Data growth and its impact on the SCOP database: new developments

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop

Fragmentation of relativistic nuclei in peripheral interactions in nuclear track emulsion

The technique of nuclear track emulsions is used to explore the fragmentation of light relativistic nuclei down to the most peripheral interactions - nuclear "white" stars. A complete pattern of therelativistic dissociation of a $^8$B nucleus with target fragment accompaniment is presented. Relativistic dissociation $^{9}$Be$\to2\alpha$ is explored using significant statistics and a relative contribution of $^{8}$Be decays from 0$^+$ and 2$^+$ states is established. Target fragment accompaniments are shown for relativistic fragmentation $^{14}$N$\to$3He+H and $^{22}$Ne$\to$5He. The leading role of the electromagnetic dissociation on heavy nuclei with respect to break-ups on target protons is demonstrated in all these cases. It is possible to conclude that the peripheral dissociation of relativistic nuclei in nuclear track emulsion is a unique tool to study many-body systems composed of lightest nuclei and nucleons in the energy scale relevant for nuclear astrophysics.Comment: 15 pages, 4 figures, 4 tables, conference: Relativistic nuclear physics: from Nuclotron to LHC energies, Kiev, June 18-22, 200

Clustering in light nuclei in fragmentation above 1 A GeV

The relativistic invariant approach is applied to analyzing the 3.3 A GeV $^{22}$Ne fragmentation in a nuclear track emulsion. New results on few-body dissociations have been obtained from the emulsion exposures to 2.1 A GeV $^{14}$N and 1.2 A GeV $^{9}$Be nuclei. It can be asserted that the use of the invariant approach is an effective means of obtaining conclusions about the behavior of systems involving a few He nuclei at a relative energy close to 1 MeV per nucleon. The first observations of fragmentation of 1.2 A GeV $^{8}$B and $^{9}$C nuclei in emulsion are described. The presented results allow one to justify the development of few-body aspects of nuclear astrophysics.Comment: 7 pages, 8 figures, 3 tables, Nuclear Physics in Astrophysics-2, 16-20 May, 2005 (ATOMKI), Debrecen, Hungar

Structures and orientational transitions in thin films of tilted hexatic smectics

We present detailed systematic studies of structural transformations in thin liquid crystal films with the smectic-C to hexatic phase transition. For the first time all possible structures reported in the literature are observed for one material (5 O.6) at the variation of temperature and thickness. In unusual modulated structures the equilibrium period of stripes is twice with respect to the domain size. We interpret these patterns in the frame work of phenomenological Landau type theory, as equilibrium phenomena produced by a natural geometric frustration in a system having spontaneous splay distortion.Comment: 7 pages, 6 figure

Фертильность продуктов мужского и женского мейоза у мейотических мутантов томата

Наведено результати дослідження фертильності мікро-і мегагаметофітів, а також розміри пилку дев'яти мейотичних мутантів томату (Lycopersicon esculentum Mill.). Всі мутації, крім мутації додаткового поділу мейозу amd викликають істотне зниження фертильності продуктів чоловічого і жіночого мейозу. Мутант amd виявляє повну стерильність і найменші розміри пилку, проте високу фертильність мегагаметофітов. The results of the study of fertility micro- and macrogametophytes, as well as the size of the pollen of nine meiotic mutants of tomato (Lycopersicon esculentum Mill.) was presented. All mutations, except mutations additional meiotic division amd cause significant reduction in fertility products of male and female meiosis. The аmd mutant reveals a complete sterility of the pollen and the smallest size, but high fertility macrogametophytes

Fertility of Micro-and Makrogametophytes Meiotic Mutants of Tomato.

Наведено результати дослідження фертильності мікро- й макрогаметофітів, а також морфометричних параметрів пилку дев’яти мейотичних мутантів томата (Lycopersicon esculentum Mill.). Усі мутації, крім мутації додаткового поділу мейозу amd, викликають істотне зниження фертильності продуктів чоловічого та жіночого мейозу. Мутант amd виявляє повну стерильність і найменші розміри пилку, проте високу фертильність макрогаметофітів. The results of the study of fertility micro- and macrogametophytes, as well as the morphometric parameters of the pollen of nine meiotic mutants of tomato (Lycopersicon esculentum Mill.) was presented. All mutations, except mutations additional meiotic division amd, cause significant reduction in fertility products of male and female meiosis. The аmd mutant reveals a complete sterility of the pollen and the smallest size, but high fertility macrogametophytes

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

Topology of "white" stars in relativistic fragmentation of light nuclei

In the present paper, experimental observations of the multifragmentation processes of light relativistic nuclei carried out by means of emulsions are reviewed. Events of the type of "white" stars in which the dissociation of relativistic nuclei is not accompanied by the production of mesons and the target-nucleus fragments are considered. A distinctive feature of the charge topology in the dissociation of the Ne, Mg, Si, and S nuclei is an almost total suppression of the binary splitting of nuclei to fragments with charges higher than 2. The growth of the nuclear fragmentation degree is revealed in an increase in the multiplicity of singly and doubly charged fragments with decreasing charge of the non-excited part of the fragmenting nucleus. The processes of dissociation of stable Li, Be, B, C, N, and O isotopes to charged fragments were used to study special features of the formation of systems consisting of the lightest $\alpha$, d, and t nuclei. Clustering in form of the $^3$He nucleus can be detected in "white" stars via the dissociation of neutron-deficient Be, B, C, and N isotopes.Comment: 20 pages, 3 figures, 9 tables, conference: Conference on Physics of Fundamental Interactions, Moscow, Russia, 1-5 Mar 2004.(Author's translation

Electromagnetic dissociation of relativistic 8^8B nuclei in nuclear track emulsion

Experimental data on fragmentation channels in peripheral interactions of $^8$B nuclei in nuclear track emulsions are presented. A detailed analysis made it possible to justify selections of events of the electromagnetic-dissociation process $^8$B $\to^7$Be + \emph{p} and to estimate its cross section. Events of $^{10}$C peripheral dissociation that were observed in the same exposure are described.Comment: 12 pages, 10 figures, 4 tables, Published in Phys.Atom.Nucl.72:690-701,200

Forestry-Selection Valuation of Genetic Reserves of Scots Pine in SE «Volodymyr-Volynsk Forestry-Hunting Economy»

У статті подано лісівничо-селекційну характеристику генетичних резерватів сосни звичайної ДП «Володимир-Волинське лісомисливське господарство». Досліджено, що генетичні резервати зростають за І–Іа бонітетом, мають добрий стан, у віці 70–80 років мають повноту 0,6–0,8. У 35–48 % дерев відсутні вади стовбура і крони. Вивчена різноманітність морфологічних форм сосни дає змогу проводити відбір дерев на комбінаційну здатність. In this article forestry-selection valuation of genetic reserves of Scots pine in SE «Volodymyr-Volynsk forestry-hunting economy» is given. The genetic reserves have І−Іа bonitet, the good health, 70-80 years old and 0,6–0,8 plenitude. 35–48 % of trees does not have the defects of trunk and crown.Роботу виконано на кафедрі ботаніки і садово- паркового господарства ВНУ ім. Лесі Українк