Size-Dependent Diffusion of Dextrans in Excised Porcine Corneal Stroma.

Delivery of therapeutic agents to the eye requires efficient transport through cellular and extracellular barriers. We evaluated the rate of diffusive transport in excised porcine corneal stroma using fluorescently labeled dextran molecules with hydrodynamic radii ranging from 1.3 to 34 nm.

Diffusion-limited encounter rate in a three-dimensional lattice of connected compartments studied by Brownian-dynamics simulations.

We considered the rate at which a diffusing particle encounters a target in a three-dimensional lattice of compartments with semipermeable walls. This work expands a previous theory [Li et al., Phys.

Effects of macromolecular crowding on the structure of a protein complex: a small-angle scattering study of superoxide dismutase.

Macromolecular crowding can alter the structure and function of biological macromolecules. We used small-angle scattering to measure the effects of macromolecular crowding on the size of a protein complex, SOD (superoxide dismutase). Crowding was induced using 400 MW PEG (polyethylene glycol),TEG (triethylene glycol), α-MG (methyl-α-glucoside), and TMAO (trimethylamine n-oxide).

Calculated rates of diffusion-limited reactions in a three-dimensional network of connected compartments: application to porous catalysts and biological systems.

We describe the diffusion limit for reaction rates in a three-dimensional system of connected compartments. This model exhibits the length-scale dependent diffusion that can be observed in many heterogeneous environments, such as porous catalysts and biological environments. We obtain a simple analytical expression for the diffusion limit applicable to any scale of the compartment confinement.

Multivalent ion screening of charged glass surface studied by streaming potential measurements.

We used streaming potential technique to measure ζ potentials for glass as a function of Co(NH3)6Cl3 concentration, KCl concentration, and pH. Charge inversion was observed only at high surface charge densities and was inhibited by increased KCl concentration. Measured ζ potentials were compared with predictions from a recent theory by dos Santos et al.

Kinetics of loop formation in worm-like chain polymers.

A common theoretical approach to calculating reaction kinetics is to approximate a high-dimensional conformational search with a one-dimensional diffusion along an effective reaction coordinate. We employed Brownian dynamics simulations to test the validity of this approximation for loop formation kinetics in the worm-like chain polymer model. This model is often used to describe polymers that exhibit backbone stiffness beyond the monomer length scale.

Separability of electrostatic and hydrodynamic forces in particle electrophoresis.

By use of optical tweezers we explicitly measure the electrostatic and hydrodynamic forces that determine the electrophoretic mobility of a charged colloidal particle. We test the ansatz of O'Brien and White [J. Chem.

DNA stretching and multivalent-cation-induced condensation.

Motivated by measurements on stretched double-stranded DNA in the presence of multivalent cations, we develop a statistical mechanical model for the compaction of an insoluble semiflexible polymer under tension. Using a mean-field approach, we determine the order of the extended-to-compact transition and provide an interpretation for the magnitude and interval of tensions over which compaction takes place. In the simplest thermodynamic limit of an infinitely long homogeneous polymer, compaction is a first-order transition that occurs at a single value of tension.

Electrostatic exclusion of neutral solutes from condensed DNA and other charged phases.

Motivated by experiments on condensed DNA phases in binary mixtures of water and a low-dielectric solute, we develop a theory for the electrostatic contribution to solute exclusion from a highly charged phase, within the continuum approximation of the medium. Because the electric field is maximum at the surface of each ion, the electrostatic energy is dominated by the Born energy; interactions between charges are of secondary importance. Neglecting interactions and considering only the competition between the Born energy and the free energy of mixing, we predict that low dielectric solutes are excluded from condensed DNA phases in water-cosolvent mixtures.

Attractive forces between cation condensed DNA double helices.

By combining single-molecule magnetic tweezers and osmotic stress on DNA assemblies, we separate attractive and repulsive components of the total intermolecular interaction between multivalent cation condensed DNA. Based on measurements of several different cations, we identify two invariant properties of multivalent cation-mediated DNA interactions: repulsive forces decay exponentially with a 2.3 +/- 0.

Interplay of ion binding and attraction in DNA condensed by multivalent cations.

We have measured forces generated by multivalent cation-induced DNA condensation using single-molecule magnetic tweezers. In the presence of cobalt hexammine, spermidine, or spermine, stretched DNA exhibits an abrupt configurational change from extended to condensed. This occurs at a well-defined condensation force that is nearly equal to the condensation free energy per unit length.

Probing the limits of the Derjaguin approximation with scanning force microscopy.

We have measured the interaction force between a silicon nitride scanning force microscopy (SFM) probe and the basal plane of highly oriented pyrolitic graphite as a function of pH and ionic concentration in aqueous solutions. Forces in the range +/- 50 pN were reconstructed from measured signals using dynamical analysis of the cantilever. We modeled the force-separation data using a flat plate electric double-layer interaction and assumed the Derjaguin approximation to adapt the flat plate geometry for the SFM probe shape.

Connecting nanoscale images of proteins with their genetic sequences.

We present a technique for reconstructing biomolecular structures from scanning force microscope data. The technique works by iteratively refining model molecules by comparison of simulated and experimental images. It can remove instrument artifacts to yield accurate dimensional measurements from tip-broadened data.