.  Topological Analysis of Linear Polymer Melts: A Statistical Approach , 2006 .

[55]  D. Schwartz,et al.  DNA Molecules in Microfluidic Oscillatory Flow. , 2005, Macromolecules.

[56]  Bumjoon J. Kim,et al.  Nanoparticle surfactants as a route to bicontinuous block copolymer morphologies. , 2007, Langmuir : the ACS journal of surfaces and colloids.

[57]  Nahum Shiffeldrim,et al.  Cyclization of short DNA fragments and bending fluctuations of the double helix. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[58]  J. D. de Pablo,et al.  Optimal allocation of replicas in parallel tempering simulations. , 2005, The Journal of chemical physics.

[59]  J J de Pablo,et al.  A mesoscale model of DNA and its renaturation. , 2009, Biophysical journal.

[60]  Alfred J. Crosby,et al.  Polymer Nanocomposites: The “Nano” Effect on Mechanical Properties , 2007 .

[61]  Q. Yan,et al.  Fast calculation of the density of states of a fluid by Monte Carlo simulations. , 2003, Physical review letters.

[62]  Po-han Lin,et al.  Molecular Simulation of Cross-Linked Epoxy and Epoxy−POSS Nanocomposite , 2009 .

[63]  Linda S. Schadler,et al.  Anisotropic self-assembly of spherical polymer-grafted nanoparticles. , 2009, Nature materials.

[64]  M. Graham,et al.  Conformation and dynamics of single DNA molecules in parallel-plate slit microchannels. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[65]  Juan J de Pablo,et al.  Fast computation of many-particle hydrodynamic and electrostatic interactions in a confined geometry. , 2007, Physical review letters.

[66]  K. Horio,et al.  Fluctuation in entanglement positions via elastic slip-links. , 2010, The Journal of chemical physics.

[67]  Craig J Hawker,et al.  General Strategies for Nanoparticle Dispersion , 2006, Science.

[68]  J. Pablo,et al.  Hyperparallel tempering Monte Carlo simulation of polymeric systems , 2000 .

[69]  M. Graham,et al.  Concentration distributions during flow of confined flowing polymer solutions at finite concentration: slit and grooved channel , 2008 .

[70]  A. Yu,et al.  Multiscale modeling and simulation of polymer nanocomposites , 2008 .

[71]  M. Kenward,et al.  Brownian dynamics simulations of single-stranded DNA hairpins. , 2009, The Journal of chemical physics.

[72]  P. Mele,et al.  Effect of Filler Particle Size on the Properties of Model Nanocomposites , 2008 .

[73]  Victor A. Beck,et al.  Dynamics of DNA Polymers in Post Arrays: Comparison of Single Molecule Experiments and Simulations , 2007 .

[74]  M. Boyce,et al.  Multiscale micromechanical modeling of polymer/clay nanocomposites and the effective clay particle , 2004 .

[75]  Tamar Schlick,et al.  Mesoscale simulations of two nucleosome-repeat length oligonucleosomes. , 2009, Physical chemistry chemical physics : PCCP.

[76]  V. Zhurkin,et al.  Modeling DNA deformations. , 2000, Current opinion in structural biology.

[77]  B. Alder,et al.  Tethered DNA dynamics in shear flow. , 2009, The Journal of chemical physics.

[78]  K. Schweizer,et al.  Contact Aggregation, Bridging, and Steric Stabilization in Dense Polymer−Particle Mixtures , 2005 .

[79]  Juan J de Pablo,et al.  DNA dynamics in a microchannel. , 2003, Physical review letters.

[80]  Tamar Schlick,et al.  Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions , 2009, Proceedings of the National Academy of Sciences.

[81]  Robert K Z Tan,et al.  YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models. , 2006, Journal of chemical theory and computation.

[82]  Tamar Schlick,et al.  Special Section On Multiscale Modeling In Biology , 2006, Multiscale Model. Simul..

[83]  Eric S. G. Shaqfeh,et al.  The dynamics of single-molecule DNA in flow , 2005 .

[84]  Sagar A. Pandit,et al.  Multiscale simulations of heterogeneous model membranes. , 2009, Biochimica et biophysica acta.

[85]  A. Lyubartsev,et al.  New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles , 1992 .

[86]  J. Šponer,et al.  Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. , 2009, Journal of chemical theory and computation.

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

[88]  Roland Faller,et al.  Coarse-grained modeling of lipids. , 2009, Chemistry and physics of lipids.

[89]  Monica H Lamm,et al.  Molecular dynamics simulation of mixed matrix nanocomposites containing polyimide and polyhedral oligomeric silsesquioxane (POSS) , 2009 .

[90]  J. Hernandez-Ortiz,et al.  Hydrodynamic effects on the translocation rate of a polymer through a pore. , 2009, The Journal of chemical physics.

[91]  Huiman Kang,et al.  Placement control of nanomaterial arrays on the surface-reconstructed block copolymer thin films. , 2009, ACS nano.

[92]  P. Nealey,et al.  Behavior of single nanoparticle/homopolymer chain in ordered structures of diblock copolymers , 2003 .

[93]  D. Long,et al.  A Microscopic Model for the Reinforcement and the Nonlinear Behavior of Filled Elastomers and Thermoplastic Elastomers (Payne and Mullins Effects) , 2008 .

[94]  Juan J de Pablo,et al.  A single-molecule barcoding system using nanoslits for DNA analysis , 2007, Proceedings of the National Academy of Sciences.

[95]  Bumjoon J. Kim,et al.  Control of nanoparticle location in block copolymers. , 2005, Journal of the American Chemical Society.

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

[97]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

[98]  C. Dellago,et al.  Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events , 2009 .

[99]  Brian J. Banaszak,et al.  A new double-rebridging technique for linear polyethylene , 2003 .

[100]  J. Pablo,et al.  Multicanonical parallel tempering , 2002, cond-mat/0201179.

[101]  Sergio Pantano,et al.  A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. , 2010, Journal of chemical theory and computation.

[102]  Theodoros E. Karakasidis,et al.  Multiscale modeling in nanomaterials science , 2007 .

[103]  P. Nealey,et al.  Monte Carlo Simulations of a Coarse-Grain Model for Block Copolymer Systems , 2008 .

[104]  D. Schwartz,et al.  A coarse grain model for DNA. , 2007, The Journal of chemical physics.

[105]  Andrew J. Senesi,et al.  Assembly and organization processes in DNA-directed colloidal crystallization , 2009, Proceedings of the National Academy of Sciences.

[106]  Thomas E Cheatham,et al.  Simulation and modeling of nucleic acid structure, dynamics and interactions. , 2004, Current opinion in structural biology.

[107]  Charles L. Brooks,et al.  Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics , 2009, International journal of molecular sciences.

[108]  Sharon C. Glotzer,et al.  Origin of Particle Clustering in a Simulated Polymer Nanocomposite and its Impact on Rheology , 2003 .

[109]  P. Nealey,et al.  Calculation of local mechanical properties of filled polymers. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[110]  J. Pablo,et al.  Hyper-parallel tempering Monte Carlo: Application to the Lennard-Jones fluid and the restricted primitive model , 1999 .

[111]  A. Balazs,et al.  Thermodynamic Behavior of Particle/Diblock Copolymer Mixtures: Simulation and Theory , 2000 .

[112]  Martin Kröger,et al.  Shortest multiple disconnected path for the analysis of entanglements in two- and three-dimensional polymeric systems , 2005, Comput. Phys. Commun..

[113]  Modesto Orozco,et al.  Recent advances in the study of nucleic acid flexibility by molecular dynamics. , 2008, Current opinion in structural biology.

[114]  N. Ghoniem,et al.  Multiscale modelling of nanomechanics and micromechanics: an overview , 2003 .

[115]  Mark P. Stoykovich,et al.  Directed assembly of cylinder-forming block copolymers into patterned structures to fabricate arrays of spherical domains and nanoparticles , 2007 .

[116]  K. Schweizer,et al.  Many body effects on the phase separation and structure of dense polymer-particle melts. , 2008, The Journal of chemical physics.

[117]  Alexander Vologodskii,et al.  Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. , 2006, Biophysical journal.

[118]  J. Rottler,et al.  A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality. , 2009, The Journal of chemical physics.

[119]  G. Schatz,et al.  DNA melting in small-molecule-DNA-hybrid dimer structures: experimental characterization and coarse-grained molecular dynamics simulations. , 2010, The journal of physical chemistry. B.

[120]  D. Schwartz,et al.  Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis , 2009, Proceedings of the National Academy of Sciences.

[121]  A. S. Krasilnikov,et al.  Basis for Structural Diversity in Homologous RNAs , 2004, Science.

[122]  W. Olson,et al.  DNA Architecture, Deformability, and Nucleosome Positioning , 2010, Journal of biomolecular structure & dynamics.

[123]  H M Berman,et al.  A standard reference frame for the description of nucleic acid base-pair geometry. , 2001, Journal of molecular biology.

[124]  Gregory A Voth,et al.  A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties. , 2005, The Journal of chemical physics.

[125]  Nikos Ch. Karayiannis,et al.  Combined Molecular Algorithms for the Generation, Equilibration and Topological Analysis of Entangled Polymers: Methodology and Performance , 2009, International journal of molecular sciences.

[126]  D. Theodorou,et al.  From atomistic simulations to slip-link models of entangled polymer melts: Hierarchical strategies for the prediction of rheological properties , 2006 .

[127]  P. Kollman,et al.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. , 1999, Journal of biomolecular structure & dynamics.

[128]  Nils B Becker,et al.  From rigid base pairs to semiflexible polymers: coarse-graining DNA. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[129]  C. Sun,et al.  A molecular dynamics simulation study of inclusion size effect on polymeric nanocomposites , 2007 .

[130]  Tamar Schlick,et al.  Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model , 2006, Proceedings of the National Academy of Sciences.

[131]  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.

[132]  R. Larson,et al.  Brownian dynamics simulations of isolated polymer molecules in shear flow near adsorbing and nonadsorbing surfaces , 2002 .

[133]  Juan J. de Pablo,et al.  Monte Carlo simulation of the chemical potential of polymers in an expanded ensemble , 1995 .

[134]  R. Hamers,et al.  Hierarchical assembly of nanoparticle superstructures from block copolymer-nanoparticle composites. , 2008, Physical review letters.

[135]  Valentina Tozzini,et al.  Multiscale modeling of proteins. , 2010, Accounts of chemical research.

[136]  Marcus Müller,et al.  Single-chain dynamics in a homogeneous melt and a lamellar microphase: a comparison between Smart Monte Carlo dynamics, slithering-snake dynamics, and slip-link dynamics. , 2008, The Journal of chemical physics.

[137]  O. Borodin,et al.  A molecular dynamics simulation and quantum chemistry study of poly(dimethylsiloxane)–silica nanoparticle interactions , 2007 .

[138]  A. Balazs,et al.  Predicting the Mesophases of Copolymer-Nanoparticle Composites , 2001, Science.

[139]  A. Yu,et al.  Molecular dynamics simulations of organoclays and polymer nanocomposites , 2008 .

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

[141]  Lee-Wei Yang,et al.  Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives , 2008, Bioinformatics and biology insights.

[142]  Mark F. Horstemeyer,et al.  Review of Hierarchical Multiscale Modeling to Describe the Mechanical Behavior of Amorphous Polymers , 2009 .

[143]  Marcus Müller,et al.  Monte Carlo Simulations of a Coarse Grain Model for Block Copolymers and Nanocomposites , 2008 .