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Full-Text Articles in Physical Sciences and Mathematics
Modeling Correlated Main-Chain Motions In Proteins For Flexible Molecular Recognition., Maria Zavodsky, Ming Lei, M. Thorpe, Anthony Day, Leslie Kuhn
Modeling Correlated Main-Chain Motions In Proteins For Flexible Molecular Recognition., Maria Zavodsky, Ming Lei, M. Thorpe, Anthony Day, Leslie Kuhn
Anthony Roy Day
We describe a new method for modeling protein and ligand main-chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large-scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystallography or NMR. A secondary goal is to assess the degree of flexibility consistent with protein–ligand recognition. Flexibility analysis of the target protein is performed using the graph-theoretic algorithm FIRST, which also identifies coupled networks of covalent and noncovalent bonds within the …
Spectral Densities Of Embedded Interfaces In Composite Materials, A. R. Mcgurn, Anthony Roy Day, D. J. Bergman, L. C. Davis, M. F. Thorpe
Spectral Densities Of Embedded Interfaces In Composite Materials, A. R. Mcgurn, Anthony Roy Day, D. J. Bergman, L. C. Davis, M. F. Thorpe
Anthony Roy Day
The effective resistivity and conductivity of two media that meet at a randomly rough interface are computed in the quasistatic limit. The results are presented in the spectral density representations of the Bergman-Milton formulation for the properties of two-component composite materials. The spectral densities are extracted from computer simulations of resistor networks in which the random interface separates two regions containing different types of resistors. In the limit that the bond lengths in the resistor network are small compared to parameters characterizing the surface roughness, the resistor network simulation approximates the continuum limit of the two-component composite. The Bergman-Milton formulation …