Role of loop entropy in the force induced melting of DNA hairpin

Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the phase diagram differs significantly with the theoretical prediction.Comment: 9 pages, 8 figures; J. Chem. Phys (2011

Time dependence of breakdown in a global fiber-bundle model with continuous damage

A time-dependent global fiber-bundle model of fracture with continuous damage is formulated in terms of a set of coupled non-linear differential equations. A first integral of this set is analytically obtained. The time evolution of the system is studied by applying a discrete probabilistic method. Several results are discussed emphasizing their differences with the standard time-dependent model. The results obtained show that with this simple model a variety of experimental observations can be qualitatively reproduced.Comment: APS style, two columns, 4 figures. To appear in Phys. Rev.

Development of a Matrix Tool for the Prediction of Vibrio Species in Oysters Harvested from North Carolina

ABSTRACT The United States has federal regulations in place to reduce the risk of seafood-related infection caused by the estuarine bacteria Vibrio vulnificus and Vibrio parahaemolyticus . However, data to support the development of regulations have been generated in a very few specific regions of the nation. More regionally specific data are needed to further understand the dynamics of human infection relating to shellfish-harvesting conditions in other areas. In this study, oysters and water were collected from four oyster harvest sites in North Carolina over an 11-month period. Samples were analyzed for the abundances of total Vibrio spp., V. vulnificus , and V. parahaemolyticus ; environmental parameters, including salinity, water temperature, wind velocity, and precipitation, were also measured simultaneously. By utilizing these data, preliminary predictive management tools for estimating the abundance of V. vulnificus bacteria in shellfish were developed. This work highlights the need for further research to elucidate the full suite of factors that drive V. parahaemolyticus abundance

Resonant Formation of dμtd\mu t Molecules in Deuterium: An Atomic Beam Measurement of Muon Catalyzed dt Fusion

Resonant formation of $d\mu t$ molecules in collisions of muonic tritium ($\mu t$) on D$_2$ was investigated using a beam of $\mu t$ atoms, demonstrating a new direct approach in muon catalyzed fusion studies. Strong epithermal resonances in $d\mu t$ formation were directly revealed for the first time. From the time-of-flight analysis of $2036\pm 116$ $dt$ fusion events, a formation rate consistent with $0.73\pm (0.16)_{meas} \pm (0.09)_{model}$ times the theoretical prediction was obtained. For the largest peak at a resonance energy of $0.423 \pm 0.037$ eV, this corresponds to a rate of $(7.1 \pm 1.8) \times 10^9$ s$^{-1}$, more than an order of magnitude larger than those at low energies.Comment: To appear in Phys. Rev. Let

X-ray emission during the muonic cascade in hydrogen

We report our investigations of X rays emitted during the muonic cascade in hydrogen employing charge coupled devices as X-ray detectors. The density dependence of the relative X-ray yields for the muonic hydrogen lines (K_alpha, K_beta, K_gamma) has been measured at densities between 0.00115 and 0.97 of liquid hydrogen density. In this density region collisional processes dominate the cascade down to low energy levels. A comparison with recent calculations is given in order to demonstrate the influence of Coulomb deexcitation.Comment: 5 pages, Tex, 4 figures, submitted to Physical Review Letter

Perforin Rapidly Induces Plasma Membrane Phospholipid Flip-Flop

The cytotoxic cell granule secretory pathway is essential for host defense. This pathway is fundamentally a form of intracellular protein delivery where granule proteases (granzymes) from cytotoxic lymphocytes are thought to diffuse through barrel stave pores generated in the plasma membrane of the target cell by the pore forming protein perforin (PFN) and mediate apoptotic as well as additional biological effects. While recent electron microscopy and structural analyses indicate that recombinant PFN oligomerizes to form pores containing 20 monomers (20 nm) when applied to liposomal membranes, these pores are not observed by propidium iodide uptake in target cells. Instead, concentrations of human PFN that encourage granzyme-mediated apoptosis are associated with pore structures that unexpectedly favor phosphatidylserine flip-flop measured by Annexin-V and Lactadherin. Efforts that reduce PFN mediated Ca influx in targets did not reduce Annexin-V reactivity. Antigen specific mouse CD8 cells initiate a similar rapid flip-flop in target cells. A lipid that augments plasma membrane curvature as well as cholesterol depletion in target cells enhance flip-flop. Annexin-V staining highly correlated with apoptosis after Granzyme B (GzmB) treatment. We propose the structures that PFN oligomers form in the membrane bilayer may include arcs previously observed by electron microscopy and that these unusual structures represent an incomplete mixture of plasma membrane lipid and PFN oligomers that may act as a flexible gateway for GzmB to translocate across the bilayer to the cytosolic leaflet of target cells

Resummation of the Divergent Perturbation Series for a Hydrogen Atom in an Electric Field

We consider the resummation of the perturbation series describing the energy displacement of a hydrogenic bound state in an electric field (known as the Stark effect or the LoSurdo-Stark effect), which constitutes a divergent formal power series in the electric field strength. The perturbation series exhibits a rich singularity structure in the Borel plane. Resummation methods are presented which appear to lead to consistent results even in problematic cases where isolated singularities or branch cuts are present on the positive and negative real axis in the Borel plane. Two resummation prescriptions are compared: (i) a variant of the Borel-Pade resummation method, with an additional improvement due to utilization of the leading renormalon poles (for a comprehensive discussion of renormalons see [M. Beneke, Phys. Rep. vol. 317, p. 1 (1999)]), and (ii) a contour-improved combination of the Borel method with an analytic continuation by conformal mapping, and Pade approximations in the conformal variable. The singularity structure in the case of the LoSurdo-Stark effect in the complex Borel plane is shown to be similar to (divergent) perturbative expansions in quantum chromodynamics.Comment: 14 pages, RevTeX, 3 tables, 1 figure; numerical accuracy of results enhanced; one section and one appendix added and some minor changes and additions; to appear in phys. rev.

Induced pseudoscalar coupling of the proton weak interaction

The induced pseudoscalar coupling $g_p$ is the least well known of the weak coupling constants of the proton's charged--current interaction. Its size is dictated by chiral symmetry arguments, and its measurement represents an important test of quantum chromodynamics at low energies. During the past decade a large body of new data relevant to the coupling $g_p$ has been accumulated. This data includes measurements of radiative and non radiative muon capture on targets ranging from hydrogen and few--nucleon systems to complex nuclei. Herein the authors review the theoretical underpinnings of $g_p$, the experimental studies of $g_p$, and the procedures and uncertainties in extracting the coupling from data. Current puzzles are highlighted and future opportunities are discussed.Comment: 58 pages, Latex, Revtex4, prepared for Reviews of Modern Physic

DNA topoisomerases participate in fragility of the oncogene RET

Fragile site breakage was previously shown to result in rearrangement of the RET oncogene, resembling the rearrangements found in thyroid cancer. Common fragile sites are specific regions of the genome with a high susceptibility to DNA breakage under conditions that partially inhibit DNA replication, and often coincide with genes deleted, amplified, or rearranged in cancer. While a substantial amount of work has been performed investigating DNA repair and cell cycle checkpoint proteins vital for maintaining stability at fragile sites, little is known about the initial events leading to DNA breakage at these sites. The purpose of this study was to investigate these initial events through the detection of aphidicolin (APH)-induced DNA breakage within the RET oncogene, in which 144 APHinduced DNA breakpoints were mapped on the nucleotide level in human thyroid cells within intron 11 of RET, the breakpoint cluster region found in patients. These breakpoints were located at or near DNA topoisomerase I and/or II predicted cleavage sites, as well as at DNA secondary structural features recognized and preferentially cleaved by DNA topoisomerases I and II. Co-treatment of thyroid cells with APH and the topoisomerase catalytic inhibitors, betulinic acid and merbarone, significantly decreased APH-induced fragile site breakage within RET intron 11 and within the common fragile site FRA3B. These data demonstrate that DNA topoisomerases I and II are involved in initiating APH-induced common fragile site breakage at RET, and may engage the recognition of DNA secondary structures formed during perturbed DNA replication