A statistical physics perspective on alignment-independent protein sequence comparison.

Motivation: Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function, and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Results: Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from “first passage probability distribution” to summarize statistics of ensemble averaged amino acid propensity values. In this paper, we introduce and elaborate this approach.

Thermal detemplation of SBA-15 mesophases. Effect of the activation protocol on the framework contraction

The potential use of the solvothermal extraction (SE) as a preliminary step to calcination for detemplating SBA-15 mesophases is investigated; aiming to reduce the amount of organics to be burnt and thereby the corresponding structural shrinkage. A systematic study was carried out by soxhlet extraction on mesophases hydrothermally aged between 90 and 130 C. The mesophases containing variable amounts of template were then treated by calcination or pyrolysis/calcination. TGA was applied to quantify the template amount after the various treatments. The as obtained materials were characterized by SAXS and Ar ad/desorption for structural and textural information while 1H NMR gave information about the integrity of the as-recycled template. The study shows that solvothermal conditions remove considerably the template, typically from 50 to 10-20 wt.%, mainly extracted from the primary mesopores. Possible reuse of the extracted template is questionable as it is poor in polyethyleneoxide compared to the synthesis block-copolymer, Pluronic P123. For all thermal protocols applied (direct calcination, calcination after solvent-extraction or pyrolysis/calcination after solvent extraction), the thermal shrinkage decreases with the aging temperature; that is consistent with the condensation degree of the silica. For each mesophase, it was found that the thermal shrinkage becomes less pronounced when the material is fully templated; thus the template can serve as structural support or can control the mass transfer of O2 and thereby the oxidation rate of the template burning. © 2013 Elsevier Inc. All rights reserved.