Discovering unique, low-energy pure water isomers: Memetic exploration, optimization, and landscape analysis

IEEE Transactions on Evolutionary Computation

Volumn 14, Issue 3, 2010, Pages 419-437

  Soh, Harold ^a,b   Ong, Yew Soon ^b   Nguyen, Quoc Chinh ^c   Nguyen, Quang Huy ^b   Habibullah, Mohamed Salahuddin ^d   Hung, Terence ^d   Kuo, Jer Lai ^e  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^d INSTITUTE OF HIGH PERFORMANCE COMPUTING   (Singapore)

^e ACADEMIA SINICA   (Taiwan)

Author keywords

Basin hopping; Isomer sampling; Landscape analysis; Memetic algorithm; Molecular optimization

Indexed keywords

BASIN HOPPING; BASIN-HOPPING ALGORITHM; EMPIRICAL MODEL; GLOBAL MINIMA; LANDSCAPE ANALYSIS; LOCAL CORRELATIONS; LOCAL SEARCH ALGORITHM; LOW ENERGIES; MEMETIC; MEMETIC ALGORITHMS; META-STABLE; MOLECULAR OPTIMIZATION; MOLECULAR SYSTEMS; MULTISTART; NUMERICAL RESULTS; PURE WATER; STOCHASTIC ALGORITHMS; UNSOLVED PROBLEMS; WATER CLUSTER;

BIOLOGY; COMPUTATIONAL CHEMISTRY; CONVERGENCE OF NUMERICAL METHODS; ISOMERS; LEARNING ALGORITHMS; OPTIMIZATION; STOCHASTIC SYSTEMS;

CLUSTERING ALGORITHMS;

EID: 77953082750     PISSN: 1089778X     EISSN: None     Source Type: Journal    
DOI: 10.1109/TEVC.2009.2033584     Document Type: Article

References (66)

1. S. S. Xantheas, " Interaction potentials for water from accurate cluster calculations, " in Intermolecular Forces and Clusters II (Structure and Bonding Series 116), Berlin: Springer-Verlag, 2005, pp. 119-148.
2. n, n ≥ 21 described by a five-site empirical potential, " Chem. Phys. Lett., vol. 415, nos. 4-6, pp. 302-307, Nov. 2005.
3. +, " Phys. Chem. Chem. Phys., vol. 7, no. 11, pp. 2324-2332, 2005.
4. G. Robinson, " Theoretical description of water, " in Water in Biology, Chemistry and Physics: Experimental Overviews and Computational Methodologies, vol. 9, Singapore: World Scientific, 1996, ch. 5, pp. 129-175.
5. C. Lee, H. Chen, and G. Fitzgerald, " Chemical bonding in water clusters, " J. Chem. Phys., vol. 102, no. 3, pp. 1266-1269, 1995.
6. n, n ≥ 21, described by an empirical potential, " Chem. Phys. Lett., vol. 286, nos. 1-2, pp. 65-72, Apr. 1998.
7. B. Bandow and B. Hartke, " Larger water clusters with edges and corners on their way to ice: Structural trends elucidated with an improved parallel evolutionary algorithm, " J. Phys. Chem. A, vol. 110, no. 17, pp. 5809-5822, 2006.
8. C. L. Brooks, N. J. Onuchic, and J. D. Wales, " Taking a walk on a landscape, " Science, vol. 293, no. 5530, pp. 612-613, Jul. 2001.
9. D. Wales, Energy Landscapes: Applications to Clusters, Biomolecules and Glasses, Cambridge, U. K.: Cambridge Univ. Press, 2004.
10. n, n = 8, 12, 16, and 20, " J. Phys. Chem., vol. 97, no. 20, pp. 5208-5210, May 1993.
11. F. H. Stillinger, " Exponential multiplicity of inherent structures, " Phys. Rev. E, vol. 59, no. 1, pp. 48-51, Jan. 1999.
12. n n ≥ 8, " J. Phys. Chem. A, vol. 112, no. 28, pp. 6257-6261, Jul. 2008.
13. P. Ballester and W. Richards, " Ultrafast shape recognition to search compound databases for similar molecular shapes." J. Comput. Chem., vol. 28, no. 10, pp. 1711-1723, Jul. 2007.
14. S. Wright, " The roles of mutation, inbreeding, crossbreeding, and selection in evolution, " in Proc. 6th Int. Congr. Genet., 1932, pp. 355-366.
15. M. Miyazaki, A. Fujii, T. Ebata, and N. Mikami, " Infrared spectro-scopic evidence for protonated water clusters forming nanoscale cages, " Science, vol. 304, no. 5674, pp. 1134-1137, May 2004.
16. n (n = 6 to 27) clusters, " Science, vol. 304, no. 5674, pp. 1137-1140, May 2004.
17. 2O) 9-11, " Phys. Chem. Chem. Phys., vol. 7, no. 5, pp. 938-944, 2005.
18. A. Wallqvist and R. D. Mountain, " Molecular models of water: Derivation and description, " in Reviews in Computational Chemistry. New York: Wiley, 2007, pp. 183-247.
19. H. W. Horn, W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, G. L. Hura, and T. Head-Gordon, " Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew, " J. Chem. Phys., vol. 120, no. 20, pp. 9665-9678, May 2004.
20. S. Liem, P. Popelier, and M. Leslie, " Simulation of liquid water using a high-rank quantum topological electrostatic potential, " Int. J. Quant. Chem., vol. 99, no. 5, pp. 685-694, Jan. 2004.
21. M. Mahoney, " A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions, " J. Chem. Phys., vol. 112, no. 20, pp. 8910-8922, May 2000.
22. S. Rick, " A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums, " J. Chem. Phys., vol. 120, no. 13, pp. 6085-6093, Apr. 2004.
23. G. Fanourgakis and S. Xantheas, " The flexible, polarizable, Thole-type interaction potential for water (TTM2-F) revisited, " J. Chem. Phys. A, vol. 110, no. 11, pp. 4100-4106, Mar. 2006.
24. L. Ojamae, " Potential models for simulations of the solvated proton in water, " J. Chem. Phys., vol. 109, no. 13, pp. 5547-5564, Oct. 1998.
25. C. Burnham and S. Xantheas, " Development of transferable interaction models for water. IV. A flexible, all-atom polarizable potential (TTM2-F) based on geometry dependent charges derived from an ab initio monomer dipole moment surface, " J. Chem. Phys., vol. 116, no. 12, pp. 5115-5124, Mar. 2002.
26. n (11≥n≥13) through a genetic evolutionary approach, " J. Chem. Phys., vol. 116, no. 19, pp. 8327-8333, May 2002.
27. B. Masek, A. Merchant, and J. Matthew, " Molecular shape comparison of angiotensin II receptor antagonists, " J. Med. Chem., vol. 36, no. 9, pp. 1230-1238, Apr. 1993.
28. A. Y. Meyer and W. G. Richards, " Similarity of molecular shape, " J. Computer-Aided Mol. Des., vol. 5, no. 5, pp. 427-439, Oct. 1991.
29. J. Grant and B. Pickup, " A Gaussian description of molecular shape, " J. Phys. Chem., vol. 99, no. 11, pp. 3503-3510, Mar. 1995.
30. A. Nicholls, N. E. MacCuish, and J. D. MacCuish, " Variable selection and model validation of 2-D and 3-D molecular descriptors, " J. Computer-Aided Mol. Des., vol. 18, nos. 7-9, pp. 451-474, Jul.-Sep. 2004.
31. J. Ochterski, " Vibrational analysis in Gaussian, " Gaussian, Inc., Wallingford, CT, Tech. Rep., 1999 [Online]. Available: http://www.gaussian. com/g whitepap/vib.htm
32. D. Lim, Y.-S. Ong, Y. Jin, B. Sendhoff, and B. S. Lee, " Efficient hierarchical parallel genetic algorithms using grid computing, " Future Generation Comput. Syst., vol. 23, no. 4, pp. 658-670, May 2007.
33. N. Noman and H. Iba, " Accelerating differential evolution using an adaptive local search, " IEEE Trans. Evol. Comput., vol. 12, no. 1, pp. 107-125, Feb. 2008.
34. Q. H. Nguyen, Y.-S. Ong, M. H. Lim, and N. Krasnogor, " Adaptive cellular memetic algorithms, " Evol. Comput., vol. 17, no. 2, pp. 231-256, May 2009.
35. M.-H. Lim, S. Gustafson, N. Krasnogor, and Y.-S. Ong, " Editorial to the first issue, " Memetic Comput., vol. 1, no. 1, pp. 1-2, Mar. 2009.
36. F. Neri and V. Tirronen, " Scale factor local search in differential evolution, " Memetic Comput., vol. 1, no. 2, pp. 153-171, Feb. 2009.
37. X. Yu, K. Tang, T. Chen, and X. Yao, " Empirical analysis of evolutionary algorithms with immigrants schemes for dynamic optimization, " Memetic Comput., vol. 1, no. 1, pp. 3-24, Mar. 2009.
38. Y.-S. Ong and A. Keane, " Meta-Lamarckian learning in memetic algorithms, " IEEE Trans. Evol. Comput., vol. 8, no. 2, pp. 99-110, Apr. 2004.
39. S. Hasan, R. Sarker, D. Essam, and D. Cornforth, " Memetic algorithms for solving job-shop scheduling problems, " Memetic Comput., vol. 1, no. 1, pp. 69-83, Mar. 2009.
40. Z. Zhu, Y. Ong, and M. Dash, " Wrapper-filter feature selection algorithm using a memetic framework, " IEEE Trans. Syst. Man Cybern. B: Cybern., vol. 37, no. 1, pp. 70-76, Feb. 2007.
41. Z. Zhu, Y.-S. Ong, and J. M. Zurada, " Identification of full and partial class relevant genes, " in Proc. IEEE/Assoc. Comput. Mach. Trans. Comput. Biol. Bioinf., vol. 99, no. 1. 2009.
42. C. Aranha and H. Iba, " The memetic tree-based genetic algorithm and its application to portfolio optimization, " Memetic Comput., vol. 1, no. 2, pp. 139-151, Apr. 2009.
43. T. Fischer, K. Bauer, P. Merz, and K. Bauer, " Solving the routing and wavelength assignment problem with a multilevel distributed memetic algorithm, " Memetic Comput., vol. 1, no. 2, pp. 101-123, Feb. 2009.
44. D. Wales and J. Doye, " Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 Atoms, " J. Phys. Chem. A, vol. 101, no. 28, pp. 5111-5116, Jul. 1997.
45. S. Kirkpatrick, C. D. Gelatt, and M. P. Vecchi, " Optimization by simulated annealing, " Science, New Ser., vol. 220, no. 4598, pp. 671-680, May 1983.
46. H. H. Hoos and T. Stützle, " SLS methods, " in Stochastic Local Search: Foundations and Applications. San Mateo, CA: Morgan Kaufmann, 2004, ch. 2, pp. 61-111.
47. N. Metropolis, A. W. Rosenbluth, A. H. Teller, and E. Teller, " Equations of state calculations by fast computing machines, " J. Chem. Phys., vol. 21, no. 6, pp. 1087-1092, Jun. 1953.
48. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, " Minimization or maximization of functions, " in Numerical Recipes: The Art of Scientific Computing, 3rd ed. Cambridge, U. K.: Cambridge Univ. Press, 2007, ch. 10, pp. 398-448.
49. D. Whitley, " The GENITOR algorithm and selection pressure: Why rank-based allocation of reproductive trials is best, " in Proc. 3rd Int. Conf. Genet. Algorithms, 1989, pp. 116-121.
50. D. E. Goldberg, " Advanced operators and techniques in genetic search, " in Genetic Algorithms in Search, Optimization and Machine Learning. Boston, MA: Addison-Wesley Longman, 1989, ch. 5, pp. 147-217.
51. T. Bäck, D. Fogel, and Z. Michalewicz, Handbook of Evolutionary Computation. New York: Taylor & Francis, 1997.
52. L. Juan, C. Zixing, and L. Jianqin, " Premature convergence in genetic algorithm: Analysis and prevention based on chaos operator, " in Proc. 3rd World Congr. Intell. Control Automat., 2000, pp. 495-499.
53. K. A. DeJong, " An analysis of the behavior of a class of genetic systems, " Ph. D. dissertation, Dept. Comput. Commun. Sci., Univ. Michigan, Ann Arbor, 1975.
54. S. W. Mahfoud, " Niching methods for genetic algorithms, " Ph. D. dissertation, Dept. Comput. Sci., Univ. Illinois at Urbana-Champaign, Urbana, 1995.
55. Y. Leung, Y. Gao, and Z. Xu, " Degree of population diversity: A perspective on premature convergence in genetic algorithms and its Markov chain analysis, " IEEE Trans. Neural Netw., vol. 8, no. 5, pp. 1165-1176, Sep. 1997.
56. S. Ronald, " Duplicate genotypes in a genetic algorithm, " in Proc. IEEE World Congr. Comput. Intel., May 1998, pp. 793-798.
57. W. Humphrey, A. Dalke, and K. Schulten, " VMD-Visual molecular dynamics, " J. Mol. Graph., vol. 14, no. 1, pp. 33-38, Feb. 1996.
58. T. Jones and S. Forrest, " Fitness distance correlation as a measure of problem difficulty for genetic algorithms, " in Proc. 6th Int. Conf. Genet. Algorithms, 1995, pp. 184-192.
59. N. Hansen and A. Ostermeier, " Completely derandomized self-adaptation in evolution strategies, " Evol. Comput., vol. 9, no. 2, pp. 159-195, Jun. 2001.
60. H. Soh and M. Kirley, " moPGA: Toward a new generation of mul-tiobjective genetic algorithms, " in Proc. IEEE Congr. Evol. Comput., Vancouver, BC, 2006, pp. 1702-1709.
61. N. Hansen, " The CMA evolution strategy: A comparing review, " in Toward a New Evolutionary Computation (Advances in Estimation of Distribution Algorithms Series). J. Lozano, P. Larranga, I. Inza, and E. Bengoetxea, Eds., New York: Springer-Verlag, 2006, pp. 75-102.
62. N. Hansen. (2008). CMA Evolution Strategy Source Code [Online]. Available: http://www.bionik.tu-berlin. de/user/niko/
63. A. Auger and N. Hansen, " A restart CMA evolution strategy with increasing population size, " in Proc. IEEE Congr. Evol. Comput., vol. 2. Sep. 2-5, 2005, pp. 1769-1776.
64. J. Arvo, " Fast random rotation matrices, " in Graphic Gems III, (Academic Press Graphic Gems Series). San Francisco, CA: Academic, 1992, pp. 117-120.
65. T. V. Bogdan, D. J. Wales, and F. Calvo, " Equilibrium thermodynamics from basin-sampling, " J. Phys. Chem., vol. 124, no. 4, p. 044102, Jan. 2006.
66. F. Calvo, J. P. K. Doye, and D. J. Wales, " Equilibrium properties of clusters in the harmonic superposition approximation, " Chem. Phys. Lett., vol. 366, nos. 1-2, pp. 176-183, Nov. 2002.