Nonlinear intrinsic variables and state reconstruction in multiscale simulations

Journal of Chemical Physics

Volumn 139, Issue 18, 2013, Pages

  Dsilva, Carmeline J ^a   Talmon, Ronen ^b   Rabin, Neta ^c   Coifman, Ronald R ^b   Kevrekidis, Ioannis G ^a,d  

^a Princeton University   (United States)

^b YALE UNIVERSITY   (United States)

^c AFEKA TEL AVIV ACADEMIC COLLEGE OF ENGINEERING   (Israel)

^d PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMISTIC SIMULATIONS; ENZYME REACTION NETWORKS; KINETIC MONTE CARLO SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MULTI-SCALE SIMULATION; REFERENCE COORDINATES; STATE RECONSTRUCTION; STOCHASTIC SIMULATIONS;

AMINO ACIDS; FILTRATION; REACTION KINETICS; STOCHASTIC MODELS;

MOLECULAR DYNAMICS;

EID: 84903370940     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4828457     Document Type: Article

References (46)

1. J. B. Tenenbaum, V. de Silva, and J. C. Langford, Science 290, 2319 (2000). 10.1126/science.290.5500.2319
2. S. T. Roweis and L. K. Saul, Science 290, 2323 (2000). 10.1126/science.290.5500.2323
3. D. L. Donoho and C. Grimes, Proc. Natl. Acad. Sci. U.S.A. 100, 5591 (2003). 10.1073/pnas.1031596100
4. M. Belkin and P. Niyogi, Neural Comput. 15, 1373 (2003). 10.1162/089976603321780317
5. R. Coifman and S. Lafon, Appl. Comput. Harmon. Anal. 21, 5 (2006). 10.1016/j.acha.2006.04.006
6. J. Bowen, A. Acrivos, and A. Oppenheim, Chem. Eng. Sci. 18, 177 (1963). 10.1016/0009-2509(63)85003-4
7. L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, and S.-J. Marrink, J. Chem. Theory Comput. 4, 819 (2008). 10.1021/ct700324x
8. E. Spiga, D. Alemani, M. T. Degiacomi, M. Cascella, and M. Dal Peraro, J. Chem. Theory Comput. 9, 3515 (2013). 10.1021/ct400137q
9. S. Izvekov, A. Violi, and G. A. Voth, J. Phys. Chem. B 109, 17019 (2005). 10.1021/jp0530496
10. M. G. Saunders and G. A. Voth, Annu. Rev. Biophys. 42, 73 (2013). 10.1146/annurev-biophys-083012-130348
11. I. Jolliffe, Principal Component Analysis (Wiley Online Library, 2005).
12. S. Lafon, Y. Keller, and R. R. Coifman, IEEE Trans. Pattern Anal. Mach. Intell. 28, 1784 (2006). 10.1109/TPAMI.2006.223
13. N. Rabin and R. Coifman, in Proceedings of the 12th SIAM International Conference on Data Mining (SDM 2012), Anaheim, California, USA (SIAM, 2012).
14. D. T. Gillespie, J. Phys. Chem. 81, 2340 (1977). 10.1021/j100540a008
15. A. Zagaris, C. Vandekerckhove, C. W. Gear, T. J. Kaper, and I. G. Kevrekidis, Discrete Contin. Dyn. Syst., Ser. B 32, 2759 (2012). 10.3934/dcds.2012.32.2759
16. P. G. Bolhuis, C. Dellago, and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 97, 5877 (2000). 10.1073/pnas.100127697
17. R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker, Proc. Natl. Acad. Sci. U.S.A. 102, 7426 (2005). 10.1073/pnas.0500334102
18. A. Singer and R. R. Coifman, Appl. Comput. Harmon. Anal. 25, 226 (2008). 10.1016/j.acha.2007.11.001
19. M. Hein and J. Y. Audibert, in Proceedings of the 22nd International Conference of Machine Learning (ACM, 2005), p. 289.
20. R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer, IEEE Trans. Image Process. 17, 1891 (2008). 10.1109/TIP.2008.2002305
21. M. A. Rohrdanz, W. Zheng, M. Maggioni, and C. Clementi, J. Chem. Phys. 134, 124116 (2011). 10.1063/1.3569857
22. F. R. Chung, Spectral Graph Theory (AMS, 1997), Vol. 92.
23. B. Nadler, S. Lafon, R. R. Coifman, and I. G. Kevrekidis, Appl. Comput. Harmon. Anal. 21, 113 (2006). 10.1016/j.acha.2005.07.004
24. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988). 10.1103/PhysRevLett.61.2635
25. P. Burt and E. Adelson, IEEE Trans. Commun. 31, 532 (1983). 10.1109/TCOM.1983.1095851
26. M. N. Do and M. Vetterli, IEEE Trans. Signal Process. 51, 2329 (2003). 10.1109/TSP.2003.815389
27. S. M. Buchman, A. B. Lee, and C. M. Schafer, Stat. Methodol. 8, 18 (2011). 10.1016/j.stamet.2009.07.002
28. D. T. Gillespie, J. Chem. Phys. 113, 297 (2000). 10.1063/1.481811
29. J. Apostolakis, P. Ferrara, and A. Caflisch, J. Chem. Phys. 110, 2099 (1999). 10.1063/1.477819
30. D. S. Chekmarev, T. Ishida, and R. M. Levy, J. Phys. Chem. B 108, 19487 (2004). 10.1021/jp048540w
31. A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005). 10.1021/jp045546c
32. T. A. Frewen, G. Hummer, and I. G. Kevrekidis, J. Chem. Phys. 131, 134104 (2009). 10.1063/1.3207882
33. A. L. Ferguson, A. Z. Panagiotopoulos, P. G. Debenedetti, and I. G. Kevrekidis, J. Chem. Phys. 134, 135103 (2011). 10.1063/1.3574394
34. D. A. Case, T. A. Darden, I. T. E. Cheatham, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, M. Crowley, R. C. Walker, W. Zhang, K. M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D. H. Mathews, M. G. Seetin, C. Sagui, V. Babin, and P. Kollman, " AMBER 10.," University of California, San Francisco, 2008.
35. R. B. Best and G. Hummer, J. Phys. Chem. B 113, 9004 (2009). 10.1021/jp901540t
36. Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. M. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. M. Wang, and P. Kollman, J. Comput. Chem. 24, 1999 (2003). 10.1002/jcc.10349
37. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
38. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995). 10.1063/1.470117
39. R. J. Loncharich, B. R. Brooks, and R. W. Pastor, Biopolymers 32, 523 (1992). 10.1002/bip.360320508
40. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977). 10.1016/0021-9991(77)90098-5
41. G. Matheron, Econ. Geol. 58, 1246 (1963). 10.2113/gsecongeo.58.8.1246
42. G. Matheron, Adv. Appl. Probab. 5, 439 (1973). 10.2307/1425829
43. R. R. Coifman and S. Lafon, Appl. Comput. Harmon. Anal. 21, 31 (2006). 10.1016/j.acha.2005.07.005
44. Y. Aït-Sahalia, Econometrica 70, 223 (2002). 10.1111/1468-0262.00274
45. Y. Aït-Sahalia and P. A. Mykland, Econometrica 71, 483 (2003). 10.1111/1468-0262.t01-1-00416
46. Y. Aït-Sahalia, Ann. Stat. 36, 906 (2008). 10.1214/ 009053607000000622