메뉴 건너뛰기




Volumn 6, Issue 1, 2011, Pages

Electrostatics and self-contact in an elastic rod approximation for DNA

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR PROCESS; DEOXYRIBONUCLEIC ACIDS; DNA LOOPING; DNA SUPERCOILING; DYNAMIC PROCESS; ELASTIC ROD; ELECTROSTATIC INTERACTIONS; EQUILIBRIUM MODELS; FLEXIBLE MOLECULES; GENETIC INFORMATION; LAC REPRESSOR; PLECTONEMES; REGULATORY PROTEIN; ROD APPROXIMATIONS; STORAGE AND RETRIEVALS; SUPERCOILED DNA;

EID: 78649931178     PISSN: 15551415     EISSN: 15551423     Source Type: Journal    
DOI: 10.1115/1.4002267     Document Type: Article
Times cited : (10)

References (32)
  • 1
    • 0038497542 scopus 로고
    • Molecular structure of nucleic acids - A structure for deoxyribose nucleic acid
    • Watson, J. D., and Crick, F. H. C, 1953, "Molecular Structure of Nucleic Acids-A Structure for Deoxyribose Nucleic Acid, " Nature (London), 171(4356), pp. 737-738.
    • (1953) Nature (London) , vol.171 , Issue.4356 , pp. 737-738
    • Watson, J.D.1    Crick, F.H.C.2
  • 2
    • 0000812966 scopus 로고
    • Molecular configuration in sodium thymonucleate
    • Franklin, R. E., and Gosling, R. G., 1953, "Molecular Configuration in Sodium Thymonucleate, " Nature (London), 171(4356), pp. 740-741.
    • (1953) Nature (London) , vol.171 , Issue.4356 , pp. 740-741
    • Franklin, R.E.1    Gosling, R.G.2
  • 4
    • 0015040327 scopus 로고
    • The writhing number of a space curve
    • Fuller, F B., 1971, "The Writhing Number of a Space Curve, " Proc. Natl. Acad. Sci. U. S. A., 68(4), pp. 815-819.
    • (1971) Proc. Natl. Acad. Sci. U. S. A , vol.68 , Issue.4 , pp. 815-819
    • Fuller, F.B.1
  • 5
    • 33749259954 scopus 로고    scopus 로고
    • Kinking occurs during molecular dynamics simulations of small DNA minicircles
    • Lankaš, F., Lavery, R., and Maddocks, J. H., 2006, "Kinking Occurs During Molecular Dynamics Simulations of Small DNA Minicircles, " Structure (London), 14(10), pp. 1527-1534.
    • (2006) Structure (London) , vol.14 , Issue.10 , pp. 1527-1534
    • Lankaš, F.1    Lavery, R.2    Maddocks, J.H.3
  • 7
    • 77952355398 scopus 로고    scopus 로고
    • A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics
    • Dans, P. D., Zeida, A., Machado, M. R., and Pantano, S., 2010, "A Coarse Grained Model for Atomic-Detailed DNA Simulations With Explicit Electrostatics, " J. Chem. Theory Comput, 6(5), pp. 1711-1725.
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.5 , pp. 1711-1725
    • Dans, P.D.1    Zeida, A.2    Machado, M.R.3    Pantano, S.4
  • 8
    • 77949889822 scopus 로고    scopus 로고
    • A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
    • Morriss-Andrews, A., Rottler, J., and Plotkin, S. S., 2010, "A Systematically Coarse-Grained Model for DNA and Its Predictions for Persistence Length, Stacking, Twist, and Chirality, " J. Chem. Phys., 132(3), p. 035105.
    • (2010) J. Chem. Phys. , vol.132 , Issue.3 , pp. 035105
    • Morriss-Andrews, A.1    Rottler, J.2    Plotkin, S.S.3
  • 9
    • 20344370700 scopus 로고    scopus 로고
    • 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., 2005, "Nonlinear Dynamics and Loop Formation in Kirchhoff Rods With Implications to the Mechanics of DNA and Cables, " J. Comput. Phys., 209(1), pp. 371-389.
    • (2005) J. Comput. Phys. , vol.209 , Issue.1 , pp. 371-389
    • Goyal, S.1    Perkins, N.C.2    Lee, C.L.3
  • 11
    • 58749116653 scopus 로고    scopus 로고
    • Computational analysis of looping of a large family of highly bent DNA by LacI
    • Lillian, T. D., Goyal, S., Kahn, J. D., Meyhöfer, E., and Perkins, N. C, 2008, "Computational Analysis of Looping of a Large Family of Highly Bent DNA by LacI, " Biophys. J., 95(12), pp. 5832-5842.
    • (2008) Biophys. J , vol.95 , Issue.12 , pp. 5832-5842
    • Lillian, T.D.1    Goyal, S.2    Kahn, J.D.3    Meyhöfer, E.4    Perkins, N.C.5
  • 12
    • 44949179469 scopus 로고    scopus 로고
    • Computational elastic rod model applied to DNA looping
    • Las Vegas, NV, Sep. 4-7
    • Lillian, T. D., Perkins, N. C, and Goyal, S., 2008, "Computational Elastic Rod Model Applied to DNA Looping, " Proceedings of ASME IDETC/CIE 2007, Las Vegas, NV, Sep. 4-7, Vol. 5, pp. 1449-1456.
    • (2008) Proceedings of ASME IDETC/CIE 2007 , vol.5 , pp. 1449-1456
    • Lillian, T.D.1    Perkins, N.C.2    Goyal, S.3
  • 15
    • 0028071373 scopus 로고
    • Entropic elasticity of lambda-phage DNA
    • Bustamante, C., Marko, J. F., Siggia, E. D., and Smith, S., 1994, "Entropic Elasticity of Lambda-Phage DNA, " Science, 265(5178), pp. 1599-1600.
    • (1994) Science , vol.265 , Issue.5178 , pp. 1599-1600
    • Bustamante, C.1    Marko, J.F.2    Siggia, E.D.3    Smith, S.4
  • 16
  • 17
    • 85015087906 scopus 로고    scopus 로고
    • Ten years of tension: Single-molecule DNA mechanics
    • Bustamante, C., Bryant, Z., and Smith, S. B., 2003, "Ten Years of Tension: Single-Molecule DNA Mechanics, " Nature (London), 421(6921), pp. 423-427.
    • (2003) Nature (London) , vol.421 , Issue.6921 , pp. 423-427
    • Bustamante, C.1    Bryant, Z.2    Smith, S.B.3
  • 18
    • 0000323998 scopus 로고    scopus 로고
    • A continuum rod model of sequence-dependent DNA structure
    • Manning, R. S., Maddocks, J. H., and Kahn, J. D., 1996, "A Continuum Rod Model of Sequence-Dependent DNA Structure, " J. Chem. Phys., 105(13), pp. 5626-5646.
    • (1996) J. Chem. Phys. , vol.105 , Issue.13 , pp. 5626-5646
    • Manning, R.S.1    Maddocks, J.H.2    Kahn, J.D.3
  • 19
    • 33745595880 scopus 로고    scopus 로고
    • Modeling the lac repressor-operator assembly: The influence of DNA looping on lac repressor conformation
    • Swigon, D., Coleman, B. D., and Olson, W. K., 2006, "Modeling the Lac Repressor-Operator Assembly: The Influence of DNA Looping on Lac Repressor conformation, " Proc. Natl. Acad. Sci. U. S. A., 103(26), pp. 9879-9884.
    • (2006) Proc. Natl. Acad. Sci. U. S. A , vol.103 , Issue.26 , pp. 9879-9884
    • Swigon, D.1    Coleman, B.D.2    Olson, W.K.3
  • 20
    • 0032168436 scopus 로고    scopus 로고
    • Rod models of DNA: Sequence-dependent anisotropic elastic modelling of local bending phenomena
    • Munteanu, M. G., Vlahovicek, K., Parthasarathy, S., Simon, I., and Pongor, S., 1998, "Rod Models of DNA: Sequence-Dependent Anisotropic Elastic Modelling of Local Bending Phenomena, " Trends Biochem. Sci., 23(9), pp. 341-347.
    • (1998) Trends Biochem. Sci. , vol.23 , Issue.9 , pp. 341-347
    • Munteanu, M.G.1    Vlahovicek, K.2    Parthasarathy, S.3    Simon, I.4    Pongor, S.5
  • 21
    • 0029066852 scopus 로고
    • Modeling superhelical DNA: Recent analytical and dynamic approaches
    • Schlick, T., 1995, "Modeling Superhelical DNA: Recent Analytical and Dynamic Approaches, " Curr. Opin. Struct. Biol., 5(2), pp. 245-262.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , Issue.2 , pp. 245-262
    • Schlick, T.1
  • 22
    • 33645086141 scopus 로고    scopus 로고
    • Modeling DNA loops using the theory of elasticity
    • Balaeff, A., Mahadevan, L., and Schulten, K., 2006, "Modeling DNA Loops Using the Theory of Elasticity, " Phys. Rev. E, 73(3), p. 031919.
    • (2006) Phys. Rev. E , vol.73 , Issue.3 , pp. 031919
    • Balaeff, A.1    Mahadevan, L.2    Schulten, K.3
  • 24
    • 0029937922 scopus 로고    scopus 로고
    • The elasticity of a single supercoiled DNA molecule
    • Strick, T. R., Allemand, J. F., Bensimon, D., Bensimon, A., and Croquette, V, 1996, "The Elasticity of a Single Supercoiled DNA Molecule, " Science, 271(5257), pp. 1835-1837.
    • (1996) Science , vol.271 , Issue.5257 , pp. 1835-1837
    • Strick, T.R.1    Allemand, J.F.2    Bensimon, D.3    Bensimon, A.4    Croquette, V.5
  • 26
    • 0027610910 scopus 로고
    • A time integration algorithm for structural dynamics with improved numerical dissipation: The generalized-alpha method
    • Chung, J., and Hulbert, G. M., 1993, "A Time Integration Algorithm for Structural Dynamics With Improved Numerical Dissipation: The Generalized-Alpha Method, " ASME J. Appl. Mech., 60(2), pp. 371-375.
    • (1993) ASME J. Appl. Mech. , vol.60 , Issue.2 , pp. 371-375
    • Chung, J.1    Hulbert, G.M.2
  • 27
    • 0029159251 scopus 로고
    • Modeling of long-range electrostatic interactions in DNA
    • Vologodskii, A., and Cozzarelli, N., 1995, "Modeling of Long-Range Electrostatic Interactions in DNA, " Biopolymers, 35(3), pp. 289-296.
    • (1995) Biopolymers , vol.35 , Issue.3 , pp. 289-296
    • Vologodskii, A.1    Cozzarelli, N.2
  • 28
    • 0030137174 scopus 로고    scopus 로고
    • Biological applications of the dynamics of twisted elastic rods
    • Klapper, I., 1996, "Biological Applications of the Dynamics of Twisted Elastic Rods, " J. Comput. Phys., 125(2), pp. 325-337.
    • (1996) J. Comput. Phys. , vol.125 , Issue.2 , pp. 325-337
    • Klapper, I.1
  • 29
    • 38149016170 scopus 로고    scopus 로고
    • Non-linear dynamic intertwining of rods with self-contact
    • Goyal, S., Perkins, N. C, and Lee, C. L., 2008, "Non-Linear Dynamic Intertwining of Rods With Self-Contact, " Int. J. Non-Linear Mech., 43(1), pp. 65-73.
    • (2008) Int. J. Non-linear Mech. , vol.43 , Issue.1 , pp. 65-73
    • Goyal, S.1    Perkins, N.C.2    Lee, C.L.3
  • 30
    • 0031555013 scopus 로고    scopus 로고
    • Comparison of hard-cylinder and screened coulomb interactions in the modeling of supercoiled DNAs
    • Delrow, J. J., Gebe, J. A., and Schurr, J. M., 1997, "Comparison of Hard-Cylinder and Screened Coulomb Interactions in the Modeling of Supercoiled DNAs, " Biopolymers, 42(4), pp. 455-470.
    • (1997) Biopolymers , vol.42 , Issue.4 , pp. 455-470
    • Delrow, J.J.1    Gebe, J.A.2    Schurr, J.M.3
  • 31
    • 0033754160 scopus 로고    scopus 로고
    • Elastic stability of DNA configurations. II. Supercoiled plasmids with self-contact
    • Coleman, B. D., Swigon, D., and Tobias, I., 2000, "Elastic Stability of DNA Configurations. II. Supercoiled Plasmids With Self-Contact, " Phys. Rev. E, 61(1), pp. 759-770.
    • (2000) Phys. Rev. E , vol.61 , Issue.1 , pp. 759-770
    • Coleman, B.D.1    Swigon, D.2    Tobias, I.3
  • 32
    • 0037269948 scopus 로고    scopus 로고
    • 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., 2003, "Instability and Self-Contact Phenomena in the Writhing of Clamped Rods, " Int. J. Mech. Sci., 45(1), pp. 161-196.
    • (2003) Int. J. Mech. Sci. , vol.45 , Issue.1 , pp. 161-196
    • Van Der Heijden, G.H.M.1    Neukirch, S.2    Goss, V.G.A.3    Thompson, J.M.T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.