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Full-Text Articles in Physics
A Novel Empirical Free Energy Function That Explains And Predicts Protein–Protein Binding Affinities, Joseph Audie, Suzanne Scarlata
A Novel Empirical Free Energy Function That Explains And Predicts Protein–Protein Binding Affinities, Joseph Audie, Suzanne Scarlata
Chemistry & Physics Faculty Publications
A free energy function can be defined as a mathematical expression that relates macroscopic free energy changes to microscopic or molecular properties. Free energy functions can be used to explain and predict the affinity of a ligand for a protein and to score and discriminate between native and non-native binding modes. However, there is a natural tension between developing a function fast enough to solve the scoring problem but rigorous enough to explain and predict binding affinities. Here, we present a novel, physics-based free energy function that is computationally inexpensive, yet explanatory and predictive. The function results from a derivation …
Local Effective Potential Theory: Nonuniqueness Of Potential And Wave Function, Viraht Sahni, Marlina Slamet, Xiao-Yin Pan
Local Effective Potential Theory: Nonuniqueness Of Potential And Wave Function, Viraht Sahni, Marlina Slamet, Xiao-Yin Pan
Physics Faculty Publications
In local effective potential energy theories such as the Hohenberg-Kohn-Sham density functional theory (HKS-DFT) and quantal density functional theory (Q-DFT) electronic systems in their ground or excited states are mapped to model systems of noninteracting fermions with equivalent density. From these models, the equivalent total energy and ionization potential are also obtained. This paper concerns the nonuniqueness of the local effective potential energy function of the model system in the mapping from a nondegenerate ground state, the nonuniqueness of the local effective potential energy function in the mapping from a nondegenerate excited state, and in the mapping to a model …