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- Jesse J Howard, John S Perkyns, B Montgomery Pettitt
- The journal of physical chemistry. B
- 2010

A renormalization of the 3D-RISM-HNC integral equation is used to study the solvent and ion distributions at neutral and negatively charged planar atomistic surfaces. The charge density of the surfaces ranged from 0.0 to 0.4116 C/m(2), and the modeled electrolyte solutions consist of the salts NaCl, KCl, and CsCl at concentrations of 0.1, 0.25, and 1.0 M in… (More)

- Jesse J Howard, Gillian C Lynch, B Montgomery Pettitt
- The journal of physical chemistry. B
- 2011

We calculate the water and ion spatial distributions around charged oligonucleotides using a renormalized three-dimensional reference interaction site theory coupled with the HNC closure. Our goal is to understand the balance between inter-DNA strand forces and solvation forces as a function of oligonucleotide length in the short strand limit. The DNA is… (More)

- Georgiy Golovko, Kamil Khanipov, +6 authors Yuriy Fofanov
- BMC Bioinformatics
- 2011

The emergence of Next Generation Sequencing technologies has made it possible for individual investigators to generate gigabases of sequencing data per week. Effective analysis and manipulation of these data is limited due to large file sizes, so even simple tasks such as data filtration and quality assessment have to be performed in several steps. This… (More)

- John S Perkyns, Gillian C Lynch, Jesse J Howard, B Montgomery Pettitt
- The Journal of chemical physics
- 2010

Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average… (More)

- Jesse J Howard, John S Perkyns, Niharendu Choudhury, B Montgomery Pettitt
- Journal of chemical theory and computation
- 2008

The hydrophobic association of two parallel graphene sheets is studied using the 3D-RISM HNC integral equations with several theoretical methods for the solvent distribution functions. The potential of mean force is calculated to study the effects of the aqueous solvent models and methods on the plates as a function of distance. The results of several… (More)

The Ornstein-Zernike (OZ) equations [1] can be used to find probability distributions of atoms in fluid states where the primary unknowns are the radial pair correlation function and the direct correlation function. In order to specify conditions of the state, certain parameters such as density and temperature are chosen. While one can find a single… (More)

- Jesse J Howard, B Montgomery Pettitt
- Journal of statistical physics
- 2011

In this review article we consider some of the current integral equation approaches and application to model polar liquid mixtures. We consider the use of multidimensional integral equations and in particular progress on the theory and applications of three dimensional integral equations. The IEs we consider may be derived from equilibrium statistical… (More)

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