Multiscale factorization method for simulating mesoscopic systems with atomic precision

Journal of Chemical Theory and Computation

Volumn 10, Issue 2, 2014, Pages 518-523

  Abi Mansour, Andrew ^a   Ortoleva, Peter J ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84894206648     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400615a     Document Type: Article

References (35)

1. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
2. Spoel, V. D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718
3. Cheluvaraja, S.; Ortoleva, P. J. J. Chem. Phys. 2010, 132, 75102-75110
4. Joshi, H.; Singharoy, A.; Sereda, Y. V.; Cheluvaraja, S. C.; Ortoleva, P. J. Prog. Bio.-Phys. Mol. Biol. 2011, 107, 200-217
5. Murtola, T.; Falck, E.; Karttunen, M.; Vattulainen, I. J. Chem. Phys. 2007, 126, 75101-75114
6. Reith, D.; Putz, M.; Muller-Plathe, F. J. Comput. Chem. 2003, 24, 1624-1636
7. Bahar, I.; Atilgan, R. A.; Erman, B. Folding Design 1997, 2, 173-181
8. Haliloglu, T.; Bahar, I.; Erman, B. Phys. Rev. Lett. 1997, 79, 3090-3093
9. Shiha, A. Y.; Arkhipov, A.; Freddolino, P. L.; Schulten, K. J. Phys. Chem. B 2006, 110, 3674-3684
10. Shiha, A. Y.; Freddolinoa, P. L.; Arkhipova, A.; Schulten, K. J. Struct. Biol. 2007, 157, 579-592
11. Marrink, S. J.; de Vries, A. H.; Mark, A. E. J. Phys. Chem. B 2004, 108, 750-760
12. Singharoy, A.; Cheluvaraja, S.; Ortoleva, P. J. J. Chem. Phys. 2011, 134, 44104-44120
13. Ortoleva, P. J. J. Phys. Chem. B 2005, 109, 21258-21266
14. Pankavich, S.; Shreif, Z.; Ortoleva, P. J. Phys. A 2008, 387, 4053-4069
15. Pankavich, S.; Shreif, Z.; Miao, Y.; Ortoleva, P. J. J. Chem. Phys. 2009, 130, 194115-194124
16. Abrams, J. B.; Tuckerman, M. E. J. Phys. Chem. B 2008, 112, 1574215757
17. Noid, W. G.; Chu, J.-W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. J. Chem. Phys. 2008, 128, 244114-244124
18. Shea, J.-E.; Oppenheim, I. J. Phys. Chem. 1996, 100, 19035-19042
19. Shea, J.-E.; Oppenheim, I. Phys. A 1997, 247, 417-443
20. Shea, J.-E.; Oppenheim, I. Phys. A 1998, 250, 265-294
21. Trotter, H. F. Proc. Am. Math. Soc. 1959, 10, 545-551
22. Hall, B. C. Lie groups, Lie algebras, and representations: an elementary introduction; Springer, 2003; Vol. 10 (III); pp 36-37.
23. Tuckerman, M.; Berne, B. J.; Martyna, G. J. J. Chem. Phys. 1992, 97, 1990-2001
24. Miao, Y.; Ortoleva, P. J. Comput. Chem. 2008, 30, 423-437
25. Miao, Y.; Johnson, J. E.; Ortoleva, P. J. J. Phys. Chem. B 2010, 114, 11181-11195
26. Singharoy, A.; Joshi, H.; Miao, Y.; Ortoleva, P. J. J. Phys. Chem. B 2012, 116, 8423-8434
27. Jaqaman, K.; Ortoleva, P. J. J. Comput. Chem. 2002, 23, 484-491
28. Pankavich, S.; Miao, Y.; Ortoleva, J.; Shreif, Z.; Ortoleva, P. J. J. Chem. Phys. 2008, 128, 234908-234921
29. Singharoy, A.; Joshi, H.; Ortoleva, P. J. J. Chem. Inf. Model. 2012, 52, 2638-2686
30. Romo, T.;; Grossfield, A. 31st Annual International Conference of the IEEE EMBS, Minneapolis, MN, Sep 2-6, 2009; pp 2332-2335.
31. Norris, G. E.; Anderson, B. F.; Baker, E. N. Acta Crystallogr. Sect. B 1991, 47, 998-1004
32. Kim, M. K.; Jernigan, R. L.; Chirikjian, G. S. J. Biophys. 2005, 89, 43-55
33. Taylor, D. J.; Wang, Q.; Bothner, B.; Natarajan, P.; Finn, M. G.; Johnson, J. E. J. Chem. Commun. 2003, 22, 2770-2771
34. Singharoy, A.; Sereda, Y.; Ortoleva, P. J. J. Chem. Theory Comput. 2012, 8, 1379-1392
35. Iserles, A. A First Course in the Numerical Analysis of Differential Equations; Cambridge University Press, 2008; pp 53-63.