CAMAC subsystem and user context utilities in ngdp framework

The ngdp framework advanced topics are described. Namely we consider work with CAMAC hardware, "selfflow" nodes for the data acquisition systems with the As-Soon-As-Possible policy, ng_mm(4) as alternative to ng_socket(4), the control subsystem, user context utilities, events representation for the ROOT package, test and debug nodes, possible advancements for netgraph(4), etc. It is shown that the {\itshape ngdp} is suitable for building lightweight DAQ systems to handle CAMAC. The investigation has been performed at the Veksler and Baldin Laboratory of High Energy Physics, JINR.Comment: 21 pages

The ngdp framework for data acquisition systems

The ngdp framework is intended to provide a base for the data acquisition (DAQ) system software. The ngdp's design key features are: high modularity and scalability; usage of the kernel context (particularly kernel threads) of the operating systems (OS), which allows to avoid preemptive scheduling and unnecessary memory--to--memory copying between contexts; elimination of intermediate data storages on the media slower than the operating memory like hard disks, etc. The ngdp, having the above properties, is suitable to organize and manage data transportation and processing for needs of essentially distributed DAQ systems. The investigation has been performed at the Veksler and Baldin Laboratory of High Energy Physics, JINR.Comment: 21 pages, 3 figure

Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps

Journal ArticleThe molecular-replacement method has been extended to locate molecules and their fragments in an electron-density map. The approach is based on a new spherically averaged phased translation function. The position of the centre of mass of a search model is found prior to determination of its orientation. The orientation is subsequently found by a phased rotation function. The technique also allows superposition of distantly related macromolecules. The method has been implemented in a computer program MOLREP and successfully tested using experimental data sets

NCS-constrained exhaustive search using oligomeric models

Copyright © 2008 International Union of CrystallographyThe efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.NI

Crystallization and preliminary X-ray analysis of human thioredoxin peroxidase-B from red blood cells.

Journal ArticleResearch Support, Non-U.S. Gov'tTwo different crystal forms of human thioredoxin peroxidase-B have been grown by vapour diffusion using polyethylene glycol 400 as a precipitant. Monoclinic P21 crystals were grown from freshly purified protein, whilst orthorhombic P212121 crystals were grown from purified protein that had been stored in ammonium sulfate, but otherwise under the same conditions. The diffraction from both crystal forms was observed to extend to beyond 2.0 A resolution using synchrotron radiation. Complete native data sets to 1.8 and 3. 7 A have been collected from the monoclinic and orthorhombic crystals, respectively.EU (HCMP Access to Large Scale Facilities grant

The structure of a tetrameric α-carbonic anhydrase fromThermovibrio ammonificansreveals a core formed around intermolecular disulfides that contribute to its thermostability

Carbonic anhydrase enzymes catalyse the reversible hydration of carbon dioxide to bicarbonate. A thermophilic Thermovibrio ammonificans α-carbonic anhydrase (TaCA) has been expressed in Escherichia coli and structurally and biochemically characterized. The crystal structure of TaCA has been determined in its native form and in two complexes with bound inhibitors. The tetrameric enzyme is stabilized by a unique core in the centre of the molecule formed by two intersubunit disulfides and a single lysine residue from each monomer that is involved in intersubunit ionic interactions. The structure of this core protects the intersubunit disulfides from reduction, whereas the conserved intrasubunit disulfides are not formed in the reducing environment of the E. coli host cytosol. When oxidized to mimic the environment of the periplasmic space, TaCA has increased thermostability, retaining 90% activity after incubation at 70°C for 1 h, making it a good candidate for industrial carbon-dioxide capture. The reduction of all TaCA cysteines resulted in dissociation of the tetrameric molecule into monomers with lower activity and reduced thermostability. Unlike other characterized α-carbonic anhydrases, TaCA does not display esterase activity towards p-nitrophenyl acetate, which appears to result from the increased rigidity of its protein scaffold

Crystallization and preliminary X-ray diffraction analysis of ω-amino acid:pyruvate transaminase from Chromobacterium violaceum

An ω-amino acid:pyruvate transaminase from C. violaceum has been purified and crystallized in two crystal forms. The structure has been solved using molecular replacement

The differential cross section for the dp-elastic scattering at 500 to 900 MeV/nucleon

The results of the differential cross section measurements of dp-elastic scattering at energies from 500 to 900 MeV/nucleon at Nuclotron JINR are reported. The data were obtained for the angular range of 70-120◦ in the center-of-mass (c.m.s.). The results are compared with existing world dat