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1
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85045107919
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edited by I. Prigogine and S. Rice Wiley, New York
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R. Berry, T. Beck, H. Davis, and J. Jellinek, in Evolution of Size Effects in Chemical Dynamics, Part 2, edited by I. Prigogine and S. Rice (Wiley, New York, 1988), pp. 75-138.
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(1988)
Evolution of Size Effects in Chemical Dynamics
, Issue.2 PART
, pp. 75-138
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Berry, R.1
Beck, T.2
Davis, H.3
Jellinek, J.4
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2
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85033041865
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For example, the Euclidean distance from the native conformation, the number of nearest-neighbor contacts that match contacts in the native conformation, and the radius of gyration have been used as order parameters
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For example, the Euclidean distance from the native conformation, the number of nearest-neighbor contacts that match contacts in the native conformation, and the radius of gyration have been used as order parameters.
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5
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0042754937
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Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding: DIMACS Workshop, edited by P. Pardalos, D. Shalloway, and G. Xue American Mathematical Society, Providence, RI
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B. Church, M. Orešič, and D. Shalloway, in Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding: DIMACS Workshop, Vol. 23 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science, edited by P. Pardalos, D. Shalloway, and G. Xue (American Mathematical Society, Providence, RI, 1996), pp. 41-64.
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(1996)
DIMACS Series in Discrete Mathematics and Theoretical Computer Science
, vol.23
, pp. 41-64
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Church, B.1
Orešič, M.2
Shalloway, D.3
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6
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85033071262
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edited by A. Conn, T. Coleman, and F. Santosa Springer, New York, in press
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D. Shalloway, in Large-Scale Optimization and Applications, Molecular Minimization, edited by A. Conn, T. Coleman, and F. Santosa (Springer, New York, in press), Vol 3.
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Large-Scale Optimization and Applications, Molecular Minimization
, vol.3
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Shalloway, D.1
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10
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0002121327
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S. Chandrasekhar, Rev. Mod. Phys. 15, 1 (1943). We assume that R is specified in Cartesian coordinates. In non-Cartesian coordinates (5) is modified by the inclusion of R-dependent Jacobean factors resulting from the implicit integrations over momentum space. To simplify the discussion, we assume that the diffusion tensor is isotropic so that D is a scalar. The Smoluchowski equation with an anisotropic diffusion tensor can be brought to the form of Eq. (5) by an apppropriate orthogonal transformation and reseating of coordinates.
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(1943)
Rev. Mod. Phys.
, vol.15
, pp. 1
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Chandrasekhar, S.1
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21
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85033044225
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The eigenfunctions corresponding to negative eigenvalues are not normalizable
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The eigenfunctions corresponding to negative eigenvalues are not normalizable.
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22
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85033064832
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note
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In quantum mechanics ψ would be called a "state function," but we do not use this term to avoid confusion with its thermodynamic meaning. 23 Without loss of generality we assume that there are no infinite potential barriers that dissect the space into completely disconnected subregions. (This would induce degenerate eigenfunctions with zero relaxation rates.) If this were the case, each subregion could be analyzed independently.
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23
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33645830747
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We previously called macrostate window functions "weighting functions" (Ref. 4). They have also been called "characteristic functions" [D. Chandler, J. Chem. Phys. 101, 9844 (1994)] and "site-localizing functions" (Ref. 20).
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(1994)
J. Chem. Phys.
, vol.101
, pp. 9844
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Chandler, D.1
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24
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85033058214
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Throughout the paper, subscripted Greek letters identify macrostates and bear no relationship to regular Greek letters such as the inverse temperature β. Summations over these macrostate indices are over all m macrostates
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Throughout the paper, subscripted Greek letters identify macrostates and bear no relationship to regular Greek letters such as the inverse temperature β. Summations over these macrostate indices are over all m macrostates.
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25
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85033037005
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b.
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b.
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26
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84940644968
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0〉 provides an alternative measure of the "information" content of the macrostate description, although its experimental interpretation is not as clear as that of Y.
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(1948)
Bell System Tech. J.
, vol.27
, pp. 379
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Shannon, C.E.1
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27
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85033043728
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note
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α is the global minimum of V(R) within the a macrostate region. This specification may be a useful approximation, but it leads to violation of window conditions (20).
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28
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85033067091
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note
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n≥m terms in eigenfunction expansion (12), since the truncated expansion would not, in general, be positive semi-definite as required for a physical reduced distribution. In contrast, this property is guaranteed by Eq. (31).
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29
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85033053793
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note
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obs and F are identical since the matrices are similar.
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30
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85033040710
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0 does not satisfy normalization condition (16), and thus is proportional to, but is not itself, a reduced distribution
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0 does not satisfy normalization condition (16), and thus is proportional to, but is not itself, a reduced distribution.
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31
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85033047388
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We explicitly display only time dependence within bra-ket vectors; the dependence on β and R is implicit
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We explicitly display only time dependence within bra-ket vectors; the dependence on β and R is implicit.
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32
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85033054947
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The equivalence of the integral and differential forms of the equations is proven in Appendix A of Ref. 4
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The equivalence of the integral and differential forms of the equations is proven in Appendix A of Ref. 4.
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33
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85033034300
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The determinant in Eq. (59) is irrelevant to the characteristic packet equations. It is included so that Eqs. (62) and (66) will be satisfied
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The determinant in Eq. (59) is irrelevant to the characteristic packet equations. It is included so that Eqs. (62) and (66) will be satisfied.
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35
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85033043770
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0 has been shown to agree to within 5% with Monte Carlo calculations of the average energy for 6- and 7-atom Lennard-Jones microclusters (Ref. 4)
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0 has been shown to agree to within 5% with Monte Carlo calculations of the average energy for 6- and 7-atom Lennard-Jones microclusters (Ref. 4).
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37
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85033036059
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Alternatively, the tanh in Eqs. (78b) and (79) could be replaced with the error function which has a similar shape (see Ref. 20 for use of the error function in a related context)
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Alternatively, the tanh in Eqs. (78b) and (79) could be replaced with the error function which has a similar shape (see Ref. 20 for use of the error function in a related context).
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38
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85033050110
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Since η is a vector, Eq. (80) represents N+1 conditions
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Since η is a vector, Eq. (80) represents N+1 conditions.
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39
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85033064690
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Equations (84) assumes that η points out of macrostate region a
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Equations (84) assumes that η points out of macrostate region a.
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40
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85033054183
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note
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-2 (η R-ξ).
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42
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85033070697
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note
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α.
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43
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85033072458
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note
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2 is negligible in the boundary regions outside of the transition regions.
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45
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0001425721
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J. Kostrowicki, L. Piela, B. J. Cherayil, and H. A. Scheraga, J. Phys. Chem. 95, 4113 (1991).
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(1991)
J. Phys. Chem.
, vol.95
, pp. 4113
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Kostrowicki, J.1
Piela, L.2
Cherayil, B.J.3
Scheraga, H.A.4
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