Mean encounter times for cell adhesion in hydrodynamic flow: analytical progress by dimensional reduction

For a cell moving in hydrodynamic flow above a wall, translational and rotational degrees of freedom are coupled by the Stokes equation. In addition, there is a close coupling of convection and diffusion due to the position-dependent mobility. These couplings render calculation of the mean encounter time between cell surface receptors and ligands on the substrate very difficult. Here we show for a two-dimensional model system how analytical progress can be achieved by treating motion in the vertical direction by an effective reaction term in the mean first passage time equation for the rotational degree of freedom. The strength of this reaction term can either be estimated from equilibrium considerations or used as a fit parameter. Our analytical results are confirmed by computer simulations and allow to assess the relative roles of convection and diffusion for different scaling regimes of interest.Comment: Reftex, postscript figures include

Determinants of Effective Population Size for Loci with Different Modes of Inheritance

Here we report an assessment of the determinants of effective population size (Ne) in species with overlapping generations. Specifically, we used a stochastic demographic model to investigate the influence of different life-history variables on Ne/N (where N = population census number) and the influence of sex differences in life-history variables on Ne for loci with dif¬ferent modes of inheritance. We applied an individual-based modeling approach to two datasets: one from a natural popu¬lation of savannah baboons (Papio cynocephalus) in the Amboseli basin of southern Kenya and one from a human tribal pop¬ulation (the Gainj of Papua New Guinea). Simulation-based estimates of Ne/N averaged 0.329 for the Amboseli baboon population (SD = 0.116, 95% CI = 0.172 – 0.537) and 0.786 for the Gainj (SD = 0.184, 95% CI = 0.498 – 1.115). Although variance in male fitness had a substantial impact on Ne/N in each of the two primate populations, ratios of Ne values for au¬tosomal and sex-linked loci exhibited no significant departures from Poisson-expected values. In each case, similarities in sex-specific Ne values were attributable to the unexpectedly high variance in female fitness. Variance in male fitness resulted primarily from age-dependent variance in reproductive success, whereas variance in female fitness resulted primarily from stochastic variance in survival during the reproductive phase

Elastic Correlations in Nucleosomal DNA Structure

The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J. Richmond and C.A. Davey, Nature {\bf 423}, 145 (2003)], it is shown that elastic correlations exist between twist, roll, tilt, and stretching of DNA, as well as the distance between phosphate groups. The twist-bend coupling term is shown to be able to capture these correlations to a large extent, and a fit to the experimental data yields a new estimate of G=25 nm for the value of the twist-bend coupling constant

Wrapping Transition and Wrapping-Mediated Interactions for Discrete Binding along an Elastic Filament: An Exact Solution

The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show that statistical mechanics of the system can be solved exactly using a path integral formalism which gives access to the full effect of thermal fluctuations, going thus beyond the usual Gaussian approximations which take into account only the contributions from the minimal energy configuration and small fluctuations about this minimal energy solution. We obtain the free energy of the wrapping-unwrapping transition of the filament around the cylinders as well as the effective interaction between two wrapped cylinders due to thermal fluctuations of the elastic filament. A change of entropy due to wrapping of the filament around the adsorbing cylinders as they move closer together is identified as an additional source of interactions between them. Such entropic wrapping effects should be distinguished from the usual entropic configuration effects in semi-flexible polymers. Our results may be applicable to the problem of adsorption of proteins as well as synthetic nano-particles on semi-flexible polymers such as DNA.Comment: 24 pages, 12 figure

Spicules and the effect of rigid rods on enclosing membrane tubes

Membrane tubes (spicules) arise in cells, or artificial membranes, in the nonlinear deformation regime due to, e.g. the growth of microtubules, actin filaments or sickle hemoglobin fibers towards a membrane. We calculate the axial force exerted by the cylindrical membrane tube, and its average radius, by taking into account steric interactions between the fluctuating membrane and the enclosed rod. The force required to confine a fluctuating membrane near the surface of the enclosed rod diverges as the separation approaches zero. This results in a smooth crossover of the axial force between a square root and a linear dependence on the membrane tension as the tension increases and the tube radius shrinks. This crossover can occur at the most physiologically relevant membrane tensions. Our work may be important in (i) interpreting experiments in which axial force is related to the tube radius or membrane tension (ii) dynamical theories for biopolymer growth in narrow tubes where these fluctuation effects control the tube radius.Comment: 10 pages, 1 figur

Controlled release nanoparticulate matter delivery system

A controlled release nanoparticulate matter delivery system includes a plurality of thermoresponsive modules containing a respective nanoparticulate matter. Each thermoresponsive module is selectively operable in at least one of a heating mode that releases the nanoparticulate matter and a cooling mode that inhibits release of the nanoparticulate matter. A control module is in electrical communication with the plurality of thermoresponsive modules. The control module is configured to determine a temperature of each thermoresponsive module and to select the at least one heating mode and cooling mode based on the temperature. The heating and cooling mode may be selected in response to a desired dosing profile and/or a biometric condition.Board of Regents, University of Texas Syste

Crystallization of the gene 45 protein from the DNA replication fork of bacteriophage T4

The gene 45 protein from bacteriophage T4 has been purified and is crystallized. This protein is part of the T4 DNA replication complex. The crystallized protein is active in complementation assays. X-ray diffraction analysis is in progress; data are measured for the native and several heavy atom derivatives. The crystals diffract to about 3.5-Å resolution

Testing Tensile and Shear Epoxy Strength at Cryogenic Temperatures

This paper covers cryogenic, tensile testing and research completed on a number of epoxies used in cryogenic applications. Epoxies are used in many different applications; however, this research focused on the use of epoxy used to bond MLI standoffs to cryogenic storage tanks and the loads imparted to the tank through the MLI. To conduct testing, samples were made from bare stainless steel, aluminum and primed aluminum. Testing involved slowly cooling test samples with liquid nitrogen then applying gradually increasing tensile loads to the epoxy. The testing evaluated the strength and durability of epoxies at cryogenic temperatures and serves as a base for future testing. The results of the tests showed that some epoxies withstood the harsh conditions while others failed. The two epoxies yielding the best results were Masterbond EP29LPSP and Scotch Weld 2216. For all metal surfaces tested, both epoxies had zero failures for up to 11.81 kg of mass

Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops

The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized DNA with lengths that are not integer multiples of the pitch take on nontrivial shapes that involve bending out of planes and formation of kinks. The effect of sequence inhomogeneity on the shape of DNA is addressed, and shown to enhance the geometrical features. These findings could shed some light on the role of DNA conformation in protein--DNA interactions

Overcoming Innocents’ Naiveté: Pre‐interrogation Decision‐making Among Innocent Suspects

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/133623/1/bsl2247.pd