Demonstrating the transferability and the descriptive power of sketch-map

Journal of Chemical Theory and Computation

Volumn 9, Issue 3, 2013, Pages 1521-1532

  Ceriotti, Michele ^a   Tribello, Gareth A ^b,c   Parrinello, Michele ^b,c  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF LUGANO   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84874907178     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct3010563     Document Type: Article

References (42)

1. Ceriotti, M.; Tribello, G. A.; Parrinello, M. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 13023-13029
2. Tribello, G. A.; Ceriotti, M.; Parrinello, M. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 5196-5201
3. Maragakis, P.; van der Vaart, A.; Karplus, M. J. Phys. Chem. B 2009, 113, 4664-4673
4. Tribello, G. A.; Ceriotti, M.; Parrinello, M. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 17509-17514
5. Piana, S.; Laio, A. J. Phys. Chem. B 2007, 111, 4553-4559
6. Wales, D. J. Energy Landscapes; Cambridge University Press: Cambridge, U. K., 2003.
7. Pártay, L. B.; Bartók, A. P.; Csányi, G. J. Phys. Chem. B 2010, 114, 10502-10512
8. Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Proteins: Struct., Funct., Genet. 1993, 17, 412
9. Garcia, A. E. Phys. Rev. Lett. 1992, 68, 2696-2699
10. Zhuravlev, P. I.; Materese, C. K.; Papoian, G. A. J. Phys. Chem. B 2009, 113, 8800-8812
11. Roweis, S. T.; Saul, L. K. Science 2000, 290, 2323-2326
12. Tenenbaum, J. B.; Silva, V. d.; Langford, J. C. Science 2000, 290, 2319-2323
13. Das, P.; Moll, M.; Stamati, H.; Kavraki, L. E.; Clementi, C. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 9885-9890
14. Coifman, R. R.; Lafon, S.; Lee, A. B.; Maggioni, M.; Nadler, B.; Warner, F.; Zucker, S. W. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 7432-7437
15. Coifman, R. R.; Lafon, S. Appl. Comput. Harmon. Anal. 2006, 21, 5-30
16. Belkin, M.; Niyogi, P. Neural Comput. 2003, 15, 1373-1396
17. Ferguson, A. L.; Panagiotopoulos, A. Z.; Debenedetti, P. G.; Kevrekidis, I. G. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 13597-13602
18. Rohrdanz, M. A.; Zheng, W.; Maggioni, M.; Clementi, C. J. Chem. Phys. 2011, 134, 124116
19. Borg, I.; Groenen, P. J. Modern Multidimensional Scaling, 2 nd ed.; Springer: New York, 2005.
20. Heiser, W. J. In Classification and Related Methods; North-Holland: Amsterdam, 1988; Chapter Multidimensional scaling with least absolute residuals, pp 455-462.
21. Spiwok, V.; Kralova, B. J. Chem. Phys. 2011, 135, 224504
22. Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103
23. Doye, J. P. K.; Wales, D. J. J. Chem. Phys. 1995, 102, 9673-9688
24. Labastie, P.; Whetten, R. L. Phys. Rev. Lett. 1990, 65, 1567-1570
25. Doye, J. P. K.; Miller, M. A.; Wales, D. J. J. Chem. Phys. 1999, 110, 6896-6906
26. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
27. Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A.; Parrinello, M. Comput. Phys. Commun. 2009, 180, 1961-1972
28. Bussi, G.; Donadio, D.; Parrinello, M. J. J. Chem. Phys. 2007, 126, 014101
29. Neirotti, J. P.; Calvo, F.; Freeman, D. L.; Doll, J. D. J. Chem. Phys. 2000, 112, 10340-10349
30. Calvo, F.; Neirotti, J. P.; Freeman, D. L.; Doll, J. D. J. Chem. Phys. 2000, 112, 10350-10357
31. Oganov, A. R.; Valle, M. J. Chem. Phys. 2009, 130, 104504
32. Tribello, G. A.; Cuny, J.; Eshet, H.; Parrinello, M. J. Chem. Phys. 2011, 135, 114109
33. Wales, D. J. Mol. Phys. 2002, 100, 3285-3306
34. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199
35. Bonomi, M.; Barducci, A.; Parrinello, M. J. Comput. Chem. 2009, 30, 1615-1621
36. Kunz, R. E.; Berry, R. S. Phys. Rev. E 1994, 49, 1895-1908
37. Kunz, R. E.; Berry, R. S. Phys. Rev. Lett. 1993, 71, 3987-3990
38. Eshet, H.; Bruneval, F.; Parrinello, M. J. Chem. Phys. 2008, 129, 026101
39. O'Keeffe, M.; Hyde, B. Crystals Structures I. Patters and Symmetry, 1 st ed.; Mineralogical Society of America: Washington, DC, 1996.
40. Steinhardt, P. J.; Nelson, D. R.; Ronchetti, M. Phys. Rev. Lett. 1981, 47, 1297-1300
41. Shamos, M. I.; Hoey, D. Closest-point problems. Proceedings of the 16th Annual Symposium on Foundations of Computer Science, IEEE: Washington, DC, USA, 1975; pp 151-162.
42. Voter, A. Introduction to the Kinetic Monte Carlo Method. In Radiation Effects in Solids; Sickafus, K.; Kotomin, E.; Uberuaga, B., Eds.; Springer: Netherlands, 2007; Vol. 235, pp 1-23.