Partly melted DNA conformations obtained with a probability peak finding method

Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate the alternative conformations that coexist in equilibrium and the range of their fluctuations. This yields a representation of the conformational ensemble at a given temperature, which is illustrated in a single diagram called a stitch profile. This article describes the methodology and discusses stitch profiles vs. the ordinary probability profiles using the phage lambda genome as an example.Comment: 11 pages, 9 figures; v3: major changes; v4: applications sectio

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

Evaluation of Three Trap Types and Five Lures for Monitoring \u3ci\u3eHylurgus Ligniperda\u3c/i\u3e (Coleoptera: Scolytidae) and Other Local Scolytids in New York

Hylurgus ligniperda (Coleoptera: Scolytidae) is a pine (Pinus spp.) pest native to Eurasia and northern Africa. In December 2000, an established population of H. ligniperda was discovered in Monroe County, New York. When surveys were initiated to determine the distribution of H. ligniperda, questions arose regarding the most effective trap and lure for survey purposes. We conducted a study in April-May 2001 to compare the effectiveness of commercially available scolytid traps and lures for attracting and capturing H. ligniperda. Traps tested included: 1) 12-unit Lindgren funnel trap, 2) Intercept panel trap, and 3) Theysohn slot-trap. Lures tested included: 1) α-pinene high release (750 mg/day) and ethanol (280 mg/ day), 2) α-pinene low release (300 mg/day) and ethanol, 3) β-pinene high release (2000 mg/day) and ethanol, 4) α-pinene low release, and 5) the “exotic bark beetle lure” [ipsdienol (0.15 mg/day), cis-verbenol (0.35 mg/day), and methylbutenol (10 mg/day)]. All three trap designs captured H. ligniperda, however, the Lindgren funnel trap caught significantly higher numbers. Capture rates of Tomicus piniperda (Coleoptera: Scolytidae) and Hylastes opacus were highest in Lindgren funnel traps; whereas Orthotomicus caelatus collections were highest in Theysohn traps. Capture rates of Ips grandicollis and Xyleborinus saxeseni did not vary significantly among trap types. Behavioral differences among scolytid species such as visual stimuli, flight and landing behavior, and host selection may explain some of these differences. Lures containing α-pinene or β-pinene and ethanol were most attractive to H. ligniperda adults, with ethanol and high-release α-pinene attracting the highest numbers in absolute terms. The exotic bark beetle lure was the least attractive lure to H. ligniperda. Attractiveness of the lures tested varied significantly for other Scolytidae, including Dendroctonus valens, H. opacus, Ips calligraphus, I. grandicollis, I. pini, O. caelatus, T. piniperda, and X. saxeseni. These differences likely were due to variation in lure release rates, host preferences, and/or species-specific pheromone attraction

Numerical simulations of a siphon mechanism for quiescent prominence formation

Quiescent prominences represent a significant challenge to our understanding of the flow of mass and energy in the outer layers of the solar atmosphere. A small number of quiescent prominences contain as much mass as the entire corona (Athay, 1976). The problem then is how to get that much material into the relatively small volume of a prominence and maintain it at a temperature of 10,000 K in close proximity to material at one million K. The thermal insulation to conduction provided by the magnetic field explains the disparate temperatures. The mass source problem is less well understood. One method for supplying mass to the prominence is to siphon it from the chromosphere. The siphon mechanism begins with a magnetic loop that evolves into a configuration with a gravitational well, such as that described by Kippenhahn and Schluter (1957). This could be formed, for example, by a twist in the magnetic field. A gravitational well could also be formed by a condensation induced sag in the field. This could further enhance the condensation process. Once this well has formed, or as it is forming, the material in the well area of the loop must cool and condense to the point where radiative losses exceed any heat input. Additional material must also flow into the well from the underlying chromosphere to supply the mass required to form the prominence. One example from a series of numerical simulations that were performed to study the formation of quiescent prominences is presented

\u3ci\u3eTomicus Piniperda\u3c/i\u3e (Coleoptera: Scolytidae): Is Shoot Feeding Required for Reproductive Maturation?

The pine shoot beetle, Tomicus piniperda (Coleoptera: Scolytidae), is a univoltine pest of pine in its native range of Europe and Asia. Tomicus piniperda is now widely established in the Great Lakes region and poses a potentially significant threat to other pine-producing areas in North America. An unusual aspect of the life history of T. piniperda is the extended period of maturation-feeding that takes place in the shoots of living pine trees and subsequent overwintering before adults reproduce the following year. We investigated the extent to which shoot-feeding is required by newly-emerged T. piniperda before introduction into Scotch pine (Pinus sylvestris) logs and before any overwintering, in order for successful reproduction to occur. Tomi­cus piniperda F1 adults successfully reproduced in pine logs in the laboratory after either no shoot-feeding or after 2 to 10 weeks of shoot-feeding. Thus, it is theoretically possible for T. piniperda to be multivoltine, yet it remains univoltine

Dynamics of a bubble formed in double stranded DNA

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let

Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev. Focus 15, story 1

Disruptant Effects of 4-Allylanisole and Verbenone on \u3ci\u3eTomicus Piniperda\u3c/i\u3e (Coleoptera: Scolytidae) Response to Baited Traps and Logs

We assessed the inhibitory effects of the host compound 4-allylanisole (release rates = 1 and 2 mg/d in 1994, and 1 and 10 mg/d in 2001) on the response of the pine shoot beetle, Tomicus piniperda (L.), adults to funnel traps baited with the attractant host compound α-pinene (release rate = 150 mg/d) in two pine Christmas tree plantations in Michigan in spring 1994 and two other plantations in spring 2001. In three of the four plantations, all doses of 4- allylanisole significantly reduced T. piniperda attraction to α-pinene-baited traps by 46 to 76%. We also tested the inhibitory effect of the antiaggregation pheromone verbenone (release rates = 2 and 4 mg/d) on T. piniperda attack density on pine bolts (average bolt length was 62 cm and diameter was 19 cm) at three sites (two pine forest stands and one Christmas tree plantation) in Michigan in 1994. Verbenone significantly reduced T. piniperda attack density by 37 to 60% at the two pine stands, but not at the Christmas tree plantation

Looking into DNA breathing dynamics via quantum physics

We study generic aspects of bubble dynamics in DNA under time dependent perturbations, for example temperature change, by mapping the associated Fokker-Planck equation to a quantum time-dependent Schroedinger equation with imaginary time. In the static case we show that the eigenequation is exactly the same as that of the $\beta$-deformed nuclear liquid drop model, without the issue of non-integer angular momentum. A universal breathing dynamics is demonstrated by using an approximate method in quantum mechanics. The calculated bubble autocorrelation function qualitatively agrees with experimental data. Under time dependent modulations, utilizing the adiabatic approximation, bubble properties reveal memory effects.Comment: 5 pages, 1 figur