Molecular dynamics methods for modeling complex interactions in biomaterials.

The molecular dynamics method is a powerful computer simulation technique which provides access to the detailed time evolution (trajectory) of a system in specified conditions, such as a particular temperature or pressure. The full trajectory of the system can be analyzed using statistical mechanics tools to obtain thermodynamical quantities and dynamical properties; the mechanism of chemical reactions and other time-dependent processes, such as diffusion, can also be revealed in high detail. When applied to model extended and complex system such as biomaterials, MD simulations represent an invaluable tool to discover structure-activity relationships and rationalize biomedical applications.

[1]  A Tilocca,et al.  First-principles string molecular dynamics: an efficient approach for finding chemical reaction pathways. , 2004, The Journal of chemical physics.

[2]  N. H. Leeuw,et al.  Shell-model molecular dynamics calculations of modified silicate glasses , 2006 .

[3]  Michele Parrinello,et al.  Glucose in Aqueous Solution by First Principles Molecular Dynamics , 1998 .

[4]  A. Tilocca,et al.  Modeling the water-bioglass interface by ab initio molecular dynamics simulations. , 2009, ACS applied materials & interfaces.

[5]  A. Tilocca,et al.  Structure and Dynamics of the Flexible Triple Helix of Water inside VPI-5 Molecular Sieves , 2002 .

[6]  N. H. Leeuw,et al.  The structure of bioactive silicate glasses : New insight from molecular dynamics simulations , 2007 .

[7]  A. Tilocca.  Short- and medium-range structure of multicomponent bioactive glasses and melts: An assessment of the performances of shell-model and rigid-ion potentials. , 2008, The Journal of chemical physics.

[8]  Pastore,et al.  Theory of ab initio molecular-dynamics calculations. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[9]  A. Tilocca.  Structure and dynamics of bioactive phosphosilicate glasses and melts from ab initio molecular dynamics simulations , 2007 .

[10]  Julian D. Gale,et al.  The General Utility Lattice Program (GULP) , 2003 .

[11]  A. Tilocca,et al.  Structural effects of phosphorus inclusion in bioactive silicate glasses. , 2007, The journal of physical chemistry. B.

[12]  A. Pukrittayakamee,et al.  Simultaneous fitting of a potential-energy surface and its corresponding force fields using feedforward neural networks. , 2009, The Journal of chemical physics.

[13]  Benjamin Lindner,et al.  Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer. , 2009, Journal of chemical theory and computation.

[14]  Pedro E. M. Lopes,et al.  Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications , 2009, Theoretical chemistry accounts.

[15]  K Y Sanbonmatsu,et al.  High performance computing in biology: multimillion atom simulations of nanoscale systems. , 2007, Journal of structural biology.

[16]  Peter L. Freddolino,et al.  Molecular dynamics simulations of the complete satellite tobacco mosaic virus. , 2006, Structure.

[17]  N. D. de Leeuw,et al.  Ab initio molecular dynamics study of 45S5 bioactive silicate glass. , 2006, The journal of physical chemistry. B.

[18]  A. Tilocca,et al.  Exploring the Surface of Bioactive Glasses: Water Adsorption and Reactivity , 2008 .

[19]  Photoelasticity of sodium silicate glass from first principles , 2004, cond-mat/0407243.

[20]  A. Tilocca.  Structural models of bioactive glasses from molecular dynamics simulations , 2009, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[21]  M. Gillan,et al.  Molecular dynamics simulation of alkali-metal diffusion in alkali-metal disilicate glasses , 1997 .

[22]  A. Tilocca,et al.  Surface signatures of bioactivity: MD simulations of 45S and 65S silicate glasses. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[23]  F Kargl,et al.  Channel formation and intermediate range order in sodium silicate melts and glasses. , 2004, Physical review letters.

[24]  M. Tuckerman,et al.  Reaction pathway of the [4 + 2] Diels-Alder adduct formation on Si(100)-2 x 1. , 2004, Journal of the American Chemical Society.

[25]  D. Marx.  Ab initio molecular dynamics: Theory and Implementation , 2000 .

[26]  Jonathan C. Knowles,et al.  Structural Characteristics of Antibacterial Bioresorbable Phosphate Glass , 2008 .

[27]  I. Bruce,et al.  Inorganic materials for bone repair or replacement applications. , 2007, Nanomedicine.

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

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

[30]  K. Powers,et al.  Effect of pH and ionic strength on the reactivity of Bioglass 45S5. , 2005, Biomaterials.

[31]  Michael L Klein,et al.  Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics. , 2005, Journal of the American Chemical Society.

[32]  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.

[33]  D. Chandler,et al.  Introduction To Modern Statistical Mechanics , 1987 .

[34]  Aneesur Rahman,et al.  Correlations in the Motion of Atoms in Liquid Argon , 1964 .

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