sobolevnrm's Yang:Q [3 articles]

Abstract

We describe a method for efficiently generating ensembles of alternate, all-atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low-frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more ...

Abstract

An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two ...

Abstract

Counterion condensation is a basic feature of 2D electrostatics exhibited by highly charged rodlike polymers such as DNA. In the framework of the Poisson Boltzmann equation with salt, we show that such a polymer of radius a attracts a condensate of thickness RM = A(axi)1/2 where xi is the Debye length and A depends weakly on the polymer charge density q0. To leading order in 1/ln(xi/a), we derive the condensate structure and show that free ions follow universal density profiles independent ...