-
1
-
-
37349074542
-
A dynamic rod model to simulate mechanics of cables and DNA
-
University of Michigan, Ann Arbor
-
Goyal S. A dynamic rod model to simulate mechanics of cables and DNA. Mechanical Engineering (2006), University of Michigan, Ann Arbor 164
-
(2006)
Mechanical Engineering
, pp. 164
-
-
Goyal, S.1
-
2
-
-
0030137174
-
Biological applications of the dynamics of twisted elastic rods
-
Klapper I. Biological applications of the dynamics of twisted elastic rods. J. Comput. Phys. 125 2 (1996) 325
-
(1996)
J. Comput. Phys.
, vol.125
, Issue.2
, pp. 325
-
-
Klapper, I.1
-
3
-
-
0038441296
-
Tendril perversion in intrinsically curved rods
-
McMillen T., and Goriely A. Tendril perversion in intrinsically curved rods. J. Nonlinear Sci. 12 3 (2002) 241
-
(2002)
J. Nonlinear Sci.
, vol.12
, Issue.3
, pp. 241
-
-
McMillen, T.1
Goriely, A.2
-
5
-
-
84941947034
-
-
Elsevier Academic Press, Amsterdam
-
Calladine C.R., Drew H.R., Luisi B.F., and Travers A.A. Understanding DNA, the Molecule and How it Works. third ed. (2004), Elsevier Academic Press, Amsterdam
-
(2004)
Understanding DNA, the Molecule and How it Works. third ed.
-
-
Calladine, C.R.1
Drew, H.R.2
Luisi, B.F.3
Travers, A.A.4
-
8
-
-
0029066852
-
Modeling superhelical DNA-recent analytical and dynamic approaches
-
Schlick T. Modeling superhelical DNA-recent analytical and dynamic approaches. Curr. Opin. Struct. Biol. 5 2 (1995) 245
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, Issue.2
, pp. 245
-
-
Schlick, T.1
-
9
-
-
0030005131
-
Simulating DNA at low resolution
-
Olson W.K. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6 2 (1996) 242
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, Issue.2
, pp. 242
-
-
Olson, W.K.1
-
10
-
-
0023274675
-
The role of the stress resultant in determining mechanical equilibria of superhelical DNA
-
Benham C.J. The role of the stress resultant in determining mechanical equilibria of superhelical DNA. Biopolymers 26 1 (1987) 9
-
(1987)
Biopolymers
, vol.26
, Issue.1
, pp. 9
-
-
Benham, C.J.1
-
11
-
-
0000511427
-
Onset of writing in circular elastic polymers
-
Benham C.J. Onset of writing in circular elastic polymers. Phys. Rev. A (General Physics) 39 5 (1989) 2582
-
(1989)
Phys. Rev. A (General Physics)
, vol.39
, Issue.5
, pp. 2582
-
-
Benham, C.J.1
-
12
-
-
0033754160
-
Elastic stability of DNA configurations. II. Supercoiled plasmids with self-contact
-
Coleman B.D., Swigon D., and Tobias I. Elastic stability of DNA configurations. II. Supercoiled plasmids with self-contact. Phys. Rev. E 61 1 (2000) 759
-
(2000)
Phys. Rev. E
, vol.61
, Issue.1
, pp. 759
-
-
Coleman, B.D.1
Swigon, D.2
Tobias, I.3
-
14
-
-
0036461761
-
Global curvature and self-contact of nonlinearly elastic curves and rods
-
Gonzalez O., Maddocks J.H., Schuricht F., and von der Mosel H. Global curvature and self-contact of nonlinearly elastic curves and rods. Calc. Var. Partial Differential Equations 14 1 (2002) 29
-
(2002)
Calc. Var. Partial Differential Equations
, vol.14
, Issue.1
, pp. 29
-
-
Gonzalez, O.1
Maddocks, J.H.2
Schuricht, F.3
von der Mosel, H.4
-
16
-
-
0000323998
-
A continuum rod model of sequence-dependent DNA structure
-
Manning R.S., Maddocks J.H., and Kahn J.D. A continuum rod model of sequence-dependent DNA structure. J. Chem. Phys. 105 13 (1996) 5626
-
(1996)
J. Chem. Phys.
, vol.105
, Issue.13
, pp. 5626
-
-
Manning, R.S.1
Maddocks, J.H.2
Kahn, J.D.3
-
19
-
-
0028184673
-
On higher buckling transitions in supercoiled DNA
-
Schlick T., Olson W.K., Westcott T., and Greenberg J.P. On higher buckling transitions in supercoiled DNA. Biopolymers 34 5 (1994) 565
-
(1994)
Biopolymers
, vol.34
, Issue.5
, pp. 565
-
-
Schlick, T.1
Olson, W.K.2
Westcott, T.3
Greenberg, J.P.4
-
21
-
-
0033968707
-
Mathematical modelling of interwound DNA supercoils
-
Stump D.M., Watson P.J., and Fraser W.B. Mathematical modelling of interwound DNA supercoils. J. Biomechanics 33 4 (2000) 407
-
(2000)
J. Biomechanics
, vol.33
, Issue.4
, pp. 407
-
-
Stump, D.M.1
Watson, P.J.2
Fraser, W.B.3
-
23
-
-
0033764926
-
Elastic stability of DNA configurations. I. General theory
-
Tobias I., Swigon D., and Coleman B.D. Elastic stability of DNA configurations. I. General theory. Phys. Rev. E 61 1 (2000) 747
-
(2000)
Phys. Rev. E
, vol.61
, Issue.1
, pp. 747
-
-
Tobias, I.1
Swigon, D.2
Coleman, B.D.3
-
24
-
-
0037269948
-
Instability and self-contact phenomena in the writhing of clamped rods
-
van der Heijden G.H.M., Neukirch S., Goss V.G.A., and Thompson J.M.T. Instability and self-contact phenomena in the writhing of clamped rods. Int. J. Mech. Sci. 45 1 (2003) 161
-
(2003)
Int. J. Mech. Sci.
, vol.45
, Issue.1
, pp. 161
-
-
van der Heijden, G.H.M.1
Neukirch, S.2
Goss, V.G.A.3
Thompson, J.M.T.4
-
25
-
-
0031976753
-
Remarks on discrete and continuous large-scale models of DNA dynamics
-
Klapper I., and Qian H. Remarks on discrete and continuous large-scale models of DNA dynamics. Biophys. J. 74 5 (1998) 2504
-
(1998)
Biophys. J.
, vol.74
, Issue.5
, pp. 2504
-
-
Klapper, I.1
Qian, H.2
-
26
-
-
20344370700
-
Nonlinear dynamics and loop formation in kirchhoff rods with implications to the mechanics of DNA and cables
-
Goyal S., Perkins N.C., and Lee C.L. Nonlinear dynamics and loop formation in kirchhoff rods with implications to the mechanics of DNA and cables. J. Comput. Phys. 209 1 (2005) 371
-
(2005)
J. Comput. Phys.
, vol.209
, Issue.1
, pp. 371
-
-
Goyal, S.1
Perkins, N.C.2
Lee, C.L.3
-
27
-
-
38149016170
-
Non-linear dynamic intertwining of rods with self-contact
-
Goyal S., Perkins N.C., and Lee C.L. Non-linear dynamic intertwining of rods with self-contact. Int. J. Non-Linear Mech. 43 (2008) 65
-
(2008)
Int. J. Non-Linear Mech.
, vol.43
, pp. 65
-
-
Goyal, S.1
Perkins, N.C.2
Lee, C.L.3
-
28
-
-
37349076968
-
Intrinsic curvature of DNA influences LacR-mediated looping
-
Goyal S., Lillian T., Blumberg S., Meiners J.C., Meyhofer E., and Perkins N.C. Intrinsic curvature of DNA influences LacR-mediated looping. Biophys. J. 93 (2007) 4342
-
(2007)
Biophys. J.
, vol.93
, pp. 4342
-
-
Goyal, S.1
Lillian, T.2
Blumberg, S.3
Meiners, J.C.4
Meyhofer, E.5
Perkins, N.C.6
-
31
-
-
33645086141
-
Modeling DNA loops using the theory of elasticity
-
Balaeff A., Mahadevan L., and Schulten K. Modeling DNA loops using the theory of elasticity. Phys. Rev. E 73 3 (2006)
-
(2006)
Phys. Rev. E
, vol.73
, Issue.3
-
-
Balaeff, A.1
Mahadevan, L.2
Schulten, K.3
-
32
-
-
33745595880
-
Modeling the lac repressor-operator assembly: the influence of DNA looping on lac repressor conformation
-
Swigon D., Coleman B.D., and Olson W.K. Modeling the lac repressor-operator assembly: the influence of DNA looping on lac repressor conformation. Proc. Nat. Acad. Sci. U.S.A. 103 26 (2006) 9879
-
(2006)
Proc. Nat. Acad. Sci. U.S.A.
, vol.103
, Issue.26
, pp. 9879
-
-
Swigon, D.1
Coleman, B.D.2
Olson, W.K.3
-
33
-
-
33645991551
-
Statistical-mechanical theory of DNA looping
-
Zhang Y., McEwen A.E., Crothers D.M., and Levene S.D. Statistical-mechanical theory of DNA looping. Biophys. J. 90 6 (2006) 1903
-
(2006)
Biophys. J.
, vol.90
, Issue.6
, pp. 1903
-
-
Zhang, Y.1
McEwen, A.E.2
Crothers, D.M.3
Levene, S.D.4
-
34
-
-
33845793417
-
Effect of supercoiling on formation of protein-mediated DNA loops
-
Purohit P.K., and Nelson P.C. Effect of supercoiling on formation of protein-mediated DNA loops. Phys. Rev. E 74 6 (2006)
-
(2006)
Phys. Rev. E
, vol.74
, Issue.6
-
-
Purohit, P.K.1
Nelson, P.C.2
-
35
-
-
0029004903
-
Crystal-structure of lac repressor core tetramer and its implications for DNA looping
-
Friedman A.M., Fischmann T.O., and Steitz T.A. Crystal-structure of lac repressor core tetramer and its implications for DNA looping. Science 268 5218 (1995) 1721
-
(1995)
Science
, vol.268
, Issue.5218
, pp. 1721
-
-
Friedman, A.M.1
Fischmann, T.O.2
Steitz, T.A.3
-
36
-
-
0029938053
-
Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
-
Lewis M., Chang G., Horton N.C., Kercher M.A., Pace H.C., Schumacher M.A., Brennan R.G., and Lu P.Z. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271 5253 (1996) 1247
-
(1996)
Science
, vol.271
, Issue.5253
, pp. 1247
-
-
Lewis, M.1
Chang, G.2
Horton, N.C.3
Kercher, M.A.4
Pace, H.C.5
Schumacher, M.A.6
Brennan, R.G.7
Lu, P.Z.8
-
37
-
-
28444490422
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
-
Dixit S.B., Beveridge D.L., Case D.A., Cheatham T.E., Giudice E., Lankas F., Lavery R., Maddocks J.H., Osman R., Sklenar H., Thayer K.M., and Varnai P. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys. J. 89 6 (2005) 3721
-
(2005)
Biophys. J.
, vol.89
, Issue.6
, pp. 3721
-
-
Dixit, S.B.1
Beveridge, D.L.2
Case, D.A.3
Cheatham, T.E.4
Giudice, E.5
Lankas, F.6
Lavery, R.7
Maddocks, J.H.8
Osman, R.9
Sklenar, H.10
Thayer, K.M.11
Varnai, P.12
-
38
-
-
10044257912
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(c(p)g) steps
-
Beveridge D.L., Barreiro G., Byun K.S., Case D.A., Cheatham T.E., Dixit S.B., Giudice E., Lankas F., Lavery R., Maddocks J.H., Osman R., Seibert E., Sklenar H., Stoll G., Thayer K.M., Varnai P., and Young M.A. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(c(p)g) steps. Biophys. J. 87 6 (2004) 3799
-
(2004)
Biophys. J.
, vol.87
, Issue.6
, pp. 3799
-
-
Beveridge, D.L.1
Barreiro, G.2
Byun, K.S.3
Case, D.A.4
Cheatham, T.E.5
Dixit, S.B.6
Giudice, E.7
Lankas, F.8
Lavery, R.9
Maddocks, J.H.10
Osman, R.11
Seibert, E.12
Sklenar, H.13
Stoll, G.14
Thayer, K.M.15
Varnai, P.16
Young, M.A.17
-
40
-
-
26944495630
-
Effects of kinks on DNA elasticity
-
Popov Y.O., and Tkachenko A.V. Effects of kinks on DNA elasticity. Phys. Rev. E 71 5 (2005)
-
(2005)
Phys. Rev. E
, vol.71
, Issue.5
-
-
Popov, Y.O.1
Tkachenko, A.V.2
-
41
-
-
2342518189
-
Spontaneous sharp bending of double-stranded DNA
-
Cloutier T.E., and Widom J. Spontaneous sharp bending of double-stranded DNA. Mol. Cell 14 3 (2004) 355
-
(2004)
Mol. Cell
, vol.14
, Issue.3
, pp. 355
-
-
Cloutier, T.E.1
Widom, J.2
-
43
-
-
1842685575
-
-
S. Goyal, N.C. Perkins, C.L. Lee, Torsional buckling and writhing dynamics of elastic cables and DNA, in: 2003 ASME Design Engineering Technical Conferences and Computers and Information in Engineering Conference, American Society of Mechanical Engineers, Chicago, IL, USA, 2003.
-
S. Goyal, N.C. Perkins, C.L. Lee, Torsional buckling and writhing dynamics of elastic cables and DNA, in: 2003 ASME Design Engineering Technical Conferences and Computers and Information in Engineering Conference, American Society of Mechanical Engineers, Chicago, IL, USA, 2003.
-
-
-
-
44
-
-
0027610910
-
A time integration algorithm for structural dynamics with improved numerical dissipation-the generalized-alpha method
-
Chung J., and Hulbert G.M. A time integration algorithm for structural dynamics with improved numerical dissipation-the generalized-alpha method. J. Appl. Mech. Trans. ASME 60 2 (1993) 371
-
(1993)
J. Appl. Mech. Trans. ASME
, vol.60
, Issue.2
, pp. 371
-
-
Chung, J.1
Hulbert, G.M.2
-
45
-
-
0036739624
-
Dynamic analysis of loop formation in cables under compression
-
Gatti-Bono C., and Perkins N.C. Dynamic analysis of loop formation in cables under compression. Int. J. Offshore Polar Eng. 12 3 (2002) 217
-
(2002)
Int. J. Offshore Polar Eng.
, vol.12
, Issue.3
, pp. 217
-
-
Gatti-Bono, C.1
Perkins, N.C.2
-
46
-
-
0018456481
-
Non-linear analysis of a twisted axially loaded elastic rod
-
Zachmann D.W. Non-linear analysis of a twisted axially loaded elastic rod. Q. Appl. Math. 37 1 (1979) 67
-
(1979)
Q. Appl. Math.
, vol.37
, Issue.1
, pp. 67
-
-
Zachmann, D.W.1
-
47
-
-
0030947539
-
Ionic effects on the elasticity of single DNA molecules
-
Baumann C.G., Smith S.B., Bloomfield V.A., and Bustamante C. Ionic effects on the elasticity of single DNA molecules. Proc. Nat. Acad. Sci. U.S.A. 94 12 (1997) 6185
-
(1997)
Proc. Nat. Acad. Sci. U.S.A.
, vol.94
, Issue.12
, pp. 6185
-
-
Baumann, C.G.1
Smith, S.B.2
Bloomfield, V.A.3
Bustamante, C.4
-
49
-
-
0029937922
-
The elasticity of a single supercoiled DNA molecule
-
Strick T.R., Allemand J.F., Bensimon D., Bensimon A., and Croquette V. The elasticity of a single supercoiled DNA molecule. Science 271 5257 (1996) 1835
-
(1996)
Science
, vol.271
, Issue.5257
, pp. 1835
-
-
Strick, T.R.1
Allemand, J.F.2
Bensimon, D.3
Bensimon, A.4
Croquette, V.5
-
50
-
-
0035039812
-
Gal repressosome contains an antiparallel DNA loop
-
Geanacopoulos M., Vasmatzis G., Zhurkin V.B., and Adhya S. Gal repressosome contains an antiparallel DNA loop. Nat. Struct. Biol. 8 5 (2001) 432
-
(2001)
Nat. Struct. Biol.
, vol.8
, Issue.5
, pp. 432
-
-
Geanacopoulos, M.1
Vasmatzis, G.2
Zhurkin, V.B.3
Adhya, S.4
-
51
-
-
18744369718
-
Multiscale method for simulating protein-DNA complexes
-
Villa E., Balaeff A., Mahadevan L., and Schulten K. Multiscale method for simulating protein-DNA complexes. Multiscale Modeling Simulation 2 4 (2004) 527
-
(2004)
Multiscale Modeling Simulation
, vol.2
, Issue.4
, pp. 527
-
-
Villa, E.1
Balaeff, A.2
Mahadevan, L.3
Schulten, K.4
-
53
-
-
0030024985
-
Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith S.B., Cui Y.J., and Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271 5250 (1996) 795
-
(1996)
Science
, vol.271
, Issue.5250
, pp. 795
-
-
Smith, S.B.1
Cui, Y.J.2
Bustamante, C.3
|