-
1
-
-
0002174423
-
-
in, Lecture Notes in Computational Science and Engineering Vol., edited by P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Marks, S. Reich, and R. D. Skeel (Springer-Verlag, Berlin)
-
S. Izrailev, S. Stepaniants, B. Isralewitz, D. Kosztin, H. Lu, F. Molnar, W. Wriggers, and K. Schulten, in Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering Vol. 4, edited by, P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Marks, S. Reich, and, R. D. Skeel, (Springer-Verlag, Berlin, 1998), pp. 39-65.
-
(1998)
Computational Molecular Dynamics: Challenges, Methods, Ideas
, vol.4
, pp. 39-65
-
-
Izrailev, S.1
Stepaniants, S.2
Isralewitz, B.3
Kosztin, D.4
Lu, H.5
Molnar, F.6
Wriggers, W.7
Schulten, K.8
-
2
-
-
0000500820
-
-
0009-2614,. 10.1016/S0009-2614(99)00388-7
-
B. Heymann and H. Grubmüller, Chem. Phys. Lett. 0009-2614 305, 202 (1999). 10.1016/S0009-2614(99)00388-7
-
(1999)
Chem. Phys. Lett.
, vol.305
, pp. 202
-
-
Heymann, B.1
Grubmüller, H.2
-
3
-
-
0035312645
-
Steered molecular dynamics and mechanical functions of proteins
-
DOI 10.1016/S0959-440X(00)00194-9
-
B. Isralewitz, M. Gao, and K. Schulten, Curr. Opin. Struct. Biol. 0959-440X 11, 224 (2001). 10.1016/S0959-440X(00)00194-9 (Pubitemid 32289426)
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.2
, pp. 224-230
-
-
Isralewitz, B.1
Gao, M.2
Schulten, K.3
-
4
-
-
0034979287
-
Probing the relation between force - Lifetime - And chemistry in single molecular bonds
-
DOI 10.1146/annurev.biophys.30.1.105
-
E. Evans, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 30, 105 (2001). 10.1146/annurev.biophys.30.1.105 (Pubitemid 32566158)
-
(2001)
Annual Review of Biophysics and Biomolecular Structure
, vol.30
, pp. 105-128
-
-
Evans, E.1
-
5
-
-
0035957720
-
Reversible unfolding of single RNA molecules by mechanical force
-
DOI 10.1126/science.1058498
-
J. Liphardt, B. Onoa, S. B. Smith, I. Tinoco, and C. Bustamante, Science 0036-8075 292, 733 (2001). 10.1126/science.1058498 (Pubitemid 32385545)
-
(2001)
Science
, vol.292
, Issue.5517
, pp. 733-737
-
-
Liphardt, J.1
Onoa, B.2
Smith, S.B.3
Tinoco Jr., I.4
Bustamante, C.5
-
6
-
-
23844508956
-
-
0031-9228,. 10.1063/1.2012462
-
C. Bustamante, J. Liphardt, and F. Ritort, Phys. Today 0031-9228 58, 43 (2005). 10.1063/1.2012462
-
(2005)
Phys. Today
, vol.58
, pp. 43
-
-
Bustamante, C.1
Liphardt, J.2
Ritort, F.3
-
7
-
-
33746675190
-
Single-molecule experiments in biological physics: Methods and applications
-
DOI 10.1088/0953-8984/18/32/R01, PII S0953898406875144, R01
-
F. Ritort, J. Phys.: Condens. Matter 0953-8984 18, R531 (2006). 10.1088/0953-8984/18/32/R01 (Pubitemid 44159969)
-
(2006)
Journal of Physics Condensed Matter
, vol.18
, Issue.32
-
-
Ritort, F.1
-
9
-
-
11944251646
-
-
0002-7863,. 10.1021/ja00109a011
-
D. B. Amabilino, P. L. Anelli, P. R. Ashton, G. R. Brown, E. Cordova, L. A. Godinez, W. Hayes, A. E. Kaifer, D. Philp, A. M. Z. Slawin, N. Spencer, J. F. Stoddart, M. S. Tolley, and D. J. Williams, J. Am. Chem. Soc. 0002-7863 117, 11142 (1995). 10.1021/ja00109a011
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11142
-
-
Amabilino, D.B.1
Anelli, P.L.2
Ashton, P.R.3
Brown, G.R.4
Cordova, E.5
Godinez, L.A.6
Hayes, W.7
Kaifer, A.E.8
Philp, D.9
Slawin, A.M.Z.10
Spencer, N.11
Stoddart, J.F.12
Tolley, M.S.13
Williams, D.J.14
-
11
-
-
44449112663
-
Folding of a donor-acceptor polyrotaxane by using noncovalent bonding interactions
-
DOI 10.1073/pnas.0711072105
-
W. Zhang, W. R. Dichtel, A. Z. Stieg, D. Benítez, J. K. Gimzewski, J. R. Heath, and J. F. Stoddart, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 105, 6514 (2008). 10.1073/pnas.0711072105 (Pubitemid 351760879)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.18
, pp. 6514-6519
-
-
Zhang, W.1
Dichtel, W.R.2
Stieg, A.Z.3
Benitez, D.4
Gimzewski, J.K.5
Heath, J.R.6
Stoddart, J.F.7
-
13
-
-
0024821263
-
Molecular mechanics. The MM3 force field for hydrocarbons. 1
-
DOI 10.1021/ja00205a001
-
N. L. Allinger, Y. H. Yuh, and J. H. Lii, J. Am. Chem. Soc. 0002-7863 111, 8551 (1989). 10.1021/ja00205a001 (Pubitemid 20021795)
-
(1989)
Journal of the American Chemical Society
, vol.111
, Issue.23
, pp. 8551-8566
-
-
Allinger, N.L.1
Yuh, Y.H.2
Lii, J.-H.3
-
14
-
-
0024843595
-
Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics
-
DOI 10.1021/ja00205a002
-
J. H. Lii and N. L. Allinger, J. Am. Chem. Soc. 0002-7863 111, 8566 (1989). 10.1021/ja00205a002 (Pubitemid 20021796)
-
(1989)
Journal of the American Chemical Society
, vol.111
, Issue.23
, pp. 8566-8575
-
-
Lii, J.-H.1
Allinger, N.L.2
-
15
-
-
0024804228
-
Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons
-
DOI 10.1021/ja00205a003
-
J. H. Lii and N. L. Allinger, J. Am. Chem. Soc. 0002-7863 111, 8576 (1989). 10.1021/ja00205a003 (Pubitemid 20021797)
-
(1989)
Journal of the American Chemical Society
, vol.111
, Issue.23
, pp. 8576-8582
-
-
Lii, J.-H.1
Allinger, N.L.2
-
16
-
-
36849122972
-
-
0021-9606,. 10.1063/1.1740409
-
R. W. Zwanzig, J. Chem. Phys. 0021-9606 22, 1420 (1954). 10.1063/1.1740409
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 1420
-
-
Zwanzig, R.W.1
-
18
-
-
84986519238
-
-
0192-8651,. 10.1002/jcc.540130812
-
S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 0192-8651 13, 1011 (1992). 10.1002/jcc.540130812
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
20
-
-
4243754128
-
-
0031-9007,. 10.1103/PhysRevLett.78.2690
-
C. Jarzynski, Phys. Rev. Lett. 0031-9007 78, 2690 (1997). 10.1103/PhysRevLett.78.2690
-
(1997)
Phys. Rev. Lett.
, vol.78
, pp. 2690
-
-
Jarzynski, C.1
-
21
-
-
54849185700
-
-
1434-6028,. 10.1140/epjb/e2008-00254-2
-
C. Jarzynski, Eur. Phys. J. B 1434-6028 64, 331 (2008). 10.1140/epjb/e2008-00254-2
-
(2008)
Eur. Phys. J. B
, vol.64
, pp. 331
-
-
Jarzynski, C.1
-
22
-
-
0037036070
-
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
-
DOI 10.1126/science.1071152
-
J. Liphardt, S. Dumont, S. B. Smith, I. Tinoco, and C. Bustamante, Science 0036-8075 296, 1832 (2002). 10.1126/science.1071152 (Pubitemid 34596263)
-
(2002)
Science
, vol.296
, Issue.5574
, pp. 1832-1835
-
-
Liphardt, J.1
Dumont, S.2
Smith, S.B.3
Tinoco Jr., I.4
Bustamante, C.5
-
24
-
-
23744478437
-
Free energy surfaces from single-molecule force spectroscopy
-
DOI 10.1021/ar040148d
-
G. Hummer and A. Szabo, Acc. Chem. Res. 0001-4842 38, 504 (2005). 10.1021/ar040148d (Pubitemid 41128402)
-
(2005)
Accounts of Chemical Research
, vol.38
, Issue.7
, pp. 504-513
-
-
Hummer, G.1
Szabo, A.2
-
25
-
-
4143087050
-
-
0021-9606,. 10.1063/1.1651473
-
S. Park and K. Schulten, J. Chem. Phys. 0021-9606 120, 5946 (2004). 10.1063/1.1651473
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 5946
-
-
Park, S.1
Schulten, K.2
-
26
-
-
34547726774
-
Experimental free energy surface reconstruction from single-molecule force spectroscopy using Jarzynski's equality
-
DOI 10.1103/PhysRevLett.99.068101
-
N. C. Harris, Y. Song, and C. -H. Kiang, Phys. Rev. Lett. 0031-9007 99, 068101 (2007). 10.1103/PhysRevLett.99.068101 (Pubitemid 47230771)
-
(2007)
Physical Review Letters
, vol.99
, Issue.6
, pp. 068101
-
-
Harris, N.C.1
Song, Y.2
Kiang, C.-H.3
-
27
-
-
78951496069
-
-
0295-5075,. 10.1209/0295-5075/82/58006
-
A. Imparato, F. Sbrana, and M. Vassalli, Europhys. Lett. 0295-5075 82, 58006 (2008). 10.1209/0295-5075/82/58006
-
(2008)
Europhys. Lett.
, vol.82
, pp. 58006
-
-
Imparato, A.1
Sbrana, F.2
Vassalli, M.3
-
28
-
-
4243802464
-
-
1063-651X,. 10.1103/PhysRevE.63.021906
-
H. J. Kreuzer and S. H. Payne, Phys. Rev. E 1063-651X 63, 021906 (2001). 10.1103/PhysRevE.63.021906
-
(2001)
Phys. Rev. e
, vol.63
, pp. 021906
-
-
Kreuzer, H.J.1
Payne, S.H.2
-
29
-
-
34548101355
-
Topography of the free-energy landscape probed via mechanical unfolding of proteins
-
DOI 10.1063/1.1931659, 234915
-
S. Kirmizialtin, L. Huang, and D. E. Makarov, J. Chem. Phys. 0021-9606 122, 234915 (2005). 10.1063/1.1931659 (Pubitemid 40925796)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.23
, pp. 1-12
-
-
Kirmizialtin, S.1
Huang, L.2
Makarov, D.E.3
-
30
-
-
47149110565
-
-
1932-7447,. 10.1021/jp7095967
-
R. W. Friddle, P. Podsiadlo, A. B. Artyukhin, and A. Noy, J. Phys. Chem. C 1932-7447 112, 4986 (2008). 10.1021/jp7095967
-
(2008)
J. Phys. Chem. C
, vol.112
, pp. 4986
-
-
Friddle, R.W.1
Podsiadlo, P.2
Artyukhin, A.B.3
Noy, A.4
-
31
-
-
67049117733
-
-
0027-8424,. 10.1073/pnas.0903003106
-
L. B. Freund, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 106, 8818 (2009). 10.1073/pnas.0903003106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 8818
-
-
Freund, L.B.1
-
33
-
-
0000526534
-
-
0002-7863,. 10.1021/ja00179a012
-
N. L. Allinger, M. Rahman, and J. H. Lii, J. Am. Chem. Soc. 0002-7863 112, 8293 (1990). 10.1021/ja00179a012
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 8293
-
-
Allinger, N.L.1
Rahman, M.2
Lii, J.H.3
-
34
-
-
0029633155
-
-
0010-4655,. 10.1016/0010-4655(95)00053-I
-
B. Roux, Comput. Phys. Commun. 0010-4655 91, 272 (1995). 10.1016/0010-4655(95)00053-I
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 272
-
-
Roux, B.1
-
35
-
-
33947398571
-
-
1549-9618,. 10.1021/ct0502864
-
J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theory Comput. 1549-9618 3, 26 (2007). 10.1021/ct0502864
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 26
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.W.3
Seok, C.4
Dill, K.A.5
-
36
-
-
0001430231
-
-
0192-8651,. 10.1002/(SICI)1096-987X(199805)19:7<726::AID-JCC4>3.0. CO;2-S
-
S. C. Harvey, R. K. Z. Tan, and T. E. Cheatham, J. Comput. Chem. 0192-8651 19, 726 (1998). 10.1002/(SICI)1096-987X(199805)19:7<726::AID- JCC4>3.0.CO;2-S
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 726
-
-
Harvey, S.C.1
Tan, R.K.Z.2
Cheatham, T.E.3
-
38
-
-
84956211161
-
-
0295-5075,. 10.1209/0295-5075/15/4/009
-
A. Halperin and E. B. Zhulina, Europhys. Lett. 0295-5075 15, 417 (1991). 10.1209/0295-5075/15/4/009
-
(1991)
Europhys. Lett.
, vol.15
, pp. 417
-
-
Halperin, A.1
Zhulina, E.B.2
-
39
-
-
34548172927
-
Force-induced globule-coil transition in single polystyrene chains in water
-
DOI 10.1021/ja068652w
-
N. Gunari, A. C. Balazs, and G. C. Walker, J. Am. Chem. Soc. 0002-7863 129, 10046 (2007). 10.1021/ja068652w (Pubitemid 47312919)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.33
, pp. 10046-10047
-
-
Gunari, N.1
Balazs, A.C.2
Walker, G.C.3
-
41
-
-
33746579687
-
Thermodynamics for single-molecule stretching experiments
-
DOI 10.1021/jp061840o
-
J. M. Rubi, D. Bedeaux, and S. Kjelstrup, J. Phys. Chem. B 1089-5647 110, 12733 (2006). 10.1021/jp061840o (Pubitemid 44139466)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.25
, pp. 12733-12737
-
-
Rubi, J.M.1
Bedeaux, D.2
Kjelstrup, S.3
-
42
-
-
64849113583
-
-
0031-9015,. 10.1143/JPSJ.17.1100
-
R. Kubo, J. Phys. Soc. Jpn. 0031-9015 17, 1100 (1962). 10.1143/JPSJ.17.1100
-
(1962)
J. Phys. Soc. Jpn.
, vol.17
, pp. 1100
-
-
Kubo, R.1
-
43
-
-
11544281834
-
-
0031-9007,. 10.1103/PhysRevLett.81.4764
-
M. Rief, J. M. Fernandez, and H. E. Gaub, Phys. Rev. Lett. 0031-9007 81, 4764 (1998). 10.1103/PhysRevLett.81.4764
-
(1998)
Phys. Rev. Lett.
, vol.81
, pp. 4764
-
-
Rief, M.1
Fernandez, J.M.2
Gaub, H.E.3
-
44
-
-
13744260911
-
Hydrodynamic effects in fast AFM single-molecule force measurements
-
DOI 10.1007/s00249-004-0430-3
-
H. Janovjak, J. Struckmeier, and D. J. Müller, Eur. Biophys. J. 0175-7571 34, 91 (2005). 10.1007/s00249-004-0430-3 (Pubitemid 40238922)
-
(2005)
European Biophysics Journal
, vol.34
, Issue.1
, pp. 91-96
-
-
Janovjak, H.1
Struckmeier, J.2
Muller, D.J.3
|