Theory and methods for rare events

[1]  T. Vegge,et al.  Hydrogen dynamics in Na3AlH6: a combined density functional theory and quasielastic neutron scattering study. , 2007, The journal of physical chemistry. B.

[2]  C. Dellago,et al.  Transition path sampling and the calculation of rate constants , 1998 .

[3]  Giovanni Ciccotti,et al.  Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology. Volume 2 (Lecture Notes in Physics) , 2006 .

[4]  A. Bensoussan,et al.  Asymptotic analysis for periodic structures , 1979 .

[5]  G. Ciccotti,et al.  Short range hydrogen diffusion in Na3AlH6. , 2011, Physical chemistry chemical physics : PCCP.

[6]  G. Ciccotti,et al.  Temperature accelerated Monte Carlo (TAMC): a method for sampling the free energy surface of non-analytical collective variables. , 2011, Physical chemistry chemical physics : PCCP.

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

[8]  A. Voter,et al.  Temperature-accelerated dynamics for simulation of infrequent events , 2000 .

[9]  G. Ciccotti,et al.  Hydrodynamics from statistical mechanics: combined dynamical-NEMD and conditional sampling to relax an interface between two immiscible liquids. , 2011, Physical chemistry chemical physics : PCCP.

[10]  M. Tuckerman,et al.  On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles , 2002 .

[11]  Exact rate calculations by trajectory parallelization and tilting. , 2009, The Journal of chemical physics.

[12]  E. Vanden-Eijnden,et al.  A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations , 2006 .

[13]  Bruce J. Berne,et al.  A molecular dynamics and Monte Carlo study of solvent effects on the conformational equilibrium of n‐butane in CCl4a),b) , 1979 .

[14]  M. Tuckerman,et al.  An Adiabatic Molecular Dynamics Method for the Calculation of Free Energy Profiles , 2002 .

[15]  Eric Vanden-Eijnden,et al.  NUMERICAL TECHNIQUES FOR MULTI-SCALE DYNAMICAL SYSTEMS WITH STOCHASTIC EFFECTS ⁄ , 2003 .

[16]  G. Ciccotti,et al.  Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates , 2008 .

[17]  Eric Vanden-Eijnden,et al.  Transition state theory: variational formulation, dynamical corrections, and error estimates. , 2005, The Journal of chemical physics.

[18]  Grubmüller,et al.  Predicting slow structural transitions in macromolecular systems: Conformational flooding. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[19]  Hans-Peter Kriegel,et al.  A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise , 1996, KDD.

[20]  W. E,et al.  Towards a Theory of Transition Paths , 2006 .

[21]  Oriele Palumbo,et al.  Point defect dynamics and evolution of chemical reactions in alanates by anelastic spectroscopy. , 2005, The journal of physical chemistry. B.

[22]  M. Sprik.  Computation of the pK of liquid water using coordination constraints , 2000 .

[23]  G. Ciccotti,et al.  Constrained reaction coordinate dynamics for the simulation of rare events , 1989 .

[24]  C. Moyses Araujo,et al.  Vacancy-mediated hydrogen desorption in NaAlH4 , 2005 .

[25]  D. Frenkel,et al.  Simulating rare events in equilibrium or nonequilibrium stochastic systems. , 2005, The Journal of chemical physics.

[26]  Ron Elber,et al.  On the assumptions underlying milestoning. , 2008, The Journal of chemical physics.

[27]  Hans-Peter Kriegel,et al.  OPTICS: ordering points to identify the clustering structure , 1999, SIGMOD '99.

[28]  Vipin Kumar,et al.  Introduction to Data Mining , 2022, Data Mining and Machine Learning Applications.

[29]  R. G. Hart,et al.  Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution , 1960, Nature.

[30]  R. Elber,et al.  Computing time scales from reaction coordinates by milestoning. , 2004, The Journal of chemical physics.

[31]  G. Ciccotti,et al.  Mapping the network of pathways of CO diffusion in myoglobin. , 2010, Journal of the American Chemical Society.

[32]  R. Durrett.  Stochastic Calculus: A Practical Introduction , 1996 .

[33]  J. MacQueen.  Some methods for classification and analysis of multivariate observations , 1967 .

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

[35]  Eric Vanden-Eijnden,et al.  Markovian milestoning with Voronoi tessellations. , 2009, The Journal of chemical physics.

[36]  M. Klein,et al.  Nosé-Hoover chains : the canonical ensemble via continuous dynamics , 1992 .

[37]  I. Tanaka,et al.  Decomposition reactions for NaAlH4, Na3AlH6, and NaH: First-principles study , 2005 .

[38]  Alessandro Laio,et al.  A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. , 2005, The journal of physical chemistry. B.

[39]  H. Jónsson,et al.  Nudged elastic band method for finding minimum energy paths of transitions , 1998 .

[40]  E. Vanden-Eijnden,et al.  Single-sweep methods for free energy calculations. , 2007, The Journal of chemical physics.

[41]  A. Laio,et al.  Assessing the accuracy of metadynamics. , 2005, The journal of physical chemistry. B.

[42]  J. VandeVondele,et al.  Canonical Adiabatic Free Energy Sampling (CAFES): A Novel Method for the Exploration of Free Energy Surfaces , 2002 .

[43]  Philipp Metzner,et al.  Illustration of transition path theory on a collection of simple examples. , 2006, The Journal of chemical physics.

[44]  David Chandler,et al.  Statistical mechanics of isomerization dynamics in liquids and the transition state approximation , 1978 .

[45]  M. Tuckerman,et al.  IN CLASSICAL AND QUANTUM DYNAMICS IN CONDENSED PHASE SIMULATIONS , 1998 .

[46]  G. Ciccotti,et al.  String method in collective variables: minimum free energy paths and isocommittor surfaces. , 2006, The Journal of chemical physics.

[47]  G. Ciccotti,et al.  Modified single sweep method for reconstructing free-energy landscapes , 2009 .

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