An algorithm for series expansions based on hierarchical rate equations

We propose a computational method to obtain series expansions in powers of time for general dynamical systems described by a set of hierarchical rate equations. The method is generally applicable to problems in both equilibrium and nonequilibrium statistical mechanics such as random sequential adsorption, diffusion-reaction dynamics, and Ising dynamics. New result of random sequential adsorption of dimers on a square lattice is presented.Comment: LaTeX, 9 pages including 1 figur

Dependence on temperature and GC content of bubble length distributions in DNA

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.Comment: 8 pages, 6 figures. Published on The Journal of Chemical Physic

Ephemeral active regions and coronal bright points: A solar maximum Mission 2 guest investigator study

A dominate association of coronal bright points (as seen in He wavelength 10830) was confirmed with the approach and subsequent disappearance of opposite polarity magnetic network. While coronal bright points do occur with ephemeral regions, this association is a factor of 2 to 4 less than with sites of disappearing magnetic flux. The intensity variations seen in He I wavelength 10830 are intermittent and often rapid, varying over the 3 minute time resolution of the data; their bright point counterparts in the C IV wavelength 1548 and 20 cm wavelength show similar, though not always coincident time variations. Ejecta are associated with about 1/3 of the dark points and are evident in the C IV and H alpha data. These results support the idea that the anti-correlation of X-ray bright points with the solar cycle can be explained by the correlation of these coronal emission structures with sites of cancelling flux, indicating that, in some cases, the process of magnetic flux removal results in the release of energy. That the intensity variations are rapid and variable suggests that this process works intermittently

DNA bubble dynamics as a quantum Coulomb problem

We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the bubble lifetime is associated with the continuum of scattering states of the repulsive Coulomb potential, at the melting temperature the Coulomb potential vanishes and the underlying first exit dynamics exhibits a long time power law tail, above the melting temperature, corresponding to an attractive Coulomb potential, the long time dynamics is controlled by the lowest bound state. Correlations and finite size effects are discussed.Comment: 4 pages, 3 figures, revte

Numerical study of the disordered Poland-Scheraga model of DNA denaturation

We numerically study the binary disordered Poland-Scheraga model of DNA denaturation, in the regime where the pure model displays a first order transition (loop exponent $c=2.15>2$). We use a Fixman-Freire scheme for the entropy of loops and consider chain length up to $N=4 \cdot 10^5$, with averages over $10^4$ samples. We present in parallel the results of various observables for two boundary conditions, namely bound-bound (bb) and bound-unbound (bu), because they present very different finite-size behaviors, both in the pure case and in the disordered case. Our main conclusion is that the transition remains first order in the disordered case: in the (bu) case, the disorder averaged energy and contact densities present crossings for different values of $N$ without rescaling. In addition, we obtain that these disorder averaged observables do not satisfy finite size scaling, as a consequence of strong sample to sample fluctuations of the pseudo-critical temperature. For a given sample, we propose a procedure to identify its pseudo-critical temperature, and show that this sample then obeys first order transition finite size scaling behavior. Finally, we obtain that the disorder averaged critical loop distribution is still governed by $P(l) \sim 1/l^c$ in the regime $l \ll N$, as in the pure case.Comment: 12 pages, 13 figures. Revised versio

Behaviors of Adult \u3ci\u3eAgrilus Planipennis\u3c/i\u3e (Coleoptera: Buprestidae)

A 2-year study was conducted in Canada (2003) and the United States (2005) to better understand searching and mating behaviors of adult Agrilus planipennis Fairmaire. In both field and laboratory, adults spent more time resting and walking than feeding or flying. The sex ratio in the field was biased towards males, which tended to hover around trees, likely looking for mates. There was more leaf feeding damage within a tree higher in the canopy than in the lower canopy early in the season, but this difference disappeared over time. In choice experiments, males attempted to mate with individuals of both sexes, but they landed more frequently on females than on males. A series of sexual behaviors was observed in the laboratory, including: exposure of the ovipositor/genitalia, sporadic jumping by males, attempted mating, and mating. Sexual behaviors were absent among 1-3 day-old beetles, but were observed regularly in 10-12 day-old beetles. Females were seen exposing their ovipositor, suggestive of pheromone-calling behavior. No courtship was observed prior to mating. Hovering, searching, and landing behaviors suggest that beetles most likely rely on visual cues during mate finding, although host-plant volatiles and/or pheromones might also be involved

\u3ci\u3eAnoplophora Glabripennis\u3c/i\u3e Within-Tree Distribution, Seasonal Development, and Host Suitability in China and Chicago

Established populations of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae), were first reported in the United States in New York in 1996, Illinois in 1998, and New Jersey in 2002. A federal quarantine and an eradication program were implemented in 1997, involving tree surveys and removal of infested trees. We recorded the number of A. glabripennis life stages found at several locations along the main trunk and major branches of naturally infested trees in China (species of Populus, Salix, and Ulmus) and Chicago, Illinois (species of Acer, Fraxinus, and Ulmus) during 1999 to 2002. Typically, A. glabripennis initiated attack near the crown base along both the trunk and main branches. The one exception to this pattern was on Populus trees in China that had branches along the entire trunk, in which case A. glabripennis initiated attack along the lower trunk. Larvae were the dominant overwintering stage in both countries. A host suitability index for A. glabripennis was calculated for each tree with the formula: (number of living life stages + number of exit holes) / number of oviposition pits. The mean host suitability index was higher on Populus and Salix than Ulmus in China, and generally higher on Acer and Ulmus than Fraxinus in Chicago. Eleven genera of trees (N = 1465 trees) were infested by A. glabripennis in Chicago; in decreasing order of tree frequency they included Acer, Ulmus, Fraxinus, Aesculus, Betula, Salix, Celtis, Malus, Pyrus, Sorbus, and Tilia. When the proportion of each genus of infested street trees (N = 958 trees in 7 genera) was compared to its proportion of all Chicago street trees based on a 2003 inventory (N = 539,613 trees in 45 genera), A. glabripennis showed a significant preference to infest the genera Acer and Ulmus. Based on our results, inspectors should focus their efforts on upper trunks and lower branches of Acer and Ulmus trees

A Survey of Laboratory Programs for First Year Medical Students

Basic science courses offered to freshmen medical students have been traditionally taught by didactic presentations and laboratory work. Various factors have prompted many departments to either markedly reduce the time allotted for the traditional, but more vulnerable, laboratory phase of these courses or drastically alter the content of the laboratory programs. Information concerning the desirability for such changes is incomplete and no evaluation has been developed to determine the effectiveness of change. Before beginning any further alterations in the laboratory programs at the Medical College of Virginia, it seemed desirable to determine anew what we wish to teach in the laboratory. This problem was approached in part by surveying the attitudes of other anatomy, biochemistry, and physiology departments

Handbook of perinatal infections, J. L. Sever, J. W. Larsen, Jr., and J. H. Grossman III, Little, Brown and Co., Boston, 1979, 199 pp

No Abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38149/1/1420230317_ftp.pd

Why is the DNA Denaturation Transition First Order?

We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between denaturated loops and the rest of the chain by exploiting recent results on scaling properties of polymer networks of arbitrary topology. The phase transition is found to be first order in d=2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let