Observation of Sommerfeld precursors on a fluid surface

We report the observation of two types of Sommerfeld precursors (or forerunners) on the surface of a layer of mercury. When the fluid depth increases, we observe a transition between these two precursor surface waves in good agreement with the predictions of asymptotic analysis. At depths thin enough compared to the capillary length, high frequency precursors propagate ahead of the ''main signal'' and their period and amplitude, measured at a fixed point, increase in time. For larger depths, low frequency ''precursors'' follow the main signal with decreasing period and amplitude. These behaviors are understood in the framework of the analysis first introduced for linear transient electromagnetic waves in a dielectric medium by Sommerfeld and Brillouin [1].Comment: to be published in Physical Review Letter

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Viral population estimation using pyrosequencing

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an EM algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies.Comment: 23 pages, 13 figure

Dislocation-induced spin tunneling in Mn-12 acetate

Comprehensive theory of quantum spin relaxation in Mn-12 acetate crystals is developed, that takes into account imperfections of the crystal structure and is based upon the generalization of the Landau-Zener effect for incoherent tunneling from excited energy levels. It is shown that linear dislocations at plausible concentrations provide the transverse anisotropy which is the main source of tunneling in Mn-12. Local rotations of the easy axis due to dislocations result in a transverse magnetic field generated by the field applied along the c-axis of the crystal, which explains the presence of odd tunneling resonances. Long-range deformations due to dislocations produce a broad distribution of tunnel splittings. The theory predicts that at subkelvin temperatures the relaxation curves for different tunneling resonances can be scaled onto a single master curve. The magnetic relaxation in the thermally activated regime follows the stretched-exponential law with the exponent depending on the field, temperature, and concentration of defects.Comment: 17 pages, 14 figures, 1 table, submitted to PR

Optimizing substitution matrix choice and gap parameters for sequence alignment

<p>Abstract</p> <p>Background</p> <p>While substitution matrices can readily be computed from reference alignments, it is challenging to compute optimal or approximately optimal gap penalties. It is also not well understood which substitution matrices are the most effective when alignment accuracy is the goal rather than homolog recognition. Here a new parameter optimization procedure, POP, is described and applied to the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global protein alignments.</p> <p>Results</p> <p>POP is compared to a recent method due to Kim and Kececioglu and found to achieve from 0.2% to 1.3% higher accuracies on pair-wise benchmarks extracted from BALIBASE. The VTML matrix series is shown to be the most accurate on several global pair-wise alignment benchmarks, with VTML200 giving best or close to the best performance in all tests. BLOSUM matrices are found to be slightly inferior, even with the marginal improvements in the bug-fixed RBLOSUM series. The PAM series is significantly worse, giving accuracies typically 2% less than VTML. Integer rounding is found to cause slight degradations in accuracy. No evidence is found that selecting a matrix based on sequence divergence improves accuracy, suggesting that the use of this heuristic in CLUSTALW may be ineffective. Using VTML200 is found to improve the accuracy of CLUSTALW by 8% on BALIBASE and 5% on PREFAB.</p> <p>Conclusion</p> <p>The hypothesis that more accurate alignments of distantly related sequences may be achieved using low-identity matrices is shown to be false for commonly used matrix types. Source code and test data is freely available from the author's web site at <url>http://www.drive5.com/pop</url>.</p