메뉴 건너뛰기




Volumn 73, Issue 1, 2013, Pages 1-23

Variational implicit solvation with solute molecular mechanics: From diffuse-interface to sharp-interface models

Author keywords

convergence; Diffuse interface; Electrostatics; Implicit solvent; Motion by mean curvature; Sharp interface; Solute molecular mechanics; Solvation; Surface energy; Van der Waals interaction

Indexed keywords

DIFFUSE INTERFACE; IMPLICIT SOLVENTS; MOTION BY MEAN CURVATURE; SHARP INTERFACE; VAN DER WAALS INTERACTIONS;

EID: 84876221909     PISSN: 00361399     EISSN: None     Source Type: Journal    
DOI: 10.1137/120883426     Document Type: Article
Times cited : (20)

References (44)
  • 2
    • 79251519623 scopus 로고    scopus 로고
    • Approximation of Helfrich's functional via diffuse interfaces
    • G. Bellettini and L. Mugnai, Approximation of Helfrich's functional via diffuse interfaces, SIAM J. Math. Anal., 42 (2010), pp. 2402-2433.
    • (2010) SIAM J. Math. Anal. , vol.42 , pp. 2402-2433
    • Bellettini, G.1    Mugnai, L.2
  • 3
    • 27944442365 scopus 로고    scopus 로고
    • Sharp-interface projection of a fluctuating phase-field model
    • R. Benítez and L. Ramírez-Piscina, Sharp-interface projection of a fluctuating phase-field model, Phys. Rev. E, 71 (2005), p. 061603.
    • (2005) Phys. Rev. e , vol.71 , pp. 061603
    • Benítez, R.1    Ramírez-Piscina, L.2
  • 5
    • 80054979521 scopus 로고    scopus 로고
    • Yukawa-field approximation of electrostatic free energy and dielectric boundary force
    • H. B. Cheng, L.-T. Cheng, and B. Li, Yukawa-field approximation of electrostatic free energy and dielectric boundary force, Nonlinearity, 24 (2011), pp. 3215-3236.
    • (2011) Nonlinearity , vol.24 , pp. 3215-3236
    • Cheng, H.B.1    Cheng, L.-T.2    Li, B.3
  • 6
    • 34548378695 scopus 로고    scopus 로고
    • Application of the level-set method to the implicit solvation of nonpolar molecules
    • L.-T. Cheng, J. Dzubiella, J. A. McCammon, and B. Li, Application of the level-set method to the implicit solvation of nonpolar molecules, J. Chem. Phys., 127 (2007), 084503.
    • (2007) J. Chem. Phys. , vol.127 , pp. 084503
    • Cheng, L.-T.1    Dzubiella, J.2    McCammon, J.A.3    Li, B.4
  • 7
    • 77956407030 scopus 로고    scopus 로고
    • Level-set minimization of potential controlled Hadwiger valuations for molecular solvation
    • L.-T. Cheng, B. Li, and Z. Wang, Level-set minimization of potential controlled Hadwiger valuations for molecular solvation, J. Comput. Phys., 229 (2010), pp. 8497-8510.
    • (2010) J. Comput. Phys. , vol.229 , pp. 8497-8510
    • Cheng, L.-T.1    Li, B.2    Wang, Z.3
  • 8
    • 70350482625 scopus 로고    scopus 로고
    • Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach
    • L.-T. Cheng, Z. Wang, P. Setny, J. Dzubiella, B. Li, and J. A. McCammon, Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach, J. Chem. Phys., 131 (2009), p. 144102.
    • (2009) J. Chem. Phys. , vol.131 , pp. 144102
    • Cheng, L.-T.1    Wang, Z.2    Setny, P.3    Dzubiella, J.4    Li, B.5    McCammon, J.A.6
  • 9
    • 65249120770 scopus 로고    scopus 로고
    • Coupling the level-set method with molecular mechanics for variational implicit solvation of nonpolar molecules
    • L.-T. Cheng, Y. Xie, J. Dzubiella, J. A. McCammon, J. Che, and B. Li, Coupling the level-set method with molecular mechanics for variational implicit solvation of nonpolar molecules, J. Chem. Theory Comput., 5 (2009), pp. 257-266.
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 257-266
    • Cheng, L.-T.1    Xie, Y.2    Dzubiella, J.3    McCammon, J.A.4    Che, J.5    Li, B.6
  • 10
    • 0036036465 scopus 로고    scopus 로고
    • Phase-field models of microstructure evolution
    • L.-Q. Chen, Phase-field models of microstructure evolution, Annu. Rev. Materials Res., 32 (2002), pp. 113-140.
    • (2002) Annu. Rev. Materials Res. , vol.32 , pp. 113-140
    • Chen, L.-Q.1
  • 11
    • 77956414486 scopus 로고    scopus 로고
    • Differential geometry based solvation model I: Eulerian formulation
    • Z. Chen, N. A. Baker, and G. W. Wei, Differential geometry based solvation model I: Eulerian formulation, J. Comput. Phys., 229 (2010), pp. 8231-8258.
    • (2010) J. Comput. Phys. , vol.229 , pp. 8231-8258
    • Chen, Z.1    Baker, N.A.2    Wei, G.W.3
  • 12
    • 4243463817 scopus 로고
    • Electrostatics in biomolecular structure and dynamics
    • M. E. Davis and J. A. McCammon, Electrostatics in biomolecular structure and dynamics, Chem. Rev., 90 (1990), pp. 509-521.
    • (1990) Chem. Rev. , vol.90 , pp. 509-521
    • Davis, M.E.1    McCammon, J.A.2
  • 13
    • 29144514194 scopus 로고    scopus 로고
    • A phase field formulation of the Willmore problem
    • DOI 10.1088/0951-7715/18/3/016
    • Q. Du, C. Liu, R. Ryham, and X. Wang, A phase field formulation of the Willmore problem, Nonlinearity, 18 (2005), pp. 1249-1267. (Pubitemid 43025962)
    • (2005) Nonlinearity , vol.18 , Issue.3 , pp. 1249-1267
    • Du, Q.1    Liu, C.2    Ryham, R.3    Wang, X.4
  • 14
    • 3242875567 scopus 로고    scopus 로고
    • A phase field approach in the numerical study of the elastic bending energy for vesicle membranes
    • DOI 10.1016/j.jcp.2004.01.029, PII S0021999104000373
    • Q. Du, C. Liu, and X. Wang, A phase field approach in the numerical study of the elastic bending energy for vesicle memberanes, J. Comput. Phys., 198 (2004), pp. 450-468. (Pubitemid 38999047)
    • (2004) Journal of Computational Physics , vol.198 , Issue.2 , pp. 450-468
    • Du, Q.1    Liu, C.2    Wang, X.3
  • 15
    • 33644682762 scopus 로고    scopus 로고
    • Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models
    • J. Dzubiella, J. M. J. Swanson, and J. A. McCammon, Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models, Phys. Rev. Lett., 96 (2006), 087802.
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 087802
    • Dzubiella, J.1    Swanson, J.M.J.2    McCammon, J.A.3
  • 16
    • 33644594508 scopus 로고    scopus 로고
    • Coupling nonpolar and polar solvation free energies in implicit solvent models
    • J. Dzubiella, J. M. J. Swanson, and J. A. McCammon, Coupling nonpolar and polar solvation free energies in implicit solvent models, J. Chem. Phys., 124 (2006), 084905.
    • (2006) J. Chem. Phys. , vol.124 , pp. 084905
    • Dzubiella, J.1    Swanson, J.M.J.2    McCammon, J.A.3
  • 19
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • DOI 10.1016/j.sbi.2004.03.009, PII S0959440X04000430
    • M. Feig and C. L. Brooks III, Recent advances in the development and applications of implicit solvent models in biomolecule simulations, Curr. Opinion Struct. Biology, 14 (2004), pp. 217-224. (Pubitemid 38495800)
    • (2004) Current Opinion in Structural Biology , vol.14 , Issue.2 , pp. 217-224
    • Feig, M.1    Brooks III, C.L.2
  • 20
    • 0001008594 scopus 로고
    • An integral formula for total gradient variation
    • W. H. Fleming and R. Rishel, An integral formula for total gradient variation, Arch.Math., 11 (1960), pp. 218-222.
    • (1960) Arch.Math. , vol.11 , pp. 218-222
    • Fleming, W.H.1    Rishel, R.2
  • 21
    • 0036873086 scopus 로고    scopus 로고
    • The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology
    • DOI 10.1002/jmr.577
    • F. Fogolari, A. Brigo, and H. Molinari, The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology, J. Mol. Recognit., 15 (2002), pp. 377-392. (Pubitemid 36101029)
    • (2002) Journal of Molecular Recognition , vol.15 , Issue.6 , pp. 377-392
    • Fogolari, F.1    Brigo, A.2    Molinari, H.3
  • 24
    • 38949141177 scopus 로고    scopus 로고
    • Review: Continuum molecular electrostatics, salt effects, and counterion binding - A review of the Poisson-Boltzmann theory and its modifications
    • DOI 10.1002/bip.20877
    • P. Grochowski and J. Trylska, Continuum molecular electrostatics, salt effects and counterion binding - A review of the Poisson-Boltzmann model and its modifications, Biopolymers, 89 (2008), pp. 93-113. (Pubitemid 351211641)
    • (2008) Biopolymers , vol.89 , Issue.2 , pp. 93-113
    • Grochowski, P.1    Trylska, J.2
  • 25
    • 4244131779 scopus 로고    scopus 로고
    • Phase-field model of mode III dynamic fracture
    • A. Karma, D. Kessler, and H. Levine, Phase-field model of mode III dynamic fracture, Phys. Rev. Lett., 87 (2001), p. 045501.
    • (2001) Phys. Rev. Lett. , vol.87 , pp. 045501
    • Karma, A.1    Kessler, D.2    Levine, H.3
  • 28
    • 33645820084 scopus 로고    scopus 로고
    • Large-scale moleculardynamics simulation of nanoscale hydrophobic interaction and nanobubble formation
    • T. Koshi, K. Yasuoka, T. Ebisuzaki, S. Yoo, and X. C. Zeng, Large-scale moleculardynamics simulation of nanoscale hydrophobic interaction and nanobubble formation, J. Chem. Phys., 123 (2005), 204707.
    • (2005) J. Chem. Phys. , vol.123 , pp. 204707
    • Koshi, T.1    Yasuoka, K.2    Ebisuzaki, T.3    Yoo, S.4    Zeng, X.C.5
  • 30
    • 0000262022 scopus 로고
    • Models of pattern formation in first-order phase transitions
    • G. Grinstein and G. Mazenko, eds., World Scientific, River Edge, NJ
    • J. S. Langer, Models of pattern formation in first-order phase transitions, in Directions in Condensed Matter Physics, G. Grinstein and G. Mazenko, eds., World Scientific, River Edge, NJ, 1986.
    • (1986) Directions in Condensed Matter Physics
    • Langer, J.S.1
  • 31
    • 84862908482 scopus 로고    scopus 로고
    • Dielectric boundary force in molecular solvation with the Poisson-Boltzmann free energy: A shape derivative approach
    • B. Li., X.-L. Cheng, and Z.-F. Zhang, Dielectric boundary force in molecular solvation with the Poisson-Boltzmann free energy: A shape derivative approach, SIAM J. Appl. Math., 71 (2011), pp. 2093-2111.
    • (2011) SIAM J. Appl. Math. , vol.71 , pp. 2093-2111
    • Li, B.1    Cheng, X.-L.2    Zhang, Z.-F.3
  • 32
    • 70350480299 scopus 로고    scopus 로고
    • Minimization of electrostatic free energy and the Poisson-Boltzmann equation for molecular solvation with implicit solvent
    • B. Li, Minimization of electrostatic free energy and the Poisson-Boltzmann equation for molecular solvation with implicit solvent, SIAM J. Math. Anal., 40 (2009), pp. 2536-2566.
    • (2009) SIAM J. Math. Anal. , vol.40 , pp. 2536-2566
    • Li, B.1
  • 33
    • 84866597924 scopus 로고    scopus 로고
    • Are hydrodynamic interactions important in the kinetics of hydrophobic collapse?
    • J. Li, J. A. Morrone, and B. J. Berne, Are hydrodynamic interactions important in the kinetics of hydrophobic collapse?, J. Phys. Chem. B, 116 (2012), pp. 11537-11544.
    • (2012) J. Phys. Chem. B , vol.116 , pp. 11537-11544
    • Li, J.1    Morrone, J.A.2    Berne, B.J.3
  • 34
    • 34250109116 scopus 로고
    • The gradient theory of phase transitions and the minimal interface criterion
    • L. Modica, The gradient theory of phase transitions and the minimal interface criterion, Arch. Ration. Mech. Anal., 98 (1987), pp. 123-142.
    • (1987) Arch. Ration. Mech. Anal. , vol.98 , pp. 123-142
    • Modica, L.1
  • 35
    • 0000265293 scopus 로고
    • Minimizers and gradient flows for singularly perturbed bi-stable potentials with a Dirichlet condition
    • N. C. Owen, J. Rubinstein, and P. Sternberg, Minimizers and gradient flows for singularly perturbed bi-stable potentials with a Dirichlet condition, Proc. Roy. Soc. London A, 429 (1990), pp. 505-532.
    • (1990) Proc. Roy. Soc. London A , vol.429 , pp. 505-532
    • Owen, N.C.1    Rubinstein, J.2    Sternberg, P.3
  • 36
    • 33749607402 scopus 로고    scopus 로고
    • On a modified conjecture of De Giorgi
    • DOI 10.1007/s00209-006-0002-6
    • M. Röger and R. Schätzle, On a modified conjecture of De Giorgi, Math. Z., 254 (2006), pp. 675-714. (Pubitemid 44546712)
    • (2006) Mathematische Zeitschrift , vol.254 , Issue.4 , pp. 675-714
    • Roger, M.1    Schatzle, R.2
  • 37
    • 0032968133 scopus 로고    scopus 로고
    • Implicit solvent models
    • DOI 10.1016/S0301-4622(98)00226-9, PII S0301462298002269
    • B. Roux and T. Simonson, Implicit solvent models, Biophys. Chem., 78 (1999), pp. 1-20. (Pubitemid 29206654)
    • (1999) Biophysical Chemistry , vol.78 , Issue.1-2 , pp. 1-20
    • Roux, B.1    Simonson, T.2
  • 39
    • 77956336109 scopus 로고    scopus 로고
    • Computational model for cell morphodynamics
    • D. Shao, W.-J. Rappel, and H. Levine, Computational model for cell morphodynamics, Phys. Rev. Lett., 105 (2010), 108104.
    • (2010) Phys. Rev. Lett. , vol.105 , pp. 108104
    • Shao, D.1    Rappel, W.-J.2    Levine, H.3
  • 41
    • 34250095380 scopus 로고
    • The effect of a singular perturbation on nonconvex variational problems
    • P. Sternberg, The effect of a singular perturbation on nonconvex variational problems, Arch. Ration. Mech. Anal., 101 (1988), pp. 209-260.
    • (1988) Arch. Ration. Mech. Anal. , vol.101 , pp. 209-260
    • Sternberg, P.1
  • 42
    • 52649175908 scopus 로고    scopus 로고
    • Asymptotic analysis of phase field formulations of bending elasticity models
    • X. Wang, Asymptotic analysis of phase field formulations of bending elasticity models, SIAM J. Math. Anal., 39 (2008), pp. 1367-1401.
    • (2008) SIAM J. Math. Anal. , vol.39 , pp. 1367-1401
    • Wang, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.