Algorithm engineering for optimal alignment of protein structure distance matrices

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model for computing optimal structural alignments based on dense inter-residue distance matrices. We therefore reformulate the problem as a special graph problem and give a tight integer linear programming model. We then present algorithm engineering techniques to handle the huge integer linear programs of real-life distance matrix alignment problems. Applying these techniques, we can compute provably optimal Dali alignments for the very first time

One-loop corrections to the Drell--Yan process in SANC (II). The neutral current case

Radiative corrections to the neutral current Drell--Yan-like processes are considered. Complete one-loop electroweak corrections are calculated within the SANC system. Theoretical uncertainties are discussed. Numerical results are presented for typical conditions of LHC experiments.Comment: 17 pages, 9 figures, 3 table

High frequency dynamics in a monatomic glass

The high frequency dynamics of glassy Selenium has been studied by Inelastic X-ray Scattering at beamline BL35XU (SPring-8). The high quality of the data allows one to pinpoint the existence of a dispersing acoustic mode for wavevectors ($Q$) of $1.5<Q<12.5$ nm$^{-1}$, helping to clarify a previous contradiction between experimental and numerical results. The sound velocity shows a positive dispersion, exceeding the hydrodynamic value by $\approx$ 10% at $Q<3.5$ nm$^{-1}$. The $Q^2$ dependence of the sound attenuation $\Gamma(Q)$, reported for other glasses, is found to be the low-$Q$ limit of a more general $\Gamma(Q) \propto \Omega(Q)^2$ law which applies also to the higher $Q$ region, where $\Omega(Q)\propto Q$ no longer holds.Comment: Phys. Rev. Lett. (Accepted

CSA: Comprehensive comparison of pairwise protein structure alignments

htmlabstractCSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl

One-loop corrections to the Drell-Yan process in SANC (I). The charged current case

Radiative corrections to the charged current Drell-Yan processes are revisited. Complete one-loop electroweak corrections are calculated within the automatic SANC system. Electroweak scheme dependence and the choice of the factorization scale are discussed. Comparisons with earlier calculations are presented.Comment: extended version submitted to EPJ

Electroweak radiative corrections to the three channels of the process f_1 bar-f_1 ZA --> 0

We have calculated the electroweak radiative corrections at the O(alpha) level to the three channels of the process f_1 bar-f_1 Z A --> 0 and implemented them into the SANC system. Here A stands for the photon and f_1 for a first generation fermion whose mass is neglected everywhere except in arguments of logarithmic functions. The symbol --> 0 means that 4-momenta of all the external particles flow inwards. We present the complete analytical results for the covariant and helicity amplitudes for three cross channels: f_1 + bar-f_1 --> Z + gamma, Z --> f_1 + bar-f_1 + gamma and f_1 + gamma --> f_1 + Z. The one-loop scalar form factors of these channels are simply related by an appropriate permutation of their arguments s,t,u. To check the correctness of our results we first of all observe the independence of the scalar form factors on the gauge parameters and the validity of the Ward identity, i.e. external photon transversality, and, secondly, compare our numerical results with the other independent calculations available to us.Comment: 19 pages, 6 figures, 10 table

Maximum Cliques in Protein Structure Comparison

Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper, we propose a new protein structure comparison method based on internal distances (DAST) which is posed as a maximum clique problem in an alignment graph. We also design an algorithm (ACF) for solving such maximum clique problems. ACF is first applied in the context of VAST, a software largely used in the National Center for Biotechnology Information, and then in the context of DAST. The obtained results on real protein alignment instances show that our algorithm is more than 37000 times faster than the original VAST clique solver which is based on Bron & Kerbosch algorithm. We furthermore compare ACF with one of the fastest clique finder, recently conceived by Ostergard. On a popular benchmark (the Skolnick set) we observe that ACF is about 20 times faster in average than the Ostergard's algorithm

Inverse bremsstrahlung contributions to Drell-Yan like processes

The contribution of the sub-process $\gamma q \to q' l_1\bar{l}_2$ in hadron-hadron interactions is considered. It is a part of one-loop electroweak radiative corrections for the Drell-Yan production of lepton pairs at hadron colliders. It is shown that this contribution should be taken into account aiming at the 1% accuracy of the Drell-Yan process theoretical description. Both the neutral and charged current cases are evaluated. Numerical results are presented for typical conditions of LHC experiments.Comment: 11 pages, 8 figure

Efekat ishrane kokoši nosilja smešama obogaćenim omega-3 masnim kiselinama na sastav masnih kiselina u jajetu

In order to investigate the effects of omega (n) 3 fatty acids on egg quality a group-control trial was organized. Trial lasted 40 days and was performed in production conditions. Total number of 1264 laying hens of Lohman Brown classic provenience were used and randomly allotted into one of four groups by 316 hens each (C-control, I experimental, II experimental and III experimental). All groups of hens were fed diets of standard ingredients and chemical composition, while feed of I, II and III experimental group of hens was supplemented with micro algae Schizochytrium spp. (DHA Gold®, Martek, USA) as a source of n- 3 fatty acids in amount of 0.5, 0.7 and 1.0 % respectively. In order to investigate the influence of micro algae Schizochytrium spp. feed supplementation on egg quality, from the aspect of content and ratio of fatty acids, random egg samples (n=10) were taken at the 10th, 20th and 40th day of the trial from each group. Egg yolk fatty acid content was determined by gas chromatography on Varian 1400 with flame ionization detector (FID detector) (on a packed column 20% LAC-3R-728 Chromosorb WAW 80-100 mesh). Significant differences in egg yolk fatty acid content as well as their ratio were determined between treatment groups. Positive influence of supplemented micro algae preparation was observed. Highest content of n-3 poly unsaturated fatty acids (PUFA n-3) was determined in egg yolks of III experimental group while lowest content was determined in egg yolks of control group of hens. Micro algae feed supplementation, at the end of the trial period, positively affected egg yolk PUFA n-6/PUFA n-3 ratio, since determined ratio of 4.24 in III experimental group was more desirable than 12.27 determined in a control group. Marine algae (Schizochytrium spp.) feed supplementation in laying hens in amounts above 0.5% significantly affected egg yolk fatty acid composition as well as ratio of n-6/n-3 PUFA. These findings support its use from nutritive, medical and economic point of view.Da bi se ispitao uticaj omega -3 masnih kiselina na kvalitet jaja postavljen je ogled sa tri eksperimentalne i jednom kontrolnom grupom. Ogled je trajao 40 dana i sproveden je u proizvodnim uslovima. Ukupan broj od 1264 kokoši nosilja Lohmann Brown classic provenijence je slučajno raspoređen u četiri grupe po 316 nosilja u svakoj (C-kontrola, I eksperimentalna, II eksperimentalna i III eksperimentalna). Sve grupe su hranjene smešama standardnog sastava, dok su eksperimentalne grupe I, II, III hranjene smešom obogaćenom mikroalgama Schizochytrium spp. (DHA Gold®, Martek, USA) kao izvorom n-3 masnih kiselina u količini od 0,5; 0,7; 1,0. U cilju ispitivanja hrane obogaćene mikroalgom Schizochytrium spp. na kvalitet jaja sa aspekta sadržaja i odnosa masnih kiselina, uzet je slučajan uzorak jaja (n=10) 10., 20., i 40. dana iz svake grupe. Sadržaj masnih kiselina u žumancetu je određen gasnim hromatografom Varian 1400 sa plamen jonizujućim detektorom (FID detector) (na koloni 20% LAC-3R-728 Chromosorb WAW 80-100 mreža). Značajne razlike u sadržaju masnih kiselina u žumancetu kao i njihov odnos su određeni između tretmana. Najveći sadržaj n-3 polinezasićenih masnih kiselina (PUFA n-3) određen je u žumancetu jaja treće eksperimentalne grupe, dok je najmanji sadržaj određen u kontrolnoj grupi. Dodavanje mikro algi smešama na kraju oglednog perioda, pozitivno je uticao na odnos PUFA n-6/PUFA n-3 u žumancetu, pošto je određen odnos od 4,24 u III eksperimentalnoj grupi što je poželjnije od 12,27 koliko je određeno u kontrolnoj grupi. Dodavanje morskih algi (Schizochytrium spp.) u smeše za kokoši nosilje u koncentraciji oko 0,5%, značajno je uticalo na sastav masnih kiselina u žumancetu jajeta kao i na odnos n-6/n-3 PUFA. Ovi rezultati opravdavaju upotrebu algi u ishrani kokoši nosilja sa nutritivne, medicinske i ekonomske tačke gledišta

Energy Scenarios for South Eastern Europe: A close look into the Western Balkans

"The Energy Scenarios for South East Europe" thematic seminar took place on the 15th of December 2015 in Vienna, Austria. The workshop was organized by Institute of Energy and Transport of the European Commission's Joint Research Centre (JRC-IET), hosted by the Energy Community Secretariat (ECS) and sponsored by the Directorate-General for Neighbourhood and Enlargement Negotiations (DG-NEAR) in the framework of the Travel Accommodation and Conference facility for Western Balkans and Turkey, a programme of dissemination activities organised by the Commission in the EU or the beneficiary country in connection with the enlargement process and the pre-accession strategy. The aim of the workshop was to bring together representatives from think tanks, scientific institutes, the academia and the private sector with government officials, the national statistical agencies and the local TSO representatives from the Western Balkan region to exchange views on potential energy technology deployment scenarios that could facilitate a low carbon development pathway for the enlargement countries, but also exchange on the methodologies utilized and identify challenges as well as potential pitfalls in this process. The workshop included three sessions of specific thematic focus. The first session provided the "regional picture" with forecasts on the development of the energy and power systems in the western Balkans. The second session discussed case studies on low carbon development trajectories for specific countries in the region; and the third session explored the role of particular technologies in this context. This report comprises of long abstracts from the workshop presentations and closes with a chapter on conclusions and recommendations that resulted from the discussion sessions