Showing papers by "Moscow State University published in 2005"

Virtual computational chemistry laboratory - design and description

Abstract: Internet technology offers an excellent opportunity for the development of tools by the cooperative effort of various groups and institutions. We have developed a multi-platform software system, Virtual Computational Chemistry Laboratory, http://www.vcclab.org, allowing the computational chemist to perform a comprehensive series of molecular indices/properties calculations and data analysis. The implemented software is based on a three-tier architecture that is one of the standard technologies to provide client-server services on the Internet. The developed software includes several popular programs, including the indices generation program, DRAGON, a 3D structure generator, CORINA, a program to predict lipophilicity and aqueous solubility of chemicals, ALOGPS and others. All these programs are running at the host institutes located in five countries over Europe. In this article we review the main features and statistics of the developed system that can be used as a prototype for academic and industry models.

Assessing computational tools for the discovery of transcription factor binding sites.

Abstract: The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

Mitochondrial metabolism of reactive oxygen species.

Abstract: Oxidative stress is considered a major contributor to etiology of both "normal" senescence and severe pathologies with serious public health implications. Mitochondria generate reactive oxygen species (ROS) that are thought to augment intracellular oxidative stress. Mitochondria possess at least nine known sites that are capable of generating superoxide anion, a progenitor ROS. Mitochondria also possess numerous ROS defense systems that are much less studied. Studies of the last three decades shed light on many important mechanistic details of mitochondrial ROS production, but the bigger picture remains obscure. This review summarizes the current knowledge about major components involved in mitochondrial ROS metabolism and factors that regulate ROS generation and removal. An integrative, systemic approach is applied to analysis of mitochondrial ROS metabolism, which is now dissected into mitochondrial ROS production, mitochondrial ROS removal, and mitochondrial ROS emission. It is suggested that mitochondria augment intracellular oxidative stress due primarily to failure of their ROS removal systems, whereas the role of mitochondrial ROS emission is yet to be determined and a net increase in mitochondrial ROS production in situ remains to be demonstrated.

Iteration of planar amplitudes in maximally supersymmetric Yang-Mills theory at three loops and beyond

Abstract: We compute the leading-color (planar) three-loop four-point amplitude of N = 4 supersymmetric Yang-Mills theory in 4 - 2{epsilon} dimensions, as a Laurent expansion about {epsilon} = 0 including the finite terms. The amplitude was constructed previously via the unitarity method, in terms of two Feynman loop integrals, one of which has been evaluated already. Here we use the Mellin-Barnes integration technique to evaluate the Laurent expansion of the second integral. Strikingly, the amplitude is expressible, through the finite terms, in terms of the corresponding one- and two-loop amplitudes, which provides strong evidence for a previous conjecture that higher-loop planar N = 4 amplitudes have an iterative structure. The infrared singularities of the amplitude agree with the predictions of Sterman and Tejeda-Yeomans based on resummation. Based on the four-point result and the exponentiation of infrared singularities, we give an exponentiated ansatz for the maximally helicity-violating n-point amplitudes to all loop orders. The 1/{epsilon}{sup 2} pole in the four-point amplitude determines the soft, or cusp, anomalous dimension at three loops in N = 4 supersymmetric Yang-Mills theory. The result confirms a prediction by Kotikov, Lipatov, Onishchenko and Velizhanin, which utilizes the leading-twist anomalous dimensions in QCD computed by Moch, Vermaseren and Vogt. Following similar logic, we are able to predict a term in the three-loop quark and gluon form factors in QCD.

PRIRODA-04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallel computing

Abstract: Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.

Magnetic nanoparticles: preparation, structure and properties

Abstract: The key methods for the preparation of magnetic nanoparticles are described systematically. The experimental data on their properties are analysed and generalised. The main theoretical views on the magnetism of nanoparticles are considered.

Continuous-time quantum Monte Carlo method for fermions

Abstract: We present a numerically exact continuous-time quantum Monte Carlo algorithm for fermions with a general interaction nonlocal in space-time The new determinantal grand-canonical scheme is based on a stochastic series expansion for the partition function in the interaction representation The method is particularly applicable for multiband, time-dependent correlations since it does not invoke the Hubbard-Stratonovich transformation The test calculations for exactly solvable models, as well results for the Green function and for the time-dependent susceptibility of the multiband supersymmetric model with a spin-flip interaction are discussed

Ipr1 gene mediates innate immunity to tuberculosis.

Abstract: An estimated eight million people are infected each year with the pathogen Mycobacterium tuberculosis, and more than two million die annually. Yet only about 10% of those infected develop tuberculosis. Genetic variation within host populations is known to be significant in humans and animals, but the nature of genetic control of host resistance to tuberculosis remains poorly understood. Previously we mapped a new genetic locus on mouse chromosome 1, designated sst1 (for supersusceptibility to tuberculosis 1). Here we show that this locus mediates innate immunity in sst1 congenic mouse strains and identify a candidate gene, Intracellular pathogen resistance 1 (Ipr1), within the sst1 locus. The Ipr1 gene is upregulated in the sst1 resistant macrophages after activation and infection, but it is not expressed in the sst1 susceptible macrophages. Expression of the Ipr1 transgene in the sst1 susceptible macrophages limits the multiplication not only of M. tuberculosis but also of Listeria monocytogenes and switches a cell death pathway of the infected macrophages from necrosis to apoptosis. Our data indicate that the Ipr1 gene product might have a previously undocumented function in integrating signals generated by intracellular pathogens with mechanisms controlling innate immunity, cell death and pathogenesis.

Polynomial identities and asymptotic methods

Abstract: Polynomial identities and PI-algebras $S_n$-representations Group gradings and group actions Codimension and colength growth Matrix invariants and central polynomials The PI-exponent of an algebra Polynomial growth and low PI-exponent Classifying minimal varieties Computing the exponent of a polynomial $G$-identities and $G\wr S_n$-action Superalgebras, *-algebras and codimension growth Lie algebras and nonassociative algebras The generalized-six-square theorem Bibliography Index.

CLASP1 and CLASP2 bind to EB1 and regulate microtubule plus-end dynamics at the cell cortex

Abstract: CLIP-associating protein (CLASP) 1 and CLASP2 are mammalian microtubule (MT) plus-end binding proteins, which associate with CLIP-170 and CLIP-115. Using RNA interference in HeLa cells, we show that the two CLASPs play redundant roles in regulating the density, length distribution and stability of interphase MTs. In HeLa cells, both CLASPs concentrate on the distal MT ends in a narrow region at the cell margin. CLASPs stabilize MTs by promoting pauses and restricting MT growth and shortening episodes to this peripheral cell region. We demonstrate that the middle part of CLASPs binds directly to EB1 and to MTs. Furthermore, we show that the association of CLASP2 with the cell cortex is MT independent and relies on its COOH-terminal domain. Both EB1- and cortex-binding domains of CLASP are required to promote MT stability. We propose that CLASPs can mediate interactions between MT plus ends and the cell cortex and act as local rescue factors, possibly through forming a complex with EB1 at MT tips.

Aqueous Dispersions of Single-wall and Multiwall Carbon Nanotubes with Designed Amphiphilic Polycations

Abstract: Poor solubility of single-walled and multiwalled carbon nanotubes (NTs) in water and organic solvents presents a considerable challenge for their purification and applications. Macromolecules can be convenient solubilizing agents for NTs and a structural element of composite materials for them. Several block copolymers with different chemical functionalities of the side groups were tested for the preparation of aqueous NT dispersions. Poly(N-cetyl-4-vinylpyridinium bromide-co-N-ethyl-4-vinylpyridinium bromide-co-4-vinylpyridine) was found to form exceptionally stable NT dispersions. It is suggested that the efficiency of macromolecular dispersion agents for NT solubilization correlates with the topological and electronic similarity of polymer-NT and NT-NT interactions in the nanotube bundles. Raman spectroscopy and atomic force and transmission electron microcopies data indicate that the polycations are wrapped around NTs forming a uniform coating 1.0-1.5 nm thick. The ability to wind around the NT originates in the hydrophobic attraction of the polymer backbone to the graphene surface and topological matching. Tetraalkylammonium functional groups in the side chains of the macromolecule create a cloud of positive charge around NTs, which makes them hydrophilic. The prepared dispersions could facilitate the processing of the nanotubes into composites with high nanotube loading for electronic materials and sensing. Positive charge on their surface is particularly important for biological and biomedical applications because it strengthens interactions with negatively charged cell membranes. A high degree of spontaneous bundle separation afforded by the polymer coating can also be beneficial for NT sorting.

Programmed and altruistic ageing.

Abstract: Ageing is widely believed to be a non-adaptive process that results from a decline in the force of natural selection. However, recent studies in Saccharomyces cerevisiae are consistent with the existence of a programme of altruistic ageing and death. We suggest that the similarities between the molecular pathways that regulate ageing in yeast, worms, flies and mice, together with evidence that is consistent with programmed death in salmon and other organisms, raise the possibility that programmed ageing or death can also occur in higher eukaryotes.

Force production by disassembling microtubules.

Abstract: Microtubules (MTs) are important components of the eukaryotic cytoskeleton: they contribute to cell shape and movement, as well as to the motions of organelles including mitotic chromosomes. MTs bind motor enzymes that drive many such movements, but MT dynamics can also contribute to organelle motility. Each MT polymer is a store of chemical energy that can be used to do mechanical work, but how this energy is converted to motility remains unknown. Here we show, by conjugating glass microbeads to tubulin polymers through strong inert linkages, such as biotin-avidin, that depolymerizing MTs exert a brief tug on the beads, as measured with laser tweezers. Analysis of these interactions with a molecular-mechanical model of MT structure and force production shows that a single depolymerizing MT can generate about ten times the force that is developed by a motor enzyme; thus, this mechanism might be the primary driving force for chromosome motion. Because even the simple coupler used here slows MT disassembly, physiological couplers may modulate MT dynamics in vivo.

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Abstract: Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and nitrite-sensitive repressor NsrR. Using comparative genomics approaches, we predict DNA-binding motifs for these transcriptional factors and describe corresponding regulons in available bacterial genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNA recognition motif. Highly conserved regulon HcpR for the hybrid cluster protein and some other redox enzymes is present in diverse anaerobic bacteria, including Clostridia, Thermotogales, and delta-proteobacteria. NnrR and DNR control denitrification in alpha- and beta-proteobacteria, respectively. Sigma-54-dependent NorR regulon found in some gamma- and beta-proteobacteria contains various enzymes involved in the NO detoxification. Repressor NsrR, which was previously known to control only nitrite reductase operon in Nitrosomonas spp., appears to be the master regulator of the nitric oxides' metabolism, not only in most gamma- and beta-proteobacteria (including well-studied species such as Escherichia coli), but also in Gram-positive Bacillus and Streptomyces species. Positional analysis and comparison of regulatory regions of NO detoxification genes allows us to propose the candidate NsrR-binding motif. The most conserved member of the predicted NsrR regulon is the NO-detoxifying flavohemoglobin Hmp. In enterobacteria, the regulon also includes two nitrite-responsive loci, nipAB (hcp-hcr) and nipC (dnrN), thus confirming the identity of the effector, i.e. nitrite. The proposed NsrR regulons in Neisseria and some other species are extended to include denitrification genes. As the result, we demonstrate considerable interconnection between various nitrogen-oxides-responsive regulatory systems for the denitrification and NO detoxification genes and evolutionary plasticity of this transcriptional network.

Role of mitochondria in the pheromone- and amiodarone-induced programmed death of yeast

Abstract: Although programmed cell death (PCD) is extensively studied in multicellular organisms, in recent years it has been shown that a unicellular organism, yeast Saccharomyces cerevisiae, also possesses death program(s). In particular, we have found that a high doses of yeast pheromone is a natural stimulus inducing PCD. Here, we show that the death cascades triggered by pheromone and by a drug amiodarone are very similar. We focused on the role of mitochondria during the pheromone/amiodarone-induced PCD. For the first time, a functional chain of the mitochondria-related events required for a particular case of yeast PCD has been revealed: an enhancement of mitochondrial respiration and of its energy coupling, a strong increase of mitochondrial membrane potential, both events triggered by the rise of cytoplasmic [Ca2+], a burst in generation of reactive oxygen species in center o of the respiratory chain complex III, mitochondrial thread-grain transition, and cytochrome c release from mitochondria. A novel mitochondrial protein required for thread-grain transition is identified.

Excitation dynamics in the LHCII complex of higher plants: Modeling based on the 2.72 angstrom crystal structure

Abstract: We have modeled steady-state spectra and energy-transfer dynamics in the peripheral plant light-harvesting complex LHCII using new structural data. The dynamics of the chlorophyll (Chl) b-->Chl a transfer and decay of selectively excited "bottleneck" Chl a and b states have been studied by femtosecond pump-probe spectroscopy. We propose an exciton model of the LHCII trimer (with specific site energies) which allows a simultaneous quantitative fit of the absorption, linear-dichroism, steady-state fluorescence spectra, and transient absorption kinetics upon excitation at different wavelengths. In the modeling we use the experimental exciton-phonon spectral density and modified Redfield theory. We have found that fast b-->a transfer is determined by a good connection of the Chls b to strongly coupled Chl a clusters, i.e., a610-a611-a612 trimer and a602-a603 and a613-a614 dimers. Long-lived components of the energy-transfer kinetics are determined by a quick population of red-shifted Chl b605 and blue-shifted Chl a604 followed by a very slow (3 ps for b605 and 12 ps for a604) flow of energy from these monomeric bottleneck sites to the Chl a clusters. The dynamics within the Chl a region is determined by fast (with time constants down to sub-100 fs) exciton relaxation within the a610-a611-a612 trimer, slower 200-300 fs relaxation within the a602-a603 and a613-a614 dimers, even slower 300-800 fs migration between these clusters, and very slow transfer from a604 to the quasi-equilibrated a sites. The final equilibrium is characterized by predominant population of the a610-a611-a612 cluster (mostly the a610 site). The location of this cluster on the outer side of the LHCII trimer probably provides a good connection with the other subunits of PSII.

Crossing the w = - 1 barrier in the D3-brane dark energy model

Abstract: We explore a possibility for the Universe to cross the $w=\ensuremath{-}1$ cosmological constant barrier for the dark energy state parameter. We consider the Universe as a slowly decaying D3-brane. The D3-brane dynamics are approximately described by a nonlocal string tachyon interaction and the backreaction of gravity is incorporated in the closed string tachyon dynamics. In a local effective approximation this model contains one phantom component and one usual field with a simple polynomial interaction. To understand cosmological properties of this system we study toy models with the same scalar fields but with modified interactions. These modifications admit polynomial superpotentials. We find restrictions on these interactions under which it is possible to reach $w=\ensuremath{-}1$ from below at large time. Explicit solutions with the dark energy state parameter crossing or not crossing the barrier $w=\ensuremath{-}1$ at large time are presented.

Supersymmetry Parameter Analysis: SPA Convention and Project

Abstract: High-precision analyses of supersymmetry parameters aim at reconstructing the fundamental supersymmetric theory and its breaking mechanism. A well defined theoretical framework is needed when higher-order corrections are included. We propose such a scheme, Supersymmetry Parameter Analysis SPA, based on a consistent set of conventions and input parameters. A repository for computer programs is provided which connect parameters in different schemes and relate the Lagrangian parameters to physical observables at LHC and high energy e+e- linear collider experiments, i.e., masses, mixings, decay widths and production cross sections for supersymmetric particles. In addition, programs for calculating high-precision low energy observables, the density of cold dark matter (CDM) in the universe as well as the cross sections for CDM search experiments are included. The SPA scheme still requires extended efforts on both the theoretical and experimental side before data can be evaluated in the future at the level of the desired precision. We take here an initial step of testing the SPA scheme by applying the techniques involved to a specific supersymmetry reference point.

The role of deliberate practice in chess expertise

Abstract: SUMMARY Two large, diverse samples of tournament-rated chess players were asked to estimate the frequency and duration of their engagement in a variety of chess-related activities. Variables representing accumulated time spent on serious study alone, tournament play, and formal instruction were all significant bivariate correlates of chess skill as measured by tournament performance ratings. Multivariate regression analyses revealed that among the activities measured, serious study alone was the strongest predictor of chess skill in both samples, and that a combination of various chessrelated activities accounted for about 40% of the variance in chess skill ratings. However, the relevance of tournament play and formal instruction to skill varied as a function of skill measurement time (peak vs. current) and age group (above vs. below 40 years). Chess players at the highest skill level (i.e. grandmasters) expended about 5000 hours on serious study alone during their first decade of serious chess play—nearly five times the average amount reported by intermediate-level players. These results provide further evidence to support the argument that deliberate practice plays a critical role in the acquisition of chess expertise, and may be useful in addressing pedagogical issues concerning the optimal allocation of time to different chess learning activities. Copyright # 2005 John Wiley & Sons, Ltd. How long does it take to become an expert in chess? Based on theoretical arguments about information processing efficiency and computer simulations of pattern recognition in chess, Simon and colleagues (Simon & Chase, 1973; Simon & Gilmartin, 1973) proposed a ‘10-year rule’ for the development of chess expertise. In other words, one needs about a decade of study in order to acquire the necessary knowledge base to perform at very high levels of tournament play (see F. Gobet & N. Charness, submitted; Expertise in chess. In K. A. Ericsson, N. Charness, P. Feltovich, & R. Hoffman (Eds.), Cambridge handbook of expertise and expert performance. New York: Cambridge University Press; Gobet, de Voogt, & Retschnitzki, 2004, for review).

Critical evaluation of stability constants of metal complexes of complexones for biomedical and environmental applications* (IUPAC Technical Report)

Abstract: Available experimental data on stability constants of proton (hydron) and metal complexes for seven complexones of particular biomedical and environmental interest: iminodiacetic acid (2,2'-azanediyldiacetic acid, IDA); (methyl-imino)diacetic acid (2,2'-(methylazanediyl)diacetic acid, MIDA); 2,2',2",2'''-{[(carboxymethyl)azanediyl]bis[(ethane-l,2-diyl)nitrilo]}tetraacetic acid (DTPA); 3.6,9,12-tetrakis(carboxymethyl )-3,6,9,12-tetraazatetradecanedioic acid (TTHA); 2,2',2"-(l,4,7-triazanonane-l,4,7-triyl)triacetic acid (NOTA); 2,2',2",2'''-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetraacetic acid (DOTA); 2,2',2",2'''-(1,4,8,11-tetraazacyclotetradecane-1,4,8,11-tetrayl)tetraacetic acid (TETA), published in 1945-2000, have been critically evaluated. Some typical errors in stability constant measurements for particular complexones are summarized. Higher quality data are selected and presented as "Recommended" or "Provisional".

Gel phantom for use in high-intensity focused ultrasound dosimetry

Abstract: An optically transparent phantom was developed for use in high-intensity focused ultrasound (US), or HIFU, dosimetry studies. The phantom is composed of polyacrylamide hydrogel, embedded with bovine serum albumin (BSA) that becomes optically opaque when denatured. Acoustic and optical properties of the phantom were characterized as a function of BSA concentration and temperature. The speed of sound (1544 m/s) and acoustic impedance (1.6 MRayls) were similar to the values in soft tissue. The attenuation coefficient was approximately 8 times lower than that of soft tissues (0.02 Np/cm/MHz for 9% BSA). The nonlinear (B/A) coefficient was similar to the value in water. HIFU lesions were readily seen during formation in the phantom. In US B-mode images, the HIFU lesions were observed as hyperechoic regions only if the cavitation activity was present. The phantom can be used for fast characterization and calibration of US-image guided HIFU devices before animal or clinical studies.

Carbon substitution in MgB2 single crystals: Structural and superconducting properties

Abstract: The growth of carbon-substituted magnesium diboride $\mathrm{Mg}{({\mathrm{B}}_{1\ensuremath{-}x}{\mathrm{C}}_{x})}_{2}$ single crystals with $0\ensuremath{\leqslant}x\ensuremath{\leqslant}0.15$ is reported, and the structural, transport, and magnetization data are presented. The superconducting transition temperature decreases monotonically with increasing carbon content in the full investigated range of substitution. By adjusting the nominal composition, ${T}_{c}$ of substituted crystals can be tuned in a wide temperature range between 10 and 39 K. Simultaneous introduction of disorder by carbon substitution and significant increase of the upper critical field ${H}_{c2}$ is observed. Comparing with the nonsubstituted compound, ${H}_{c2}$ at 15 K for $x=0.05$ is enhanced by more than a factor of 2 for $H$ oriented both perpendicular and parallel to the $ab$ plane. This enhancement is accompanied by a reduction of the ${H}_{c2}$-anisotropy coefficient $\ensuremath{\gamma}$ from 4.5 (for the nonsubstituted compound) to 3.4 and 2.8 for the crystals with $x=0.05$ and 0.095, respectively. At temperatures below 10 K, the single crystal with larger carbon content shows ${H}_{c2}$ (defined at zero resistance) higher than 7 and 24 T for $H$ oriented perpendicular and parallel to the $ab$ plane, respectively. Observed increase of ${H}_{c2}$ cannot be explained by the change in the coherence length due to the disorder-induced decrease of the mean free path only.