메뉴 건너뛰기




Volumn 51, Issue , 2013, Pages 102-110

State reduction in molecular simulations

Author keywords

Data mining; Diffusion Maps; Local Feature Analysis; Model reduction; Principal Component Analysis

Indexed keywords

DATA-MINING TOOLS; DIFFUSION MAPS; ILLUSTRATIVE EXAMPLES; LARGE SYSTEM; LOCAL FEATURE ANALYSIS; MODEL REDUCTION; MOLECULAR SIMULATIONS; STATE REDUCTION;

EID: 84874017363     PISSN: 00981354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compchemeng.2012.06.029     Document Type: Article
Times cited : (12)

References (62)
  • 3
    • 84874019603 scopus 로고    scopus 로고
    • Problems of learning on manifolds. Ph.D. Thesis
    • Belkin, M., (2003). Problems of learning on manifolds. Ph.D. Thesis.
    • (2003)
    • Belkin, M.1
  • 4
    • 0042378381 scopus 로고    scopus 로고
    • Laplacian eigenmaps for dimensionality reduction and data representation
    • Belkin M., Niyogi P. Laplacian eigenmaps for dimensionality reduction and data representation. Neural Computation 2003, 15(6):1373-1396.
    • (2003) Neural Computation , vol.15 , Issue.6 , pp. 1373-1396
    • Belkin, M.1    Niyogi, P.2
  • 5
    • 26944439046 scopus 로고    scopus 로고
    • Towards a theoretical foundation for Laplacian-based manifold methods
    • Belkin M., Niyogi P. Towards a theoretical foundation for Laplacian-based manifold methods. Learning theory, Proceedings, Vol. 3559 2005, 486-500.
    • (2005) Learning theory, Proceedings, Vol. 3559 , pp. 486-500
    • Belkin, M.1    Niyogi, P.2
  • 6
    • 0037615148 scopus 로고    scopus 로고
    • Reconstructing a three-dimensional model with arbitrary errors
    • Berger B., Kleinberg J., Leighton T. Reconstructing a three-dimensional model with arbitrary errors. Journal of the ACM 1999, 46(2):212-235.
    • (1999) Journal of the ACM , vol.46 , Issue.2 , pp. 212-235
    • Berger, B.1    Kleinberg, J.2    Leighton, T.3
  • 7
    • 67649494492 scopus 로고    scopus 로고
    • Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
    • Best R.B., Hummer G. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. Journal of Physical Chemistry B 2009, 113(26):9004-9015.
    • (2009) Journal of Physical Chemistry B , vol.113 , Issue.26 , pp. 9004-9015
    • Best, R.B.1    Hummer, G.2
  • 10
    • 0038589165 scopus 로고    scopus 로고
    • The anatomy of a large-scale hypertextual web search engine
    • Brin S., Page L. The anatomy of a large-scale hypertextual web search engine. Computer Networks and ISDN Systems 1998, 30(1-7):107-117.
    • (1998) Computer Networks and ISDN Systems , vol.30 , Issue.1-7 , pp. 107-117
    • Brin, S.1    Page, L.2
  • 11
    • 78649693330 scopus 로고    scopus 로고
    • High-dimensional density estimation via SCA: An example in the modelling of hurricane tracks
    • Buchman S., Lee A., Schafer C. High-dimensional density estimation via SCA: An example in the modelling of hurricane tracks. Statistical Methodology 2011, 8(1):18-30.
    • (2011) Statistical Methodology , vol.8 , Issue.1 , pp. 18-30
    • Buchman, S.1    Lee, A.2    Schafer, C.3
  • 14
    • 0031910020 scopus 로고    scopus 로고
    • Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin
    • Caves L.S.D., Evanseck J.D., Karplus M. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin. Protein Science 1998, 7(3):649-666.
    • (1998) Protein Science , vol.7 , Issue.3 , pp. 649-666
    • Caves, L.S.D.1    Evanseck, J.D.2    Karplus, M.3
  • 16
    • 0003365565 scopus 로고    scopus 로고
    • Spectral graph theory
    • Published for the Conference Board of the mathematical sciences by the American Mathematical Society, Providence, RI
    • Chung F.R.K. Spectral graph theory. Regional conference series in mathematics 1997, Published for the Conference Board of the mathematical sciences by the American Mathematical Society, Providence, RI.
    • (1997) Regional conference series in mathematics
    • Chung, F.R.K.1
  • 18
    • 33745398604 scopus 로고    scopus 로고
    • Geometric harmonics: A novel tool for multiscale out-of-sample extension of empirical functions
    • Coifman R.R., Lafon S. Geometric harmonics: A novel tool for multiscale out-of-sample extension of empirical functions. Applied and Computational Harmonic Analysis 2006, 21(1):31-52.
    • (2006) Applied and Computational Harmonic Analysis , vol.21 , Issue.1 , pp. 31-52
    • Coifman, R.R.1    Lafon, S.2
  • 25
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G.M., Zhang W., et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry 2003, 24(16):1999-2012.
    • (2003) Journal of Computational Chemistry , vol.24 , Issue.16 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.M.5    Zhang, W.6
  • 30
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia A.E. Large-amplitude nonlinear motions in proteins. Physical Review Letters 1992, 68(17):2696-2699.
    • (1992) Physical Review Letters , vol.68 , Issue.17 , pp. 2696-2699
    • Garcia, A.E.1
  • 32
    • 0037865691 scopus 로고    scopus 로고
    • Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
    • Hummer G., Kevrekidis I.G. Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations. Journal of Chemical Physics 2003, 118(23):10762-10773.
    • (2003) Journal of Chemical Physics , vol.118 , Issue.23 , pp. 10762-10773
    • Hummer, G.1    Kevrekidis, I.G.2
  • 35
    • 84893482610 scopus 로고
    • Solution for best rotation to relate 2 sets of vectors
    • Kabsch W. Solution for best rotation to relate 2 sets of vectors. Acta Crystallographica Section A 1976, 32:922-923.
    • (1976) Acta Crystallographica Section A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 36
    • 12944249776 scopus 로고
    • Discussion of solution for best rotation to relate 2 sets of vectors
    • Kabsch W. Discussion of solution for best rotation to relate 2 sets of vectors. Acta Crystallographica Section A 1978, 34:827-828.
    • (1978) Acta Crystallographica Section A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 37
    • 3042720018 scopus 로고    scopus 로고
    • Equation-free: The computer-aided analysis of complex multiscale systems
    • Kevrekidis I.G., Gear C.W., Hummer G. Equation-free: The computer-aided analysis of complex multiscale systems. AIChE Journal 2004, 50(7).
    • (2004) AIChE Journal , vol.50 , Issue.7
    • Kevrekidis, I.G.1    Gear, C.W.2    Hummer, G.3
  • 39
    • 0041775676 scopus 로고    scopus 로고
    • Diffusion kernels on graphs and other discrete input spaces
    • Kondor R., Lafferty J. Diffusion kernels on graphs and other discrete input spaces. Proceedings of the ICML 2002.
    • (2002) Proceedings of the ICML
    • Kondor, R.1    Lafferty, J.2
  • 40
    • 84874021815 scopus 로고    scopus 로고
    • Diffusion Maps and geometric harmonics. Ph.D. Thesis
    • Lafon, S. S. (2004). Diffusion Maps and geometric harmonics. Ph.D. Thesis.
    • (2004)
    • Lafon, S.S.1
  • 41
    • 58149367504 scopus 로고
    • Understanding complex chemical kinetics with computational singular perturbation
    • Lam S., Goussis D. Understanding complex chemical kinetics with computational singular perturbation. Symposium (International) on Combustion 1989, 22(1):931-941.
    • (1989) Symposium (International) on Combustion , vol.22 , Issue.1 , pp. 931-941
    • Lam, S.1    Goussis, D.2
  • 42
    • 26444531014 scopus 로고    scopus 로고
    • Local and global feature extraction for face recognition
    • Lee Y., Lee K., Pan S. Local and global feature extraction for face recognition. Lecture Notes in Computer Science 2005, 3546:219-228.
    • (2005) Lecture Notes in Computer Science , vol.3546 , pp. 219-228
    • Lee, Y.1    Lee, K.2    Pan, S.3
  • 43
    • 45949083297 scopus 로고    scopus 로고
    • Optimal control of diffusion-convection-reaction processes using reduced-order models
    • Li M., Christofides P.D. Optimal control of diffusion-convection-reaction processes using reduced-order models. Computers and Chemical Engineering 2007, 32(9).
    • (2007) Computers and Chemical Engineering , vol.32 , Issue.9
    • Li, M.1    Christofides, P.D.2
  • 44
    • 0026869597 scopus 로고
    • Langevin dynamics of peptides - the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide
    • Loncharich R.J., Brooks B.R., Pastor R.W. Langevin dynamics of peptides - the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers 1992, 32(5):523-535.
    • (1992) Biopolymers , vol.32 , Issue.5 , pp. 523-535
    • Loncharich, R.J.1    Brooks, B.R.2    Pastor, R.W.3
  • 45
    • 0026833045 scopus 로고
    • Simplifying chemical-kinetics - intrinsic low-dimensional manifolds in composition space
    • Maas U., Pope S.B. Simplifying chemical-kinetics - intrinsic low-dimensional manifolds in composition space. Combustion and Flame 1992, 88(3-4):239-264.
    • (1992) Combustion and Flame , vol.88 , Issue.3-4 , pp. 239-264
    • Maas, U.1    Pope, S.B.2
  • 48
    • 84874018451 scopus 로고    scopus 로고
    • November). The pagerank citation ranking: Bringing order to the web. Technical report
    • Page, L., Brin, S., Motwani, R., Winograd, T. (1999, November). The pagerank citation ranking: Bringing order to the web. Technical report.
    • (1999)
    • Page, L.1    Brin, S.2    Motwani, R.3    Winograd, T.4
  • 49
    • 0000209334 scopus 로고    scopus 로고
    • Local Feature Analysis: A general statistical theory for object representation
    • Penev P.S., Atick J.J. Local Feature Analysis: A general statistical theory for object representation. Computation in Neural Systems 1996, 7:477-500.
    • (1996) Computation in Neural Systems , vol.7 , pp. 477-500
    • Penev, P.S.1    Atick, J.J.2
  • 50
    • 84874021737 scopus 로고    scopus 로고
    • Heterogeneous datasets representation and learning using Diffusion Maps and Laplacian pyramids
    • Rabin N., Coifman R.R. Heterogeneous datasets representation and learning using Diffusion Maps and Laplacian pyramids. 2012 SIAM international conference on data mining 2012, 189-199.
    • (2012) 2012 SIAM international conference on data mining , pp. 189-199
    • Rabin, N.1    Coifman, R.R.2
  • 51
    • 0034704222 scopus 로고    scopus 로고
    • Nonlinear dimensionality reduction by locally linear embedding
    • Roweis S.T., Saul L.K. Nonlinear dimensionality reduction by locally linear embedding. Science 2000, 290(5500):2323-2326.
    • (2000) Science , vol.290 , Issue.5500 , pp. 2323-2326
    • Roweis, S.T.1    Saul, L.K.2
  • 52
    • 33646940952 scopus 로고
    • Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of n-alkanes. Journal of Computational Physics 1977, 23(3):327-341.
    • (1977) Journal of Computational Physics , vol.23 , Issue.3 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 53
    • 0347243182 scopus 로고    scopus 로고
    • Nonlinear component analysis as a kernel eigenvalue problem
    • Schölkopf B., Smola A., Müller K.R. Nonlinear component analysis as a kernel eigenvalue problem. Neural Computation 1998, 10(5):1299-1319.
    • (1998) Neural Computation , vol.10 , Issue.5 , pp. 1299-1319
    • Schölkopf, B.1    Smola, A.2    Müller, K.R.3
  • 56
    • 70349494198 scopus 로고    scopus 로고
    • Coarse-graining the dynamics of a driven interface in the presence of mobile impurities: Effective description via Diffusion Maps
    • Sonday B.E., Haataja M., Kevrekidis I.G. Coarse-graining the dynamics of a driven interface in the presence of mobile impurities: Effective description via Diffusion Maps. Physical Review E 2009, 80(3).
    • (2009) Physical Review E , vol.80 , Issue.3
    • Sonday, B.E.1    Haataja, M.2    Kevrekidis, I.G.3
  • 57
    • 84874022169 scopus 로고    scopus 로고
    • (submitted for publication). Manifold learning techniques and model reduction applied to dissipative PDES. SIAM Journal on Applied Dynamical Systems. Can be obtained as 1011.5197 at arxiv.org.
    • Sonday, B. E., Singer, A., Gear, C. W., Kevrekidis, I. G. (submitted for publication). Manifold learning techniques and model reduction applied to dissipative PDES. SIAM Journal on Applied Dynamical Systems. Can be obtained as 1011.5197 at arxiv.org.
    • Sonday, B.E.1    Singer, A.2    Gear, C.W.3    Kevrekidis, I.G.4
  • 58
    • 0034704229 scopus 로고    scopus 로고
    • A global geometric framework for nonlinear dimensionality reduction
    • Tenenbaum J.B., de Silva V., Langford J.C. A global geometric framework for nonlinear dimensionality reduction. Science 2000, 290(5500):2319-2323.
    • (2000) Science , vol.290 , Issue.5500 , pp. 2319-2323
    • Tenenbaum, J.B.1    de Silva, V.2    Langford, J.C.3
  • 61
    • 33745587301 scopus 로고    scopus 로고
    • Local Feature Analysis: A statistical theory for reproducible essential dynamics of large macromolecules
    • Zhang Z., Wriggers W. Local Feature Analysis: A statistical theory for reproducible essential dynamics of large macromolecules. Proteins: Structure, Function, and Bioinformatics 2006, 64:391-403.
    • (2006) Proteins: Structure, Function, and Bioinformatics , vol.64 , pp. 391-403
    • Zhang, Z.1    Wriggers, W.2
  • 62
    • 56349126308 scopus 로고    scopus 로고
    • Coarse-graining protein structures with local multivariate features from molecular dynamics
    • Zhang Z., Wriggers W. Coarse-graining protein structures with local multivariate features from molecular dynamics. Journal of Physical Chemistry B 2008, 112:14026-14035.
    • (2008) Journal of Physical Chemistry B , vol.112 , pp. 14026-14035
    • Zhang, Z.1    Wriggers, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.