-
1
-
-
0000086155
-
DNA strand separation studied by single molecule force measurements
-
Bockelmann, U., B. Essevaz-Roulet, and F. Heslot 1998. DNA strand separation studied by single molecule force measurements. Phys. Rev. E. 58:2386-2394.
-
(1998)
Phys. Rev. E
, vol.58
, pp. 2386-2394
-
-
Bockelmann, U.1
Essevaz-Roulet, B.2
Heslot, F.3
-
2
-
-
0002296942
-
A new algorithm for Monte Carlo simulation of Ising spin systems
-
Bortz, A. B., M. H. Kalos, and J. L. Lebowitz. 1975. A new algorithm for Monte Carlo simulation of Ising spin systems. J. Comput. Phys. 17:10-18.
-
(1975)
J. Comput. Phys.
, vol.17
, pp. 10-18
-
-
Bortz, A.B.1
Kalos, M.H.2
Lebowitz, J.L.3
-
3
-
-
0030919776
-
Prediction of sequentially optimal RNA secondary structures
-
Breton, N., C. Jacob, and P. Daegelen. 1997. Prediction of sequentially optimal RNA secondary structures. J. Biomol. Struct. Dyn. 14:727-740.
-
(1997)
J. Biomol. Struct. Dyn.
, vol.14
, pp. 727-740
-
-
Breton, N.1
Jacob, C.2
Daegelen, P.3
-
4
-
-
0028071373
-
Entropic elasticity of lambda-phage DNA
-
Bustamante, C., J. F. Marko, E. D. Siggia, and S. B. Smith. 1994. Entropic elasticity of lambda-phage DNA. Science. 265:1599-1600.
-
(1994)
Science
, vol.265
, pp. 1599-1600
-
-
Bustamante, C.1
Marko, J.F.2
Siggia, E.D.3
Smith, S.B.4
-
5
-
-
0034069612
-
Single-molecule studies of DNA mechanics
-
Bustamante, C., S. B. Smith, J. Liphardt, and D. Smith. 2000. Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol. 10:279-285.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 279-285
-
-
Bustamante, C.1
Smith, S.B.2
Liphardt, J.3
Smith, D.4
-
6
-
-
0023364038
-
The chemistry of self-splicing RNA and RNA enzymes
-
Cech, T. R. 1987. The chemistry of self-splicing RNA and RNA enzymes. Science. 236:1532-1539.
-
(1987)
Science
, vol.236
, pp. 1532-1539
-
-
Cech, T.R.1
-
7
-
-
0003017978
-
Strucuture and mechanism of the large catalytic RNAs: Group I and group II introns and ribonuclease P
-
R. F. Gesteland and J. F. Atkins, editors. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
-
Cech, T. R. 1993. Strucuture and mechanism of the large catalytic RNAs: group I and group II introns and ribonuclease P. In The RNA World. R. F. Gesteland and J. F. Atkins, editors. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 239-269.
-
(1993)
The RNA World
, pp. 239-269
-
-
Cech, T.R.1
-
8
-
-
2342470819
-
Slow nucleic acid unzipping kinetics from sequence-defined barriers
-
Cocco, S., S. F. Marko, and R. Monasson. 2003. Slow nucleic acid unzipping kinetics from sequence-defined barriers. Eur. Phys. J. E. Soft Matter. 10:153-161.
-
(2003)
Eur. Phys. J. E. Soft Matter
, vol.10
, pp. 153-161
-
-
Cocco, S.1
Marko, S.F.2
Monasson, R.3
-
9
-
-
0037146606
-
Small RNAs make big splash
-
Couzin, J. 2002. Small RNAs make big splash. Science. 298:2296-2297.
-
(2002)
Science
, vol.298
, pp. 2296-2297
-
-
Couzin, J.1
-
10
-
-
0031001349
-
Dynamic strength of molecular adhesion bonds
-
Evans, E., and K. Ritchie. 1997. Dynamic strength of molecular adhesion bonds. Biophys. J. 72:1541-1555.
-
(1997)
Biophys. J.
, vol.72
, pp. 1541-1555
-
-
Evans, E.1
Ritchie, K.2
-
12
-
-
0034021259
-
RNA folding at elementary step resolution
-
Flamm, C., W. Fontana, I. Hofacker, and P. Schuster. 2000. RNA folding at elementary step resolution. RNA: 6:325-338.
-
(2000)
RNA
, vol.6
, pp. 325-338
-
-
Flamm, C.1
Fontana, W.2
Hofacker, I.3
Schuster, P.4
-
13
-
-
0037623306
-
Mechanically probing the folding pathway of single RNA molecules
-
Gerland, U., R. Bundschuh, and T. Hwa. 2003. Mechanically probing the folding pathway of single RNA molecules. Biophys. J. 84:2831-2840.
-
(2003)
Biophys. J.
, vol.84
, pp. 2831-2840
-
-
Gerland, U.1
Bundschuh, R.2
Hwa, T.3
-
14
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie, D. T. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys. 22:403-434.
-
(1976)
J. Comp. Phys.
, vol.22
, pp. 403-434
-
-
Gillespie, D.T.1
-
15
-
-
0029061125
-
The computer simulation of RNA folding pathways using a genetic algorithm
-
Gultyaev, A. P., F. H. D. van Batenburg, and C. W. A. Pleij. 1995. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:37-51.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 37-51
-
-
Gultyaev, A.P.1
Van Batenburg, F.H.D.2
Pleij, C.W.A.3
-
16
-
-
2342459158
-
Probing complex RNA structures by mechanical force
-
Harlepp, S., T. M. Marchal, J. Robert, J.-F. Leger, A. Xayaphoummine, H. Isambert, and D. Chatenay. 2003. Probing complex RNA structures by mechanical force. Eur. Phys. J. E. Soft Matter. 12:605-613.
-
(2003)
Eur. Phys. J. E. Soft Matter
, vol.12
, pp. 605-613
-
-
Harlepp, S.1
Marchal, T.M.2
Robert, J.3
Leger, J.-F.4
Xayaphoummine, A.5
Isambert, H.6
Chatenay, D.7
-
17
-
-
0043123153
-
The Vienna RNA secondary structure server
-
Hofacker, I. L. 2003. The Vienna RNA secondary structure server. Nucleic Acids Res. 31:3429-3431.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
18
-
-
0000718479
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I. L., W. Fontana, P. F. Stadler, S. Bonhoeffer. M. Takcer, and P. Schuster. 1994. Fast folding and comparison of RNA secondary structures. Monatsh. Chemie. 107:2903-2912.
-
(1994)
Monatsh. Chemie
, vol.107
, pp. 2903-2912
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, S.4
Takcer, M.5
Schuster, P.6
-
19
-
-
0038650860
-
Kinetics from nonequilibrium single-molecule pulling experiments
-
Hummer, G., and A. Szabo. 2003. Kinetics from nonequilibrium single-molecule pulling experiments. Biophys. J. 85:5-15.
-
(2003)
Biophys. J.
, vol.85
, pp. 5-15
-
-
Hummer, G.1
Szabo, A.2
-
20
-
-
0041335634
-
Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments
-
Hyeon, C.-H., and D. Thirumalai. 2003. Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments. Proc. Natl. Acad. Sci. USA. 100:10249-10253.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 10249-10253
-
-
Hyeon, C.-H.1
Thirumalai, D.2
-
21
-
-
0034612331
-
Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
-
Isambert, H., and E. D. Siggia. 2000. Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc. Natl. Acad. Sci. USA. 97:6515-6520.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 6515-6520
-
-
Isambert, H.1
Siggia, E.D.2
-
22
-
-
36049060531
-
Diffusion constants near the critical point for time-dependent Ising models
-
Kawasaki, K. 1966. Diffusion constants near the critical point for time-dependent Ising models. Phys. Rev. 145:224-230.
-
(1966)
Phys. Rev.
, vol.145
, pp. 224-230
-
-
Kawasaki, K.1
-
23
-
-
0037036070
-
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
-
Liphardt, J., B. S. Dumont, S. B. Smith, I. Tinoco, and C. Bustamante. 2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science. 296:1832-1835.
-
(2002)
Science
, vol.296
, pp. 1832-1835
-
-
Liphardt, J.1
Dumont, B.S.2
Smith, S.B.3
Tinoco, I.4
Bustamante, C.5
-
24
-
-
0035957720
-
Reversible unfolding of single RNA molecules by mechanical force
-
Liphardt, J., B. Onoa, S. B. Smith, I. Tinoco, and C. Bustamante. 2001. Reversible unfolding of single RNA molecules by mechanical force. Science. 292:733-737.
-
(2001)
Science
, vol.292
, pp. 733-737
-
-
Liphardt, J.1
Onoa, B.2
Smith, S.B.3
Tinoco, I.4
Bustamante, C.5
-
25
-
-
37649026744
-
Unfolding single RNA molecules by mechanical force: A stochastic kinetic method
-
Liu, F., and Z.-c. Ou-Yang. 2004. Unfolding single RNA molecules by mechanical force: a stochastic kinetic method. Phys. Rev. E. 70:040901-040904.
-
(2004)
Phys. Rev. E
, vol.70
, pp. 040901-040904
-
-
Liu, F.1
Ou-Yang, Z.-C.2
-
26
-
-
37649027722
-
Single molecule statistics and the polynucleotide unzipping transition
-
Lubensky, D. K., and D. R. Nelson. 2002. Single molecule statistics and the polynucleotide unzipping transition. Phys. Rev. E. 65:031917.
-
(2002)
Phys. Rev. E
, vol.65
, pp. 031917
-
-
Lubensky, D.K.1
Nelson, D.R.2
-
27
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
McCaskill, J. S. 1993. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 29:1105-1119.
-
(1993)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
28
-
-
0027219835
-
A kinetic model of RNA folding
-
Mironov, A., and V. F. Lebedev. 1993. A kinetic model of RNA folding. Biosystems. 30:49-56.
-
(1993)
Biosystems
, vol.30
, pp. 49-56
-
-
Mironov, A.1
Lebedev, V.F.2
-
30
-
-
0242417558
-
Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme
-
Onoa, B., S. Dumont, J. Liphardt, S. B. Smith, I. Tinoco, and C. Bustamante. 2003. Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science. 299:1892-1895.
-
(2003)
Science
, vol.299
, pp. 1892-1895
-
-
Onoa, B.1
Dumont, S.2
Liphardt, J.3
Smith, S.B.4
Tinoco, I.5
Bustamante, C.6
-
32
-
-
0037109040
-
A two-state kinetic model for the unfolding of single molecules by mechanical force
-
Ritort, F., C. Bustamante, and I. Tinoco, Jr. 2002. A two-state kinetic model for the unfolding of single molecules by mechanical force. Proc. Natl. Acad. Sci. USA. 99:13544-13548.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 13544-13548
-
-
Ritort, F.1
Bustamante, C.2
Tinoco Jr., I.3
-
33
-
-
0033524952
-
A dynamic programming algorithm for RNA structure prediction including pseudoknots
-
Rivas, E., and S. R. Eddy. 1999. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285:2053-2068.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2053-2068
-
-
Rivas, E.1
Eddy, S.R.2
-
34
-
-
0030024985
-
Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
36
-
-
0031047888
-
Stretching DNA with optical tweezers
-
Wang, M. D., H. Yin, R. Landick, J. Gelles, and S. M. Block. 1997. Stretching DNA with optical tweezers. Biophys. J. 72:1335-1346.
-
(1997)
Biophys. J.
, vol.72
, pp. 1335-1346
-
-
Wang, M.D.1
Yin, H.2
Landick, R.3
Gelles, J.4
Block, S.M.5
-
37
-
-
0034901419
-
Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions
-
Zhang, Y., H. Zhou, and Z.-C. Ou-Yang. 2001. Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions. Biophys. J. 81:1133-1143.
-
(2001)
Biophys. J.
, vol.81
, pp. 1133-1143
-
-
Zhang, Y.1
Zhou, H.2
Ou-Yang, Z.-C.3
-
38
-
-
0019876473
-
Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information
-
Zuker, M., and P. Stiegler. 1981. Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9:133-148.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|