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Volumn 15, Issue 1-3, 2008, Pages 339-362

Microscopic mechanics of biomolecules in living cells

Author keywords

Biomolecules; Configurational entropy; Jarzynski identity; Mechanical properties; Molecular dynamics

Indexed keywords

BIOLOGY AND GENETICS; CELL BIOLOGY; CONDENSED MATTER; CONFIGURATIONAL ENTROPY; CYTOSKELETAL FILAMENTS; DNA TRANSCRIPTIONS; EXPERIMENTAL TECHNIQUES; HYDROGEN BONDINGS; HYDROPHOBIC INTERACTIONS; IN-VITRO; JARZYNSKI IDENTITY; KEY ISSUES; LIFE-SCIENCES; LIVING CELL; MECHANICAL FORCE; MECHANICAL RESPONSE; MECHANOCHEMICALS; MODELLING METHOD; MOLECULAR MOTORS; NON EQUILIBRIUM THERMODYNAMICS; SOLID MECHANICS; THEORETICAL MODELS; VAN DER WAALS; WEAK FORCE;

EID: 73449125475     PISSN: 18748554     EISSN: 18748562     Source Type: Journal    
DOI: 10.1007/s10820-008-9104-2     Document Type: Article
Times cited : (7)

References (101)
  • 1
    • 10244261513 scopus 로고    scopus 로고
    • A simplified model to determine the contribution of strain energy in the failure process of thin biological membranes during cutting
    • 10.1111/j.1475-1305.2004.00165.x
    • C.F. Doran B.A.O. McCormack A. Macey 2004 A simplified model to determine the contribution of strain energy in the failure process of thin biological membranes during cutting Strain 40 173 179 10.1111/j.1475-1305.2004.00165.x
    • (2004) Strain , vol.40 , pp. 173-179
    • Doran, C.F.1    McCormack, B.A.O.2    MacEy, A.3
  • 2
    • 0034209635 scopus 로고    scopus 로고
    • Orientation and loading condition dependence of fracture toughness in cortical bone
    • DOI 10.1016/S0928-4931(00)00142-9, PII S0928493100001429, Containing papers presented at the International Conference on Advanced Materials 1999, Symposium R: Materials Research Inspired by Biological Systems, June 1999, Beijing, China
    • Z. Feng J. Rho S. Han I. Ziv 2000 Orientation and loading condition dependence of fracture toughness in cortical bone Mat. Sci. Eng. C 11 41 46 10.1016/S0928-4931(00)00142-9 (Pubitemid 30613568)
    • (2000) Materials Science and Engineering C , vol.11 , Issue.1 , pp. 41-46
    • Feng, Z.1    Rho, J.2    Han, S.3    Ziv, I.4
  • 4
    • 15844388388 scopus 로고    scopus 로고
    • Finding inspiration in argiope trifasciata spider silk fiber
    • 10.1007/s11837-005-0218-7 1:CAS:528:DC%2BD2MXhvFCrs7k%3D
    • M. Elices J. Pérez-Rigueiro G.R. Plaza G.V. Guinea 2005 Finding inspiration in argiope trifasciata spider silk fiber JOM J. 57 60 66 10.1007/s11837-005-0218-7 1:CAS:528:DC%2BD2MXhvFCrs7k%3D
    • (2005) JOM J. , vol.57 , pp. 60-66
    • Elices, M.1    Pérez-Rigueiro, J.2    Plaza, G.R.3    Guinea, G.V.4
  • 5
    • 5544311564 scopus 로고
    • Perspectives on neural network models and their relevance to neurobiology
    • 10.1088/0305-4470/22/12/001 1989JPhA.22.1959T 1004903
    • G. Toulouse 1989 Perspectives on neural network models and their relevance to neurobiology J. Phys. A Math. Gen. 22 1959 1960 10.1088/0305-4470/22/12/001 1989JPhA...22.1959T 1004903
    • (1989) J. Phys. A Math. Gen. , vol.22 , pp. 1959-1960
    • Toulouse, G.1
  • 6
    • 0031615095 scopus 로고    scopus 로고
    • Correlative light and electron microscopy of the cytoskeleton of cultured cells
    • DOI 10.1016/S0076-6879(98)98045-4
    • T.M. Svitkina G.G. Borisy 1998 Correlative light and electron microscopy of the cytoskeleton of cultured cells Meth. Enzym. 298 570 576 9751908 10.1016/S0076-6879(98)98045-4 1:CAS:528:DyaK1MXltlyh (Pubitemid 28450779)
    • (1998) Methods in Enzymology , vol.298 , pp. 570-592
    • Svitkina, T.M.1    Borisy, G.G.2
  • 7
    • 0032996355 scopus 로고    scopus 로고
    • DNA-protein cooperative binding through variable-range elastic coupling
    • 10096873 1:CAS:528:DyaK1MXit1Kqurs%3D 1999BpJ.76.1725R
    • J. Rudnick R. Bruinsma 1999 DNA-protein cooperative binding through variable-range elastic coupling Biophys. J. 76 1725 1733 10096873 1:CAS:528:DyaK1MXit1Kqurs%3D 1999BpJ....76.1725R
    • (1999) Biophys. J. , vol.76 , pp. 1725-1733
    • Rudnick, J.1    Bruinsma, R.2
  • 8
    • 0037151013 scopus 로고    scopus 로고
    • Transcriptional regulation of a contractile gene by mechanical forces applied through integrins in osteoblasts
    • DOI 10.1074/jbc.M203130200
    • J. Wang M. Su J. Fan A. Seth C.A. McCulloch 2002 Transcriptional regulation of a contractile gene by mechanical forces applied through integrins in osteoblasts J. Biol. Chem. 277 22889 22895 11953441 10.1074/jbc.M203130200 1:CAS:528:DC%2BD38XltVGrsr0%3D (Pubitemid 34967271)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.25 , pp. 22889-22895
    • Wang, J.1    Su, M.2    Fan, J.3    Seth, A.4    McCulloch, C.A.5
  • 9
    • 7244239227 scopus 로고    scopus 로고
    • A DNA nanomachine based on a duplex-triplex transition
    • DOI 10.1002/anie.200460789
    • Y. Chen S.-H. Lee C. Mao 2004 A DNA nanomachine based on a duplex-triplex transition Angew. Chem. Int. Ed. 43 5335 5338 10.1002/anie.200460789 1:CAS:528:DC%2BD2cXptVanur0%3D (Pubitemid 39433911)
    • (2004) Angewandte Chemie - International Edition , vol.43 , Issue.40 , pp. 5335-5338
    • Chen, Y.1    Lee, S.-H.2    Mao, C.3
  • 10
    • 8944235343 scopus 로고    scopus 로고
    • Theoretical estimates of mechanical properties of the endothelial cell cytoskeleton
    • R.I. Satchey C.F. Dewey 1996 Theoretical estimates of mechanical properties of the endothelial cell cytoskeleton J. Biophys. 71 109 118
    • (1996) J. Biophys. , vol.71 , pp. 109-118
    • Satchey, R.I.1    Dewey, C.F.2
  • 11
    • 30344454380 scopus 로고    scopus 로고
    • Neuroligins and neurexins: Linking cell adhesion, synapse formation and cognitive function
    • DOI 10.1016/j.tins.2005.11.003, PII S0166223605003000
    • C. Dean T. Dresbach 2006 Neuroligins and neurexins: linking cell adhesion, synapse formation and cognitive function Trends Neurosci. 29 21 29 16337696 10.1016/j.tins.2005.11.003 1:CAS:528:DC%2BD28XksVSnsg%3D%3D (Pubitemid 43063127)
    • (2006) Trends in Neurosciences , vol.29 , Issue.1 , pp. 21-29
    • Dean, C.1    Dresbach, T.2
  • 12
    • 0033930954 scopus 로고    scopus 로고
    • E-cadherin-catenin cell-cell adhesion complex and human cancer
    • DOI 10.1046/j.1365-2168.2000.01513.x
    • B.P.L. Wijnhoven W.N.M. Dinjens M. Pignatelli 2000 E-cadherin-catenin cell-cell adhesion complex and human cancer Br. J. Surg. 87 992 1005 10931041 10.1046/j.1365-2168.2000.01513.x 1:STN:280:DC%2BD3cvhvVaqtA%3D%3D (Pubitemid 30496847)
    • (2000) British Journal of Surgery , vol.87 , Issue.8 , pp. 992-1005
    • Wijnhoven, B.P.L.1    Dinjens, W.N.M.2    Pignatelli, M.3
  • 13
    • 0034755942 scopus 로고    scopus 로고
    • Molecular complexity and dynamics of cell-matrix adhesions
    • 11707509 1:CAS:528:DC%2BD3MXot12gtbg%3D
    • E. Zamir B. Geiger 2001 Molecular complexity and dynamics of cell-matrix adhesions J. Cell Sci. 114 3577 3579 11707509 1:CAS:528:DC%2BD3MXot12gtbg%3D
    • (2001) J. Cell Sci. , vol.114 , pp. 3577-3579
    • Zamir, E.1    Geiger, B.2
  • 15
    • 27944497333 scopus 로고    scopus 로고
    • Tissue cells feel and respond to the stiffness of their substrate
    • DOI 10.1126/science.1116995
    • D.E. Discher P. Janmey Y. Wang 2005 Tissue cells feel and respond to the stiffness of their substrate Science 310 1139 1143 16293750 10.1126/science. 1116995 2005Sci...310.1139D 1:CAS:528:DC%2BD2MXht1WgtLbF (Pubitemid 41681732)
    • (2005) Science , vol.310 , Issue.5751 , pp. 1139-1143
    • Discher, D.E.1    Janmey, P.2    Wang, Y.-L.3
  • 16
    • 34249936024 scopus 로고    scopus 로고
    • Forces and bond dynamics in cell adhesion
    • DOI 10.1126/science.1137592
    • E.A. Evans D. Calderwood 2007 Forces and bond dynamics in cell adhesion Science 316 1148 1153 17525329 10.1126/science.1137592 2007Sci...316.1148E 1:CAS:528:DC%2BD2sXls1Kit7Y%3D (Pubitemid 46877469)
    • (2007) Science , vol.316 , Issue.5828 , pp. 1148-1153
    • Evans, E.A.1    Calderwood, D.A.2
  • 17
    • 3242796694 scopus 로고    scopus 로고
    • Dealing with mechanics: Mechanisms of force transduction in cells
    • DOI 10.1016/j.tibs.2004.05.003, PII S0968000404001239
    • P.A. Janmey D.A. Weitz 2004 Dealing with mechanics: mechanisms of force transduction in cells Trends Biochem. Sci. 29 364 370 15236744 10.1016/j.tibs.2004.05.003 1:CAS:528:DC%2BD2cXlsVSls7w%3D (Pubitemid 38968753)
    • (2004) Trends in Biochemical Sciences , vol.29 , Issue.7 , pp. 364-370
    • Janmey, P.A.1    Weitz, D.A.2
  • 18
    • 14744281200 scopus 로고    scopus 로고
    • Growth and shape stability of a biological membrane adhesion complex in the diffusion-mediated regime
    • DOI 10.1073/pnas.0500368102
    • V.B. Shenoy L.B. Freund 2005 Growth and shape stability of a biological membrane adhesion complex in the diffusion-mediated regime Proc. Natl. Acad. Sci. USA 102 3213 3218 15728395 10.1073/pnas.0500368102 2005PNAS..102.3213S 1:CAS:528:DC%2BD2MXitl2lt7g%3D (Pubitemid 40328025)
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.9 , pp. 3213-3218
    • Shenoy, V.B.1    Freund, L.B.2
  • 19
    • 84891683670 scopus 로고
    • Reconstruction of tissues by dissociated cells
    • Steinberg, M.: Reconstruction of tissues by dissociated cells. Science 141, 401-408 (1963)
    • (1963) Science 141 , pp. 401-408
    • Steinberg, M.1
  • 20
    • 0030589504 scopus 로고    scopus 로고
    • Adhesion in development: An historical overview
    • Steinberg, M.: Adhesion in development: an historical overview. Dev. Biol. 180, 377-388 (1996)
    • (1996) Dev. Biol. , vol.180 , pp. 377-388
    • Steinberg, M.1
  • 21
    • 0018101150 scopus 로고
    • Models for the specific adhesion of cells to cells
    • 347575 10.1126/science.347575 1978Sci.200.618B 1:CAS:528: DyaE1cXktlyns7Y%3D
    • G.I. Bell 1978 Models for the specific adhesion of cells to cells Science 200 618 627 347575 10.1126/science.347575 1978Sci...200..618B 1:CAS:528:DyaE1cXktlyns7Y%3D
    • (1978) Science , vol.200 , pp. 618-627
    • Bell, G.I.1
  • 22
    • 0035236352 scopus 로고    scopus 로고
    • The living state of matter
    • 1:STN:280:DC%2BD38%2FhvVyiuw%3D%3D
    • M. Buiatti M. Buiatti 2001 The living state of matter Riv. Biol. Biol. Forum 94 59 82 1:STN:280:DC%2BD38%2FhvVyiuw%3D%3D
    • (2001) Riv. Biol. Biol. Forum , vol.94 , pp. 59-82
    • Buiatti, M.1    Buiatti, M.2
  • 23
    • 0141990843 scopus 로고    scopus 로고
    • Towards a statistical characterisation of the living state of matter
    • 1073.92001 10.1016/S0960-0779(03)00427-2 1:CAS:528:DC%2BD3sXnvFaisbc%3D 2033864
    • M. Buiatti M. Buiatti 2004 Towards a statistical characterisation of the living state of matter Chaos Sol. Fract. 20 55 66 1073.92001 10.1016/S0960-0779(03)00427-2 1:CAS:528:DC%2BD3sXnvFaisbc%3D 2033864
    • (2004) Chaos Sol. Fract. , vol.20 , pp. 55-66
    • Buiatti, M.1    Buiatti, M.2
  • 24
    • 36649002612 scopus 로고    scopus 로고
    • Multiscale modeling in advanced materials research-challenges, novel methods, and emerging applications
    • de Pablo, J.J., Curtin, W.A. (guest eds.)
    • de Pablo, J.J., Curtin, W.A. (guest eds.): Multiscale modeling in advanced materials research-challenges, novel methods, and emerging applications. MRS Bull. 32(11) (2007)
    • (2007) MRS Bull. , vol.32 , Issue.11
  • 25
    • 33747610222 scopus 로고    scopus 로고
    • Nature designs tough collagen: Explaining the nanostructure of collagen fibrils
    • DOI 10.1073/pnas.0603216103
    • M. Buehler 2006 Nature designs tough collagen: explaining the nanostructure of collagen fibrils Proc. Natl. Acad. Sci. USA 103 12285 12290 16895989 10.1073/pnas.0603216103 2006PNAS..10312285B 1:CAS:528: DC%2BD28Xos1Kls7o%3D (Pubitemid 44267251)
    • (2006) Proceedings of the National Academy of Sciences of the United States of America , vol.103 , Issue.33 , pp. 12285-12290
    • Buehler, M.J.1
  • 26
    • 0036833168 scopus 로고    scopus 로고
    • Mechanics of biomolecules
    • DOI 10.1016/S0022-5096(02)00035-2, PII S0022509602000352
    • G. Bao 2002 Mechanics of biomolecules J. Mech. Phys. Sol. 50 2237 2274 1013.92018 10.1016/S0022-5096(02)00035-2 2002JMPSo..50.2237B 1:CAS:528:DC%2BD38XmsVOntL0%3D (Pubitemid 34946672)
    • (2002) Journal of the Mechanics and Physics of Solids , vol.50 , Issue.11 , pp. 2237-2274
    • Bao, G.1
  • 27
    • 34547191723 scopus 로고    scopus 로고
    • Cell surface mechanics and the control of cell shape, tissue patterns and morphogenesis
    • 10.1038/nrm2222 1:CAS:528:DC%2BD2sXotVaht7g%3D
    • T. Lecuit P.-F. Lenne 2002 Cell surface mechanics and the control of cell shape, tissue patterns and morphogenesis Nat. Rev. Mol. Cell Biol. 8 633 644 10.1038/nrm2222 1:CAS:528:DC%2BD2sXotVaht7g%3D
    • (2002) Nat. Rev. Mol. Cell Biol. , vol.8 , pp. 633-644
    • Lecuit, T.1    Lenne, P.-F.2
  • 28
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • 9138555 1:CAS:528:DyaK2sXhsVeisbo%3D 1997BpJ.72.1047G
    • M.K. Gilson J.A. Given B.L. Bush A. McCammon 1997 The statistical-thermodynamic basis for computation of binding affinities: a critical review Biophys. J. 72 1047 1069 9138555 1:CAS:528:DyaK2sXhsVeisbo%3D 1997BpJ....72.1047G
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, A.4
  • 31
    • 0029623184 scopus 로고
    • Computational methods for predicting binding free energy in ligand-receptor complexes
    • 10.1021/jm00026a001
    • R. Aiay M. Murcko 1995 Computational methods for predicting binding free energy in ligand-receptor complexes J. Med. Chem. 38 4953 4967 10.1021/jm00026a001
    • (1995) J. Med. Chem. , vol.38 , pp. 4953-4967
    • Aiay, R.1    Murcko, M.2
  • 32
    • 85005687495 scopus 로고
    • The free-energy of xenon binding to myoglobin from molecular-dynamics simulation
    • 1:CAS:528:DyaL2sXltFWgt78%3D
    • J. Hermans S. Shankar 1986 The free-energy of xenon binding to myoglobin from molecular-dynamics simulation Isr. J. Chem. 27 225 227 1:CAS:528: DyaL2sXltFWgt78%3D
    • (1986) Isr. J. Chem. , vol.27 , pp. 225-227
    • Hermans, J.1    Shankar, S.2
  • 33
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
    • 8842206 1:CAS:528:DyaK28XkslOqtb4%3D 1996BpJ.71.670R
    • B. Roux M. Nina R. Pomes J.C. Smith 1996 Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study Biophys. J. 71 670 681 8842206 1:CAS:528: DyaK28XkslOqtb4%3D 1996BpJ....71..670R
    • (1996) Biophys. J. , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomes, R.3    Smith, J.C.4
  • 34
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • 10.1021/ma50003a019 1:CAS:528:DyaL3MXhvFWmsbY%3D 1981Mamol.14.325K
    • M. Karplus S. Kushick 1981 Method for estimating the configurational entropy of macromolecules Macromolecules 14 325 332 10.1021/ma50003a019 1:CAS:528:DyaL3MXhvFWmsbY%3D 1981Mamol..14..325K
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, S.2
  • 35
    • 0001064378 scopus 로고
    • Free energy determination of polypeptide conformations generated by molecular dynamics simulations
    • 10.1021/ma00140a029 1:CAS:528:DyaL2cXlslWksLk%3D 1984Mamol.17.2044D
    • A. Di Nola H.J.C. Berendsen O. Edholm 1984 Free energy determination of polypeptide conformations generated by molecular dynamics simulations Macromolecules 17 2044 2050 10.1021/ma00140a029 1:CAS:528:DyaL2cXlslWksLk%3D 1984Mamol..17.2044D
    • (1984) Macromolecules , vol.17 , pp. 2044-2050
    • Di Nola, A.1    Berendsen, H.J.C.2    Edholm, O.3
  • 36
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • 10.1016/0009-2614(93)89366-P 1993CPL.215.617S 1:CAS:528: DyaK2cXhtVOksb8%3D
    • J. Schlitter 1993 Estimation of absolute and relative entropies of macromolecules using the covariance matrix Chem. Phys. Lett. 215 617 621 10.1016/0009-2614(93)89366-P 1993CPL...215..617S 1:CAS:528:DyaK2cXhtVOksb8%3D
    • (1993) Chem. Phys. Lett. , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 37
    • 0034323089 scopus 로고    scopus 로고
    • Absolute entropies from molecular dynamics simulation trajectories
    • DOI 10.1063/1.1309534
    • H. Schaefer A.E. Mark W.F. van Gunsteren 2000 Absolute entropies from molecular dynamics simulations trajectories J. Chem. Phys. 113 7809 7817 10.1063/1.1309534 2000JChPh.113.7809S (Pubitemid 32023177)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.18 , pp. 7809-7817
    • Schafer, H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 38
    • 0030987036 scopus 로고    scopus 로고
    • Molecular dynamics study of unbinding of the avidin-biotin complex
    • S. Izrailev S. Stepaniants M. Balsera Y. Oono K. Schulten 1997 Molecular dynamics study of unbinding of the avidin-biotin complex Biophys. J. 72 1568 1581 9083662 1:CAS:528:DyaK2sXitFeisbk%3D (Pubitemid 27133097)
    • (1997) Biophysical Journal , vol.72 , Issue.4 , pp. 1568-1581
    • Izrailev, S.1    Stepaniants, S.2    Balsera, M.3    Oono, Y.4    Schulten, K.5
  • 40
    • 0031001349 scopus 로고    scopus 로고
    • Dynamic strength of molecular adhesion bonds
    • 9083660 1:CAS:528:DyaK2sXitFeisbs%3D
    • E. Evans K. Ritchie 1997 Dynamic strength of molecular adhesion bonds Biophys. J. 72 1541 1555 9083660 1:CAS:528:DyaK2sXitFeisbs%3D
    • (1997) Biophys. J. , vol.72 , pp. 1541-1555
    • Evans, E.1    Ritchie, K.2
  • 41
    • 0030834853 scopus 로고    scopus 로고
    • Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations
    • 9414212 1:CAS:528:DyaK2sXnsl2murc%3D
    • B. Isralewitz S. Izrailev K. Schulten 1997 Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations Biophys. J. 73 2972 2979 9414212 1:CAS:528:DyaK2sXnsl2murc%3D
    • (1997) Biophys. J. , vol.73 , pp. 2972-2979
    • Isralewitz, B.1    Izrailev, S.2    Schulten, K.3
  • 42
    • 0030787462 scopus 로고    scopus 로고
    • Stability and dynamics of G-actin: Back-door water diffusion and behavior of a subdomain 3/4 loop
    • 9251782 1:CAS:528:DyaK2sXkvFCmtbc%3D
    • W. Wriggers K. Schulten 1997 Stability and dynamics of G-actin: back-door water diffusion and behavior of a subdomain 3/4 loop Biophys. J. 73 624 639 9251782 1:CAS:528:DyaK2sXkvFCmtbc%3D
    • (1997) Biophys. J. , vol.73 , pp. 624-639
    • Wriggers, W.1    Schulten, K.2
  • 43
    • 0033445338 scopus 로고    scopus 로고
    • Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations
    • 10.1016/S0301-0104(99)00164-0 1999CP.247.141L 1:CAS:528: DyaK1MXks1Omtbo%3D
    • H. Lu K. Schulten 1999 Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations Chem. Phys. 247 141 153 10.1016/S0301-0104(99)00164-0 1999CP....247..141L 1:CAS:528:DyaK1MXks1Omtbo%3D
    • (1999) Chem. Phys. , vol.247 , pp. 141-153
    • Lu, H.1    Schulten, K.2
  • 44
    • 0034612284 scopus 로고    scopus 로고
    • Unfolding proteins by external forces and temperature: The importance of topology and energetics
    • DOI 10.1073/pnas.100124597
    • E. Paci M. Karplus 2000 Unfolding proteins by external forces and temperature: the importance of topology and energetics Proc. Natl. Acad. Sci. USA 97 6521 6526 10823892 10.1073/pnas.100124597 2000PNAS...97.6521P 1:CAS:528:DC%2BD3cXktFajtL8%3D (Pubitemid 30412746)
    • (2000) Proceedings of the National Academy of Sciences of the United States of America , vol.97 , Issue.12 , pp. 6521-6526
    • Paci, E.1    Karplus, M.2
  • 46
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
    • 10.1063/1.1590311 2003JChPh.119.3559P 1:CAS:528:DC%2BD3sXlvVWktr0%3D
    • S. Park F. Khalili-Araghi E. Tajkhorshid K. Schulten 2003 Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality J. Chem. Phys. 119 3559 3566 10.1063/1.1590311 2003JChPh.119.3559P 1:CAS:528:DC%2BD3sXlvVWktr0%3D
    • (2003) J. Chem. Phys. , vol.119 , pp. 3559-3566
    • Park, S.1    Khalili-Araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 47
    • 34347403503 scopus 로고    scopus 로고
    • Entropic elasticity controls nanomechanics of single tropocollagen molecules
    • DOI 10.1529/biophysj.106.102616
    • M.J. Buehler S.Y. Wong 2007 Entropic elasticity controls nanomechanics of single tropocollagen molecules Biophys. J. 93 37 43 17434941 10.1529/biophysj.106.102616 1:CAS:528:DC%2BD2sXntVKqt7c%3D 2007BpJ....93...37B (Pubitemid 47041649)
    • (2007) Biophysical Journal , vol.93 , Issue.1 , pp. 37-43
    • Buehler, M.J.1    Wong, S.Y.2
  • 48
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • 10.1103/PhysRevLett.78.2690 1997PhRvL.78.2690J 1:CAS:528: DyaK2sXisVSrt7c%3D
    • C. Jarzynski 1997 Nonequilibrium equality for free energy differences Phys. Rev. Lett. 78 2690 2693 10.1103/PhysRevLett.78.2690 1997PhRvL..78.2690J 1:CAS:528:DyaK2sXisVSrt7c%3D
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 49
    • 0000765761 scopus 로고    scopus 로고
    • Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences
    • C. Jarzynski 1997 Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences Phys. Rev. E 60 2721 2726
    • (1997) Phys. Rev. E , vol.60 , pp. 2721-2726
    • Jarzynski, C.1
  • 50
    • 0000186593 scopus 로고    scopus 로고
    • Path-ensemble averages in systems driven far from equilibrium
    • 10.1103/PhysRevE.61.2361 2000PhRvE.61.2361C 1:CAS:528: DC%2BD3cXhs1Cjs74%3D
    • G.E. Crooks 2000 Path-ensemble averages in systems driven far from equilibrium Phys. Rev. E 61 2361 2366 10.1103/PhysRevE.61.2361 2000PhRvE..61.2361C 1:CAS:528:DC%2BD3cXhs1Cjs74%3D
    • (2000) Phys. Rev. E , vol.61 , pp. 2361-2366
    • Crooks, G.E.1
  • 51
    • 33749997463 scopus 로고    scopus 로고
    • The Jarzynski identity derived from general Hamiltonian or non-Hamiltonian dynamics reproducing NVT or NPT ensembles
    • DOI 10.1063/1.2338535
    • M.A. Cuendet 2006 The Jarzynski identity derived from general Hamiltonian or non-Hamiltonian dynamics reproducing NVT or NPT ensembles J. Chem. Phys. 125 144109 17042581 10.1063/1.2338535 2006JChPh.125n4109C 1:CAS:528: DC%2BD28XhtFWjt7rP (Pubitemid 44570775)
    • (2006) Journal of Chemical Physics , vol.125 , Issue.14 , pp. 144109
    • Cuendet, M.A.1
  • 52
    • 17044382128 scopus 로고    scopus 로고
    • Enhancing the accuracy, the efficiency and the scope of free energy simulations
    • 15837174 10.1016/j.sbi.2005.03.001 1:CAS:528:DC%2BD2MXjtlaltb0%3D
    • T. Rodinger R. Pomés 2005 Enhancing the accuracy, the efficiency and the scope of free energy simulations Curr. Opin. Struct. Biol. 15 164 170 15837174 10.1016/j.sbi.2005.03.001 1:CAS:528:DC%2BD2MXjtlaltb0%3D
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 164-170
    • Rodinger, T.1    Pomés, R.2
  • 53
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • DOI 10.1016/S0959-440X(00)00194-9
    • B. Isralewitz M. Gao K. Schulten 2001 Steered molecular dynamics and mechanical functions of proteins Curr. Opin. Struct. Biol. 11 224 230 11297932 10.1016/S0959-440X(00)00194-9 1:CAS:528:DC%2BD3MXjsVyisro%3D (Pubitemid 32289426)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.2 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 54
    • 34249930159 scopus 로고    scopus 로고
    • Single-molecule experiments in vitro and in silico
    • DOI 10.1126/science.1137591
    • M. Sotomayor K. Schulten 2007 Single-molecule experiments in vitro and in silico Science 316 1144 1148 17525328 10.1126/science.1137591 2007Sci...316.1144S 1:CAS:528:DC%2BD2sXls1Kit7g%3D (Pubitemid 46877468)
    • (2007) Science , vol.316 , Issue.5828 , pp. 1144-1148
    • Sotomayor, M.1    Schulten, K.2
  • 55
    • 0032028924 scopus 로고    scopus 로고
    • Atomistic simulations of materials fracture and the link between atomic and Continuum length scales
    • 1:CAS:528:DyaK1cXisVOmtrY%3D
    • F. Cleri S.R. Phillpot D. Wolf S. Yip 1998 Atomistic simulations of materials fracture and the link between atomic and Continuum length scales J. Amer. Cer. Soc. 81 501 516 1:CAS:528:DyaK1cXisVOmtrY%3D
    • (1998) J. Amer. Cer. Soc. , vol.81 , pp. 501-516
    • Cleri, F.1    Phillpot, S.R.2    Wolf, D.3    Yip, S.4
  • 56
    • 21244498669 scopus 로고    scopus 로고
    • Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA
    • DOI 10.1529/biophysj.104.046912
    • S.A. Harris Z.A. Sands C.A. Laughton 2005 Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA Biophys. J. 88 1684 1691 15626714 10.1529/biophysj.104.046912 1:CAS:528:DC%2BD2MXis1WhtLs%3D (Pubitemid 40976185)
    • (2005) Biophysical Journal , vol.88 , Issue.3 , pp. 1684-1691
    • Harris, S.A.1    Sands, Z.A.2    Laughton, C.A.3
  • 57
    • 0024294636 scopus 로고
    • No code for recognition
    • 3419498 10.1038/335294a0 1988Natur.335.294M 1:STN:280: DyaL1czjsVKruw%3D%3D
    • B. Matthews 1988 No code for recognition Nature 335 294 295 3419498 10.1038/335294a0 1988Natur.335..294M 1:STN:280:DyaL1czjsVKruw%3D%3D
    • (1988) Nature , vol.335 , pp. 294-295
    • Matthews, B.1
  • 58
    • 0029065860 scopus 로고
    • DNA recognition code of transcription factors
    • 7567917 10.1093/protein/8.4.319 1:CAS:528:DyaK2MXntVelt7c%3D
    • M. Suzuki S. Brenner M. Gerstein N. Yagi 1995 DNA recognition code of transcription factors Protein Eng. 8 319 328 7567917 10.1093/protein/8.4.319 1:CAS:528:DyaK2MXntVelt7c%3D
    • (1995) Protein Eng. , vol.8 , pp. 319-328
    • Suzuki, M.1    Brenner, S.2    Gerstein, M.3    Yagi, N.4
  • 59
    • 0034682882 scopus 로고    scopus 로고
    • Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
    • DOI 10.1006/jmbi.2000.3918
    • C. Pabo L. Nekludova 2000 Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol. 301 597 624 10966773 10.1006/jmbi.2000.3918 1:CAS:528:DC%2BD3cXmtVKmtbw%3D (Pubitemid 30706831)
    • (2000) Journal of Molecular Biology , vol.301 , Issue.3 , pp. 597-624
    • Pabo, C.O.1    Nekludova, L.2
  • 60
    • 0028071373 scopus 로고
    • Entropic elasticity of lambda-phage DNA
    • 8079175 10.1126/science.8079175 1994Sci.265.1599B 1:STN:280: DyaK2czmtVamsw%3D%3D
    • C. Bustamante J.F. Marko E.D. Siggia S. Smith 1994 Entropic elasticity of lambda-phage DNA Science 265 1599 1600 8079175 10.1126/science.8079175 1994Sci...265.1599B 1:STN:280:DyaK2czmtVamsw%3D%3D
    • (1994) Science , vol.265 , pp. 1599-1600
    • Bustamante, C.1    Marko, J.F.2    Siggia, E.D.3    Smith, S.4
  • 62
    • 0028375446 scopus 로고
    • Bending and twisting elasticity of DNA
    • 10.1021/ma00082a015 1:CAS:528:DyaK2cXpvFKluw%3D%3D 1994Mamol.27.981M
    • J.F. Marko E.D. Siggia 1994 Bending and twisting elasticity of DNA Macromolecules 27 981 987 10.1021/ma00082a015 1:CAS:528:DyaK2cXpvFKluw%3D%3D 1994Mamol..27..981M
    • (1994) Macromolecules , vol.27 , pp. 981-987
    • Marko, J.F.1    Siggia, E.D.2
  • 65
    • 41649096570 scopus 로고    scopus 로고
    • There and (slowly) back again: Entropy-driven hysteresis in a model of DNA overstretching
    • 17981894 10.1529/biophysj.107.117036 1:CAS:528:DC%2BD1cXjslequr4%3D
    • S. Whitelam S. Pronk P.L. Geissler 2008 There and (slowly) back again: entropy-driven hysteresis in a model of DNA overstretching Biophys. J. 94 2452 2469 17981894 10.1529/biophysj.107.117036 1:CAS:528:DC%2BD1cXjslequr4%3D
    • (2008) Biophys. J. , vol.94 , pp. 2452-2469
    • Whitelam, S.1    Pronk, S.2    Geissler, P.L.3
  • 66
    • 0029909230 scopus 로고    scopus 로고
    • Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure
    • DOI 10.1021/ja961751x, PII S0002786396017519
    • M.W. Konrad J.I. Bolonick 1996 Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure J. Am. Chem. Soc. 118 10989 10994 10.1021/ja961751x 1:CAS:528:DyaK28XmsFOisL8%3D (Pubitemid 26399722)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.45 , pp. 10989-10994
    • Konrad, M.W.1    Bolonick, J.I.2
  • 67
    • 0344327079 scopus 로고    scopus 로고
    • Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads
    • DOI 10.1007/s002490050224
    • A.D. MacKerell G.U. Lee 1999 Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads Eur. Biophys. J. 28 415 426 10413863 10.1007/s002490050224 1:CAS:528:DyaK1MXjsVGjurk%3D (Pubitemid 29287524)
    • (1999) European Biophysics Journal , vol.28 , Issue.5 , pp. 415-426
    • MacKerell Jr., A.D.1    Lee, G.U.2
  • 68
    • 0033861876 scopus 로고    scopus 로고
    • Model energy landscapes and the force-induced dissociation of ligand-receptor bonds
    • 10968985 1:CAS:528:DC%2BD3cXmsVaku7g%3D 10.1016/S0006-3495(00)76375-2
    • T. Strunz K. Oroszlan H.J. Guntherodt M. Henger 2000 Model energy landscapes and the force-induced dissociation of ligand-receptor bonds Biophys. J. 79 1206 1212 10968985 1:CAS:528:DC%2BD3cXmsVaku7g%3D 10.1016/S0006-3495(00) 76375-2
    • (2000) Biophys. J. , vol.79 , pp. 1206-1212
    • Strunz, T.1    Oroszlan, K.2    Guntherodt, H.J.3    Henger, M.4
  • 69
    • 46749084254 scopus 로고    scopus 로고
    • Simulation of the mechanical strength of a single collagen molecule
    • 10.1529/biophysj.107.120659 1:CAS:528:DC%2BD1cXnslWltr4%3D
    • P.J. in't Veld M.J. Stevens 2008 Simulation of the mechanical strength of a single collagen molecule Biophys. J. 95 33 39 10.1529/biophysj.107.120659 1:CAS:528:DC%2BD1cXnslWltr4%3D
    • (2008) Biophys. J. , vol.95 , pp. 33-39
    • In'T Veld, P.J.1    Stevens, M.J.2
  • 70
    • 0031011695 scopus 로고    scopus 로고
    • Reversible unfolding of individual titin immunoglobulin domains by AFM
    • DOI 10.1126/science.276.5315.1109
    • M. Rief M. Gautel F. Oesterhelt J.M. Fernandez H. Gaub 1997 Reversible unfolding of individual titin immunoglobulin domains by AFM Science 276 1109 1112 9148804 10.1126/science.276.5315.1109 1:CAS:528:DyaK2sXjt12qtLc%3D (Pubitemid 27218118)
    • (1997) Science , vol.276 , Issue.5315 , pp. 1109-1112
    • Rief, M.1    Gautel, M.2    Oesterhelt, F.3    Fernandez, J.M.4    Gaub, H.E.5
  • 71
    • 0031002460 scopus 로고    scopus 로고
    • Folding-unfolding transitions in single titin molecules characterized with laser tweezers
    • DOI 10.1126/science.276.5315.1112
    • M.S.Z. Kellermayer S.B. Smith H.L. Granzier C. Bustamante 1997 Folding-unfolding transitions in single titin molecules characterized with laser tweezers Science 276 1112 1116 9148805 10.1126/science.276.5315.1112 1:CAS:528:DyaK2sXjt12qtbc%3D (Pubitemid 27218119)
    • (1997) Science , vol.276 , Issue.5315 , pp. 1112-1116
    • Kellermayer, M.S.Z.1    Smith, S.B.2    Granzier, H.L.3    Bustamante, C.4
  • 72
    • 0032516205 scopus 로고    scopus 로고
    • The molecular elasticity of the extracellular matrix protein tenascin
    • DOI 10.1038/30270
    • A.F. Oberhauser P.E. Marszalek H.P. Erickson J.M. Fernandez 1998 The molecular elasticity of the extracellular matrix protein tenascin Nature 393 181 185 9603523 10.1038/30270 1998Natur.393..181O 1:CAS:528:DyaK1cXjt1ahur8%3D (Pubitemid 28242260)
    • (1998) Nature , vol.393 , Issue.6681 , pp. 181-185
    • Oberhauser, A.F.1    Marszalek, P.E.2    Erickson, H.P.3    Fernandez, J.M.4
  • 73
    • 0033523904 scopus 로고    scopus 로고
    • Mechanical unfolding intermediates in titin modules
    • DOI 10.1038/47083
    • P.E. Marszalek H. Lu H. Li M. Carrion-Vazquez A.F. Oberhauser K. Schulten J.M. Fernandez 1999 Mechanical unfolding intermediates in titin modules Nature 402 100 103 10573426 10.1038/47083 1999Natur.402..100M 1:CAS:528: DyaK1MXntlCmsL0%3D (Pubitemid 29533524)
    • (1999) Nature , vol.402 , Issue.6757 , pp. 100-103
    • Marszalek, P.E.1    Lu, H.2    Li, H.3    Carrion-Vazquez, M.4    Oberhauser, A.F.5    Schulten, K.6    Fernandez, J.M.7
  • 75
    • 8544278061 scopus 로고    scopus 로고
    • Chemistry on a single protein, vascular cell adhesion molecule-1, during forced unfolding
    • DOI 10.1074/jbc.M404103200
    • N. Bhasin P. Carl S. Harper G. Feng H. Lu D.W. Speicher D.E. Discher 2004 Chemistry on a single protein, vascular cell adhesion molecule-1, during forced unfolding J. Biol. Chem. 279 45865 45874 15308645 10.1074/jbc.M404103200 1:CAS:528:DC%2BD2cXovVCntro%3D (Pubitemid 39491579)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.44 , pp. 45865-45874
    • Bhasin, N.1    Carl, P.2    Harper, S.3    Feng, G.4    Lu, H.5    Speicher, D.W.6    Discher, D.E.7
  • 78
    • 0031003997 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of a Brownian motor
    • DOI 10.1126/science.276.5314.917
    • R. Dean Astumian 1997 Thermodynamics and kinetics of a brownian motor Science 276 917 922 10.1126/science.276.5314.917 (Pubitemid 27209083)
    • (1997) Science , vol.276 , Issue.5314 , pp. 917-922
    • Astumian, R.D.1
  • 79
    • 0034660532 scopus 로고    scopus 로고
    • Two-headed binding of a processive myosin to F-actin
    • DOI 10.1038/35015592
    • M.L. Walker S.A. Burgess J.R. Sellers F. Wang J.A. Hammer J. Trinick P.J. Knight 2000 Two-headed binding of a processive myosin to F-actin Nature 405 804 807 10866203 10.1038/35015592 2000Natur.405..804W 1:CAS:528: DC%2BD3cXksVyjsrs%3D (Pubitemid 30407854)
    • (2000) Nature , vol.405 , Issue.6788 , pp. 804-807
    • Walker, M.L.1    Burgess, S.A.2    Sellers, J.R.3    Wang, F.4    Hammer III, J.A.5    Trinick, J.6    Knight, P.J.7
  • 80
    • 33749439041 scopus 로고    scopus 로고
    • Kinesin's biased stepping mechanism: Amplification of neck linker zippering
    • DOI 10.1529/biophysj.106.087049
    • W.H. Mather R.F. Fox 2006 Kinesin's biased stepping mechanism: amplification of neck linker zippering Biophys. J. 91 2416 2426 16844749 10.1529/biophysj.106.087049 1:CAS:528:DC%2BD28XhtVSktrbM 2006BpJ....91.2416M (Pubitemid 44511698)
    • (2006) Biophysical Journal , vol.91 , Issue.7 , pp. 2416-2426
    • Mather, W.H.1    Fox, R.F.2
  • 81
    • 33847013578 scopus 로고
    • Muscle structure and theories of contraction
    • Huxley, A.F.: Muscle structure and theories of contraction. Prog. Biophys. Biophys. Chem. 7, 255-318 (1957)
    • (1957) Prog. Biophys. Biophys. Chem. , vol.7 , pp. 255-318
    • Huxley, A.F.1
  • 82
    • 0016122530 scopus 로고
    • Muscular contraction-review lecture
    • Huxley, A.F.: Muscular contraction-review lecture. J. Physiol. (London) 243, 1-43 (1974)
    • (1974) J. Physiol. (London) , vol.243 , pp. 1-43
    • Huxley, A.F.1
  • 83
    • 0001533859 scopus 로고    scopus 로고
    • Rectified brownian movement in molecular and cell biology
    • 10.1103/PhysRevE.57.2177 1998PhRvE.57.2177F 1:CAS:528:DyaK1cXhtFCntbk%3D
    • R.F. Fox 1998 Rectified brownian movement in molecular and cell biology Phys. Rev. E 57 2177 2203 10.1103/PhysRevE.57.2177 1998PhRvE..57.2177F 1:CAS:528:DyaK1cXhtFCntbk%3D
    • (1998) Phys. Rev. E , vol.57 , pp. 2177-2203
    • Fox, R.F.1
  • 84
    • 34548407835 scopus 로고    scopus 로고
    • Superelasticity, energy dissipation and strain hardening of vimentin coiled-coil intermediate filaments: Atomistic and continuum studies
    • DOI 10.1007/s10853-007-1719-2, Nano- and micromechanica I prperties of hieracrhal biological materials: Linking mechanics, chemistry and biology
    • T. Ackbarow M.J. Buehler 2007 Superelasticity, energy dissipation and strain hardening of vimentin coiled-coil intermediate filaments: atomistic and continuum studies J. Mater. Sci. 42 8771 8787 10.1007/s10853-007-1719-2 1:CAS:528:DC%2BD2sXpvVWqurg%3D 2007JMatS..42.8771A (Pubitemid 47353300)
    • (2007) Journal of Materials Science , vol.42 , Issue.21 , pp. 8771-8787
    • Ackbarow, T.1    Buehler, M.J.2
  • 85
    • 0037036070 scopus 로고    scopus 로고
    • 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 Jr. C. Bustamante 2002 Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality Science 296 1832 1835 12052949 10.1126/science.1071152 2002Sci...296.1832L 1:CAS:528:DC%2BD38Xktl2rt7Y%3D (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
  • 86
    • 0036790894 scopus 로고    scopus 로고
    • Escaping free energy minima
    • 12271136 10.1073/pnas.202427399 2002PNAS.9912562L 1:CAS:528: DC%2BD38XnvFGiurc%3D
    • A. Laio M. Parrinello 2002 Escaping free energy minima Proc. Natl. Acad. Sci. USA 99 12562 12566 12271136 10.1073/pnas.202427399 2002PNAS...9912562L 1:CAS:528:DC%2BD38XnvFGiurc%3D
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12562-12566
    • Laio, A.1    Parrinello, M.2
  • 87
    • 33644772083 scopus 로고    scopus 로고
    • Equilibrium free energies from nonequilibrium metadynamics
    • DOI 10.1103/PhysRevLett.96.090601, 090601
    • G. Bussi A. Laio M. Parrinello 2006 Equilibrium free energies from nonequilibrium metadynamics Phys. Rev. Lett. 96 090601 16606249 10.1103/PhysRevLett.96.090601 2006PhRvL..96i0601B 1:CAS:528:DC%2BD28XitlSis7o%3D (Pubitemid 43346714)
    • (2006) Physical Review Letters , vol.96 , Issue.9 , pp. 1-4
    • Bussi, G.1    Laio, A.2    Parrinello, M.3
  • 88
    • 29144483372 scopus 로고    scopus 로고
    • Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
    • 16375469 10.1063/1.2132286 2005JChPh.123v4106P 1:CAS:528: DC%2BD2MXhtlGhsrzJ
    • M. Praprotnik L. Delle Site K. Kremer 2005 Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly J. Chem. Phys. 123 224106 16375469 10.1063/1.2132286 2005JChPh.123v4106P 1:CAS:528:DC%2BD2MXhtlGhsrzJ
    • (2005) J. Chem. Phys. , vol.123 , pp. 224106
    • Praprotnik, M.1    Delle Site, L.2    Kremer, K.3
  • 89
    • 28844494903 scopus 로고    scopus 로고
    • Coarse-grained model of proteins incorporating atomistic detail of the active site
    • 16384187 10.1103/PhysRevLett.95.218102 2005PhRvL.95u8102N 1:CAS:528:DC%2BD2MXht1ejt77F
    • M. Neri C. Anselmi M. Cascella A. Maritan P. Carloni 2005 Coarse-grained model of proteins incorporating atomistic detail of the active site Phys. Rev. Lett. 95 218102 16384187 10.1103/PhysRevLett.95.218102 2005PhRvL..95u8102N 1:CAS:528:DC%2BD2MXht1ejt77F
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 218102
    • Neri, M.1    Anselmi, C.2    Cascella, M.3    Maritan, A.4    Carloni, P.5
  • 90
    • 33748266722 scopus 로고    scopus 로고
    • Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
    • DOI 10.1021/jp062700h
    • Q. Shi S. Izvekov G.A. Voth 2006 Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel J. Phys. Chem. B 110 15045 15048 16884212 10.1021/jp062700h 1:CAS:528:DC%2BD28XmvF2nur0%3D (Pubitemid 44318467)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.31 , pp. 15045-15048
    • Shi, Q.1    Izvekov, S.2    Voth, G.A.3
  • 91
    • 22844456329 scopus 로고    scopus 로고
    • Using simplified protein representation as a reference potential for all-atom calculations of folding free energy
    • 1:CAS:528:DC%2BD3cXjsV2htbk%3D
    • Z.Z. Fan J.K. Hwang A. Warshel 1999 Using simplified protein representation as a reference potential for all-atom calculations of folding free energy Theor. Chem. Acc. 103 77 80 1:CAS:528:DC%2BD3cXjsV2htbk%3D
    • (1999) Theor. Chem. Acc. , vol.103 , pp. 77-80
    • Fan, Z.Z.1    Hwang, J.K.2    Warshel, A.3
  • 93
    • 32644458379 scopus 로고    scopus 로고
    • Resolution exchange simulation
    • DOI 10.1103/PhysRevLett.96.028105
    • E. Lyman F.M. Ytreberg D.M. Zuckerman 2006 Resolution exchange simulation Phys. Rev. Lett. 96 028105 16486650 10.1103/PhysRevLett.96.028105 2006PhRvL..96b8105L 1:CAS:528:DC%2BD28XmslKiuw%3D%3D (Pubitemid 43248299)
    • (2006) Physical Review Letters , vol.96 , Issue.2 , pp. 028105
    • Lyman, E.1    Ytreberg, F.M.2    Zuckerman, D.M.3
  • 94
  • 95
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • 10.1021/jp036508g 1:CAS:528:DC%2BD3sXptlKjsb4%3D
    • S.J. Marrink A.H. de Vries A.E. Mark 2004 Coarse grained model for semiquantitative lipid simulations J. Phys. Chem. B 108 750 760 10.1021/jp036508g 1:CAS:528:DC%2BD3sXptlKjsb4%3D
    • (2004) J. Phys. Chem. B , vol.108 , pp. 750-760
    • Marrink, S.J.1    De Vries, A.H.2    Mark, A.E.3
  • 96
    • 0037044173 scopus 로고    scopus 로고
    • Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations
    • DOI 10.1063/1.1498463
    • J.C. Shillcock R. Lipowsky 2002 Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations J. Chem. Phys. 117 5048 5061 10.1063/1.1498463 2002JChPh.117.5048S 1:CAS:528:DC%2BD38XmsVWmtLY%3D (Pubitemid 35048409)
    • (2002) Journal of Chemical Physics , vol.117 , Issue.10 , pp. 5048-5061
    • Shillcock, J.C.1    Lipowsky, R.2
  • 97
    • 34347250453 scopus 로고    scopus 로고
    • The coordination of protein motors and the kinetic behavior of microtubule - A computational study
    • DOI 10.1016/j.bpc.2007.05.008, PII S0301462207001147
    • Q. Chen D.Y. Li K. Oiwa 2007 The coordination of protein motors and the kinetic behavior of microtubule-a computational study Biophys. Chem. 129 60 69 17566632 10.1016/j.bpc.2007.05.008 1:CAS:528:DC%2BD2sXnsFKqsr8%3D (Pubitemid 47002121)
    • (2007) Biophysical Chemistry , vol.129 , Issue.1 , pp. 60-69
    • Chen, Q.1    Li, D.Y.2    Oiwa, K.3
  • 98
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: in serial and in parallel
    • DOI 10.1016/j.sbi.2007.03.004, PII S0959440X07000346, Theory and Simulation / Mecromolecular Assemblages
    • G.S. Ayton W.G. Noid G.A. Voth 2007 Multiscale modeling of biomolecular systems: in serial and in parallel Curr. Opin. Struct. Biol. 17 192 198 17383173 10.1016/j.sbi.2007.03.004 1:CAS:528:DC%2BD2sXksFehtLc%3D (Pubitemid 46584804)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.2 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 100
    • 34447515841 scopus 로고    scopus 로고
    • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    • DOI 10.1002/prot.21371
    • A.P. Heath L.E. Kavraki C. Clementi 2007 From coarse-grain to all-atom: toward multiscale analysis of protein landscapes Proteins Struct. Funct. Bioinfo. 68 646 661 10.1002/prot.21371 1:CAS:528:DC%2BD2sXnvFymsbw%3D (Pubitemid 47068305)
    • (2007) Proteins: Structure, Function and Genetics , vol.68 , Issue.3 , pp. 646-661
    • Heath, A.P.1    Kavraki, L.E.2    Clementi, C.3
  • 101
    • 33845386474 scopus 로고    scopus 로고
    • Viral structural transitions: An all-atom multiscale theory
    • DOI 10.1063/1.2400858
    • Y. Miao P.J. Ortoleva 2006 Viral structural transitions: an all-atom multiscale theory J. Chem. Phys. 125 214901 17166043 10.1063/1.2400858 2006JChPh.125u4901M 1:CAS:528:DC%2BD28XhtlejtbnF (Pubitemid 44907427)
    • (2006) Journal of Chemical Physics , vol.125 , Issue.21 , pp. 214901
    • Miao, Y.1    Ortoleva, P.J.2


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