메뉴 건너뛰기




Volumn 370, Issue 1969, 2012, Pages 2877-2899

Decoding the energy landscape: Extracting structure, dynamics and thermodynamics

Author keywords

Energy landscapes; Global optimization; Self organization

Indexed keywords

DYNAMICS; GLOBAL OPTIMIZATION; MORPHOLOGY; POTENTIAL ENERGY SURFACES; QUANTUM CHEMISTRY; THERMODYNAMICS;

EID: 84861946897     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2011.0208     Document Type: Article
Times cited : (75)

References (148)
  • 2
    • 0042797442 scopus 로고    scopus 로고
    • Cambridge, UK: Cambridge University Press
    • Wales, D. J. 2003 Energy landscapes. Cambridge, UK: Cambridge University Press.
    • (2003) Energy Landscapes
    • Wales, D.J.1
  • 3
    • 84973654655 scopus 로고
    • Zur quantentheorie der molekeln.
    • (doi:10.1002/andp.19273892002)
    • Born, M. & Oppenheimer, J. R. 1927 Zur quantentheorie der molekeln. Ann. Phys. 84, 457-484. (doi:10.1002/andp.19273892002)
    • (1927) Ann. Phys. , vol.84 , pp. 457-484
    • Born, M.1    Oppenheimer, J.R.2
  • 5
    • 0037113209 scopus 로고    scopus 로고
    • Bifurcation tunneling dynamics in the water trimer
    • DOI 10.1063/1.1509750
    • Keutsch, F. N., Saykally, R. J. & Wales, D. J. 2002 Bifurcation tunneling dynamics in the water trimer. J. Chem. Phys. 117, 8823-8835. (doi:10.1063/1.1509750) (Pubitemid 35457586)
    • (2002) Journal of Chemical Physics , vol.117 , Issue.19 , pp. 8823-8835
    • Keutsch, F.N.1    Saykally, R.J.2    Wales, D.J.3
  • 6
    • 75749138541 scopus 로고    scopus 로고
    • Emergent complexity from simple anisotropic building blocks: Shells, tubes and spirals
    • (doi:10.1021/nn9013565)
    • Fejer, S. N., Chakrabarti, D. &Wales, D. J. 2010 Emergent complexity from simple anisotropic building blocks: shells, tubes and spirals. ACS Nano 4, 219-228. (doi:10.1021/nn9013565)
    • (2010) ACS Nano , vol.4 , pp. 219-228
    • Fejer, S.N.1    Chakrabarti, D.2    Wales, D.J.3
  • 7
    • 79955850981 scopus 로고    scopus 로고
    • Self-assembly of anisotropic particles
    • (doi:10.1039/c0sm01289k)
    • Fejer, S. N., Chakrabarti, D. & Wales, D. J. 2011 Self-assembly of anisotropic particles. Soft Matter 7, 3553-3564. (doi:10.1039/c0sm01289k)
    • (2011) Soft Matter , vol.7 , pp. 3553-3564
    • Fejer, S.N.1    Chakrabarti, D.2    Wales, D.J.3
  • 8
    • 0000710399 scopus 로고
    • On hills and dales
    • Maxwell, J. C. 1870 On hills and dales. Phil. Mag. 40, 421-427.
    • (1870) Phil. Mag. , vol.40 , pp. 421-427
    • Maxwell, J.C.1
  • 9
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: Throwing ropes over rough mountain passes, in the dark
    • (doi:10.1146/annurev.physchem.53.082301.113146)
    • Bolhuis, P. G., Chandler, D., Dellago, C. & Geissler, P. L. 2002 Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53, 291-318. (doi:10.1146/annurev.physchem.53. 082301.113146)
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 11
    • 33746567202 scopus 로고    scopus 로고
    • One-dimensional free-energy profiles of complex systems: Progress variables that preserve the barriers
    • DOI 10.1021/jp060039b
    • Krivov, S. V. & Karplus, M. 2006 One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers. J. Phys. Chem. B 110, 12 689-12 698. (doi:10.1021/jp060039b) (Pubitemid 44139460)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.25 , pp. 12689-12698
    • Krivov, S.V.1    Karplus, M.2
  • 12
    • 39749156392 scopus 로고    scopus 로고
    • Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a -sheet miniprotein
    • DOI 10.1002/prot.21565
    • Muff, S. & Caflisch, A. 2008 Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a b-sheet miniprotein. Proteins Struct. Func. Bioinf. 70, 1185-1195. (doi:10.1002/prot.21565) (Pubitemid 351304079)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.4 , pp. 1185-1195
    • Muff, S.1    Caflisch, A.2
  • 13
    • 52949137003 scopus 로고    scopus 로고
    • Diffusive reaction dynamics on invariant free energy profiles
    • (doi:10.1073/pnas.0800228105)
    • Krivov, S. V. & Karplus, M. 2008 Diffusive reaction dynamics on invariant free energy profiles. Proc. Natl Acad. Sci. USA 105, 13 841-13 846. (doi:10.1073/pnas.0800228105)
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 13841-13846
    • Krivov, S.V.1    Karplus, M.2
  • 14
    • 42149175435 scopus 로고    scopus 로고
    • Transition networks for modeling the kinetics of conformational change in macromolecules
    • (doi:10.1016/j.sbi.2008.01.008)
    • Noé, F. & Fischer, S. 2008 Transition networks for modeling the kinetics of conformational change in macromolecules. Curr. Opin. Struct. Biol. 18, 154-162. (doi:10.1016/j.sbi.2008.01.008)
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 154-162
    • Noé, F.1    Fischer, S.2
  • 15
    • 69249194661 scopus 로고    scopus 로고
    • Pitfalls of choosing an order parameter for rare event calculations
    • (doi:10.1063/1.3204008)
    • Dickson, B. M., Makarov, D. E. & Henkelman, G. 2009 Pitfalls of choosing an order parameter for rare event calculations. J. Chem. Phys. 131, 074108. (doi:10.1063/1.3204008)
    • (2009) J. Chem. Phys. , vol.131 , pp. 074108
    • Dickson, B.M.1    Makarov, D.E.2    Henkelman, G.3
  • 16
    • 77749324287 scopus 로고    scopus 로고
    • Energy landscapes: Some new horizons
    • (doi:10.1016/j.sbi.2009.12.011)
    • Wales, D. J. 2010 Energy landscapes: some new horizons. Curr. Opin. Struct. Biol. 20, 3-10. (doi:10.1016/j.sbi.2009.12.011)
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 3-10
    • Wales, D.J.1
  • 17
    • 0000370391 scopus 로고    scopus 로고
    • The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
    • Becker, O. M. & Karplus, M. 1997 The topology of multidimensional potential energy surfaces: theory and application to peptide structure and kinetics. J. Chem. Phys. 106, 1495-1517. (doi:10.1063/1.473299) (Pubitemid 127627069)
    • (1997) Journal of Chemical Physics , vol.106 , Issue.4 , pp. 1495-1517
    • Becker, O.M.1    Karplus, M.2
  • 18
    • 0032552138 scopus 로고    scopus 로고
    • Archetypal energy landscapes
    • DOI 10.1038/29487
    • Wales, D. J., Miller, M. A. & Walsh, T. R. 1998 Archetypal energy landscapes. Nature 394, 758-760. (doi:10.1038/29487) (Pubitemid 28391634)
    • (1998) Nature , vol.394 , Issue.6695 , pp. 758-760
    • Wales, D.J.1    Miller, M.A.2    Walsh, T.R.3
  • 19
    • 0037115811 scopus 로고    scopus 로고
    • Free energy disconnectivity graphs: Application to peptide models
    • (doi:10.1063/1.1517606)
    • Krivov, S. V. & Karplus, M. 2002 Free energy disconnectivity graphs: application to peptide models. J. Chem. Phys. 117, 10 894-10 903. (doi:10.1063/1.1517606)
    • (2002) J. Chem. Phys. , vol.117 , pp. 10894-10903
    • Krivov, S.V.1    Karplus, M.2
  • 20
    • 0037460544 scopus 로고    scopus 로고
    • Free energy landscapes of model peptides and proteins
    • (doi:10.1063/1.1540099)
    • Evans, D. A. & Wales, D. J. 2003 Free energy landscapes of model peptides and proteins. J. Chem. Phys. 118, 3891-3897. (doi:10.1063/1.1540099)
    • (2003) J. Chem. Phys. , vol.118 , pp. 3891-3897
    • Evans, D.A.1    Wales, D.J.2
  • 21
    • 0000986911 scopus 로고
    • Vapor phase homogenous nucleation and the thermodynamic properties of small clusters of argon atoms
    • (doi:10.1063/1.1675790)
    • McGinty, D. J. 1971 Vapor phase homogenous nucleation and the thermodynamic properties of small clusters of argon atoms. J. Chem. Phys. 55, 580-588. (doi:10.1063/1.1675790)
    • (1971) J. Chem. Phys. , vol.55 , pp. 580-588
    • McGinty, D.J.1
  • 22
    • 36849104342 scopus 로고
    • Vibrational frequencies and entropies of small clusters of atoms
    • (doi:10.1063/1.1677650)
    • Burton, J. J. 1972 Vibrational frequencies and entropies of small clusters of atoms. J. Chem. Phys. 56, 3133-3138. (doi:10.1063/1.1677650)
    • (1972) J. Chem. Phys. , vol.56 , pp. 3133-3138
    • Burton, J.J.1
  • 23
    • 0001968287 scopus 로고
    • Structure and dynamics of simple microclusters
    • (doi:10.1002/9780470142592.ch2)
    • Hoare, M. R. 1979 Structure and dynamics of simple microclusters. Adv. Chem. Phys. 40, 49-135. (doi:10.1002/9780470142592.ch2)
    • (1979) Adv. Chem. Phys. , vol.40 , pp. 49-135
    • Hoare, M.R.1
  • 24
    • 0042091834 scopus 로고
    • Packing structures and transitions in liquids and solids
    • (doi:10.1126/science.225.4666.983)
    • Stillinger, F. H. & Weber, T. A. 1984 Packing structures and transitions in liquids and solids. Science 225, 983-989. (doi:10.1126/science. 225.4666.983)
    • (1984) Science , vol.225 , pp. 983-989
    • Stillinger, F.H.1    Weber, T.A.2
  • 25
    • 0000486979 scopus 로고
    • The structure of small clusters: Multiple normal modes model
    • (doi:10.1063/1.464070)
    • Franke, G., Hilf, E. R. & Borrmann, P. 1993 The structure of small clusters: multiple normal modes model. J. Chem. Phys. 98, 3496-3502. (doi:10.1063/1.464070)
    • (1993) J. Chem. Phys. , vol.98 , pp. 3496-3502
    • Franke, G.1    Hilf, E.R.2    Borrmann, P.3
  • 26
    • 77953560530 scopus 로고
    • Coexistence in small inert gas clusters
    • (doi:10.1080/00268979300100141)
    • Wales, D. J. 1993 Coexistence in small inert gas clusters. Mol. Phys. 78, 151-171. (doi:10.1080/00268979300100141)
    • (1993) Mol. Phys. , vol.78 , pp. 151-171
    • Wales, D.J.1
  • 27
    • 0002971332 scopus 로고    scopus 로고
    • Energy landscapes: From clusters to biomolecules
    • (doi:10.1002/ 9780470141748.ch1)
    • Wales, D. J., Doye, J. P. K., Miller, M. A., Mortenson, P. N. & Walsh, T. R. 2000 Energy landscapes: from clusters to biomolecules. Adv. Chem. Phys. 115, 1-111. (doi:10.1002/ 9780470141748.ch1)
    • (2000) Adv. Chem. Phys. , vol.115 , pp. 1-111
    • Wales, D.J.1    Doye, J.P.K.2    Miller, M.A.3    Mortenson, P.N.4    Walsh, T.R.5
  • 28
    • 56649088054 scopus 로고    scopus 로고
    • Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide
    • (doi:10.1016/ j.cplett.2008. 10.085)
    • Strodel, B. & Wales, D. J. 2008 Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide. Chem. Phys. Lett. 466, 105-115. (doi:10.1016/ j.cplett.2008.10.085)
    • (2008) Chem. Phys. Lett. , vol.466 , pp. 105-115
    • Strodel, B.1    Wales, D.J.2
  • 30
    • 0009990848 scopus 로고
    • Basins of attraction for stationary-points on a potential-energy surface
    • (doi:10.1039/ft9928800653)
    • Wales, D. J. 1992 Basins of attraction for stationary-points on a potential-energy surface. J. Chem. Soc. Faraday Trans. 88, 653-657. (doi:10.1039/ft9928800653)
    • (1992) J. Chem. Soc. Faraday Trans. , vol.88 , pp. 653-657
    • Wales, D.J.1
  • 31
    • 33947168305 scopus 로고    scopus 로고
    • Low-temperature structural transitions: Circumventing the broken-ergodicity problem
    • (doi:10.1103/PhysRevLett.98.105701)
    • Sharapov, V. A., Meluzzi, D. & Mandelshtam, V. A. 2007 Low-temperature structural transitions: circumventing the broken-ergodicity problem. Phys. Rev. Lett. 98, 105701. (doi:10.1103/PhysRevLett.98.105701)
    • (2007) Phys. Rev. Lett. , vol.98 , pp. 105701
    • Sharapov, V.A.1    Meluzzi, D.2    Mandelshtam, V.A.3
  • 32
    • 37049129198 scopus 로고
    • Symmetries of activated complexes
    • (doi:10.1039/tf9686400371)
    • Murrell, J. N. & Laidler, K. J. 1968 Symmetries of activated complexes. Trans. Faraday Soc. 64, 371-377. (doi:10.1039/tf9686400371)
    • (1968) Trans. Faraday Soc. , vol.64 , pp. 371-377
    • Murrell, J.N.1    Laidler, K.J.2
  • 33
    • 0000773869 scopus 로고
    • Über die Geschwindigkeitskonstante von Austauschreaktionen.
    • Pelzer, H. & Wigner, E. 1932 Über die Geschwindigkeitskonstante von Austauschreaktionen. Z. Phys. Chem. B15, 445-463.
    • (1932) Z. Phys. Chem. , vol.B15 , pp. 445-463
    • Pelzer, H.1    Wigner, E.2
  • 34
    • 36849129335 scopus 로고
    • The absolute rate of reactions in condensed phases
    • (doi:10.1063/1.1749713)
    • Wynne-Jones, W. F. K. & Eyring, H. 1935 The absolute rate of reactions in condensed phases. J. Chem. Phys. 3, 492-502. (doi:10.1063/1. 1749713)
    • (1935) J. Chem. Phys. , vol.3 , pp. 492-502
    • Wynne-Jones, W.F.K.1    Eyring, H.2
  • 35
    • 1342296307 scopus 로고
    • The activated complex and the absolute rate of chemical reactions
    • (doi:10.1021/cr60056a006)
    • Eyring, H. 1935 The activated complex and the absolute rate of chemical reactions. Chem. Rev. 17, 65-77. (doi:10.1021/cr60056a006)
    • (1935) Chem. Rev. , vol.17 , pp. 65-77
    • Eyring, H.1
  • 36
    • 37049147605 scopus 로고
    • Some applications of the transition state method to the calculation of reaction velocities, especially in solution
    • (doi:10.1039/tf9353100875)
    • Evans, M. G. & Polanyi, M. 1935 Some applications of the transition state method to the calculation of reaction velocities, especially in solution. Trans. Faraday Soc. 31, 875-894. (doi:10.1039/tf9353100875)
    • (1935) Trans. Faraday Soc. , vol.31 , pp. 875-894
    • Evans, M.G.1    Polanyi, M.2
  • 37
    • 84966262179 scopus 로고
    • Updating quasi-Newton matrices with limited storage
    • (doi:10.1090/S0025-5718-1980-0572855-7)
    • Nocedal, J. 1980 Updating quasi-Newton matrices with limited storage. Math. Comput. 35, 773-782. (doi:10.1090/S0025-5718-1980-0572855-7)
    • (1980) Math. Comput. , vol.35 , pp. 773-782
    • Nocedal, J.1
  • 38
    • 33646887390 scopus 로고
    • On the limited memory BFGS method for large scale optimization
    • Liu, D. & Nocedal, J. 1989 On the limited memory BFGS method for large scale optimization. Math. Prog. 45, 503-528. (doi:10.1007/BF01589116) (Pubitemid 20660315)
    • (1989) Mathematical Programming, Series B , vol.45 , Issue.3 , pp. 503-528
    • Liu Dong, C.1    Nocedal Jorge2
  • 39
    • 0000327364 scopus 로고    scopus 로고
    • A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives
    • Henkelman, G. & Jónsson, H. 1999 A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives. J. Chem. Phys. 111, 7010-7022. (doi:10.1063/1.480097) (Pubitemid 129579526)
    • (1999) Journal of Chemical Physics , vol.111 , Issue.15 , pp. 7010-7022
    • Henkelman, G.1    Jonsson, H.2
  • 40
    • 0034513054 scopus 로고    scopus 로고
    • Climbing image nudged elastic band method for finding saddle points and minimum energy paths
    • DOI 10.1063/1.1329672
    • Henkelman, G., Uberuaga, B. P. & Jónsson, H. 2000 A climbing image nudged elastic band method for finding saddle points and minimum energy paths. J. Chem. Phys. 113, 9901-9904. (doi:10.1063/1.1329672) (Pubitemid 32076883)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.22 , pp. 9901-9904
    • Henkelman, G.1    Uberuaga, B.P.2    Jonsson, H.3
  • 41
    • 1242329035 scopus 로고    scopus 로고
    • Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
    • DOI 10.1063/1.1323224
    • Henkelman, G. & Jónsson, H. 2000 Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points. J. Chem. Phys. 113, 9978-9985. (doi:10.1063/1.1323224) (Pubitemid 32076892)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.22 , pp. 9978-9985
    • Henkelman, G.1    Jonsson, H.2
  • 42
    • 0035584869 scopus 로고    scopus 로고
    • Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table
    • DOI 10.1063/1.1415500
    • Henkelman, G. & Jónsson, H. 2001 Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table. J. Chem. Phys. 115, 9657-9666. (doi:10.1063/1.1415500) (Pubitemid 33147327)
    • (2001) Journal of Chemical Physics , vol.115 , Issue.21 , pp. 9657-9666
    • Henkelman, G.1    Jonsson, H.2
  • 43
    • 0001476184 scopus 로고    scopus 로고
    • Defect migration in crystalline silicon
    • (doi:10.1103/PhysRevB.59.3969)
    • Munro, L. J. & Wales, D. J. 1999 Defect migration in crystalline silicon. Phys. Rev. B 59, 3969-3980. (doi:10.1103/PhysRevB.59.3969)
    • (1999) Phys. Rev. B , vol.59 , pp. 3969-3980
    • Munro, L.J.1    Wales, D.J.2
  • 44
    • 0001361692 scopus 로고    scopus 로고
    • 10 and defect migration in crystalline silicon
    • DOI 10.1016/S0009-2614(01)00334-7, PII S0009261401003347
    • Kumeda, Y., Munro, L. J. & Wales, D. J. 2001 Transition states and rearrangement mechanisms from hybrid eigenvector-following and density functional theory: application to C10H10 and defect migration in crystalline silicon. Chem. Phys. Lett. 341, 185-194. (doi:10.1016/S0009-2614(01)00334-7) (Pubitemid 33630794)
    • (2001) Chemical Physics Letters , vol.341 , Issue.1-2 , pp. 185-194
    • Kumeda, Y.1    Wales, D.J.2    Munro, L.J.3
  • 45
    • 1442282189 scopus 로고    scopus 로고
    • A doubly nudged elastic band method for finding transition states
    • (doi:10.1063/1.1636455)
    • Trygubenko, S. A. & Wales, D. J. 2004 A doubly nudged elastic band method for finding transition states. J. Chem. Phys. 120, 2082-2094. (doi:10.1063/1.1636455)
    • (2004) J. Chem. Phys. , vol.120 , pp. 2082-2094
    • Trygubenko, S.A.1    Wales, D.J.2
  • 46
    • 21644454399 scopus 로고    scopus 로고
    • Finding pathways between distant local minima
    • (doi:10.1063/1.1931587)
    • Carr, J. M., Trygubenko, S. A. & Wales, D. J. 2005 Finding pathways between distant local minima. J. Chem. Phys. 122, 234903. (doi:10.1063/1. 1931587)
    • (2005) J. Chem. Phys. , vol.122 , pp. 234903
    • Carr, J.M.1    Trygubenko, S.A.2    Wales, D.J.3
  • 48
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multipleminima problem in protein folding
    • (doi:10.1073/ pnas.84.19.6611)
    • Li, Z. & Scheraga, H. A. 1987 Monte Carlo-minimization approach to the multipleminima problem in protein folding. Proc. Natl Acad. Sci. USA 84, 6611-6615. (doi:10.1073/ pnas.84.19.6611)
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 49
    • 0000560869 scopus 로고    scopus 로고
    • Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms
    • Wales, D. J. & Doye, J. P. K. 1997 Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J. Phys. Chem. A 101, 5111-5116. (doi:10.1021/jp970984n) (Pubitemid 127578169)
    • (1997) Journal of Physical Chemistry A , vol.101 , Issue.28 , pp. 5111-5116
    • Wales, D.J.1    Doye, J.P.K.2
  • 50
    • 0033610078 scopus 로고    scopus 로고
    • Global optimization of clusters, crystals, and biomolecules
    • DOI 10.1126/science.285.5432.1368
    • Wales, D. J. & Scheraga, H. A. 1999 Global optimization of clusters, crystals and biomolecules. Science 285, 1368-1372. (doi:10.1126/science.285. 5432.1368) (Pubitemid 29411661)
    • (1999) Science , vol.285 , Issue.5432 , pp. 1368-1372
    • Wales, D.J.1    Scheraga, H.A.2
  • 53
    • 0037145606 scopus 로고    scopus 로고
    • Discrete path sampling
    • DOI 10.1080/00268970210162691
    • Wales, D. J. 2002 Discrete path sampling. Mol. Phys. 100, 3285-3305. (doi:10.1080/0026 8970210162691) (Pubitemid 35446132)
    • (2002) Molecular Physics , vol.100 , Issue.20 , pp. 3285-3305
    • Wales, D.J.1
  • 54
    • 4444353833 scopus 로고    scopus 로고
    • Some further applications of discrete path sampling to cluster isomerization
    • (doi:10.1080/00268970410001703363)
    • Wales, D. J. 2004 Some further applications of discrete path sampling to cluster isomerization. Mol. Phys. 102, 891-908. (doi:10.1080/ 00268970410001703363)
    • (2004) Mol. Phys. , vol.102 , pp. 891-908
    • Wales, D.J.1
  • 55
    • 33745044234 scopus 로고    scopus 로고
    • Energy landscapes: Calculating pathways and rates
    • (doi:10.1080/01442350600676921)
    • Wales, D. J. 2006 Energy landscapes: calculating pathways and rates. Int. Rev. Phys. Chem. 25, 237-282. (doi:10.1080/01442350600676921)
    • (2006) Int. Rev. Phys. Chem. , vol.25 , pp. 237-282
    • Wales, D.J.1
  • 56
    • 66749117149 scopus 로고    scopus 로고
    • Calculating rate constants and committor probabilities for transition networks by graph transformation
    • (doi:10.1063/1.3133782)
    • Wales, D. J. 2009 Calculating rate constants and committor probabilities for transition networks by graph transformation. J. Chem. Phys. 130, 204111. (doi:10.1063/1.3133782)
    • (2009) J. Chem. Phys. , vol.130 , pp. 204111
    • Wales, D.J.1
  • 57
    • 67650886042 scopus 로고    scopus 로고
    • Exploring the free energy landscape: From dynamics to networks and back
    • (doi:10.1371/journal.pcbi.1000415)
    • Prada-Gracia, D., Gómez-Gardenes, J., Echenique, P. & Fernando, F. 2009 Exploring the free energy landscape: from dynamics to networks and back. PLoS Comput. Biol. 5, e1000415. (doi:10.1371/journal.pcbi.1000415)
    • (2009) PLoS Comput. Biol. , vol.5
    • Prada-Gracia, D.1    Gómez-Gardenes, J.2    Echenique, P.3    Fernando, F.4
  • 59
    • 33751283977 scopus 로고    scopus 로고
    • Potential energy and free energy landscapes
    • DOI 10.1021/jp0680544
    • Wales, D. J. & Bogdan, T. V. 2006 Potential energy and free energy landscapes. J. Phys. Chem. B 110, 20 765-20 776. (doi:10.1021/jp0680544) (Pubitemid 44797331)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.42 , pp. 20765-20776
    • Wales, D.J.1    Bogdan, T.V.2
  • 60
    • 0000290506 scopus 로고
    • A dense non-crystallographic packing of equal spheres
    • (doi:10.1107/S0365110X6200239X)
    • Mackay, A. L. 1962 A dense non-crystallographic packing of equal spheres. Acta Crystallogr. 15, 916-918. (doi:10.1107/S0365110X6200239X)
    • (1962) Acta Crystallogr. , vol.15 , pp. 916-918
    • MacKay, A.L.1
  • 61
    • 0000672765 scopus 로고    scopus 로고
    • Evolution of the potential energy surface with size for Lennard-Jones clusters
    • Doye, J. P. K., Miller, M. A. & Wales, D. J. 1999 Evolution of the potential energy surface with size for Lennard-Jones clusters. J. Chem. Phys. 111, 8417-8428. (doi:10.1063/1.480217) (Pubitemid 129591020)
    • (1999) Journal of Chemical Physics , vol.111 , Issue.18 , pp. 8417-8428
    • Doye, J.P.K.1    Miller, M.A.2    Wales, D.J.3
  • 62
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • DOI 10.1016/0263-7855(96)00018-5
    • Humphrey, W., Dalke, A. & Schulten, K. 1996 VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38. (doi:10.1016/0263-7855(96)00018-5) (Pubitemid 26152973)
    • (1996) Journal of Molecular Graphics , vol.14 , Issue.1 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 63
    • 0001633897 scopus 로고
    • On the calculation of certain crystal potential constants, and on the cubic crystal of least potential energy
    • (doi:10.1098/rspa.1925.0047)
    • Jones, J. E. & Ingham, A. E. 1925 On the calculation of certain crystal potential constants, and on the cubic crystal of least potential energy. Proc. R. Soc. Lond. A 107, 636-653. (doi:10.1098/rspa.1925.0047)
    • (1925) Proc. R. Soc. Lond. A , vol.107 , pp. 636-653
    • Jones, J.E.1    Ingham, A.E.2
  • 65
    • 0023449962 scopus 로고
    • Spin glasses and the statistical mechanics of protein folding
    • (doi:10.1073/pnas.84.21.7524)
    • Bryngelson, J. D. & Wolynes, P. G. 1987 Spin glasses and the statistical mechanics of protein folding. Proc. Natl Acad. Sci. USA 84, 7524-7528. (doi:10.1073/pnas.84.21.7524)
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 66
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • (doi:10.1002/prot.340210302)
    • Bryngelson, J. D., Onuchic, J. N., Socci, N. D. & Wolynes, P. G. 1995 Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins Struct. Funct. Gen. 21, 167-195. (doi:10.1002/prot.340210302)
    • (1995) Proteins Struct. Funct. Gen. , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 67
    • 0028963362 scopus 로고
    • Toward an outline of the topography of a realistic protein-folding funnel
    • (doi:10.1073/pnas.92.8.3626)
    • Onuchic, J. N., Wolynes, P. G., Luthey-Schulten, Z. & Socci, N. D. 1995 Toward an outline of the topography of a realistic protein-folding funnel. Proc. Natl Acad. Sci. USA 92, 3626-3630. (doi:10.1073/pnas.92.8.3626)
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 3626-3630
    • Onuchic, J.N.1    Wolynes, P.G.2    Luthey-Schulten, Z.3    Socci, N.D.4
  • 68
    • 0028949547 scopus 로고
    • Theoretical studies of protein folding and unfolding
    • (doi:10.1016/0959-440X(95)80010-X)
    • Karplus, M. & Šali, A. 1995 Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5, 58-73. (doi:10.1016/0959- 440X(95)80010-X)
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 58-73
    • Karplus, M.1    Šali, A.2
  • 69
    • 0034581317 scopus 로고    scopus 로고
    • The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
    • DOI 10.1016/S0065-3233(00)53003-4
    • Onuchic, J. N., Nymeyer, H., García, A. E., Chahine, J. & Socci, N. D. 2000 The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Adv. Proteins Chem. 53, 87-152. (doi:10.1016/S0065-3233(00)53003-4) (Pubitemid 34194293)
    • (2000) Advances in Protein Chemistry , vol.53 , pp. 87-152
    • Onuchic, J.N.1    Nymeyer, H.2    Garcia, A.E.3    Chahine, J.4    Socci, N.D.5
  • 70
    • 0026723063 scopus 로고
    • Protein folding funnels: A kinetic approach to the sequence-structure relationship
    • (doi:10.1073/pnas.89.18.8721)
    • Leopold, P. E., Montal, M. & Onuchic, J. N. 1992 Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc. Natl Acad. Sci. USA 89, 8721-8725. (doi:10.1073/pnas.89.18.8721)
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 8721-8725
    • Leopold, P.E.1    Montal, M.2    Onuchic, J.N.3
  • 71
    • 0030628825 scopus 로고    scopus 로고
    • Theory of protein folding: The energy landscape perspective
    • Onuchic, J. N., Luthey-Schulten, Z. & Wolynes, P. G. 1997 Theory of protein folding: the energy landscape perspective. Annu. Rev. Phys. Chem. 48, 545-600. (doi:10.1146/annurev.physchem.48.1.545) (Pubitemid 127443918)
    • (1997) Annual Review of Physical Chemistry , vol.48 , Issue.1 , pp. 545-600
    • Onuchic, J.N.1    Luthey-Schulten, Z.2    Wolynes, P.G.3
  • 72
    • 0000984574 scopus 로고
    • Magic numbers and growth sequences of small face-centred-cubic and decahedral clusters
    • (doi:10.1016/ S0009-2614(95) 01223-0)
    • Doye, J. P. K. & Wales, D. J. 1995 Magic numbers and growth sequences of small face-centred-cubic and decahedral clusters. Chem. Phys. Lett. 247, 339-347. (doi:10.1016/ S0009-2614(95)01223-0)
    • (1995) Chem. Phys. Lett. , vol.247 , pp. 339-347
    • Doye, J.P.K.1    Wales, D.J.2
  • 73
    • 0000494238 scopus 로고
    • Molecular dynamics study of melting and freezing of small Lennard-Jones clusters
    • (doi:10.1021/j100303a014)
    • Honeycutt, J. D. & Andersen, H. C. 1987 Molecular dynamics study of melting and freezing of small Lennard-Jones clusters. J. Phys. Chem. 91, 4950-4963. (doi:10.1021/j100303a014)
    • (1987) J. Phys. Chem. , vol.91 , pp. 4950-4963
    • Honeycutt, J.D.1    Andersen, H.C.2
  • 74
    • 0006840487 scopus 로고
    • Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters
    • (doi:10.1007/BF01426907)
    • Northby, J. A., Xie, J., Freeman, D. L. & Doll, J. D. 1989 Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters. Z. Phys. D 12, 69-71. (doi:10.1007/BF01426907)
    • (1989) Z. Phys. D , vol.12 , pp. 69-71
    • Northby, J.A.1    Xie, J.2    Freeman, D.L.3    Doll, J.D.4
  • 75
    • 0000483044 scopus 로고
    • Theoretical studies of the energetics and structures of atomic clusters
    • (doi:10.1063/1.457447)
    • Xie, J., Northby, J. A., Freeman, D. L. & Doll, J. D. 1989 Theoretical studies of the energetics and structures of atomic clusters. J. Chem. Phys. 91, 612-619. (doi:10.1063/1.457447)
    • (1989) J. Chem. Phys. , vol.91 , pp. 612-619
    • Xie, J.1    Northby, J.A.2    Freeman, D.L.3    Doll, J.D.4
  • 76
    • 0000542127 scopus 로고
    • Stability of face centered cubic and icosahedral Lennard-Jones clusters
    • (doi:10.1063/1.455848)
    • van de Waal, B. W. 1989 Stability of face centered cubic and icosahedral Lennard-Jones clusters. J. Chem. Phys. 90, 3407-3408. (doi:10.1063/1.455848)
    • (1989) J. Chem. Phys. , vol.90 , pp. 3407-3408
    • Van De Waal, B.W.1
  • 78
    • 0008676361 scopus 로고
    • Stability of relaxed Lennard-Jones models made of 500 to 6000 atoms
    • (doi:10.1007/BF01426911)
    • Raoult, B., Farges, J., de Feraudy, M. F. & Torchet, G. 1989 Stability of relaxed Lennard-Jones models made of 500 to 6000 atoms. Z. Phys. D 12, 85-87. (doi:10.1007/BF01426911)
    • (1989) Z. Phys. D , vol.12 , pp. 85-87
    • Raoult, B.1    Farges, J.2    De Feraudy, M.F.3    Torchet, G.4
  • 79
    • 0012503497 scopus 로고
    • Structure and magic numbers of large Lennard-Jones quasicrystals and crystals
    • (doi:10.1016/0375-9601(92)90762-B)
    • Hasse, R. W. 1991 Structure and magic numbers of large Lennard-Jones quasicrystals and crystals. Phys. Lett. A 161, 130-134. (doi:10.1016/0375- 9601(92)90762-B)
    • (1991) Phys. Lett. A , vol.161 , pp. 130-134
    • Hasse, R.W.1
  • 80
    • 29444443292 scopus 로고
    • The energetics and structure of nickel clusters: Size dependence
    • (doi:10.1063/1.460169)
    • Cleveland, C. L. & Landman, U. 1991 The energetics and structure of nickel clusters: size dependence. J. Chem. Phys. 94, 7376-7396. (doi:10.1063/1.460169)
    • (1991) J. Chem. Phys. , vol.94 , pp. 7376-7396
    • Cleveland, C.L.1    Landman, U.2
  • 81
    • 0001161222 scopus 로고
    • Icosahedral, decahedral, fcc, and defect-fcc structural models for Arn clusters, n >500: How plausible are they?
    • (doi:10.1063/1.464946)
    • van de Waal, B. W. 1993 Icosahedral, decahedral, fcc, and defect-fcc structural models for Arn clusters, n >500: how plausible are they? J. Chem. Phys. 98, 4909-4919. (doi:10.1063/ 1.464946)
    • (1993) J. Chem. Phys. , vol.98 , pp. 4909-4919
    • Van De Waal, B.W.1
  • 82
    • 0001739738 scopus 로고    scopus 로고
    • No evidence for size-dependent icosahedral → fee structural transition in rare-gas clusters
    • van de Waal, B. W. 1996 No evidence for size-dependent icosahedral → fcc structural transition in rare-gas clusters. Phys. Rev. Lett. 76, 1083-1086. (doi:10.1103/PhysRevLett.76.1083) (Pubitemid 126617624)
    • (1996) Physical Review Letters , vol.76 , Issue.7 , pp. 1083-1086
    • Van De Waal, B.W.1
  • 84
    • 0036492418 scopus 로고    scopus 로고
    • Crossover among structural motifs in transition and noble-metal clusters
    • DOI 10.1063/1.1448484
    • Baletto, F., Ferrando, R., Montalenti, F. & Mottet, C. 2002 Crossover among structural motifs in transition and noble-metal clusters. J. Chem. Phys. 116, 3856-3863. (doi:10.1063/1.1448484) (Pubitemid 34923823)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.9 , pp. 3856-3863
    • Baletto, F.1    Ferrando, R.2    Fortunelli, A.3    Montalenti, F.4    Mottet, C.5
  • 85
    • 0037088376 scopus 로고    scopus 로고
    • Entropic effects on the structure of Lennard-Jones clusters
    • DOI 10.1063/1.1469616
    • Doye, J. P. K. & Calvo, F. 2002 Entropic effects on the structure of Lennard-Jones clusters. J. Chem. Phys. 116, 8307-8317. (doi:10.1063/1.1469616) (Pubitemid 34599828)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.19 , pp. 8307-8317
    • Doye, J.P.K.1    Calvo, F.2
  • 86
    • 0000595770 scopus 로고
    • Free energy barriers to melting in atomic clusters
    • (doi:10.1063/1.467771)
    • Lynden-Bell, R. M. & Wales, D. J. 1994 Free energy barriers to melting in atomic clusters. J. Chem. Phys. 101, 1460-1476. (doi:10.1063/1. 467771)
    • (1994) J. Chem. Phys. , vol.101 , pp. 1460-1476
    • Lynden-Bell, R.M.1    Wales, D.J.2
  • 87
    • 78049317315 scopus 로고    scopus 로고
    • Generalized simulated tempering for exploring strong phase transitions
    • (doi:10.1063/1.3503503)
    • Kim, J. & Straub, J. E. 2010 Generalized simulated tempering for exploring strong phase transitions. J. Chem. Phys. 133, 154101. (doi:10.1063/1.3503503)
    • (2010) J. Chem. Phys. , vol.133 , pp. 154101
    • Kim, J.1    Straub, J.E.2
  • 88
    • 34547649536 scopus 로고    scopus 로고
    • Structural transitions in the 309-atom magic number Lennard-Jones cluster
    • (doi:10.1063/1.2173260)
    • Noya, E. G. & Doye, J. P. K. 2006 Structural transitions in the 309-atom magic number Lennard-Jones cluster. J. Chem. Phys. 124, 104503. (doi:10.1063/1.2173260)
    • (2006) J. Chem. Phys. , vol.124 , pp. 104503
    • Noya, E.G.1    Doye, J.P.K.2
  • 89
    • 65349189938 scopus 로고    scopus 로고
    • Refined kinetic transition networks for the GB1 hairpin peptide
    • (doi:10.1039/b820649j)
    • Carr, J. M. & Wales, D. J. 2009 Refined kinetic transition networks for the GB1 hairpin peptide. Phys. Chem. Chem. Phys. 11, 3341-3354. (doi:10.1039/b820649j)
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 3341-3354
    • Carr, J.M.1    Wales, D.J.2
  • 90
    • 0028500779 scopus 로고
    • A short linear peptide that folds into a native stable b-hairpin in aqueous solution
    • (doi:10.1038/nsb0994-584)
    • Blanco, F. J., Rivas, G. & Serrano, L. 1994 A short linear peptide that folds into a native stable b-hairpin in aqueous solution. Nat. Struct. Biol. 1, 584-590. (doi:10.1038/nsb0994-584)
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 584-590
    • Blanco, F.J.1    Rivas, G.2    Serrano, L.3
  • 91
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of -hairpin formation
    • DOI 10.1038/36626
    • Muñoz, V., Thompson, P. A., Hofrichter, J. & Eaton, W. A. 1997 Folding dynamics and mechanism of b-hairpin formation. Nature 390, 196-199. (doi:10.1038/36626) (Pubitemid 27507992)
    • (1997) Nature , vol.390 , Issue.6656 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 92
    • 27344454693 scopus 로고    scopus 로고
    • Hairpin folding rates reflect mutations within and remote from the turn region
    • (doi:10.1073/pnas.0504392102)
    • Olsen, K. A., Fesinmeyer, R. M., Stewart, J. M. & Andersen, N. H. 2005 Hairpin folding rates reflect mutations within and remote from the turn region. Proc. Natl Acad. Sci. USA 102, 15 483-15 489. (doi:10.1073/pnas. 0504392102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15483-15489
    • Olsen, K.A.1    Fesinmeyer, R.M.2    Stewart, J.M.3    Andersen, N.H.4
  • 93
    • 67749147584 scopus 로고    scopus 로고
    • Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories
    • (doi:10.1073/pnas.0901178106)
    • Chung, H. S., Louis, J. M. & Eaton, W. A. 2009 Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories. Proc. Natl Acad. Sci. USA 106, 11 837-11 844. (doi:10.1073/pnas.0901178106)
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 11837-11844
    • Chung, H.S.1    Louis, J.M.2    Eaton, W.A.3
  • 94
    • 0025769350 scopus 로고
    • A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G
    • Gronenborn, A. M., Filpula, D. R., Essig, N. Z., Achari, A., Whitlow, M., Wingfield, P. T. & Clore, G. M. 1991 A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253, 657-661. (doi:10.1126/science.1871600) (Pubitemid 21917198)
    • (1991) Science , vol.253 , Issue.5020 , pp. 657-661
    • Gronenborn, A.M.1    Filpula, D.R.2    Essig, N.Z.3    Achari, A.4    Whitlow, M.5    Wingfield, P.T.6    Clore, G.M.7
  • 95
    • 0034646218 scopus 로고    scopus 로고
    • Mechanisms and kinetics of b-hairpin formation
    • (doi:10.1073/pnas.97.6.2544)
    • Klimov, D. K. & Thirumalai, D. 2000 Mechanisms and kinetics of b-hairpin formation. Proc. Natl Acad. Sci. USA 97, 2544-2549. (doi:10.1073/pnas.97.6.2544)
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 2544-2549
    • Klimov, D.K.1    Thirumalai, D.2
  • 96
    • 0035850758 scopus 로고    scopus 로고
    • Beta-Hairpin folding simulations in atomistic detail using an implicit solvent model
    • DOI 10.1006/jmbi.2001.5033
    • Zagrovic, B., Sorin, E. J. & Pande, V. 2001 Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313, 151-169. (doi:10.1006/jmbi.2001.5033) (Pubitemid 33001172)
    • (2001) Journal of Molecular Biology , vol.313 , Issue.1 , pp. 151-169
    • Zagrovic, B.1    Sorin, E.J.2    Pande, V.3
  • 97
    • 0142027789 scopus 로고    scopus 로고
    • Transition-path sampling of b-hairpin folding
    • (doi:10.1073/pnas.1534924100)
    • Bolhuis, P. G. 2003 Transition-path sampling of b-hairpin folding. Proc. Natl Acad. Sci. USA 100, 12 129-12 134. (doi:10.1073/pnas.1534924100)
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12129-12134
    • Bolhuis, P.G.1
  • 98
    • 3242681886 scopus 로고    scopus 로고
    • Folding of the GB1 hairpin peptide from discrete path sampling
    • (doi:10.1063/1.1759317)
    • Evans, D. A. & Wales, D. J. 2004 Folding of the GB1 hairpin peptide from discrete path sampling. J. Chem. Phys. 121, 1080-1090. (doi:10.1063/1. 1759317)
    • (2004) J. Chem. Phys. , vol.121 , pp. 1080-1090
    • Evans, D.A.1    Wales, D.J.2
  • 99
    • 11244289252 scopus 로고    scopus 로고
    • Kinetic pathways of b-hairpin (un)folding in explicit solvent
    • DOI 10.1529/biophysj.104.048744
    • Bolhuis, P. G. 2005 Kinetic pathways of b-hairpin (un)folding in explicit solvent. Biophys. J. 88, 50-61. (doi:10.1529/biophysj.104.048744) (Pubitemid 40070657)
    • (2005) Biophysical Journal , vol.88 , Issue.1 , pp. 50-61
    • Bolhuis, P.G.1
  • 100
    • 34548273698 scopus 로고    scopus 로고
    • Folding time predictions from allatom replica exchange simulations
    • DOI 10.1016/j.jmb.2007.07.010, PII S0022283607009242
    • Yang, S., Onuchic, J. N., García, A. E. & Levine, H. 2007 Folding time predictions from allatom replica exchange simulations. J. Mol. Biol. 372, 756-763. (doi:10.1016/j.jmb.2007.07.010) (Pubitemid 47321796)
    • (2007) Journal of Molecular Biology , vol.372 , Issue.3 , pp. 756-763
    • Yang, S.1    Onuchic, J.N.2    Garcia, A.E.3    Levine, H.4
  • 101
    • 0001591728 scopus 로고    scopus 로고
    • Relaxation dynamics of C60
    • (doi:10.1063/1.477319)
    • Walsh, T. R. & Wales, D. J. 1998 Relaxation dynamics of C60. J. Chem. Phys. 109, 6691-6700. (doi:10.1063/1.477319)
    • (1998) J. Chem. Phys. , vol.109 , pp. 6691-6700
    • Walsh, T.R.1    Wales, D.J.2
  • 102
    • 0038413961 scopus 로고    scopus 로고
    • Scratching the surface of buckminsterfullerene: The barriers for Stone-Wales transformation through symmetric and asymmetric transition states
    • DOI 10.1021/ja0288744
    • Bettinger, H. F., Yakobsen, B. I. & Scuseria, G. E. 2003 Scratching the surface of buckminsterfullerene: the barriers for Stone-Wales transformation through symmetric and asymmetric transition states. J. Am. Chem. Soc. 125, 5572-5580. (doi:10.1021/ja0288744) (Pubitemid 36582765)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.18 , pp. 5572-5580
    • Bettinger, H.F.1    Yakobson, B.I.2    Scuseria, G.E.3
  • 103
    • 0038521428 scopus 로고    scopus 로고
    • 60 fullerenes
    • DOI 10.1016/S0009-2614(03)00668-7, PII S0009261403006687
    • Kumeda, Y. & Wales, D. J. 2003 Ab initio study of rearrangements between C60 fullerenes. Chem. Phys. Lett. 374, 125-131. (doi:10.1016/S0009- 2614(03)00668-7) (Pubitemid 36613943)
    • (2003) Chemical Physics Letters , vol.374 , Issue.1-2 , pp. 125-131
    • Kumeda, Y.1    Wales, D.J.2
  • 105
    • 0025187901 scopus 로고
    • Solid C60: A new form of carbon
    • (doi:10.1038/347354a0)
    • Krätschmer, W., Lamb, L. D., Fostiropoulos, K. & Huffman, D. R. 1990 Solid C60: a new form of carbon. Nature 347, 354-358. (doi:10.1038/ 347354a0)
    • (1990) Nature , vol.347 , pp. 354-358
    • Krätschmer, W.1    Lamb, L.D.2    Fostiropoulos, K.3    Huffman, D.R.4
  • 106
    • 62349137229 scopus 로고    scopus 로고
    • Simulations of rigid bodies in an angle-axis framework
    • (doi:10.1073/pnas.0906676106)
    • Chakrabarti, D. & Wales, D. 2009 Simulations of rigid bodies in an angle-axis framework. Phys. Chem. Chem. Phys. 11, 1970-1976. (doi:10.1073/pnas.0906676106)
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 1970-1976
    • Chakrabarti, D.1    Wales, D.2
  • 107
    • 73949088302 scopus 로고    scopus 로고
    • Rational design of helical architectures
    • (doi:10.1073/pnas.0906676106)
    • Chakrabarti, D., Fejer, S. N. & Wales, D. J. 2009 Rational design of helical architectures. Proc. Natl Acad. Sci. USA 106, 20 164-20 167. (doi:10.1073/pnas.0906676106)
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 20164-20167
    • Chakrabarti, D.1    Fejer, S.N.2    Wales, D.J.3
  • 108
    • 33846216327 scopus 로고    scopus 로고
    • The directional contact distance of two ellipsoids: Coarsegrained potentials for anisotropic interactions
    • (doi:10.1063/1.2102897)
    • Paramonov, L. & Yaliraki, S. N. 2005 The directional contact distance of two ellipsoids: coarsegrained potentials for anisotropic interactions. J. Chem. Phys. 123, 194111. (doi:10.1063/ 1.2102897)
    • (2005) J. Chem. Phys. , vol.123 , pp. 194111
    • Paramonov, L.1    Yaliraki, S.N.2
  • 109
  • 110
    • 3543052006 scopus 로고    scopus 로고
    • Thermodynamics of global optimization
    • Doye, J. P. K. & Wales, D. J. 1998 Thermodynamics of global optimization. Phys. Rev. Lett. 80, 1357-1360. (doi:10.1103/PhysRevLett.80.1357) (Pubitemid 128622893)
    • (1998) Physical Review Letters , vol.80 , Issue.7 , pp. 1357-1360
    • Doye, J.P.K.1    Wales, D.J.2
  • 111
    • 0000162848 scopus 로고    scopus 로고
    • Structural relaxation in Morse clusters: Energy landscapes
    • DOI 10.1063/1.478067, PII S0021960699030019
    • Miller, M. A., Doye, J. P. K. & Wales, D. J. 1999 Structural relaxation in Morse clusters: energy landscapes. J. Chem. Phys. 110, 328-334. (doi:10.1063/1.478067) (Pubitemid 129708056)
    • (1999) Journal of Chemical Physics , vol.110 , Issue.1 , pp. 328-334
    • Miller, M.A.1    Doye, J.P.K.2    Wales, D.J.3
  • 112
    • 0000672766 scopus 로고    scopus 로고
    • The double-funnel energy landscape of the 38-atom Lennard-Jones cluster
    • (doi:10.1063/1.478595)
    • Doye, J. P. K., Miller, M. A. & Wales, D. J. 1999 The double-funnel energy landscape of the 38-atom Lennard-Jones cluster. J. Chem. Phys. 110, 6896-6906. (doi:10.1063/1.478595)
    • (1999) J. Chem. Phys. , vol.110 , pp. 6896-6906
    • Doye, J.P.K.1    Miller, M.A.2    Wales, D.J.3
  • 113
    • 0033682989 scopus 로고    scopus 로고
    • Phase changes in 38 atom Lennard- Jones clusters. I. A parallel tempering study in the canonical ensemble
    • (doi:10.1063/1.481671)
    • Neirotti, J. P., Calvo, F., Freeman, D. L. & Doll, J. D. 2000 Phase changes in 38 atom Lennard- Jones clusters. I. A parallel tempering study in the canonical ensemble. J. Chem. Phys. 112, 10 340-10 349. (doi:10.1063/1.481671)
    • (2000) J. Chem. Phys. , vol.112 , pp. 10340-10349
    • Neirotti, J.P.1    Calvo, F.2    Freeman, D.L.3    Doll, J.D.4
  • 114
    • 0033701180 scopus 로고    scopus 로고
    • Phase changes in 38 atom Lennard-Jones clusters. II. A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical ensembles
    • (doi:10.1063/1.481672)
    • Calvo, F., Neirotti, J. P., Freeman, D. L. & Doll, J. D. 2000 Phase changes in 38 atom Lennard-Jones clusters. II. A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical ensembles. J. Chem. Phys. 112, 10 350-10 357. (doi:10.1063/1.481672)
    • (2000) J. Chem. Phys. , vol.112 , pp. 10350-10357
    • Calvo, F.1    Neirotti, J.P.2    Freeman, D.L.3    Doll, J.D.4
  • 115
    • 0000624250 scopus 로고    scopus 로고
    • The dynamics of structural transitions in sodium chloride clusters
    • Doye, J. P. K. & Wales, D. J. 1999 The dynamics of structural transitions in sodium chloride clusters. J. Chem. Phys. 111, 11 070-11 079. (doi:10.1063/1.480465) (Pubitemid 129585479)
    • (1999) Journal of Chemical Physics , vol.111 , Issue.24 , pp. 11070-11079
    • Doye, J.P.K.1    Wales, D.J.2
  • 116
    • 36749117884 scopus 로고
    • Revised TIPS for simulations of liquid water and aqueous solutions
    • (doi:10.1063/1.444325)
    • Jorgensen, W. L. 1982 Revised TIPS for simulations of liquid water and aqueous solutions. J. Chem. Phys. 77, 4156-4163. (doi:10.1063/1.444325)
    • (1982) J. Chem. Phys. , vol.77 , pp. 4156-4163
    • Jorgensen, W.L.1
  • 117
    • 4243754961 scopus 로고
    • Computer simulation of local order in condensed phases of silicon
    • (doi:10.1103/PhysRevB.31.5262)
    • Stillinger, F. H. & Weber, T. A. 1985 Computer simulation of local order in condensed phases of silicon. Phys. Rev. B 31, 5262-5271. (doi:10.1103/PhysRevB.31.5262)
    • (1985) Phys. Rev. B , vol.31 , pp. 5262-5271
    • Stillinger, F.H.1    Weber, T.A.2
  • 118
    • 0034897831 scopus 로고    scopus 로고
    • Energy landscapes of model glass formers
    • (doi:10.1103/PhysRevB.64.024205)
    • Middleton, T. F. & Wales, D. J. 2001 Energy landscapes of model glass formers. Phys. Rev. B 64, 024205. (doi:10.1103/PhysRevB.64.024205)
    • (2001) Phys. Rev. B , vol.64 , pp. 024205
    • Middleton, T.F.1    Wales, D.J.2
  • 119
    • 26444451608 scopus 로고    scopus 로고
    • Diagnosing broken ergodicity using an energy fluctuation metric
    • (doi:10.1063/1.2035080)
    • de Souza, V. K. & Wales, D. J. 2005 Diagnosing broken ergodicity using an energy fluctuation metric. J. Chem. Phys. 123, 134504. (doi:10.1063/1.2035080)
    • (2005) J. Chem. Phys. , vol.123 , pp. 134504
    • De Souza, V.K.1    Wales, D.J.2
  • 120
    • 33646634660 scopus 로고
    • Local order and structural transitions in amorphous metal-metalloid alloys
    • (doi:10.1103/PhysRevB.31.1954)
    • Weber, T. A. & Stillinger, F. H. 1985 Local order and structural transitions in amorphous metal-metalloid alloys. Phys. Rev. B 31, 1954-1963. (doi:10.1103/PhysRevB.31.1954)
    • (1985) Phys. Rev. B , vol.31 , pp. 1954-1963
    • Weber, T.A.1    Stillinger, F.H.2
  • 121
    • 4243306133 scopus 로고
    • Scaling behavior in the b-relaxation regime of a supercooled Lennard-Jones mixture
    • Kob, W. & Andersen, H. C. 1994 Scaling behavior in the b-relaxation regime of a supercooled Lennard-Jones mixture. Phys. Rev. Lett. 73, 1376-1379. (doi:10.1103/PhysRevLett.73.1376) (Pubitemid 24975870)
    • (1994) Physical Review Letters , vol.73 , Issue.10 , pp. 1376-1379
    • Kob, W.1    Andersen, H.C.2
  • 122
    • 6144288607 scopus 로고
    • Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture: the van Hove correlation function.
    • (doi:10.1103/PhysRevE.51.4626)
    • Kob, W. & Andersen, H. C. 1995 Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture: the van Hove correlation function. Phys. Rev. E 51, 4626-4641. (doi:10.1103/PhysRevE.51.4626)
    • (1995) Phys. Rev. e , vol.51 , pp. 4626-4641
    • Kob, W.1    Andersen, H.C.2
  • 123
    • 6444235056 scopus 로고
    • Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. II. Intermediate scattering function and dynamic susceptibility
    • (doi:10.1103/PhysRevE.52.4134)
    • Kob, W. & Andersen, H. C. 1995 Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture. II. Intermediate scattering function and dynamic susceptibility. Phys. Rev. E 52, 4134-4153. (doi:10.1103/PhysRevE. 52.4134)
    • (1995) Phys. Rev. e , vol.52 , pp. 4134-4153
    • Kob, W.1    Andersen, H.C.2
  • 124
    • 0032508044 scopus 로고    scopus 로고
    • Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid
    • DOI 10.1038/31146
    • Sastry, S., Debenedetti, P. G. & Stillinger, F. H. 1998 Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid. Nature 393, 554-557. (doi:10.1038/31189) (Pubitemid 28319239)
    • (1998) Nature , vol.393 , Issue.6685 , pp. 554-557
    • Sastry, S.1    Debenedetti, P.G.2    Stillinger, F.H.3
  • 126
    • 0042942352 scopus 로고    scopus 로고
    • Inherent structure entropy of supercooled liquids
    • Sciortino, F., Kob, W. & Tartaglia, P. 1999 Inherent structure entropy of supercooled liquids. Phys. Rev. Lett. 83, 3214-3217. (doi:10.1103/PhysRevLett.83.3214) (Pubitemid 129582867)
    • (1999) Physical Review Letters , vol.83 , Issue.16 , pp. 3214-3217
    • Sciortino, F.1    Kob, W.2    Tartaglia, P.3
  • 127
    • 0037426227 scopus 로고    scopus 로고
    • Energy landscapes of model glass formers. II. Results for constant pressure
    • (doi:10.1063/1.1545096)
    • Middleton, T. F. & Wales, D. J. 2003 Energy landscapes of model glass formers. II. Results for constant pressure. J. Chem. Phys. 118, 4583-4593. (doi:10.1063/1.1545096)
    • (2003) J. Chem. Phys. , vol.118 , pp. 4583-4593
    • Middleton, T.F.1    Wales, D.J.2
  • 128
    • 0035124789 scopus 로고    scopus 로고
    • Extension of the fluctuation-dissipation theorem to the physical aging of a model glass-forming liquid
    • DOI 10.1103/PhysRevLett.86.107
    • Sciortino, F. & Tartaglia, P. 2001 Extension of the fluctuation-dissipation theorem to the physical aging of a model glass-forming liquid. Phys. Rev. Lett. 86, 107-110. (doi:10.1103/ PhysRevLett.86.107) (Pubitemid 32131744)
    • (2001) Physical Review Letters , vol.86 , Issue.1 , pp. 107-110
    • Sciortino, F.1    Tartaglia, P.2
  • 129
    • 0035843149 scopus 로고    scopus 로고
    • The relationship between fragility, configurational entropy and the potential energy landscape of glass-forming liquids
    • DOI 10.1038/35051524
    • Sastry, S. 2001 The relationship between fragility, configurational entropy and the potential energy landscape of glass-forming liquids. Nature 409, 164-167. (doi:10.1038/35051524) (Pubitemid 32146167)
    • (2001) Nature , vol.409 , Issue.6817 , pp. 164-167
    • Sastry, S.1
  • 130
  • 131
    • 0038731355 scopus 로고    scopus 로고
    • Crystal phases of a glass-forming Lennard-Jones mixture
    • (doi:10.1103/PhysRevE.67.011403)
    • Fernández, J. R. & Harrowell, P. 2003 Crystal phases of a glass-forming Lennard-Jones mixture. Phys. Rev. E 67, 011403. (doi:10.1103/PhysRevE.67.011403)
    • (2003) Phys. Rev. e , vol.67 , pp. 011403
    • Fernández, J.R.1    Harrowell, P.2
  • 132
    • 55349083642 scopus 로고    scopus 로고
    • Energy landscapes for diffusion: Analysis of cage-breaking processes
    • (doi:10.1063/1.2992128)
    • de Souza, V. K. & Wales, D. J. 2008 Energy landscapes for diffusion: analysis of cage-breaking processes. J. Chem. Phys. 129, 164507. (doi:10.1063/1.2992128)
    • (2008) J. Chem. Phys. , vol.129 , pp. 164507
    • De Souza, V.K.1    Wales, D.J.2
  • 133
    • 72049086718 scopus 로고    scopus 로고
    • Computing the viscosity of supercooled liquids. II. Silica and strong-fragile crossover behavior
    • (doi:10.1063/1.3243854)
    • Kushima, A., Lin, X., Li, J., Qian, X., Eapen, J., Mauro, J. C., Diep, P. & Yip, S. 2009 Computing the viscosity of supercooled liquids. II. Silica and strong-fragile crossover behavior. J. Chem. Phys. 131, 164505. (doi:10.1063/1.3243854)
    • (2009) J. Chem. Phys. , vol.131 , pp. 164505
    • Kushima, A.1    Lin, X.2    Li, J.3    Qian, X.4    Eapen, J.5    Mauro, J.C.6    Diep, P.7    Yip, S.8
  • 134
    • 11344259128 scopus 로고
    • A topographic view of supercooled liquids and glass formation
    • (doi:10.1126/science.267.5206.1935)
    • Stillinger, F. H. 1995 A topographic view of supercooled liquids and glass formation. Science 267, 1935-1939. (doi:10.1126/science.267.5206.1935)
    • (1995) Science , vol.267 , pp. 1935-1939
    • Stillinger, F.H.1
  • 135
    • 0037467228 scopus 로고    scopus 로고
    • Hopping in a supercooled Lennard-Jones liquid: Metabasins, waiting time distribution and diffusion
    • (doi:10.1088/ 0953-8984/15/11/309)
    • Doliwa, B. & Heuer, A. 2003 Hopping in a supercooled Lennard-Jones liquid: metabasins, waiting time distribution and diffusion. J. Phys. Condens. Matter 15, S849-S858. (doi:10.1088/ 0953-8984/15/11/309)
    • (2003) J. Phys. Condens. Matter , vol.15
    • Doliwa, B.1    Heuer, A.2
  • 136
    • 0035860455 scopus 로고    scopus 로고
    • A microscopic basis for the global appearance of energy landscapes
    • (doi:10.1126/science.1062565)
    • Wales, D. J. 2001 A microscopic basis for the global appearance of energy landscapes. Science 293, 2067-2069. (doi:10.1126/science.1062565)
    • (2001) Science , vol.293 , pp. 2067-2069
    • Wales, D.J.1
  • 139
    • 3042551557 scopus 로고    scopus 로고
    • New results for phase transitions from catastrophe theory
    • (doi:10.1063/1.1740756)
    • Bogdan, T. V. & Wales, D. J. 2004 New results for phase transitions from catastrophe theory. J. Chem. Phys. 120, 11090-11099. (doi:10.1063/1. 1740756)
    • (2004) J. Chem. Phys. , vol.120 , pp. 11090-11099
    • Bogdan, T.V.1    Wales, D.J.2
  • 140
    • 5244245983 scopus 로고
    • A correlation of reaction rates
    • (doi:10.1021/ja01607a027)
    • Hammond, G. S. 1955 A correlation of reaction rates. J. Am. Chem. Soc. 77, 334-338. (doi:10.1021/ja01607a027)
    • (1955) J. Am. Chem. Soc. , vol.77 , pp. 334-338
    • Hammond, G.S.1
  • 142
    • 85010384444 scopus 로고
    • Cambridge, UK: Cambridge University Press
    • Thompson, D. W. 1961 On growth and form. Cambridge, UK: Cambridge University Press.
    • (1961) On Growth and Form
    • Thompson, D.W.1
  • 144
    • 0000460062 scopus 로고    scopus 로고
    • Symmetry, near-symmetry and energetics
    • PII S000926149800044X
    • Wales, D. J. 1998 Symmetry, near-symmetry and energetics. Chem. Phys. Lett. 285, 330-336. (doi:10.1016/S0009-2614(98)00044-X) (Pubitemid 128339112)
    • (1998) Chemical Physics Letters , vol.285 , Issue.5-6 , pp. 330-336
    • Wales, D.J.1
  • 145
    • 33744632076 scopus 로고    scopus 로고
    • Erratum
    • (doi:10.1016/S0009-2614(98)00893-8)
    • Wales, D. J. 1998 Erratum. Chem. Phys. Lett. 294, 262. (doi:10.1016/S0009-2614(98)00893-8)
    • (1998) Chem. Phys. Lett. , vol.294 , pp. 262
    • Wales, D.J.1
  • 147
    • 0000329743 scopus 로고    scopus 로고
    • Thermodynamics and symmetry of protein-like heteropolymers
    • (doi:10.1103/PhysRevLett.79.3534)
    • Nelson, E. D., Teneyck, L. F. & Onuchic, J. N. 1997 Thermodynamics and symmetry of protein-like heteropolymers. Phys. Rev. Lett. 79, 3534-3537. (doi:10.1103/PhysRevLett.79.3534)
    • (1997) Phys. Rev. Lett. , vol.79 , pp. 3534-3537
    • Nelson, E.D.1    Teneyck, L.F.2    Onuchic, J.N.3
  • 148
    • 0032169011 scopus 로고    scopus 로고
    • Proposed mechanism for stability of proteins to evolutionary mutations
    • (doi:10.1073/pnas.95.18.10682)
    • Nelson, E. D. & Onuchic, J. N. 1997 Proposed mechanism for stability of proteins to evolutionary mutations. Proc. Natl Acad. Sci. USA 95, 10 682-10 686. (doi:10.1073/pnas.95.18.10682)
    • (1997) Proc. Natl Acad. Sci. USA , vol.95 , pp. 10682-10686
    • Nelson, E.D.1    Onuchic, J.N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.