Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling
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[1] Sanford Weisberg,et al. Computing science and statistics : proceedings of the 30th Symposium on the Interface, Minneapolis, Minnesota, May 13-16, 1998 : dimension reduction, computational complexity and information , 1998 .
[2] S. Whittington,et al. Monte carlo study of the interacting self-avoiding walk model in three dimensions , 1996 .
[3] Srikanth Sastry,et al. The relationship between fragility, configurational entropy and the potential energy landscape of glass-forming liquids , 2000, Nature.
[4] D. Wales. Energy landscapes of clusters bound by short-ranged potentials. , 2010, Chemphyschem : a European journal of chemical physics and physical chemistry.
[5] H. Scheraga,et al. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[6] R. Berry,et al. Solid‐Liquid Phase Behavior in Microclusters , 2007 .
[7] Jonathan P. K. Doye,et al. An order parameter approach to coexistence in atomic clusters , 1995 .
[8] Nature of vibrational eigenmodes in topologically disordered solids , 2001, cond-mat/0108336.
[9] P. Debenedetti,et al. The distribution of tetravalent network glasses , 1996 .
[10] Liquid limits: glass transition and liquid-gas spinodal boundaries of metastable liquids. , 2000, Physical review letters.
[11] D. Wales,et al. How the range of pair interactions governs features of multidimensional potentials , 1990 .
[12] B. Berne,et al. Smart walking: A new method for Boltzmann sampling of protein conformations , 1997 .
[13] Thermodynamics and equilibrium structure of Ne38 cluster: quantum mechanics versus classical. , 2005, The Journal of chemical physics.
[14] A. Heuer,et al. Why is the density of inherent structures of a Lennard-Jones-type system Gaussian? , 2000 .
[15] Potential energy landscape of a model glass former: thermodynamics, anharmonicities, and finite size effects. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[16] J. Nocedal. Updating Quasi-Newton Matrices With Limited Storage , 1980 .
[17] H. Stanley,et al. Thermodynamic and structural aspects of the potential energy surface of simulated water. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.
[18] R. Franzosi,et al. Theorem on the origin of phase transitions. , 2003, Physical Review Letters.
[19] A. Voter,et al. Smart Darting Monte Carlo , 2001 .
[20] Paul G. Mezey,et al. Catchment region partitioning of energy hypersurfaces, I , 1981 .
[21] Watanabe,et al. Direct dynamical calculation of entropy and free energy by adiabatic switching. , 1990, Physical review letters.
[22] F. Sciortino,et al. Thermodynamics of supercooled liquids in the inherent-structure formalism: a case study , 2000 .
[23] J. Doye,et al. Evolution of the Potential Energy Surface with Size for Lennard-Jones Clusters , 1999, cond-mat/9903305.
[24] J. Doye,et al. Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms. , 2012, Nanoscale.
[25] Vladimir A Mandelshtam,et al. Low-temperature structural transitions: circumventing the broken-ergodicity problem. , 2007, Physical review letters.
[26] D. Landau,et al. Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.
[27] Janet E. Jones,et al. On the Calculation of Certain Crystal Potential Constants, and on the Cubic Crystal of Least Potential Energy , 1925 .
[28] P. Bunker,et al. Molecular symmetry and spectroscopy , 1979 .
[29] S. Weerasinghe,et al. Absolute classical densities of states for very anharmonic systems and applications to the evaporation of rare gas clusters , 1993 .
[30] H. C. Longuet-Higgins. The symmetry groups of non-rigid molecules , 1963 .
[31] Jonathan P. K. Doye,et al. Stationary points and dynamics in high-dimensional systems , 2003 .
[32] Sahand Hormoz,et al. Design principles for self-assembly with short-range interactions , 2011, Proceedings of the National Academy of Sciences.
[33] David J. Wales,et al. Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations. , 2012, Journal of chemical theory and computation.
[34] J. Doye,et al. Thermodynamics and the Global Optimization of Lennard-Jones clusters , 1998, cond-mat/9806020.
[35] Schober,et al. Low-frequency vibrations in a model glass. , 1996, Physical review. B, Condensed matter.
[36] Dhagash Mehta,et al. Finding all the stationary points of a potential-energy landscape via numerical polynomial-homotopy-continuation method. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.
[37] P. Haarhoff. The density of vibrational energy levels of polyatomic molecules , 1964 .
[38] F. Stillinger,et al. A Topographic View of Supercooled Liquids and Glass Formation , 1995, Science.
[39] J. Straub,et al. Replica exchange statistical temperature molecular dynamics algorithm. , 2012, The journal of physical chemistry. B.
[40] J. Doye,et al. THE DOUBLE-FUNNEL ENERGY LANDSCAPE OF THE 38-ATOM LENNARD-JONES CLUSTER , 1998, cond-mat/9808265.
[41] R. Stephen Berry,et al. The onset of nonrigid dynamics and the melting transition in Ar7 , 1986 .
[42] Jonathan P. K. Doye,et al. Characterization of anharmonicities on complex potential energy surfaces: Perturbation theory and simulation , 2001 .
[43] J. Doye,et al. Dynamics and thermodynamics of supercooled liquids and glasses from a model energy landscape , 2001 .
[44] Wang,et al. Replica Monte Carlo simulation of spin glasses. , 1986, Physical review letters.
[45] F. Calvo,et al. Configurational density of states from molecular dynamics simulations , 1995 .
[46] J. Doye,et al. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.
[47] Eberhard R. Hilf,et al. The structure of small clusters: Multiple normal-modes model , 1993 .
[48] M. Hoare. Structure and Dynamics of Simple Microclusters , 2007 .
[49] M. Brenner,et al. The Free-Energy Landscape of Clusters of Attractive Hard Spheres , 2010, Science.
[50] J. Straub,et al. Statistical-temperature Monte Carlo and molecular dynamics algorithms. , 2006, Physical review letters.
[51] D. Mehta,et al. Energy-landscape analysis of the two-dimensional nearest-neighbor φ⁴ model. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.
[52] David Jackson McGinty,et al. Vapor phase homogeneous nucleation and the thermodynamic properties of small clusters of argon atoms , 1971 .
[53] D. Wales,et al. Equilibrium density of states and thermodynamic properties of a model glass former. , 2007, The Journal of chemical physics.
[54] Y. Sugita,et al. Multidimensional replica-exchange method for free-energy calculations , 2000, cond-mat/0009120.
[55] Vladimir A Mandelshtam,et al. Self-consistent phonons revisited. I. The role of thermal versus quantum fluctuations on structural transitions in large Lennard-Jones clusters. , 2012, The Journal of chemical physics.
[56] P. Steinhardt,et al. Bond-orientational order in liquids and glasses , 1983 .
[57] J. J. Burton. Vibrational Frequencies and Entropies of Small Clusters of Atoms , 1972 .
[58] Alan M. Ferrenberg,et al. Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.
[59] R. Whetten,et al. Statistical thermodynamics of the cluster solid-liquid transition. , 1990, Physical review letters.
[60] J. Pablo,et al. Density of states of a binary Lennard-Jones glass , 2003, cond-mat/0305666.
[61] J. Doye,et al. The Structure and Stability of Atomic Liquids: From Clusters to Bulk , 1996, Science.
[62] Jorge Nocedal,et al. On the limited memory BFGS method for large scale optimization , 1989, Math. Program..
[63] G. Parisi,et al. Lennard-Jones binary mixture: A thermodynamical approach to glass transition , 2000 .
[64] Jonathan P. K. Doye,et al. Calculation of thermodynamic properties of small Lennard‐Jones clusters incorporating anharmonicity , 1995 .
[65] J. Straub,et al. Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables. , 2011, The Journal of chemical physics.
[66] D. L. Freeman,et al. Phase changes in 38-atom Lennard-Jones clusters. II. A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical ensembles , 2000, physics/0003072.
[67] P. Frantsuzov,et al. Size-temperature phase diagram for small Lennard-Jones clusters. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.
[68] Jonathan P. K. Doye,et al. TOPICAL REVIEW: The effect of the range of the potential on the structure and stability of simple liquids: from clusters to bulk, from sodium to ? , 1996 .
[69] Vladimir A Mandelshtam,et al. Structural transitions and melting in LJ(74-78) Lennard-Jones clusters from adaptive exchange Monte Carlo simulations. , 2006, The journal of physical chemistry. A.
[70] H. Scheraga,et al. Global optimization of clusters, crystals, and biomolecules. , 1999, Science.
[71] David J. Wales,et al. Symmetry, near-symmetry and energetics , 1998 .
[72] Juan J de Pablo,et al. Density-of-states Monte Carlo simulation of a binary glass. , 2004, Physical review letters.
[73] U H Hansmann,et al. New Monte Carlo algorithms for protein folding. , 1999, Current opinion in structural biology.
[74] K. Jordan,et al. On the convergence of parallel tempering Monte Carlo simulations of LJ38. , 2005, The journal of physical chemistry. A.
[75] F. Stillinger,et al. Distinguishing Vibrational and Structural Equilibration Contributions to Thermal Expansion , 1999 .
[76] Vladimir A Mandelshtam,et al. Solid-solid structural transformations in Lennard-Jones clusters: accurate simulations versus the harmonic superposition approximation. , 2007, The journal of physical chemistry. A.
[77] David J. Wales,et al. Coexistence in small inert gas clusters , 1993 .
[78] David J. Wales,et al. Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide , 2008 .
[79] Daan Frenkel,et al. COMPUTER-SIMULATION STUDY OF FREE-ENERGY BARRIERS IN CRYSTAL NUCLEATION , 1992 .
[80] J. Doye,et al. Structural consequences of the range of the interatomic potential A menagerie of clusters , 1997, cond-mat/9709201.
[81] David J Wales,et al. Potential energy and free energy landscapes. , 2006, The journal of physical chemistry. B.
[82] K. Hukushima,et al. Exchange Monte Carlo Method and Application to Spin Glass Simulations , 1995, cond-mat/9512035.
[83] Unattainability of a purely topological criterion for the existence of a phase transition for nonconfining potentials. , 2004, Physical review letters.
[84] D. Wales. A Microscopic Basis for the Global Appearance of Energy Landscapes , 2001, Science.
[85] F. Stillinger,et al. Packing Structures and Transitions in Liquids and Solids , 1984, Science.
[86] Taming the rugged landscape: production, reordering, and stabilization of selected cluster inherent structures in the X13-nYn system. , 2004, The Journal of chemical physics.
[87] David J. Wales,et al. Some further applications of discrete path sampling to cluster isomerization , 2004 .
[88] D. L. Freeman,et al. Phase changes in 38-atom Lennard-Jones clusters. I. A parallel tempering study in the canonical ensemble , 2000, physics/0003068.
[89] David J Wales,et al. Equilibrium thermodynamics from basin-sampling. , 2006, The Journal of chemical physics.
[90] E. Curotto. Isomerizations and relative kinetic stability of LJn clusters in a carrier gas , 2001 .
[91] D. Frenkel,et al. Colloidal self-assembly: designed to yield. , 2011, Nature materials.
[92] F. Sciortino,et al. Inherent Structure Entropy of Supercooled Liquids , 1999, cond-mat/9906081.
[93] Dhagash Mehta,et al. Phase transitions detached from stationary points of the energy landscape. , 2011, Physical review letters.
[94] Alan M. Ferrenberg,et al. New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.
[95] U. Hansmann. Parallel tempering algorithm for conformational studies of biological molecules , 1997, physics/9710041.
[96] J. Doye,et al. The effect of the range of the potential on the structures of clusters , 1995 .