Similarity-Detection and Localization

The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a threshold value. The onset of detection is a continuous phase transition which can be viewed as a localization-delocalization transition. The ``fidelity'' of the alignment is the order parameter of that transition; it leads to criteria for the selection of optimal alignment parameters.Comment: 4 pages including 4 figures (308kb post-script file

MC64: A web platform to test bioinformatics algorithms in a many-core architecture

New analytical methodologies, like the so-called "next-generation sequencing" (NGS), allow the sequencing of full genomes with high speed and reduced price. Yet, such technologies generate huge amounts of data that demand large raw computational power. Many-core technologies can be exploited to overcome the involved bioinformatics bottleneck. Indeed, such hardware is currently in active development. We have developed parallel bioinformatics algorithms for many-core microprocessors containing 64 cores each. Thus, the MC64 web platform allows executing high-performance alignments (Needleman-Wunsch, Smith-Waterman and ClustalW) of long sequences. The MC64 platform can be accessed via web browsers, allowing easy resource integration into third-party tools. Furthermore, the results obtained from the MC64 include time-performance statistics that can be compared with other platform

How and why DNA barcodes underestimate the diversity of microbial eukaryotes

Background: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. Principal Findings: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependant. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. Conclusions: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous ''cryptic species'' will become discernable with the future acquisition of genomic and metagenomic sequences

Sintering Kinetics of Plasma-Sprayed Zirconia TBCs

A model of the sintering exhibited by EB-PVD TBCs, based on principles of free energy minimization, was recently published by Hutchinson et al. In the current paper, this approach is applied to sintering of plasma-sprayed TBCs and comparisons are made with experimental results. Predictions of through-thickness shrinkage and changing pore surface area are compared with experimental data obtained by dilatometry and BET analysis respectively. The sensitivity of the predictions to initial pore architecture and material properties are assessed. The model can be used to predict the evolution of contact area between overlying splats. This is in turn related to the through-thickness thermal conductivity, using a previously-developed analytical model

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences

In this article, we introduce PicXAA-Web, a web-based platform for accurate probabilistic alignment of multiple biological sequences. The core of PicXAA-Web consists of PicXAA, a multiple protein/DNA sequence alignment algorithm, and PicXAA-R, an extension of PicXAA for structural alignment of RNA sequences. Both PicXAA and PicXAA-R are probabilistic non-progressive alignment algorithms that aim to find the optimal alignment of multiple biological sequences by maximizing the expected accuracy. PicXAA and PicXAA-R greedily build up the alignment from sequence regions with high local similarity, thereby yielding an accurate global alignment that effectively captures local similarities among sequences. PicXAA-Web integrates these two algorithms in a user-friendly web platform for accurate alignment and analysis of multiple protein, DNA and RNA sequences. PicXAA-Web can be freely accessed at http://gsp.tamu.edu/picxaa/

Generalized Interpolation Material Point Approach to High Melting Explosive with Cavities Under Shock

Criterion for contacting is critically important for the Generalized Interpolation Material Point(GIMP) method. We present an improved criterion by adding a switching function. With the method dynamical response of high melting explosive(HMX) with cavities under shock is investigated. The physical model used in the present work is an elastic-to-plastic and thermal-dynamical model with Mie-Gr\"uneissen equation of state. We mainly concern the influence of various parameters, including the impacting velocity $v$, cavity size $R$, etc, to the dynamical and thermodynamical behaviors of the material. For the colliding of two bodies with a cavity in each, a secondary impacting is observed. Correspondingly, the separation distance $D$ of the two bodies has a maximum value $D_{\max}$ in between the initial and second impacts. When the initial impacting velocity $v$ is not large enough, the cavity collapses in a nearly symmetric fashion, the maximum separation distance $D_{\max}$ increases with $v$. When the initial shock wave is strong enough to collapse the cavity asymmetrically along the shock direction, the variation of $D_{\max}$ with $v$ does not show monotonic behavior. Our numerical results show clear indication that the existence of cavities in explosive helps the creation of ``hot spots''.Comment: Figs.2,4,7,11 in JPG format; Accepted for publication in J. Phys. D: Applied Physic

Banding, Excitability and Chaos in Active Nematic Suspensions

Motivated by the observation of highly unstable flowing states in suspensions of microtubules and kinesin, we analyze a model of mutually-propelled filaments suspended in a solvent. The system undergoes a mean-field isotropic-nematic transition for large enough filament concentrations when the nematic order parameter is allowed to vary in space and time. We analyze the model in two contexts: a quasi-one-dimensional channel with no-slip walls and a two-dimensional box with periodic boundaries. Using stability analysis and numerical calculations we show that the interplay between non-uniform nematic order, activity, and flow results in a variety of complex scenarios that include spontaneous banded laminar flow, relaxation oscillations, and chaos.Comment: 15 pages, 15 figure

Local alignment of two-base encoded DNA sequence

<p>Abstract</p> <p>Background</p> <p>DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity.</p> <p>Results</p> <p>We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions.</p> <p>Conclusion</p> <p>The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data.</p

Characterization of the Rheological, Mucoadhesive, and Drug Release Properties of Highly Structured Gel Platforms for Intravaginal Drug Delivery

This investigation describes the formulation and characterization of rheologically structured vehicles (RSVs) designed for improved drug delivery to the vagina. Interactive, multicomponent, polymeric platforms were manufactured containing hydroxyethylcellulose (HEC, 5 % w/w) polyvinylpyrrolidone (PVP, 4 % w/w), Pluronic (PL, 0 or 10 % w/w), and either polycarbophil (PC, 3 % w/w) or poly(methylvinylether-co-maleic anhydride) (Gantrez S97, 3 % w/w) as a mucoadhesive agent. The rheological (torsional and dynamic), mechanical (com-pressional), and mucoadhesive properties were characterized and shown to be dependent upon the mucoadhesive agent used and the inclusion/exclusion of PL. The dynamic rheological properties of the gel platforms were also assessed following dilution with simulated vaginal fluid (to mimic in vivo dilution). RSVs containing PC were more rheologically structured than comparator formulations containing GAN. This trend was also reflected in formulation hardness, compressibility, consistency, and syringeability. Moreover, formulations containing PL (10% w/w) were more rheologically structured than formulations devoid of PL. Dilution with simulated vaginal fluids significantly decreased rheological structure, although RSVs still retained a highly elastic structure (G ′&gt; G′ ′ and tan δ &lt; 1). Furthermore, RSVs exhibited sustained drug release properties that were shown to be dependent upon their rheological structure. It is considered that these semisolid drug delivery systems may be useful as site-retentive platforms for the sustained delivery of therapeutic agents to the vagina