SYSTEMS AND METHODS FOR IDENTIFYING THERMODYNAMIC EFFECTS OF ATOMIC CHANGES TO POLYMERS

摘要

Systems and methods for evaluating thermodynamics of atomic changes in a polymer include using a first portion of a refined derived set of three-dimensional coordinates for a derivation of the polymer, which incorporates the atomic change under study, to compute a first effective atomistic Hessian. A second effective atomistic Hessian is computed using a second portion of a refined native set of three-dimensional coordinates for the native polymer. Atoms in the first and second portions are identical. A thermodynamic property of the first portion is determined using the refined derived set of three-dimensional coordinates and the first effective atomistic Hessian. A thermodynamic property of the second portion of the native polymer is determined using the refined native set of three-dimensional coordinates and the second effective atomistic Hessian. The effect of the atomic changes is quantified by taking the difference between the calculated thermodynamic properties of the first and second portions.

主权项

1. A method of identifying a thermodynamic effect of an atomic replacement, insertion or deletion in a polymer, the method comprising:
at a computer system having one or more processors and memory storing one or more programs to be executed by the one of more processors: (A) using a set of three-dimensional coordinates {y1, . . . , yN} for a derivation of the polymer, the derivation of the polymer formed by incorporating the atomic replacement, insertion or deletion into the polymer, to compute a first effective atomistic Hessian of a first portion of the derivation of the polymer, wherein each respective yi in {y1, . . . , yN} is a three dimensional coordinate for an atom in a first plurality of atoms in the derivation of the polymer; (B) using a native set of three-dimensional coordinates {x1, . . . , xM} for the native polymer to compute a second effective atomistic Hessian of a second portion of the native polymer, wherein each respective xi in {x1, . . . , xM} is a three dimensional coordinate for an atom in a second plurality of atoms in the native version of the polymer; (C) computing a thermodynamic property of the first portion of the derivation of the polymer using the derived set of three-dimensional coordinates {y1, . . . , yN} and the first effective atomistic Hessian; and (D) computing a thermodynamic property of the second portion of the native polymer using the native set of three-dimensional coordinates {x1, . . . , xM} and the second effective atomistic Hessian.