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Updated: Aug 15, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
Monte Carlo simulation of an inhomogeneous dielectric continuum model for B-DNA
Scott Grandison1, Robert Penfold, Jean-Marc Vanden-Broeck
1School of Mathematics, University of East Anglia, Norwich, UKNR4 7TJ. s.grandison@uea.ac.uk
Abstract:
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.
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