RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps

Motivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies in the fitted component. Results: Here we present the RIBFIND server, a tool for identifying rigid bodies in protein structures. The server identifies rigid bodies in proteins by calculating spatial proximity between their secondary structural elements. Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk

The study of the effect of aluminum powders dispersion on the oxidation and kinetic characteristics

Differential-scanning calorimetry (DSC) and thermogravimetric analysis (TG) were used to study micro-sized aluminum powder ASD-4 and nano-sized powder Alex. The dependence of the oxidation process on the dispersion of the sample particles is shown. The influence of thermogravimetric conditions on the thermal regime of the process was considered, and its kinetic parameters were determined. Calculations of the activation energy and the pre-exponential factor were carried out

Special features of the 9^9Be→\to2He fragmentation in emulsion at an energy of 1.2~A~GeV

The results of investigations of the relativistic $^9$Be nucleus fragmentation in emulsion which entails the production of two He fragments of an energy of 1.2~A~GeV are presented. The results of the angular measurements of the $^9$Be$\to$2He events are analyzed. The $^9$Be$\to^8$Be+n fragmentation channel involving the $^8$Be decay from the ground (0$^+$) and the first excited (2$^+$) states to two $\alpha$ particles is observed to be predominant.Comment: 10 pages, 6 figures, conference: Conference on Physics of Fundamental Interactions, Moscow, Russia, 5-9 Dec 2005 (Author's translation

Global Spiral Modes in NGC 1566: Observations and Theory

We present an observational and theoretical study of the spiral structure in galaxy NGC 1566. A digitized image of NGC 1566 in I-band was used for measurements of the radial dependence of amplitude variations in the spiral arms. We use the known velocity dispersion in the disk of NGC 1566, together with its rotation curve, to construct linear and 2D nonlinear simulations which are then compared with observations. A two-armed spiral is the most unstable linear global mode in the disk of NGC 1566. The nonlinear simulations are in agreement with the results of the linear modal analysis, and the theoretical surface amplitude and the velocity residual variations across the spiral arms are in qualitative agreement with the observations. The spiral arms found in the linear and nonlinear simulations are considerably shorter than those observed in the disk of NGC 1566. We argue therefore, that the surface density distribution in the disk of the galaxy NGC 1566 was different in the past, when spiral structure in NGC 1566 was linearly growing.Comment: 41 pages, 20 figures, to be published in the Astrophysical Journa

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