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A stationary‐wave model of enzyme catalysis
Author(s) -
Canepa Carlo
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21264
Subject(s) - embedding , amplitude , debye , phase space , space (punctuation) , molecular dynamics , physics , phase (matter) , chemistry , potential energy , classical mechanics , thermodynamics , computational chemistry , quantum mechanics , computer science , artificial intelligence , operating system
An expression for the external force driving a system of two coupled oscillators in the condensed phase was derived in the frame of the Debye theory of solids. The time dependence and amplitude of the force is determined by the size of the cell embedding the coupled oscillators and its Debye temperature (θ D ). The dynamics of the driven system of oscillators were followed in the two regimes of (a) low θ D and cell diameter, as a model of liquid water, and (b) large θ D and cell diameter, as a model of the core of a protein. The response in potential energy of the reference oscillator was computed for all possible values of the internal parameters of the system under investigation. For protein cores, the region in the parameter space of high maximum potential energy of the reference oscillator is considerably extended with respect to the corresponding simulation for water. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010