-
1
-
-
19044363437
-
-
PRLTAO 0031-9007,. 10.1103/PhysRevLett.88.198101
-
E. Carlon, E. Orlandini, and A. L. Stella, Phys. Rev. Lett. PRLTAO 0031-9007 88, 198101 (2002). 10.1103/PhysRevLett.88.198101
-
(2002)
Phys. Rev. Lett.
, vol.88
, pp. 198101
-
-
Carlon, E.1
Orlandini, E.2
Stella, A.L.3
-
2
-
-
85014002810
-
-
PLEEE8 1063-651X,. 10.1103/PhysRevE.68.021911
-
B. Mergell, M. R. Ejtehadi, and R. Everaers, Phys. Rev. E PLEEE8 1063-651X 68, 021911 (2003). 10.1103/PhysRevE.68.021911
-
(2003)
Phys. Rev. e
, vol.68
, pp. 021911
-
-
Mergell, B.1
Ejtehadi, M.R.2
Everaers, R.3
-
3
-
-
26944440021
-
Mesoscopic modeling for nucleic acid chain dynamics
-
DOI 10.1103/PhysRevE.71.051902, 051902
-
M. Sales-Pardo, R. Guimera, A. A. Moreira, J. Widom, and L. A. N. Amaral, Phys. Rev. E PLEEE8 1063-651X 71, 051902 (2005). 10.1103/PhysRevE.71.051902 (Pubitemid 41480965)
-
(2005)
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
, vol.71
, Issue.5
, pp. 1-13
-
-
Sales-Pardo, M.1
Guimera, R.2
Moreira, A.A.3
Widom, J.4
Amaral, L.A.N.5
-
4
-
-
33748469169
-
Computer simulation study of molecular recognition in model DNA microarrays
-
DOI 10.1529/biophysj.106.086173
-
A. Jayaraman, C. K. Hall, and J. Genzer, Biophys. J. BIOJAU 0006-3495 91, 2227 (2006). 10.1529/biophysj.106.086173 (Pubitemid 44352405)
-
(2006)
Biophysical Journal
, vol.91
, Issue.6
, pp. 2227-2236
-
-
Jayaraman, A.1
Hall, C.K.2
Genzer, J.3
-
5
-
-
77951916314
-
-
PPCPFQ 1463-9076,. 10.1039/b916183j
-
G. Zheng, L. Czapla, A. R. Srinivasan, and W. K. Olson, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 12, 1399 (2010). 10.1039/b916183j
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 1399
-
-
Zheng, G.1
Czapla, L.2
Srinivasan, A.R.3
Olson, W.K.4
-
6
-
-
77951569390
-
-
PRLTAO 0031-9007,. 10.1103/PhysRevLett.104.178101
-
T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. PRLTAO 0031-9007 104, 178101 (2010). 10.1103/PhysRevLett.104.178101
-
(2010)
Phys. Rev. Lett.
, vol.104
, pp. 178101
-
-
Ouldridge, T.E.1
Louis, A.A.2
Doye, J.P.K.3
-
7
-
-
0034227561
-
-
JPCBFK 1089-5647,. 10.1021/jp000550j
-
K. Drukker and G. C. Schatz, J. Phys. Chem. B JPCBFK 1089-5647 104, 6108 (2000). 10.1021/jp000550j
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 6108
-
-
Drukker, K.1
Schatz, G.C.2
-
8
-
-
0035151619
-
Model simulations of DNA denaturation dynamics
-
DOI 10.1063/1.1329137
-
K. Drukker, G. Wu, and G. C. Schatz, J. Chem. Phys. JCPSA6 0021-9606 114, 579 (2001). 10.1063/1.1329137 (Pubitemid 32088417)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.1
, pp. 579-590
-
-
Drukker, K.1
Wu, G.2
Schatz, G.C.3
-
9
-
-
26044467569
-
Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA
-
DOI 10.1063/1.2038767, 124911
-
S. P. Mielke, N. Grønbech-Jensen, V. V. Krishnan, W. H. Fink, and C. J. Benham, J. Chem. Phys. JCPSA6 0021-9606 123, 124911 (2005). 10.1063/1.2038767 (Pubitemid 41407821)
-
(2005)
Journal of Chemical Physics
, vol.123
, Issue.12
, pp. 1-11
-
-
Mielke, S.P.1
Gronbech-Jensen, N.2
Krishnan, V.V.3
Fink, W.H.4
Benham, C.J.5
-
10
-
-
62249141027
-
-
JCPSA6 0021-9606,. 10.1063/1.3078795
-
M. Kenward and K. D. Dorfman, J. Chem. Phys. JCPSA6 0021-9606 130, 095101 (2009). 10.1063/1.3078795
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 095101
-
-
Kenward, M.1
Dorfman, K.D.2
-
12
-
-
0020962967
-
-
JBSDD6 0739-1102
-
B. Tidor, K. K. Irikura, B. R. Brooks, and M. Karplus, J. Biomol. Struct. Dyn. JBSDD6 0739-1102 1, 231 (1983).
-
(1983)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 231
-
-
Tidor, B.1
Irikura, K.K.2
Brooks, B.R.3
Karplus, M.4
-
14
-
-
35949004903
-
-
PLEEE8 1063-651X,. 10.1103/PhysRevE.52.4217
-
F. Zhang and M. A. Collins, Phys. Rev. E PLEEE8 1063-651X 52, 4217 (1995). 10.1103/PhysRevE.52.4217
-
(1995)
Phys. Rev. e
, vol.52
, pp. 4217
-
-
Zhang, F.1
Collins, M.A.2
-
15
-
-
0032735433
-
-
BIOJAU 0006-3495,. 10.1016/S0006-3495(99)77074-8
-
N. Bruant, D. Flatters, R. Lavery, and D. Genest, Biophys. J. BIOJAU 0006-3495 77, 2366 (1999). 10.1016/S0006-3495(99)77074-8
-
(1999)
Biophys. J.
, vol.77
, pp. 2366
-
-
Bruant, N.1
Flatters, D.2
Lavery, R.3
Genest, D.4
-
16
-
-
0034820744
-
MD simulations of homomorphous PNA, DNA, and RNA single strands: Characterization and comparison of conformations and dynamics
-
DOI 10.1021/ja0032632
-
S. Sen and L. Nilsson, J. Am. Chem. Soc. JACSAT 0002-7863 123, 7414 (2001). 10.1021/ja0032632 (Pubitemid 32879459)
-
(2001)
Journal of the American Chemical Society
, vol.123
, Issue.30
, pp. 7414-7422
-
-
Sen, S.1
Nilsson, L.2
-
17
-
-
14244271476
-
-
BIPMAA 0006-3525,. 10.1002/1097-0282(2000)56:4<232::AID-BIP10037>3. 0.CO;2-H
-
T. E. Cheatham III and M. A. Young, Biopolymers BIPMAA 0006-3525 56, 232 (2000). 10.1002/1097-0282(2000)56:4<232::AID-BIP10037>3.0.CO;2-H
-
(2000)
Biopolymers
, vol.56
, pp. 232
-
-
Cheatham III, T.E.1
Young, M.A.2
-
18
-
-
0036280718
-
-
ACHRE4 0001-4842,. 10.1021/ar010026a
-
J. Norberg and L. Nilsson, Acc. Chem. Res. ACHRE4 0001-4842 35, 465 (2002). 10.1021/ar010026a
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 465
-
-
Norberg, J.1
Nilsson, L.2
-
19
-
-
6944220065
-
Ion motions in molecular dynamics simulations on DNA
-
DOI 10.1073/pnas.0406435101
-
S. Y. Ponomarev, K. M. Thayer, and D. L. Beveridge, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 101, 14771 (2004). 10.1073/pnas.0406435101 (Pubitemid 39410750)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.41
, pp. 14771-14775
-
-
Ponornarev, S.Y.1
Thayer, K.M.2
Beveridge, D.L.3
-
20
-
-
17444405896
-
A coarse-grained model for double-helix molecules in solution: Spontaneous helix formation and equilibrium properties
-
DOI 10.1063/1.1869417, 124906
-
H. L. Tepper and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 122, 124906 (2005). 10.1063/1.1869417 (Pubitemid 40537498)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.12
, pp. 1-11
-
-
Tepper, H.L.1
Voth, G.A.2
-
21
-
-
32344437326
-
Towards more realistic dynamical models for DNA secondary structure
-
DOI 10.1016/j.cplett.2005.12.009, PII S0009261405018841
-
S. Buyukdagli, M. Sanrey, and M. Joyeux, Chem. Phys. Lett. CHPLBC 0009-2614 419, 434 (2006). 10.1016/j.cplett.2005.12.009 (Pubitemid 43220507)
-
(2006)
Chemical Physics Letters
, vol.419
, Issue.4-6
, pp. 434-438
-
-
Buyukdagli, S.1
Sanrey, M.2
Joyeux, M.3
-
22
-
-
33847626738
-
A coarse grain model for DNA
-
DOI 10.1063/1.2431804
-
T. A. Knotts IV, N. Rathore, D. C. Schwartz, and J. J. de Pablo, J. Chem. Phys. JCPSA6 0021-9606 126, 084901 (2007). 10.1063/1.2431804 (Pubitemid 46357459)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.8
, pp. 084901
-
-
Knotts, T.A.1
Rathore, N.2
Schwartz, D.C.3
De Pablo, J.J.4
-
24
-
-
70450257682
-
-
PPCPFQ 1463-9076,. 10.1039/b912067j
-
A. Noy, I. Soteras, F. J. Luque, and M. Orozco, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 11, 10596 (2009). 10.1039/b912067j
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 10596
-
-
Noy, A.1
Soteras, I.2
Luque, F.J.3
Orozco, M.4
-
25
-
-
77949889822
-
-
JCPSA6 0021-9606,. 10.1063/1.3269994
-
A. Morriss-Andrews, J. Rottler, and S. S. Plotkin, J. Chem. Phys. JCPSA6 0021-9606 132, 035105 (2010). 10.1063/1.3269994
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 035105
-
-
Morriss-Andrews, A.1
Rottler, J.2
Plotkin, S.S.3
-
26
-
-
0034257985
-
-
PLEEE8 1063-651X,. 10.1103/PhysRevE.62.3958
-
M. S. Causo, B. Coluzzi, and P. Grassberger, Phys. Rev. E PLEEE8 1063-651X 62, 3958 (2000). 10.1103/PhysRevE.62.3958
-
(2000)
Phys. Rev. e
, vol.62
, pp. 3958
-
-
Causo, M.S.1
Coluzzi, B.2
Grassberger, P.3
-
27
-
-
34548008374
-
Modeling DNA in confinement: A comparison between the brownian dynamics and lattice Boltzmann method
-
DOI 10.1021/ma070729t
-
Y. L. Chen, H. Ma, M. D. Graham, and J. J. de Pablo, Macromolecules MAMOBX 0024-9297 40, 5978 (2007). 10.1021/ma070729t (Pubitemid 47280875)
-
(2007)
Macromolecules
, vol.40
, Issue.16
, pp. 5978-5984
-
-
Chen, Y.-L.1
Ma, H.2
Graham, M.D.3
De Pablo, J.J.4
-
28
-
-
40149097626
-
The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores
-
DOI 10.1063/1.2831777
-
A. Izmitli, D. C. Schwartz, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. JCPSA6 0021-9606 128, 085102 (2008). 10.1063/1.2831777 (Pubitemid 351328732)
-
(2008)
Journal of Chemical Physics
, vol.128
, Issue.8
, pp. 085102
-
-
Izmitli, A.1
Schwartz, D.C.2
Graham, M.D.3
De Pablo, J.J.4
-
29
-
-
4043110893
-
-
PRLTAO 0031-9007,. 10.1103/PhysRevLett.88.028102
-
D. Marenduzzo, S. M. Bhattacharjee, A. Maritan, E. Orlandini, and F. Seno, Phys. Rev. Lett. PRLTAO 0031-9007 88, 028102 (2001). 10.1103/PhysRevLett. 88.028102
-
(2001)
Phys. Rev. Lett.
, vol.88
, pp. 028102
-
-
Marenduzzo, D.1
Bhattacharjee, S.M.2
Maritan, A.3
Orlandini, E.4
Seno, F.5
-
30
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
DOI 10.1093/nar/gkg595
-
M. Zuker, Nucleic Acids Res. NARHAD 0305-1048 31, 3406 (2003). 10.1093/nar/gkg595 (Pubitemid 37442169)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3406-3415
-
-
Zuker, M.1
-
31
-
-
0032478096
-
Cleaving DNA with DNA
-
DOI 10.1073/pnas.95.5.2233
-
N. Carmi, S. R. Balkhi, and R. R. Breaker, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 95, 2233 (1998). 10.1073/pnas.95.5.2233 (Pubitemid 28145924)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.5
, pp. 2233-2237
-
-
Carmi, N.1
Balkhi, S.R.2
Breaker, R.R.3
-
33
-
-
72149121596
-
-
BIOJAU 0006-3495,. 10.1016/j.bpj.2009.09.003
-
M. Kenward and K. D. Dorfman, Biophys. J. BIOJAU 0006-3495 97, 2785 (2009). 10.1016/j.bpj.2009.09.003
-
(2009)
Biophys. J.
, vol.97
, pp. 2785
-
-
Kenward, M.1
Dorfman, K.D.2
-
34
-
-
0003803285
-
-
(Univ. Science, Sausalito, CA)
-
V. A. Bloomfield, D. M. Crothers, and I. Tinoco, Nucleic Acids: Structures, Properties, and Functions (Univ. Science, Sausalito, CA, 2000).
-
(2000)
Nucleic Acids: Structures, Properties, and Functions
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco, I.3
-
35
-
-
70849103169
-
-
PNASA6 0027-8424,. 10.1073/pnas.0904721106
-
E. J. Sambriski, D. C. Schwartz, and J. J. De Pablo, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 18125 (2009). 10.1073/pnas.0904721106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 18125
-
-
Sambriski, E.J.1
Schwartz, D.C.2
De Pablo, J.J.3
-
36
-
-
0031568919
-
Product differentiation by analysis of DNA melting curves during the polymerase chain reaction
-
DOI 10.1006/abio.1996.9916
-
K. M. Ririe, R. P. Rasmussen, and C. T. Wittwer, Anal. Biochem. ANBCA2 0003-2697 245, 154 (1997). 10.1006/abio.1996.9916 (Pubitemid 27082244)
-
(1997)
Analytical Biochemistry
, vol.245
, Issue.2
, pp. 154-160
-
-
Ririe, K.M.1
Rasmussen, R.P.2
Wittwer, C.T.3
-
37
-
-
0035060502
-
-
CLCHAU 0009-9147
-
R. H. Lipsky, C. M. Mazzanti, J. G. Rudolph, K. Xu, G. Vyas, D. Bozak, M. Q. Radel, and D. Goldman, Clin. Chem. CLCHAU 0009-9147 47, 635 (2001).
-
(2001)
Clin. Chem.
, vol.47
, pp. 635
-
-
Lipsky, R.H.1
Mazzanti, C.M.2
Rudolph, J.G.3
Xu, K.4
Vyas, G.5
Bozak, D.6
Radel, M.Q.7
Goldman, D.8
-
38
-
-
0036849582
-
-
NARHAD 0305-1048,. 10.1093/nar/gkf597
-
A. T. Phan and J. L. Mergny, Nucleic Acids Res. NARHAD 0305-1048 30, 4618 (2002). 10.1093/nar/gkf597
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4618
-
-
Phan, A.T.1
Mergny, J.L.2
|