Towards Reliable Automatic Protein Structure Alignment

A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based on local structure similarity. In this work, we propose a method to incorporate global information in obtaining optimal alignments and superpositions. Our method, when applied to optimizing the TM-score and the GDT score, produces significantly better results than current state-of-the-art protein structure alignment tools. Specifically, if the highest TM-score found by TMalign is lower than (0.6) and the highest TM-score found by one of the tested methods is higher than (0.5), there is a probability of (42%) that TMalign failed to find TM-scores higher than (0.5), while the same probability is reduced to (2%) if our method is used. This could significantly improve the accuracy of fold detection if the cutoff TM-score of (0.5) is used. In addition, existing structure alignment algorithms focus on structure similarity alone and simply ignore other important similarities, such as sequence similarity. Our approach has the capacity to incorporate multiple similarities into the scoring function. Results show that sequence similarity aids in finding high quality protein structure alignments that are more consistent with eye-examined alignments in HOMSTRAD. Even when structure similarity itself fails to find alignments with any consistency with eye-examined alignments, our method remains capable of finding alignments highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Green function techniques in the treatment of quantum transport at the molecular scale

The theoretical investigation of charge (and spin) transport at nanometer length scales requires the use of advanced and powerful techniques able to deal with the dynamical properties of the relevant physical systems, to explicitly include out-of-equilibrium situations typical for electrical/heat transport as well as to take into account interaction effects in a systematic way. Equilibrium Green function techniques and their extension to non-equilibrium situations via the Keldysh formalism build one of the pillars of current state-of-the-art approaches to quantum transport which have been implemented in both model Hamiltonian formulations and first-principle methodologies. We offer a tutorial overview of the applications of Green functions to deal with some fundamental aspects of charge transport at the nanoscale, mainly focusing on applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references, submitted to Springer series "Lecture Notes in Physics

РЕКОНСТРУКЦИЯ ПАЛЬЦЕВ КИСТИ С ИСПОЛЬЗОВАНИЕМ ТРАДИЦИОННЫХ И МИКРОХИРУРГИЧЕСКИХ МЕТОДИК

The authors presents a new method of hand and finger reconstruction, which makes it possible to restore finger surface and bony frame by transfer of vascularized osteo-cutaneous grafts on microvessel anastomoses and transposition of the radial flap on peripheral pedicle. Lipocutaneous flaps on temporary pedicles provide coverage for the most part of the reconstructed digit as well as for the present hand defects. Complete acceptance of segments was achieved in 92,8% of cases. In all the cases of successful segment acceptance bony frame stability in the reconstructed digits and restoration of the bilateral hand grip were achieved.Представлен и обоснован авторский подход к реконструкции пальцев кисти, заключающийся в восстановлении костного остова и рабочей поверхности пальцев путем свободной пересадки кровоснабжаемых кожно-костных комплексов на микрососудистых анастомозах или несвободной пересадки лучевого лоскута предплечья на дистальной сосудистой ножке. На первом этапе реконструкции большую часть реконструируемых пальцев, а также имеющиеся дефекты кисти закрывали кожно-жировыми лоскутами на временной питающей ножке. Полное приживление комплексов тканей отмечено в 92,8% наблюдений. Во всех этих случаях достигнута стабильность костного остова сформированных пальцев, а также восстановлен или улучшен двусторонний схват кисти

ON MANAGING THE USE OF SURROGATES IN GENERAL NONLINEAR OPTIMIZATION AND MDO

This paper is concerned with a trust-region approximation management framework (AMF) for solving the nonlinear programming problem, in general, and multidisciplinary optimization problems, in particular. The intent of the AMF methodology is to facilitate the solution of optimization problems with high-fidelity models. While such models are designed to approximate the physical phenomena they describe to a high degree of accuracy, their use in a repetitive procedure, for example, iterations of an optimization or a search algorithm, make such use prohibitively expensive. An improvement in design with lower-fidelity, cheaper models, however, does not guarantee a corresponding improvement for the higher-fidelity problem. The AMF methodology proposed here is based on a class of multilevel methods for constrained optimization and is designed to manage the use of variable-fidelity approximations or models in a systematic way that assures convergence to critical points of the original, high-fidelity problem