Biomedical Engineering Reference
In-Depth Information
7. Alder, B.J., Wainwright, T.E.: Phase transition for a hard sphere system. J. Chem. Phys.
27
,
2 (1957)
8. Rapaport, D.C.: Molecular-dynamics simulation of polymer-chains with excluded volume.
J.Phys.AMath.Gen.
11
, L213-L217 (1978)
9. Rapaport, D.C.: Event scheduling problem in molecular dynamic simulation. J. Comput. Phys.
34
, 184-201 (1980)
10. Denlinger, M.A., Hall, C.K.: Molecular dynamics simulation results for the pressure of hard-
chain fluids. Mol. Phys.
71
, 541-559 (1990)
11. Alejandre, J., Chapela, G.A.: Molecular-dynamics for discontinuous potentials.3. compress-
ibility factors and structure of hard polyatomic fluids. Mol. Phys.
61
, 1119-1130 (1987)
12. Chapela, G.A., Martinezcasas, S.E., Alejandre, J.: Molecular-dynamics for discontinuous
potentials.1. General-method and simulation of hard polyatomic-molecules. Mol. Phys.
53
,
139-159 (1984)
13. Smith, A.V., Hall, C.K.: alpha-helix formation: discontinuous molecular dynamics on an
intermediate-resolution protein model. Proteins-Struct. Func. Genet.
44
, 344-360 (2001)
14. Smith, S.W., Hall, C.K., Freeman, B.D.: Large-scale molecular-dynamics study of entangled
hard-chain fluids. Phys. Rev. Lett.
75
, 1316-1319 (1995)
15. Smith, S.W., Hall, C.K., Freeman, B.D.: Molecular dynamics for polymeric fluids using
discontinuous potentials. J. Comput. Phys.
134
, 16-30 (1997)
16. Zhou, Y., Karplus, M.: Folding thermodynamics of a model three-helix-bundle protein. Proc.
Natl. Acad. Sci. U. S. A.
94
, 14429-14432 (1997)
17. Zhou, Y., Karplus, M.: Interpreting the folding kinetics of helical proteins. Nature
401
,
400-403 (1999)
18. Ding, F., Borreguero, J.M., Buldyrey, S.V., Stanley, H.E., Dokholyan, N.V.: Mechanism for the
alpha-helix to beta-hairpin transition. Proteins
53
, 220-228 (2003)
19. Ding, F., Buldyrev, S.V., Dokholyan, N.V.: Folding Trp-cage to NMR resolution native
structure using a coarse-grained protein model. Biophys. J.
88
, 147-155 (2005)
20. Ding, F., Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., Shakhnovich, E.I.: Molecular
dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis
mechanism. J. Mol. Biol.
324
, 851-857 (2002)
21. Ding, F., Tsao, D., Nie, H., Dokholyan, N.V.: Ab initio folding of proteins with all-atom
discrete molecular dynamics. Structure
16
, 1010-1018 (2008)
22. Peng, S., Ding, F., Urbanc, B., Buldyrev, S.V., Cruz, L., Stanley, H.E., Dokholyan, N.V.:
Discrete molecular dynamics simulations of peptide aggregation. Phys. Rev. E Stat. Nonlin.
Soft Matter Phys.
69
, 041908 (2004)
23. Rahman, A.: Correlations in motion of atoms in liquid argon. Phys. Rev. A Gen. Phys.
136
,
A405-A411 (1964)
24. Stilling, F.h., Rahman, A.: Improved simulation of liquid water by molecular-dynamics.
J. Chem. Phys.
60
, 1545-1557 (1974)
25. McCammon, J.A., Gelin, B.R., Karplus, M.: Dynamics of folded proteins. Nature
267
,
585-590 (1977)
26. Shirts, M., Pande, V.S.: COMPUTING: screen savers of the world unite! Science
290
,
1903-1904 (2000)
27. Piana, S., Sarkar, K., Lindorff-Larsen, K., Guo, M., Gruebele, M., Shaw, D.E.: Computational
design and experimental testing of the fastest-folding beta-sheet protein. J. Mol. Biol.
405
,
43-48 (2010)
28. Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O., Eastwood, M.P., Bank,
J.A., Jumper, J.M., Salmon, J.K., Shan, Y., Wriggers, W.: Atomic-level characterization of the
structural dynamics of proteins. Science
330
, 341-346 (2010)
29. Borreguero, J.M., Urbanc, B., Lazo, N.D., Buldyrev, S.V., Teplow, D.B., Stanley, H.E.: Folding
events in the 21-30 region of amyloid beta-protein (Abeta) studied in silico. Proc. Natl. Acad.
Sci. U. S. A.
102
, 6015-6020 (2005)
Search WWH ::
Custom Search