Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency.

A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles.

Effect of pH and Molecular Length on the Structure and Dynamics of Linear and Short-Chain Branched Poly(ethylene imine) in Dilute Solution: Scaling Laws from Detailed Molecular Dynamics Simulations.

Atomistic molecular dynamics (MD) simulations are carried out to examine the effect of molecular weight (= 0.6, 0.86, 1.

Theoretical modeling of fluid flow in cellular biological media: an overview.

Fluid-structure interactions strongly affect, in multiple ways, the structure and function of cellular biological media, such as tissues, biofilms, and cell-entrapping gels. Mathematical models and computer simulation are important tools in advancing our understanding of these interactions, interpreting experimental observations, and designing novel processes and biomaterials. In this paper, we present a comprehensive survey and highlight promising directions of future research on theoretical modeling of momentum transport in cellular biological media with focus on the formulation of governing equations and the calculation of material properties both theoretically and experimentally.

A multiscale theoretical model for diffusive mass transfer in cellular biological media.

An integrated methodology is developed for the theoretical analysis of solute transport and reaction in cellular biological media, such as tissues, microbial flocs, and biofilms. First, the method of local spatial averaging with a weight function is used to establish the equation which describes solute conservation at the cellular biological medium scale, starting with a continuum-based formulation of solute transport at finer spatial scales. Second, an effective-medium model is developed for the self-consistent calculation of the local diffusion coefficient in the cellular biological medium, including the effects of the structural heterogeneity of the extra-cellular space and the reversible adsorption to extra-cellular polymers.