Monte Carlo simulation of an inhomogeneous dielectric continuum model for B-DNA

Grandison, Scott, Penfold, Robert and Vanden-Broeck, Jean-Marc (2005) Monte Carlo simulation of an inhomogeneous dielectric continuum model for B-DNA. Physical Chemistry Chemical Physics, 7 (19). pp. 3486-3495. ISSN 1463-9076

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Thermodynamic and structural properties of the counterion atmosphere surrounding B-DNA are calculated by Monte Carlo simulation in a spatially inhomogeneous, but piecewise uniform, dielectric continuum cell model — the “barbarous” model. A boundary element formulation is implemented to study the sensitivity of these properties with respect to perturbations in the location of discontinuous dielectric boundaries relative to fixed and mobile charges. High concentrations are considered corresponding to the liquid crystalline hexagonally ordered phase of DNA. Primitive model results are verified against other simulation reports and a comparison of barbarous model predictions with experimental data is discussed. The internal energy, osmotic coefficient, radial distributions and the population ratio of counterions in the geometrically resolved major and minor grooves are all found to strongly depend on the dielectric boundary position. This suggests that a self-consistent development of the model should consider a free surface problem where the boundary is not specified a priori.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Faculty of Science > School of Mathematics
Depositing User: Rhiannon Harvey
Date Deposited: 31 Jan 2012 15:49
Last Modified: 11 Mar 2024 01:07
DOI: 10.1039/B508393A

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