Direct determination of the base-pair force constant of DNA from the acoustic phonon dispersion of the double helix.

Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3 N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83 N/m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.

Nonlinear diffusion in two-dimensional ordered porous media based on a free volume theory.

A continuum nonlinear diffusion model is developed to describe molecular transport in ordered porous media. An existing generic van der Waals equation of state based free volume theory of binary diffusion coefficients is modified and introduced into the two-dimensional diffusion equation. The resulting diffusion equation is solved numerically with the alternating-direction fully implicit method under Neumann boundary conditions. Two types of pore structure symmetries are considered, hexagonal and cubic. The former is modeled as parallel channels while in case of the latter equal-sized channels are placed perpendicularly thus creating an interconnected network. First, general features of transport in both systems are explored, followed by the analysis of the impact of molecular properties on diffusion inside and out of the porous matrix. The influence of pore size on the diffusion-controlled release kinetics is assessed and the findings used to comment recent experimental studies of drug release profiles from ordered mesoporous silicates.

Atomistic model of DNA: phonons and base-pair opening.

A fully atomistic model of B-DNA using the CHARMM (chemistry at Harvard molecular mechanics) force field is presented. Molecular dynamics simulations were used to prepare an equilibrium structure. The Hessian of interatomic forces obtained from CHARMM for the equilibrium structure was used as input to a large scale phonon calculation. The calculated dispersion relations at low frequency are compared with recently published experimental data, which shows the model to have good accuracy for the low frequency, vibrational modes of DNA. These are discussed in the context of base-pair opening. In addition to the widely reported modes at, or below, approximately 12.5 meV, a continuous band of modes with strong base-pair opening character is found up to 40 meV, which coincides with the typical denaturation temperature of DNA.