Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

Journal of Chemical Physics

Volumn 136, Issue 16, 2012, Pages

  Bauler, Patricia ^a   Huber, Gary A ^a   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; BROWNIAN DYNAMICS; CONTINUUM METHOD; DIFFUSION CONTROLLED REACTIONS; DIFFUSION METHOD; DIFFUSION SYSTEMS; HYBRID FINITE ELEMENTS; MULTIDIMENSIONAL SYSTEMS; RADIALLY SYMMETRIC; RATE DETERMINING STEP; STOCHASTIC METHODS; TEST CASE;

BROWNIAN MOVEMENT; FINITE ELEMENT METHOD;

DIFFUSION;

ARTICLE; DIFFUSION; MOLECULAR DYNAMICS;

DIFFUSION; MOLECULAR DYNAMICS SIMULATION;

EID: 84860475629     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4704808     Document Type: Article

References (34)

1. I. Ouporov, H. Knull, A. Huber, and K. Thomasson, Biophys. J. 80, 2527 (2001). 10.1016/S0006-3495(01)76224-8
2. A. Spaar, C. Dammer, R. R. Gabdoulline, and R. C. Wade, Biophys. J. 90, 1913 (2006). 10.1529/biophysj.105.075507
3. S. Northrup, J. Boles, and J. Reynolds, J. Chem. Phys. 91, 5991 (1987). 10.1021/j100307a036
4. J. Hake and G. T. Lines, Biophys. J. 94, 4184 (2008). 10.1529/biophysj.106.103523
5. S. Lu, A. Michailova, J. Saucerman, Y. Cheng, Z. Yu, T. Kaiser, W. Li, R. Bank, M. Holst, J. McCammon, T. Hayashi, M. Hoshijima, P. Arzberger, and A. McCulloch, IEEE Eng. Med. Biol. Mag. 28, 46 (2009). 10.1109/MEMB.2009.931787
6. T. Bartol, B. Land, E. Salpeter, and M. Salpeter, Biophys. J. 59, 1290 (1991). 10.1016/S0006-3495(91)82344-X
7. J. Smart and J. McCammon, Biophys. J. 75, 1679 (1998). 10.1016/S0006-3495(98)77610-6
8. K. Tai, S. Bond, H. MacMillan, N. Baker, M. Holst, and J. McCammon, Biophys. J. 84, 2234 (2003). 10.1016/S0006-3495(03)75029-2
9. J. Antosiewicz, M. K. Gilson, I. H. Lee, and J. A. McCammon, Biophys. J. 68, 62 (1995). 10.1016/S0006-3495(95)80159-1
10. C. L. Lopreore, T. M. Bartol, J. S. Coggan, D. X. Keller, G. E. Sosinsky, M. H. Ellisman, and T. J. Sejnowski, Biophys. J. 95, 2624 (2008). 10.1529/biophysj.108.132167
11. D. Ermak and J. McCammon, J. Chem. Phys. 69, 1352 (1978). 10.1063/1.436761
12. S. Northrup, S. Allison, and J. McCammon, J. Chem. Phys. 80, 1517 (1984). 10.1063/1.446900
13. H. Zhou, J. Chem. Phys. 92, 3092 (1990). 10.1063/1.457907
14. B. Luty, J. McCammon, and H. Zhou, J. Chem. Phys. 97, 5682 (1992). 10.1063/1.463777
15. P. Bauler, G. Huber, T. Leyh, and J. A. McCammon, J. Phys. Chem. Lett. 1, 1332 (2010). 10.1021/jz1002007
16. Y. Song, Y. Zhang, T. Shen, C. Bajaj, J. McCammon, and N. Baker, Biophys. J. 86, 2017 (2004). 10.1016/S0006-3495(04)74263-0
17. G. A. Huber and J. A. McCammon, Comput. Phys. Commun. 181, 1896 (2010). 10.1016/j.cpc.2010.07.022
18. R. Gabdoulline and R. Wade, Biophys. J. 72, 1917 (1997). 10.1016/S0006-3495(97)78838-6
19. S. Northrup, T. Laughner, and G. Stevenson, MACRODOX macromolecular simulation program, Department of Chemistry, Tennessee Technological University, Cookeville, TN, 1997; online at iweb.tntech.edu/macrodox/macrodox.html.
20. J. Madura, J. Briggs, R. Wade, M. Davis, B. Luty, A. Ilin, J. Antosiewicz, M. Gilson, B. Bagheri, L. Scott, and J. McCammon, Comput. Phys. Commun. 91, 57 (1995). 10.1016/0010-4655(95)00043-F
21. M. Dlugosz, P. Zielinski, and J. Trylska, J. Comput. Chem. 32, 2734 (2011). 10.1002/jcc.21847
22. T. Geyer, BMC Biophys. 4, (2011). 10.1186/2046-1682-4-7
23. S. R. McGuffee and A. H. Elcock, PLoS Comput. Biol. 6, e1000694 (2010). 10.1371/journal.pcbi.1000694
24. Y. Cheng, J. K. Suen, D. Zhang, S. D. Bond, Y. Zhang, Y. Song, N. A. Baker, C. L. Bajaj, M. J. Holst, and J. A. McCammon, Biophys. J. 92, 3397 (2007). 10.1529/biophysj.106.102533
25. B. Lu, Y. C. Zhou, G. A. Huber, S. D. Bond, M. J. Holst, and J. A. McCammon, J. Chem. Phys. 127, (2007). 10.1063/1.2775933
26. Y. C. Zhou, B. Lu, G. A. Huber, M. J. Holst, and J. A. McCammon, J. Phys. Chem. B 112, 270 (2008). 10.1021/jp074900e
27. Y. Cheng, C. Chang, Z. Yu, Y. Zhang, M. Sun, T. S. Leyh, M. J. Holst, and J. A. McCammon, Biophys. J. 95, 4659 (2008). 10.1529/biophysj.108.140038
28. T. Geyer, C. Gorba, and V. Helms, J. Chem. Phys. 120, 4573 (2004). 10.1063/1.1647522
29. C. Gorba, T. Geyer, and V. Helms, J. Chem. Phys. 121, 457 (2004). 10.1063/1.1755668
30. W. Im, S. Seefeld, and B. Roux, Biophys. J. 79, 788 (2000). 10.1016/S0006-3495(00)76336-3
31. J. Crank, The Mathematics of Diffusion, 2nd ed. (Clarendon Press, Oxford, 1975).
32. E. Hairer and G. Wanner, J. Comput. App. Math. 111, 93 (1999). 10.1016/S0377-0427(99)00134-X
33. Y. Cheng, Z. Yu, M. Hoshijima, M. J. Holst, A. D. McCulloch, J. A. McCammon, and A. P. Michailova, PLoS Comput. Biol. 6, (2010). 10.1371/journal.pcbi.1000972
34. S. Lindert, P. M. Kekenes-Huskey, G. Huber, L. Pierce, and J. A. McCammon, Dynamics and Calcium Association to the N-Terminal Regulatory Domain of Human Cardiac Troponin C: A Multiscale Computational Study., J. Phys. Chem. B (in press). 10.1021/jp212173f