Thermodynamics of Twisted DNA with Solvent Interaction

The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over $\sim 10^7 - 10^8$ base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.Comment: The Journal of Chemical Physics (2011) in pres

Patterned Geometries and Hydrodynamics at the Vortex Bose Glass Transition

Patterned irradiation of cuprate superconductors with columnar defects allows a new generation of experiments which can probe the properties of vortex liquids by confining them to controlled geometries. Here we show that an analysis of such experiments that combines an inhomogeneous Bose glass scaling theory with the hydrodynamic description of viscous flow of vortex liquids can be used to infer the critical behavior near the Bose glass transition. The shear viscosity is predicted to diverge as $|T-T_{BG}|^{-z}$ at the Bose glass transition, with $z\simeq 6$ the dynamical critical exponent.Comment: 5 pages, 4 figure

Translational Correlations in the Vortex Array at the Surface of a Type-II Superconductor

We discuss the statistical mechanics of magnetic flux lines in a finite-thickness slab of type-II superconductor. The long wavelength properties of a flux-line liquid in a slab geometry are described by a hydrodynamic free energy that incorporates the boundary conditions on the flux lines at the sample's surface as a surface contribution to the free energy. Bulk and surface weak disorder are modeled via Gaussian impurity potentials. This free energy is used to evaluate the two-dimensional structure factor of the flux-line tips at the sample surface. We find that surface interaction always dominates in determining the decay of translational correlations in the asymptotic long-wavelength limit. On the other hand, such large length scales have not been probed by the decoration experiments. Our results indicate that the translational correlations extracted from the analysis of the Bitter patterns are indeed representative of behavior of flux lines in the bulk.Comment: 23 pages, 1 figure (not included), harvmac.tex macro needed (e-mail requests to [email protected] SU-CM-92-01

The effect of neuronal conditional knock-out of peroxisome proliferator-activated receptors in the MPTP mouse model of Parkinson's disease

This study was supported by Parkinson’s Disease Foundation (IRGP 09-11 (P.T.)), the Royal Society (2006/R1 (P.T.)), the Wellcome Trust (WT080782MF (P.T.)), the Biotechnology and Biological Sciences Research Council (P.T. and H.L.M.), the National Institutes of Health (DK057978) (R.M.E.), and by grants from the Leona M. and Harry B. Helmsley Charitable Trust (R.M.E.), the Glenn Foundation for Medical Research (R.M.E.), and the Ellison Medical Foundation (R.M.E.). R.M.E. is an investigator at the Howard Hughes Medical Institute and March of Dimes Chair in Molecular and Developmental Biology at the Salk Institute. The authors would like to thank Lynne J. Hocking, University of Aberdeen, for her assistance with the statistics. We are grateful to the staff of the Medical Research Facility for their help with the animal care and the microscopy core facility at the University of Aberdeen for the use of microscopy equipment.Peer reviewedPublisher PD

Factors Influencing the Adoption of Fodder Production Techniques by Milk Producers in Dhankuta District, Eastern Nepal

Many districts are food-deficient in Nepal. Increased milk consumption could improve human health and nutrition, while milk sales can provide families with a valuable source of income. However, milk production in Nepal is low, mainly because of the poor nutritional status of livestock, which can be attributed in part to a fodder deficit. However there is potential to increase fodder production, and some innovative fodder production techniques have been tried and proven locally. These include planting of fodder trees, fodder grasses and fodder crops. As the level of adoption of these techniques is variable, a survey was undertaken to quantify adoption levels by milk producers in Eastern Nepal, together with factors influencing adoption levels

Hydrodynamic Simulations of Propagating Warps and Bending Waves In Accretion Discs

We present the results of a study of propagating warp or bending waves in accretion discs. Three dimensional hydrodynamic simulations were performed using SPH, and the results of these are compared with calculations based on the linear theory of warped discs. We consider primarily the physical regime in which the dimensionless viscosity parameter `alpha' < H/r, the disc aspect ratio, so that bending waves are expected to propagate. We also present calculations in which `alpha' > H/r, where the warps are expected to behave diffusively. Small amplitude perturbations are studied in both Keplerian and slightly non Keplerian discs, and we find that the SPH results can be reasonably well fitted by those of the linear theory. The main results of these calculations are: (1) the warp in Keplerian discs when `alpha' < H/r propagates with little dispersion and damps at a rate expected from estimates of the code viscosity, (2) warps evolve diffusively when `alpha' > H/r, (3) the non Keplerian discs exhibit a substantially more dispersive behaviour of the warps. Initially imposed higher amplitude nonlinear warping disturbances were studied in Keplerian discs. The results indicate that nonlinear warps can lead to the formation of shocks, and that the evolution of the warp becomes less wave-like and more diffusive in character. This work is relevant to the study of the warped accretion discs that may occur around Kerr black holes or in misaligned binary systems. The results indicate that SPH can accurately model the hydrodynamics of warped discs, even when using rather modest numbers of particles.Comment: 14 pages, 9 figures, to appear in MNRA

Remote sensing of vigor loss in conifers due to dwarf mistletoe

The initial operation of a multiband/multidate tower-tramway test site in northeastern Minnesota for the development of specifications for subsequent multiband aerial photography of more extensive study areas was completed. Multiband/multidate configurations suggested by the tower-tramway studies were and will be flown with local equipment over the Togo test site. This site was photographed by the NASA RB57F aircraft in August and September 1971. It appears that, of all the film/filter combinations attempted to date (including optical recombining of several spectral band images via photo enhancement techniques), Ektachrome infrared film with a Wratten 12 filter is the best for detecting dwarf mistletoe, and other tree diseases as well. Using this film/filter combination, infection centers are easily detectable even on the smallest photo scale (1:100,000) obtained on the Togo site

Mapping the magic numbers in binary Lennard-Jones clusters

Using a global optimization approach that directly searches for the composition of greatest stability, we have been able to find the particularly stable structures for binary Lennard-Jones clusters with up to 100 atoms for a range of Lennard-Jones parameters. In particular, we have shown that just having atoms of different size leads to a remarkable stabilization of polytetrahedral structures, including both polyicosahedral clusters and at larger sizes structures with disclination lines.Comment: 5 pages, 5 figure

Pinning and Tribology of Tethered Monolayers on Disordered Substrates

We study the statistical mechanics and dynamics of crystalline films with a fixed internal connectivity on a random substrate. Defect free triangular lattices exhibit a sharp transition to a low temperature glassy phase with anomalous phonon fluctuations and a nonlinear force-displacement law with a continuously variable exponent, similar to the vortex glass phase of directed lines in 1+1 dimensions. The periodicity of the tethered monolayer acts like a filter which amplifies particular Fourier components of the disorder. However, the absence of annealed topological defects like dislocations is crucial: the transition is destroyed when the constraint of fixed connectivity is relaxed and dislocations are allowed to proliferate.Comment: revtex, preprint style, 27 pages. This submission is a revision of cond-mat/9607184. The revisions affect only Appendix B, Appendix C, and Eqs. 2.27, 2.28, 2.3