Protein sliding and hopping kinetics on DNA

Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (1) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of ms; (2) sliding dominates the root mean square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (3) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; furthermore, (4) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins

Canonical form of master equations and characterization of non-Markovianity

Master equations govern the time evolution of a quantum system interacting with an environment, and may be written in a variety of forms. Time-independent or memoryless master equations, in particular, can be cast in the well-known Lindblad form. Any time-local master equation, Markovian or non-Markovian, may in fact also be written in a Lindblad-like form. A diagonalisation procedure results in a unique, and in this sense canonical, representation of the equation, which may be used to fully characterize the non-Markovianity of the time evolution. Recently, several different measures of non-Markovianity have been presented which reflect, to varying degrees, the appearance of negative decoherence rates in the Lindblad-like form of the master equation. We therefore propose using the negative decoherence rates themselves, as they appear in the canonical form of the master equation, to completely characterize non-Markovianity. The advantages of this are especially apparent when more than one decoherence channel is present. We show that a measure proposed by Rivas et al. is a surprisingly simple function of the canonical decoherence rates, and give an example of a master equation that is non-Markovian for all times t>0, but to which nearly all proposed measures are blind. We also give necessary and sufficient conditions for trace distance and volume measures to witness non-Markovianity, in terms of the Bloch damping matrix.Comment: v2: Significant update, with many new results and one new author. 12 pages; v3: Minor clarifications, to appear in PRA; v4: matches published versio

The Removal of Artificially Generated Polarization in SHARP Maps

We characterize the problem of artificial polarization for the Submillimeter High Angular Resolution Polarimeter (SHARP) through the use of simulated data and observations made at the Caltech Submillimeter Observatory (CSO). These erroneous, artificial polarization signals are introduced into the data through misalignments in the bolometer sub-arrays plus pointing drifts present during the data-taking procedure. An algorithm is outlined here to address this problem and correct for it, provided that one can measure the degree of the sub-array misalignments and telescope pointing drifts. Tests involving simulated sources of Gaussian intensity profile indicate that the level of introduced artificial polarization is highly dependent upon the angular size of the source. Despite this, the correction algorithm is effective at removing up to 60% of the artificial polarization during these tests. The analysis of Jupiter data taken in January 2006 and February 2007 indicates a mean polarization of 1.44%+/-0.04% and 0.95%+/-0.09%, respectively. The application of the correction algorithm yields mean reductions in the polarization of approximately 0.15% and 0.03% for the 2006 and 2007 data sets, respectively.Comment: 19 pages, 7 figure

Discovery of Resolved Debris Disk Around HD 131835

We report the discovery of the resolved disk around HD 131835 and present the analysis and modeling of its thermal emission. HD 131835 is a ~15 Myr A2 star in the Scorpius-Centaurus OB association at a distance of 122.7 +16.2 -12.8 parsec. The extended disk has been detected to ~1.5" (200 AU) at 11.7 {\mu}m and 18.3 {\mu}m with T-ReCS on Gemini South. The disk is inclined at an angle of ~75{\deg} with the position angle of ~61{\deg}. The flux of HD 131835 system is 49.3+-7.6 mJy and 84+-45 mJy at 11.7 {\mu}m and 18.3 {\mu}m respectively. A model with three grain populations gives a satisfactory fit to both the spectral energy distribution and the images simultaneously. This best-fit model is composed of a hot continuous power-law disk and two rings. We characterized the grain temperature profile and found that the grains in all three populations are emitting at temperatures higher than blackbodies. In particular, the grains in the continuous disk are unusually warm; even when considering small graphite particles as the composition.Comment: 11 pages, 5 figures, Accepted for Publication in Ap

Analytical solution of the Gross-Neveu model at finite density

Recent numerical calculations have shown that the ground state of the Gross-Neveu model at finite density is a crystal. Guided by these results, we can now present the analytical solution to this problem in terms of elliptic functions. The scalar potential is the superpotential of the non-relativistic Lame Hamiltonian. This model can also serve as analytically solvable toy model for a relativistic superconductor in the Larkin-Ovchinnikov-Fulde-Ferrell phase.Comment: 5 pages, no figures, revtex; vs2: appendix with analytical proof of self-consistency adde

Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture

<p>Abstract</p> <p>Background</p> <p>The biological dimensions of genes are manifold. These include genomic properties, (e.g., X/autosomal linkage, recombination) and functional properties (e.g., expression level, tissue specificity). Multiple properties, each generally of subtle influence individually, may affect the evolution of genes or merely be (auto-)correlates. Results of multidimensional analyses may reveal the relative importance of these properties on the evolution of genes, and therefore help evaluate whether these properties should be considered during analyses. While numerous properties are now considered during studies, most work still assumes the stereotypical solitary gene as commonly depicted in textbooks. Here, we investigate the <it>Drosophila melanogaster </it>genome to determine whether deviations from the stereotypical gene architecture correlate with other properties of genes.</p> <p>Results</p> <p>Deviations from the stereotypical gene architecture were classified as the following gene constellations: Overlapping genes were defined as those that overlap in the 5-prime, exonic, or intronic regions. Chromatin co-clustering genes were defined as genes that co-clustered within 20 kb of transcriptional territories. If this scheme is applied the stereotypical gene emerges as a rare occurrence (7.5%), slightly varied schemes yielded between ~1%-50%. Moreover, when following our scheme, paired-overlapping genes and chromatin co-clustering genes accounted for 50.1 and 42.4% of the genes analyzed, respectively. Gene constellation was a correlate of a number of functional and evolutionary properties of genes, but its statistical effect was ~1-2 orders of magnitude lower than the effects of recombination, chromosome linkage and protein function. Analysis of datasets on male reproductive proteins showed these were biased in their representation of gene constellations and evolutionary rate Ka/Ks estimates, but these biases did not overwhelm the biologically meaningful observation of high evolutionary rates of male reproductive genes.</p> <p>Conclusion</p> <p>Given the rarity of the solitary stereotypical gene, and the abundance of gene constellations that deviate from it, the presence of gene constellations, while once thought to be exceptional in large Eukaryote genomes, might have broader relevance to the understanding and study of the genome. However, according to our definition, while gene constellations can be significant correlates of functional properties of genes, they generally are weak correlates of the evolution of genes. Thus, the need for their consideration would depend on the context of studies.</p