Mitosis method for directly calculating the interfacial free energy of nuclei

Molecular Simulation

Volumn 36, Issue 7-8, 2010, Pages 498-504

  Duff, Nathan ^a   Peters, Baron ^a,b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

interfacial free energy; lattice model; nucleation; polymorph selection; surface tension

Indexed keywords

ALTERNATIVE METHODS; CRITICAL NUCLEI; EXPLICIT SOLVENTS; INTERFACIAL FREE ENERGY; LATTICE GAS MODEL; LATTICE MODEL; LATTICE MODELS; MOLECULAR LEVELS; NANO SCALE; NUCLEATION RATE; PHASE TRANSFORMATION; PURE COMPONENT SYSTEMS; REAL CRYSTALS; REAL SOLUTIONS;

CHEMICAL POTENTIAL; CHEMICALS; COMPUTER SIMULATION; CRYSTAL LATTICES; FREE ENERGY; POLYMORPHISM; SURFACE PROPERTIES; SURFACE TENSION;

NUCLEATION;

EID: 77955438461     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2010.483684     Document Type: Article

References (67)

1. P.R. ten Wolde and D. Frenkel, Computer simulation study of gas-liquid nucleation in a Lennard-Jones system, J. Chem. Phys. 109 (1998), pp. 9901-9918.
2. P.R. ten Wolde and D. Frenkel, Enhancement of protein crystal nucleation by critical density fluctuations, Science 277 (1997), pp. 1975-1978.
3. S. Auer and D. Frenkel, Prediction of absolute crystal-nucleation rate in hard-sphere colloids, Nature 409 (2001), pp. 1020-1023.
4. S. Auer and D. Frenkel, Numerical prediction of absolute crystallization rates in hard-sphere colloids, J. Chem. Phys. 120 (2004), pp. 3015-3029.
5. C. Valeriani, E. Sanz, and D. Frenkel, Rate of homogeneous crystal nucleation in molten NaCl, J. Chem. Phys. 122 (2005), 194501.
6. A.C. Pan and D. Chandler, Dynamics of nucleation in the Ising model, J. Phys. Chem. B 108 (2004), pp. 19681-19686.
7. K. Brendel, G.T. Barkema, and H. Van Beijeren, Nucleation times in the two-dimensional Ising model, Phys. Rev. E 71 (2005), 031601.
8. B. Peters and B.L. Trout, Obtaining reaction coordinates by likelihood maximization, J. Chem. Phys. 125 (2006), 054108.
9. B. Peters, Competing nucleation pathways in a mixture of oppositely charged colloids: Out-of-equilibrium nucleation revisited, J. Chem. Phys. 131 (2009), 244103.
10. N. Duff and B. Peters, Nucleation in a Potts lattice gas model of crystallization from solution, J. Chem. Phys. 131 (2009), 184101.
11. J.M. Leyssale, J. Delhommelle, and C. Millot, Hit and miss of classical nucleation theory as revealed by a molecular simulation study of crystal nucleation in supercooled sulfur hexafluoride, J. Chem. Phys. 127 (2007), 044504.
12. D. Moroni, P.R. ten Wolde, and P.G. Bolhuis, Interplay between structure and size in a critical crystal nucleus, Phys. Rev. Lett. 94 (2005), 235703.
13. S. Auer, C.M. Dobson, and M. Vendruscolo, Characterization of the nucleation barriers for protein aggregation and amyloid formation, HFSP J. 1 (2007), pp. 137-146.
14. S. Auer, C.M. Dobson, M. Vendruscolo, and A. Maritan, Selftemplated nucleation in peptide and protein aggregation, Phys. Rev. Lett. 101 (2008), 258101.
15. S. Punnathanam and P.A. Monson, Crystal nucleation in binary hard sphere mixtures: A Monte Carlo simulation study, J. Chem. Phys. 125 (2006), 024508.
16. B. Chen, J.I. Siepmann, K.J. Oh, and M.L. Klein, Aggregationvolume-bias Monte Carlo simulations of vapor-liquid nucleation barriers for Lennard-Jonesium, J. Chem. Phys. 115 (2001), 10903-10913.
17. B. Chen, J.I. Siepmann, and M.L. Klein, Simulating vapor-liquid nucleation of water: A combined histogram-reweighting and aggregation-volume- bias Monte Carlo investigation for fixedcharge and polarizable models, J. Phys. Chem. A 109 (2005), pp. 1137-1145.
18. B. Chen, J.I. Siepmann, K.J. Oh, and M.L. Klein, Simulating vapor-liquid nucleation of n-alkanes, J. Chem. Phys. 116 (2002), pp. 4317-4329.
19. F. Trudu, D. Donadio, and M. Parrinello, Freezing of a Lennard-Jones fluid: From nucleation to spinodal regime, Phys. Rev. Lett. 97 (2006), 105701.
20. B. Chen, H. Kim, S.J. Keasler, and R.B. Nellas, An aggregationvolume-bias Monte Carlo investigation on the condensation of a Lennard-Jones vapor below the triple point and crystal nucleation in cluster systems: An in-depth evaluation of the classical nucleation theory, J. Phys. Chem. B 112 (2008), pp. 4067-4078.
21. B. Chen, J.I. Siepmann, and M.L. Klein, Simulating the nucleation of water/ethanol and water/n-nonane mixtures: Mutual enhancement and two-pathway mechanism, J. Am. Chem. Soc. 125 (2003), pp. 3113-3118.
22. T. Zykova-Timan, C. Valeriani, E. Sanz, D. Frenkel, and E. Tosatti, Irreducible finite-size effects in the surface free energy of NaCl crystals from crystal-nucleation data, Phys. Rev. Lett. 100 (2008), 036103.
23. L. Maibaum, Phase transformation near the classical limit of stability, Phys. Rev. Lett. 101 (2008), 256102.
24. A.R. Browning, M.F. Doherty, and G.H. Fredrickson, Nucleation and polymorph selection in a model colloidal fluid, Phys. Rev. E 77 (2008), 041604.
25. D. Moroni, P.R. ten Wolde, and P.G. Bolhuis, Interplay between structure and size in a critical crystal nucleus, Phys. Rev. Lett. 94 (2005), p. 235703.
26. R. Radhakrishnan and B.L. Trout, Nucleation of hexagonal ice (Ih) in liquid water, J. Am. Chem. Soc. 125 (2003), pp. 7743-7747.
27. S. Punnathanam and D.S. Corti, Homogeneous bubble nucleation in stretched fluids: Cavity formation in the superheated Lennard-Jones liquid, Ind. Eng. Chem. Res. 41 (2002), pp. 1113-1121.
28. C. Desgranges and J. Delhommelle, Molecular mechanism for the cross-nucleation between polymorphs, J. Am. Chem. Soc. 128 (2006), pp. 10368-10369.
29. S.M. Kathmann, G.K. Schenter, B.C. Garrett, B. Chen, and J.I. Siepmann, Thermodynamics and kinetics of nanoclusters controlling gas-to-particle nucleation, J. Phys. Chem. C 113 (2009), pp. 10354-10370.
30. Z.-J. Wang, C. Valeriani, and D. Frenkel, Homogeneous bubble nucleation driven by local hot spots: A molecular dynamics study, J. Phys. Chem. B 113 (2009), pp. 3776-3784.
31. R. Du, V.S. Pande, A.Y. Grosberg, T. Tanaka, and E.S. Shakhnovich, On the transition coordinate for protein folding, J. Chem. Phys. 108 (1998), pp. 334-350.
32. P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler, Transition path sampling: Throwing ropes over rough mountain passes, in the dark, Annu, Rev. Phys. Chem. 53 (2002), pp. 291-318.
33. J. Wedekind, D. Reguera, and R. Strey, Finite-size effects in simulations of nucleation, J. Chem. Phys. 125 (2006), 214505.
34. B. Widom, Some topics in the theory of fluids, J. Chem. Phys. 39 (1963), pp. 2808-2812.
35. M. Mezei, A cavity-biased (T, V, m) Monte Carlo method for the computer simulation of fluids, Mol. Phys. 40 (1980), p. 901.
36. M. Laso, J.J. de Pablo, and U.W. Suter, Simulation of phase equilibria for chain molecules, J. Chem. Phys. 97 (1992), pp. 2817-2819.
37. G.C.A.M. Mooij, D. Frenkel, and B. Smit, Direct simulation of phase equilibria of chain molecules, J. Phys.: Condens. Matter 4 (1992), pp. L255-L259.
38. M.G. Martin and J.I. Siepmann, Predicting multicomponent phase equilibria and free energies of transfer for alkanes by molecular simulation, J. Am. Chem. Soc. 119 (1997), pp. 8921-8924.
39. W. Shi and E.J. Maginn, Continuous fractional component Monte Carlo: An adaptive biasing method for open system atomistic simulations, J. Chem. Theory Comput. 3 (2007), pp. 1451-1463.
40. J.J. De Pablo and J.M. Prausnitz, Phase equilibria for fluid mixtures from Monte-Carlo simulation, Fluid Phase Equilib. 53 (1989), pp. 177-189.
41. D.A. Kofke and E.D. Glandt, Monte-Carlo simulation of multicomponent equilibria in a semigrand canonical ensemble, Mol. Phys. 64 (1988), pp. 1105-1131.
42. P.G. Debenedetti, Metastable liquids: Concepts and principles, Princeton University Press, Princeton, NJ, 1996.
43. D. Kashchiev, Nucleation: Basic theory with applications, Butterworth Heinemann, Oxford, 2000.
44. G.W. Adams, J.L. Schmitt, and R.A. Zalabsky, The homogeneous nucleation of nonane, J. Chem. Phys. 81 (1984), pp. 5074-5078.
45. J.L. Schmitt, R.A. Zalabsky, and G.W. Adams, Homogeneous nucleation of toluene, J. Chem. Phys. 79 (1983), pp. 4496-4501.
46. M.A. Sharaf and R.A. Dobbins, A comparison of measured nucleation rates with the predictions of several theories of homogeneous nucleation, J. Chem. Phys. 77 (1982), pp. 1517-1526.
47. R. Strey, P.E. Wagner, and T. Schmeling, Homogeneous nucleation rates for n-alcohol vapors measured in a two-piston expansion chamber, J. Chem. Phys. 84 (1986), pp. 2325-2335.
48. J.K. Lee, J.A. Barker, and G.M. Pound, Surface structure and surface tension: Perturbation theory and Monte Carlo calculation, J. Chem. Phys. 60 (1974), pp. 1976-1980.
49. T.S. Jain and J.J. de Pablo, Calculation of interfacial tension from density of states, J. Chem. Phys. 118 (2003), pp. 4226-4229.
50. J.R. Errington and D.A. Kofke, Calculation of surface tension via area sampling, J. Chem. Phys. 127 (2007), 174709.
51. E. Lindahl, B. Hess, and D. Van der Spoel, GROMACS 3.0: A package for molecular simulation and trajectory analysis, J. Mol. Model. 7 (2001), pp. 306-317.
52. P.K. Weiner and P.A. Kollman, AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions, J. Comput. Chem. 2 (1981), pp. 287-303.
53. J.C. Phillips,R.Braun,W.Wang, J.Gumbart, E. Tajkhorshid,E. Villa, C. Chipot, R.D. Skeel, L. Kalé, and K. Schulten, Scalable molecular dynamics with NAMD, J. Comput. Chem. 26 (2005), pp. 1781-1802.
54. B.R. Brooks, C.L. Brooks, III, A.D. Mackerell, Jr, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R.M. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York, and M. Karplus, CHARMM: The biomolecular simulation program, J. Comput. Chem. 30 (2009), pp. 1545-1614.
55. S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys. 117 (1995), pp. 1-19.
56. M.A. Lovette, A.R. Browning, D.W. Griffin, J.P. Sizemore, R.C. Snyder, and M.F. Doherty, Crystal shape engineering, Ind. Eng. Chem. Res. 47 (2008), pp. 9812-9833.
57. K. Kim, I.S. Lee, A. Centrone, T.A. Hatton, and A.S. Myerson, Formation of nanosized organic molecular crystals on engineered surfaces, J. Am. Chem. Soc. 131 (2009), pp. 18212-18213.
58. I.M. Lifshitz and V.V. Slyozov, The kinetics of precipitation from supersaturated solid solutions, J. Phys. Chem. Solids 19 (1961), pp. 35-50.
59. O. Krichevsky and J. Stavans, Ostwald ripening in a twodimensional system: Correlation effects, Phys. Rev. E 52 (1995), pp. 1818-1827.
60. D. Frenkel and B. Smit, Understanding molecular simulation: From algorithms to applications, Academic Press, San Diego, 2002.
61. G.M. Torrie and J.P. Valleau, Non-physical sampling distributions in Monte-Carlo free-energy estimation -Umbrella sampling, J. Comput. Phys. 23 (1977), pp. 187-199.
62. B.C. Knott, N. Duff, M.F. Doherty, and B. Peters, Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation, J. Chem. Phys. 131 (2009), 224112.
63. N. Duff and B. Peters, Erratum: "Nucleation in a Potts lattice gas model of crystallization from solution [J. Chem. Phys. 131 (2009) 184101]"
64. J. Chem. Phys. 132 (2010), 129901.
65. L. Maibaum, Comment on "elucidating the mechanism of nucleation near the gas-liquid spinodal", Phys. Rev. Lett. 101 (2008), 019601.
66. K.F. Riley, M.P. Hobson, and S.J. Bence, Mathematical methods for physics and engineering, Cambridge University Press, Cambridge, 2006.
67. D. Chandler, Introduction to modern statistical mechanics, Oxford University Press, New York, 1987.