Metadynamics studies of crystal nucleation

Crystallization processes are characterized by activated events, thus the application of enhanced sampling techniques such as metadynamics in order to study phenomena occurring at the molecular scale through molecular modelling. This paper provides an introduction to metadynamics and an overview of its applications in the context of crystal nucleation.

[1]  M. Parrinello,et al.  A time-independent free energy estimator for metadynamics. , 2015, The journal of physical chemistry. B.

[2]  Marco Mazzotti,et al.  Insight into the nucleation of urea crystals from the melt , 2015 .

[3]  Marco Mazzotti,et al.  Molecular-dynamics simulations of urea nucleation from aqueous solution , 2014, Proceedings of the National Academy of Sciences.

[4]  Michele Parrinello,et al.  Well-tempered metadynamics converges asymptotically. , 2014, Physical review letters.

[5]  Michele Parrinello,et al.  1,3,5-Tris(4-bromophenyl)benzene prenucleation clusters from metadynamics. , 2014, Acta crystallographica. Section C, Structural chemistry.

[6]  Massimiliano Bonomi,et al.  PLUMED 2: New feathers for an old bird , 2013, Comput. Phys. Commun..

[7]  Marco Mazzotti,et al.  Controlling and predicting crystal shapes: the case of urea. , 2013, Angewandte Chemie.

[8]  Jörg Behler,et al.  Fast Crystallization of the Phase Change Compound GeTe by Large-Scale Molecular Dynamics Simulations. , 2013, The journal of physical chemistry letters.

[9]  M. Parrinello,et al.  Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. , 2013, Journal of chemical theory and computation.

[10]  M. Parrinello,et al.  From metadynamics to dynamics. , 2013, Physical review letters.

[11]  A. Gavezzotti Molecular Level Insights on the Liquid–Solid Transition of Large Organics by Biased Monte Carlo Simulations , 2013 .

[12]  Michele Parrinello,et al.  Transient Polymorphism in NaCl. , 2013, Journal of Chemical Theory and Computation.

[13]  G. Galli,et al.  Ice nucleation at the nanoscale probes no man’s land of water , 2013, Nature Communications.

[14]  Gregory C. Rutledge,et al.  Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene , 2013 .

[15]  M. Doherty,et al.  Homogeneous nucleation of methane hydrates: unrealistic under realistic conditions. , 2012, Journal of the American Chemical Society.

[16]  Marco Mazzotti,et al.  Uncovering molecular details of urea crystal growth in the presence of additives. , 2012, Journal of the American Chemical Society.

[17]  P. Vekilov Crystal nucleation: Nucleus in a droplet. , 2012, Nature materials.

[18]  L. Leibler,et al.  Heterogeneous nucleation of organic crystals mediated by single-molecule templates. , 2012, Nature materials.

[19]  Germany,et al.  Neural network interatomic potential for the phase change material GeTe , 2012, 1201.2026.

[20]  G. Galli,et al.  Homogeneous ice nucleation from supercooled water. , 2011, Physical chemistry chemical physics : PCCP.

[21]  B. Trout,et al.  Computer simulations of homogeneous nucleation of benzene from the melt. , 2011, The journal of physical chemistry. B.

[22]  V. Molinero,et al.  Structural transformation in supercooled water controls the crystallization rate of ice , 2011, Nature.

[23]  A. Gavezzotti Can a computer crystallize a liquid? Molecular simulation of continuous trajectories from liquid to crystalline n-hexane , 2011 .

[24]  J. Anwar,et al.  Uncovering molecular processes in crystal nucleation and growth by using molecular simulation. , 2011, Angewandte Chemie.

[25]  Christoph Dellago,et al.  UvA-DARE ( Digital Academic Repository ) Role of the prestructured surface cloud in crystal nucleation , 2011 .

[26]  Erik E. Santiso,et al.  A general set of order parameters for molecular crystals. , 2011, The Journal of chemical physics.

[27]  D. Quigley,et al.  Sampling the structure of calcium carbonate nanoparticles with metadynamics. , 2011, The Journal of chemical physics.

[28]  J. Gale,et al.  Water is the key to nonclassical nucleation of amorphous calcium carbonate. , 2010, Journal of the American Chemical Society.

[29]  David Quigley,et al.  Structural control of crystal nuclei by an eggshell protein. , 2010, Angewandte Chemie.

[30]  Yan Liang,et al.  Direct observation of nucleation and growth in amyloid self-assembly. , 2010, Journal of the American Chemical Society.

[31]  Donald G. Truhlar,et al.  Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods , 2010 .

[32]  Michele Ceriotti,et al.  Solid-liquid interface free energy through metadynamics simulations , 2009, 0911.2615.

[33]  M. Parrinello,et al.  Enhanced sampling in the well-tempered ensemble. , 2009, Physical review letters.

[34]  B. Peters Competing nucleation pathways in a mixture of oppositely charged colloids: out-of-equilibrium nucleation revisited. , 2009, The Journal of chemical physics.

[35]  M. Parrinello,et al.  A molecular dynamics study of the early stages of calcium carbonate growth. , 2009, The journal of physical chemistry. B.

[36]  Massimiliano Bonomi,et al.  Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics , 2009, J. Comput. Chem..

[37]  Rosalind J Allen,et al.  Forward flux sampling for rare event simulations , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[38]  Massimiliano Bonomi,et al.  PLUMED: A portable plugin for free-energy calculations with molecular dynamics , 2009, Comput. Phys. Commun..

[39]  Valeria Molinero,et al.  Water modeled as an intermediate element between carbon and silicon. , 2009, The journal of physical chemistry. B.

[40]  D. Quigley,et al.  Free energy and structure of calcium carbonate nanoparticles during early stages of crystallization. , 2008, The Journal of chemical physics.

[41]  L. Gago-Duport,et al.  Amorphous calcium carbonate biomineralization in the earthworm's calciferous gland: pathways to the formation of crystalline phases. , 2008, Journal of structural biology.

[42]  P M Rodger,et al.  Metadynamics simulations of ice nucleation and growth. , 2008, The Journal of chemical physics.

[43]  M. Parrinello,et al.  Well-tempered metadynamics: a smoothly converging and tunable free-energy method. , 2008, Physical review letters.

[44]  S. Rice,et al.  ADVANCES IN CHEMICAL PHYSICS , 2002 .

[45]  Michele Parrinello,et al.  Generalized neural-network representation of high-dimensional potential-energy surfaces. , 2007, Physical review letters.

[46]  R. Sear Nucleation: theory and applications to protein solutions and colloidal suspensions , 2007 .

[47]  Michele Parrinello,et al.  Freezing of a Lennard-Jones fluid: from nucleation to spinodal regime. , 2006, Physical review letters.

[48]  Simone Marsili,et al.  Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations. , 2006, The journal of physical chemistry. B.

[49]  J. Harding,et al.  The challenge of biominerals to simulations , 2006 .

[50]  A. Laio,et al.  Equilibrium free energies from nonequilibrium metadynamics. , 2006, Physical Review Letters.

[51]  A. Laio,et al.  Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. , 2006, The journal of physical chemistry. B.

[52]  David J. Earl,et al.  Parallel tempering: theory, applications, and new perspectives. , 2005, Physical chemistry chemical physics : PCCP.

[53]  Peter G Bolhuis,et al.  Interplay between structure and size in a critical crystal nucleus. , 2005, Physical review letters.

[54]  D. Frenkel,et al.  Rate of homogeneous crystal nucleation in molten NaCl. , 2005, The Journal of chemical physics.

[55]  J. Harding,et al.  Simulation of organic monolayers as templates for the nucleation of calcite crystals. , 2004, Langmuir : the ACS journal of surfaces and colloids.

[56]  P. Vekilov,et al.  Dense Liquid Precursor for the Nucleation of Ordered Solid Phases from Solution, Crystal Growth and Design , 2004 .

[57]  D. Zahn Atomistic mechanism of NaCl nucleation from an aqueous solution. , 2004, Physical review letters.

[58]  Bernhardt L Trout,et al.  Nucleation of hexagonal ice (Ih) in liquid water. , 2003, Journal of the American Chemical Society.

[59]  Peter G. Bolhuis,et al.  Transition path sampling on diffusive barriers , 2003 .

[60]  S. Weiner,et al.  Biologically Formed Amorphous Calcium Carbonate , 2003, Connective tissue research.

[61]  D. Muller,et al.  Direct observation of defect-mediated cluster nucleation , 2002, Nature materials.

[62]  D. Schüler,et al.  The biomineralization of magnetosomes in Magnetospirillum gryphiswaldense , 2002, International microbiology : the official journal of the Spanish Society for Microbiology.

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

[64]  Shinji Saito,et al.  Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing , 2002, Nature.

[65]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[66]  Peidong Yang,et al.  Direct Observation of Vapor-Liquid-Solid Nanowire Growth , 2001 .

[67]  Andrew Schofield,et al.  Real-Space Imaging of Nucleation and Growth in Colloidal Crystallization , 2001, Science.

[68]  D. Frenkel,et al.  Prediction of absolute crystal-nucleation rate in hard-sphere colloids , 2001, Nature.

[69]  B. Luo,et al.  Water activity as the determinant for homogeneous ice nucleation in aqueous solutions , 2000, Nature.

[70]  Dimo Kashchiev,et al.  Nucleation : basic theory with applications , 2000 .

[71]  R. B. Frankel,et al.  Bacterial magnetosomes: microbiology, biomineralization and biotechnological applications , 1999, Applied Microbiology and Biotechnology.

[72]  Daan Frenkel,et al.  Computer simulation study of gas–liquid nucleation in a Lennard-Jones system , 1998 .

[73]  A. McPherson,et al.  ATOMIC-FORCE-MICROSCOPY STUDIES OF PHASE SEPARATIONS IN MACROMOLECULAR SYSTEMS , 1998 .

[74]  D. Frenkel,et al.  Enhancement of protein crystal nucleation by critical density fluctuations. , 1997, Science.

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

[76]  Pieter Rein ten Wolde,et al.  Numerical calculation of the rate of crystal nucleation in a Lennard‐Jones system at moderate undercooling , 1996 .

[77]  Pablo G. Debenedetti,et al.  Metastable Liquids: Concepts and Principles , 1996 .

[78]  M. J. Ruiz-Montero,et al.  Numerical evidence for bcc ordering at the surface of a critical fcc nucleus. , 1995, Physical review letters.

[79]  Andrew E. Torda,et al.  Local elevation: A method for improving the searching properties of molecular dynamics simulation , 1994, J. Comput. Aided Mol. Des..

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

[81]  P. Steinhardt,et al.  Bond-orientational order in liquids and glasses , 1983 .

[82]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[83]  C. Tanford Macromolecules , 1994, Nature.