Showing papers by "Russian Academy of Sciences published in 2003"

PRIMUS: a Windows PC-based system for small-angle scattering data analysis

Abstract: A program suite for one-dimensional small-angle scattering data processing running on IBM-compatible PCs under Windows 9x/NT/2000/XP is presented. The main program, PRIMUS, has a menu-driven graphical user interface calling computational modules to perform data manipulation and analysis. Experimental data in binary OTOKO format can be reduced by calling the program SAPOKO, which includes statistical analysis of time frames, averaging and scaling. Tools to generate the angular axis and detector response files from diffraction patterns of calibration samples, as well as binary to ASCII transformation programs, are available. Several types of ASCII files can be directly imported into PRIMUS, in particular, sasCIF or ILL-type files are read without modification. PRIMUS provides basic data manipulation functions (averaging, background subtraction, merging of data measured in different angular ranges, extrapolation to zero sample concentration, etc.) and computes invariants from Guinier and Porod plots. Several external modules coupled with PRIMUS via pop-up menus enable the user to evaluate the characteristic functions by indirect Fourier transformation, to perform peak analysis for partially ordered systems and to find shape approximations in terms of three-parametric geometrical bodies. For the analysis of mixtures, PRIMUS enables model-independent singular value decomposition or linear fitting if the scattering from the components is known. An interface is also provided to the general non-linear fitting program MIXTURE, which is designed for quantitative analysis of multicomponent systems represented by simple geometrical bodies, taking shape and size polydispersity as well as interparticle interference effects into account.

Uniqueness of ab initio shape determination in small-angle scattering

Abstract: Scattering patterns from geometrical bodies with different shapes and anisometry (solid and hollow spheres, cylinders, prisms) are computed and the shapes are reconstructed ab initio using envelope function and bead modelling methods. A procedure is described to analyze multiple solutions provided by bead modeling methods and to estimate stability and reliability of the shape reconstruction. It is demonstrated that flat shapes are more difficult to restore than elongated ones and types of shapes are indicated, which require additional information for reliable shape reconsrtuction from the scattering data.

L3,∞-solutions of the Navier-Stokes equations and backward uniqueness

Abstract: It is shown that the L3,∞-solutions of the Cauchy problem for the three-dimensional Navier-Stokes equations are smooth.

Strong spatial dispersion in wire media in the very large wavelength limit

Abstract: It is found that there exist composite media that exhibit strong spatial dispersion even in the very large wavelength limit. This follows from the study of lattices of ideally conducting parallel thin wires (wire media). In fact, our analysis reveals that the description of this medium by means of a local dispersive uniaxial dielectric tensor is not complete, leading to unphysical results for the propagation of electromagnetic waves at any frequencies. Since nonlocal constitutive relations have been usually considered in the past as a second-order approximation, meaningful in the short-wavelength limit, the aforementioned result presents a relevant theoretical interest. In addition, since such wire media have been recently used as a constituent of some discrete artificial media (or metamaterials), the reported results open the question of the relevance of the spatial dispersion in the characterization of these artificial media.

Constant elevation of southern Tibet over the past 15 million years

Abstract: The uplift of the Tibetan plateau, an area that is 2,000 km wide, to an altitude of about 5,000 m has been shown to modify global climate and to influence monsoon intensity. Mechanical and thermal models for homogeneous thickening of the lithosphere make specific predictions about uplift rates of the Tibetan plateau, but the precise history of the uplift of the plateau has yet to be confirmed by observations. Here we present well-preserved fossil leaf assemblages from the Namling basin, southern Tibet, dated to approximately 15 Myr ago, which allow us to reconstruct the temperatures within the basin at that time. Using a numerical general circulation model to estimate moist static energy at the location of the fossil leaves, we reconstruct the elevation of the Namling basin 15 Myr ago to be 4,689 +/- 895 m or 4,638 +/- 847 m, depending on the reference data used. This is comparable to the present-day altitude of 4,600 m. We conclude that the elevation of the southern Tibetan plateau probably has remained unchanged for the past 15 Myr.

Nonlinear properties of left-handed metamaterials.

Abstract: We analyze the properties of microstructured materials with negative refraction, the so-called left-handed metamaterials. We consider a two-dimensional periodic structure created by arrays of wires and split-ring resonators embedded into a nonlinear dielectric, and calculate the effective nonlinear electric permittivity and magnetic permeability. We demonstrate that the hysteresis-type dependence of the magnetic permeability on the field intensity allows changing the material properties from left- to right-handed and back. These effects can be treated as the second-order phase transitions in the transmission properties induced by the variation of an external field.

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution.

Abstract: A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies - on ribosomes and on the allosteric protein aspartate transcarbamoylase - illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

Climate change and Arctic ecosystems: 2. Modeling, paleodata‐model comparisons, and future projections

Abstract: Large variations in the composition, structure, and function of Arctic ecosystems are determined by climatic gradients, especially of growing-season warmth, soil moisture, and snow cover. A unified circumpolar classification recognizing five types of tundra was developed. The geographic distributions of vegetation types north of 55degreesN, including the position of the forest limit and the distributions of the tundra types, could be predicted from climatology using a small set of plant functional types embedded in the biogeochemistry-biogeography model BIOME4. Several palaeoclimate simulations for the last glacial maximum (LGM) and mid-Holocene were used to explore the possibility of simulating past vegetation patterns, which are independently known based on pollen data. The broad outlines of observed changes in vegetation were captured. LGM simulations showed the major reduction of forest, the great extension of graminoid and forb tundra, and the restriction of low- and high-shrub tundra (although not all models produced sufficiently dry conditions to mimic the full observed change). Mid-Holocene simulations reproduced the contrast between northward forest extension in western and central Siberia and stability of the forest limit in Beringia. Projection of the effect of a continued exponential increase in atmospheric CO2 concentration, based on a transient ocean-atmosphere simulation including sulfate aerosol effects, suggests a potential for larger changes in Arctic ecosystems during the 21st century than have occurred between mid-Holocene and present. Simulated physiological effects of the CO2 increase (to >700 ppm) at high latitudes were slight compared with the effects of the change in climate.

A Protein-Chameleon: Conformational Plasticity of α-Synuclein, a Disordered Protein Involved in Neurodegenerative Disorders

Abstract: Under the physiological conditions in vitro, α-synuclein, a conservative presynaptic protein, the aggregation and fibrillation of which is assumed to be involved into the pathogenesis of Parkinson's disease and several other neurodegenerative disorders, known as synucleinopathies, is characterized by the lack of rigid well-defined structure; i.e., it belongs to the class of intrinsically unstructured proteins. Intriguingly, α-synuclein is characterized by a remarkable conformational plasticity, adopting a series of different conformations depending on the environment. For example, this protein may either stay substantially unfolded, or adopt an amyloidogenic partially folded conformation, or fold into α-helical or β-structural species, both monomeric and oligomeric. Furthermore, it might form several morphologically different types of aggregates, including oligomers (spheres or doughnuts), amorphous aggregates, and or amyloid-like fibrils. The peculiarities of this astonishing conformational beha...

Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR

Abstract: Novel phylogenetic lineages of as yet uncultivated crenarchaeota have been frequently detected in low to moderate-temperature, marine and terrestrial environments. In order to gain a more comprehensive view on the distribution and diversity of Crenarchaeota in moderate habitats, we have studied 18 different terrestrial and freshwater samples by 16S rDNA-based phylogenetic surveys. In seven different soil samples of diverse geographic areas in Europe (forest, grassland, ruderal) and Asia (permafrost, ruderal) as well as in two microbial mats, we have consistently found one particular lineage of crenarchaeota. The diversity of Crenarchaeota in freshwater sediments was considerably higher with respresentative 16S rDNA sequences distributed over four different groups within the moderate crenarchaeota. Systematic analysis of a 16S rDNA universal library from a sandy ecosystem containing 800 clones exclusively revealed the presence of the soil-specific crenarchaeotal cluster. With primers specific for non-thermophilic crenarchaeota we established a rapid method to quantify archaeal 16S rDNA in real time PCR. The relative abundance of crenarchaeotal rDNA was 0.5-3% in the bulk soil sample and only 0.16% in the rhizosphere of the sandy ecosystem. A nearby agricultural setting yielded a relative abundance of 0.17% crenarchaeotal rDNA. In total our data suggest that soil crenarchaeota represent a stable and specific component of the microbiota in terrestrial habitats.

Fabrication and characterization of n-ZnO/p-AlGaN heterojunction light-emitting diodes on 6H-SiC substrates

Abstract: We report on the fabrication of n-ZnO/p-AlGaN heterojunction light-emitting diodes on 6H-SiC substrates. Hydride vapor phase epitaxy was used to grow p-type AlGaN, while chemical vapor deposition was used to produce the n-type ZnO layers. Diode-like, rectifying I-V characteristics, with threshold voltage ~3.2V and low reverse leakage current ~10(-7)A, are observed at room temperature. Intense ultraviolet emission with a peak wavelength near 389 mn is observed when the diode is forward biased; this emission is found to be stable at temperatures up to 500K and shown to originate from recombination within the ZnO.

Electric Explosion of Wires as a Method for Preparation of Nanopowders

Abstract: The development of the method of electric explosion of wires and research results concerning preparation of nanopowders by this method has been reviewed. The method is highly productive (up to 200g/h), provides powders with an average particle size of 20–100nm, and requires an energy consumption of about 25kWh/kg. Several characteristics of the nanopowders will be given and their applications will be exemplified too.

The iau 2000 resolutions for astrometry celestial mechanics and metrology in the relativistic framework: explanatory supplement

Abstract: We discuss the IAU resolutions B1.3, B1.4, B1.5, and B1.9 that were adopted during the 24th General Assembly in Manchester, 2000, and provides details on and explanations for these resolutions. It is explained why they present significant progress over the corresponding IAU 1991 resolutions and why they are necessary in the light of present accuracies in astrometry, celestial mechanics, and metrology. In fact, most of these resolutions are consistent with astronomical models and software already in use. The metric tensors and gravitational potentials of both the Barycentric Celestial Reference System and the Geocentric Celestial Reference System are defined and discussed. The necessity and relevance of the two celestial reference systems are explained. The transformations of coordinates and gravitational potentials are discussed. Potential coefficients parameterizing the post-Newtonian gravitational potentials are expounded. Simplified versions of the time transformations suitable for modern clock accuracies are elucidated. Various approximations used in the resolutions are explicated and justified. Some models (e.g., for higher spin moments) that serve the purpose of estimating orders of magnitude have actually never been published before.

Contact order revisited: Influence of protein size on the folding rate

Abstract: Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical model of protein folding that predicts that logarithm of the folding rate decreases with the protein chain length L as L(2/3), and by the finding that the folding rates of multistate folding proteins strongly correlate with their sizes and have very bad correlation with CO, we reexamined the dependence of folding rate on CO and L in attempt to find a structural parameter that determines folding rates for the totality of proteins. We show that the Abs_CO = CO x L, is able to predict rather accurately folding rates for both two-state and multistate folding proteins, as well as short peptides, and that this Abs_CO scales with the protein chain length as L(0.70 +/- 0.07) for the totality of studied single-domain proteins and peptides.

Properties of heavy quarkonia and B c mesons in the relativistic quark model

Abstract: The mass spectra and electromagnetic decay rates of charmonium, bottomonium, and ${B}_{c}$ mesons are comprehensively investigated in the relativistic quark model. The presence of only heavy quarks allows the expansion in powers of their velocities. All relativistic corrections of order ${v}^{2}{/c}^{2},$ including retardation effects and one-loop radiative corrections, are systematically taken into account in the computations of the mass spectra. The obtained wave functions are used for the calculation of radiative magnetic dipole $(M1)$ and electric dipole $(E1)$ transitions. It is found that relativistic effects play a substantial role. Their account and the proper choice of the Lorentz structure of the quark-antiquark interaction in a meson is crucial for bringing theoretical predictions in accord with experimental data. A detailed comparison of the calculated decay rates and branching fractions with available experimental data for radiative decays of charmonium and bottomonium is presented. The possibilities to observe the currently missing spin-singlet S and P states as well as D states in bottomonium are discussed. The results for ${B}_{c}$ masses and decays are compared with other quark model predictions.

Secular total solar irradiance trend during solar cycles 21–23

Abstract: [1] A series of satellite total solar irradiance (TSI) observations can be combined in a precise solar magnetic cycle length composite TSI database by determining the relationship between two non-overlapping components: ACRIM1 and ACRIM2. [Willson and Hudson, 1991; Willson, 1994] An ACRIM composite TSI time series using the Nimbus7/ERB results [Hoyt et al., 1992] to relate ACRIM1 and ACRIM2 demonstrates a secular upward trend of 0.05 percent-per-decade between consecutive solar activity minima. [Willson, 1997] A PMOD TSI composite using ERBS [Lee et al., 1995] comparisons to relate ACRIM1 and ACRIM2 [Frohlich and Lean, 1998] differs from the ACRIM composite in two significant respects: a negligible trend between solar minima and lower TSI at solar maxima. Our findings indicate the lower PMOD trend and lower PMOD TSI at the maxima of solar cycles 22 and 23 are artifacts of ERBS degradation. Lower PMOD TSI during the maximum of cycle 21 results from modifications of Nimbus7/ERB and ACRIM1 published results that produces better agreement with a TSI/solar proxy model [Foukal and Lean, 1988; Lean et al., 1995; Frohlich and Lean, 1998].

EcR isoforms in Drosophila: testing tissue-specific requirements by targeted blockade and rescue.

Abstract: The three Drosophila EcR isoforms differ only at their N termini; thus, they share the conserved ligand-binding domain transcriptional activation function (AF2) and only differ in the unconserved A/B region, which contains a second, isoform-specific, activation function (AF1). We have developed a dominant-negative mutant EcR (EcR-DN), expressed it in flies with the GAL4/UAS system, and used it to block ecdysone signaling in eight tissues or groups of tissues. Localized EcR-DN arrests ecdysone-dependent development in the target cells and often — because of a molting checkpoint — arrests development globally. Simultaneously expressing individual wild-type EcR isoforms in the same target tissues suppresses the EcR-DN phenotype and identifies the rescuing isoform as sufficient to support the development of the target. Every isoform, and even an N-terminal truncated EcR that lacks any AF1, supports development in the fat body, eye discs, salivary glands, EH-secreting neurosecretory cells and in the dpp expression domain, implying that AF1 is dispensable in these tissues. By contrast, only EcR-A is able to support development in the margins of the wing discs, and only EcR-B2 can do so in the larval epidermis and the border cells of the developing egg chamber. In light of our results, the simplest explanations for the widespread spatial and temporal variations in EcR isoform titers appear untenable.

Air temperature triggers the recovery of evergreen boreal forest photosynthesis in spring

Abstract: The timing of the commencement of photosynthesis (P-*) in spring is an important determinant of growing-season length and thus of the productivity of boreal forests. Although controlled experiments have shed light on environmental mechanisms triggering release from photoinhibition after winter, quantitative research for trees growing naturally in the field is scarce. In this study, we investigated the environmental cues initiating the spring recovery of boreal coniferous forest ecosystems under field conditions. We used meteorological data and above-canopy eddy covariance measurements of the net ecosystem CO2 exchange (NEE) from five field stations located in northern and southern Finland, northern and southern Sweden, and central Siberia. The within- and intersite variability for P-* was large, 30-60 days. Of the different climate variables examined, air temperature emerged as the best predictor for P-* in spring. We also found that 'soil thaw', defined as the time when near-surface soil temperature rapidly increases above 0degreesC, is not a useful criterion for P-*. In one case, photosynthesis commenced 1.5 months before soil temperatures increased significantly above 0degreesC. At most sites, we were able to determine a threshold for air-temperature-related variables, the exceeding of which was required for P-*. A 5-day running-average temperature (T-5) produced the best predictions, but a developmental-stage model (S) utilizing a modified temperature sum concept also worked well. But for both T-5 and S, the threshold values varied from site to site, perhaps reflecting genetic differences among the stands or climate-induced differences in the physiological state of trees in late winter/early spring. Only at the warmest site, in southern Sweden, could we obtain no threshold values for T-5 or S that could predict P-* reliably. This suggests that although air temperature appears to be a good predictor for P-* at high latitudes, there may be no unifying ecophysiological relationship applicable across the entire boreal zone.

Protein folding revisited. A polypeptide chain at the folding: misfolding: nonfolding cross-roads: which way to go?

Abstract: The structure-function paradigm claims that a specific function of a protein is determined by its unique and rigid three-dimensional (3D) structure. Thus, following its biosynthesis on the ribosome, a protein must fold to be functional. This idea represents one of the cornerstones of modern biology. Numerous cases when, due to the effect of environmental factors or because of genetic defects (mutations), a polypeptide chain has lost its capability to gain a proper functional 3D structure (i.e. became misfolded), seem to confirm this concept. Consequences of such misfolding are well known and represent lost of function, aggregation, development of conformational disorders and cell death. However, the recent revelation of countless examples of intrinsically disordered proteins has cast doubt on the general validity of the structure-function paradigm and revealed an intriguing route of functional disorder. Thus, in a living cell, a polypeptide chain chooses between three potential fates - functional folding, potentially deadly misfolding and mysterious nonfolding. This choice is dictated by the peculiarities of amino acid sequence and/or by the pressure of environmental factors. The aim of the present review is to outline some interesting features of these three routes.

Photometry and Spectroscopy of the Type IIP SN 1999em from Outburst to Dust Formation

Abstract: We present photometry and spectra of the Type IIP supernova 1999em in NGC 1637 from several days after the outburst till day 642. The radioactive tail of the recovered bolometric light curve of SN 1999em indicates that the amount of the ejected 5 6 Ni is 0.02 M O .. The Ha and HeI 10 830-A lines at the nebular epoch show that the distribution of the bulk of 5 6 Ni can be represented approximately by a sphere of 5 6 Ni with a velocity of 1500 km s - 1 , which is shifted towards the far hemisphere by about 400 km s - 1 . The fine structure of the Ha at the photospheric epoch reminiscent of the 'Bochum event' in SN 1987A is analysed in terms of two plausible models: bipolar 5 6 Ni jets and non-monotonic behaviour of the Ha optical depth combined with the one-sided 5 6 Ni ejection. The late-time spectra show a dramatic transformation of the [O I] 6300-A line profile between days 465 and 510, which we interpret as an effect of dust condensation during this period. Late-time photometry supports the dust formation scenario after day 465. The [O I] line profile suggests that the dust occupies a sphere with velocity 800 km s - 1 and optical depth >> 10. The latter exceeds the optical depth of the dusty zone in SN 1987A by more than 10 times. Use is made of the Expanding Photosphere Method to estimate the distance and the explosion time, D 7.83 Mpc and t 0 ≃ 1999 October 24.5 UT, in accord with observational constraints on the explosion time and with other results of detailed studies of the method. The plateau brightness and duration combined with the expansion velocity suggest a pre-supernova radius of 120-150 R O ., ejecta mass of 10-11 M O . and explosion energy of (0.5-1) x 10 5 1 erg. The ejecta mass combined with the neutron star and a conservative assumption about mass loss implies the main sequence progenitor of M m s 12-14 M O .. The derived mass range is in agreement with the upper limit to the mass found using pre-supernova field images by Smartt et al. From the [OI] 6300, 6364 A doublet luminosity we infer the oxygen mass to be a factor four lower than in SN 1987A which is consistent with the estimated SN 1999em progenitor mass according to nucleosynthesis and stellar evolution theory. We note a 'second-plateau' behaviour of the light curve after the main plateau at the beginning of the radioactive tail. This feature seems to be common to SNe IIP with low 5 6 Ni mass.

Climate change and Arctic ecosystems: 1. Vegetation changes north of 55°N between the last glacial maximum, mid‐Holocene, and present

Abstract: A unified scheme to assign pollen samples to vegetation types was used to reconstruct vegetation patterns north of 55°N at the last glacial maximum (LGM) and mid-Holocene (6000 years B.P.). The pollen data set assembled for this purpose represents a comprehensive compilation based on the work of many projects and research groups. Five tundra types (cushion forb tundra, graminoid and forb tundra, prostrate dwarf-shrub tundra, erect dwarf-shrub tundra, and low- and high-shrub tundra) were distinguished and mapped on the basis of modern pollen surface samples. The tundra-forest boundary and the distributions of boreal and temperate forest types today were realistically reconstructed. During the mid-Holocene the tundra-forest boundary was north of its present position in some regions, but the pattern of this shift was strongly asymmetrical around the pole, with the largest northward shift in central Siberia (∼200 km), little change in Beringia, and a southward shift in Keewatin and Labrador (∼200 km). Low- and high-shrub tundra extended farther north than today. At the LGM, forests were absent from high latitudes. Graminoid and forb tundra abutted on temperate steppe in northwestern Eurasia while prostrate dwarf-shrub, erect dwarf-shrub, and graminoid and forb tundra formed a mosaic in Beringia. Graminoid and forb tundra is restricted today and does not form a large continuous biome, but the pollen data show that it was far more extensive at the LGM, while low- and high-shrub tundra were greatly reduced, illustrating the potential for climate change to dramatically alter the relative areas occupied by different vegetation types.

High-Accuracy ab Initio Rotation-Vibration Transitions for Water

Abstract: The spectrum of water vapor is of fundamental importance for a variety of processes, including the absorption and retention of sunlight in Earth's atmosphere. Therefore, there has long been an urgent need for a robust and accurate predictive model for this spectrum. In our work on the high-resolution spectrum of water, we report first-principles calculations that approach experimental accuracy. To achieve this, we performed exceptionally large electronic structure calculations and considered a variety of effects, including quantum electrodynamics, which have routinely been neglected in studies of small many-electron molecules. The high accuracy of the resulting ab initio procedure is demonstrated for the main isotopomers of water.

Hypoxia-Induced Stroke Tolerance in the Mouse Is Mediated by Erythropoietin

Abstract: Background and Purpose— Cellular response to hypoxia is mainly controlled by hypoxia-inducible factor 1 (HIF-1). The HIF-1 target gene erythropoietin (EPO) has been described as neuroprotective. Th...