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Biomedical subjects

V V Volkov

Publications and source records attributed to V V Volkov.

At least 19 recordsLinked to original sources
PubMed2004

Quasicoherent oscillations induced by nonthermal electrons during magnetic reconnection in the T-10 tokamak.

Small-scale quasicoherent oscillations of the x-ray emissivity and magnetic field perturbations are observed in the T-10 tokamak during abrupt growth of the m=2, n=1 magnetohydrodynamic modes at the density limit disruption. Analysis indicates a possible link between the small-scale oscillations and nonthermal electron beams induced around the X points of the m=2, n=1 magnetic island during reconnection of magnetic field lines at the disruption instability.

Journal Article↗
PubMed2004

Lorentz phase microscopy of magnetic materials.

We propose a method of Lorentz phase microscopy for in situ studies and imaging magnetic materials in transmission electron microscopy (TEM) based on the solution of the magnetic transport-of-intensity equation. We also describe the appropriate way of solving this equation that may be useful for understanding and practical use of non-holographic methods for phase retrieval in electron microscopy, especially in imaging magnetic materials. The method is simple, since it is primarily based on classical Fresnel imaging. On the other hand, it is quantitative and can be applied in any TEM without changing the basic hardware. Therefore, it may well find important practical applications in ultramicroscopy and modern magnetic materials research.

Journal Article↗
PubMed2004

On the transport of intensity technique for phase retrieval.

The Transport of Intensity technique is becoming a viable alternative to electron holography for phase retrieval in Transmission Electron Microscopy. However, several issues are still to be clarified in order to ascertain the applicability of the technique; among them, the controversy regarding its geometrical or wave-optical nature, as related to the phase detection limit. We show here that the Transport of Intensity is a wave-optical technique that works in a special regime of small defocus where the image intensity is linear with the defocus parameter. By a simple analytical example we show that the Transport of Intensity correctly reconstructs the electron optical phase shift even when the phase is smaller than pi, a value defining the boundary between the geometrical and wave approaches. Another example is given, the reconstruction of a phase jump, accompanied with experimental support showing that phase retrieval by Electron Holography and Transport of Intensity techniques yields results in good agreement.

Algorithms↗
PubMed2003

Phase imaging and nanoscale currents in phase objects imaged with fast electrons.

We derive the magnetic transport-of-intensity equation (MTIE) that links defocused contrast of magnetic nanoobjects imaged by partially coherent electron waves to their micromagnetic parameters. This provides Maxwell's explanation for observable contrast in terms of the Z component of currents existing around vortices in superconductors and domain vortices and walls in ferromagnets. The solution of the MTIE via Fourier transform is used for quantitative mapping of magnetic flux and projected induction in magnetic and superconducting materials imaged by Lorentz microscopy.

Journal Article↗
PubMed2002

A new symmetrized solution for phase retrieval using the transport of intensity equation.

We propose a novel symmetrization method for solving the transport of intensity equation (TIE) using fast Fourier transforms for situations where the input images may or may not exhibit spatial periodicity. The method is derived from the analysis of intensity conservation law and the internal symmetry of the TIE, and is illustrated for both a computational and an experimental data set.

Journal Article↗
PubMed2001

The relaxation dynamics of the excited electronic states of retinal in bacteriorhodopsin by two-pump-probe femtosecond studies.

We present the results of two-pump and probe femtosecond experiments designed to follow the relaxation dynamics of the lowest excited state (S(1)) populated by different modes. In the first mode, a direct (S(0) --> S(1)) radiative excitation of the ground state is used. In the second mode, an indirect excitation is used where the S(1) state is populated by the use of two femtosecond laser pulses with different colors and delay times between them. The first pulse excites the S(0) --> S(1) transition whereas the second pulse excites the S(1) --> S(n) transition. The nonradiative relaxation from the S(n) state populates the lowest excited state. Our results suggest that the S(1) state relaxes faster when populated nonradiatively from the S(n) state than when pumped directly by the S(0) --> S(1) excitation. Additionally, the S(n) --> S(1) nonradiative relaxation time is found to change by varying the delay time between the two pump pulses. The observed dependence of the lowest excited state population as well as its dependence on the delay between the two pump pulses are found to fit a kinetic model in which the S(n) state populates a different surface (called S'(1)) than the one being directly excited (S(1)). The possible involvement of the A(g) type states, the J intermediate, and the conical intersection leading to the S(0) or to the isomerization product (K intermediate) are discussed in the framework of the proposed model.

Bacteriorhodopsins↗
PubMed2001

Understanding magnetic structures in permanent magnets via in situ Lorentz microscopy, interferometric and non-interferometric phase-reconstructions.

We present our observations of field- and orientation-dependence of magnetic domains and their reversal nucleation at grain boundaries in polycrystalline Nd2Fe14B, using Fresnel- and Foucault-Lorentz microscopy. The local magnetization associated with the domain and domain-wall in Nd2Fe14B and in precipitated Fe particles was mapped using an interferometric holography as well as a novel non-interferometric method based on the 'transport of intensity' equation.

Journal Article↗
PubMed2001

[Hernioplasty with a dermal autograft in recurrent and postoperative hernias].

Long-term results of treatment of ventral recurrent and postoperative hernias by Yanov's method from 1988 till 2000 in 160 patients aged from 19 to 65 years were studied. Depending on the type of hernia the autodermal strip, flap or their combination were used for plasty of hernial ring. Recurrence was in 6.2% patients, wound suppuration--in 4.3%. One elderly patient died of postoperative pneumonia.

Adult↗
PubMed1998

Quaternary structure of V1 and F1 ATPase: significance of structural homologies and diversities.

The V1 ATPase from the tobacco hornworm Manduca sexta and the Escherichia coli F1 ATPase were characterized by small-angle X-ray scattering (SAXS). The radii of gyration (Rg) of the complexes were 6.2 +/- 0.1 and 4.7 +/- 0.02 nm, respectively. The shape of the M. sexta V1 ATPase was determined ab initio from the scattering data showing six masses, presumed to be the A and B subunits, arranged in an alternating manner about a 3-fold axis. A seventh mass with a length of about 11.0 nm extends perpendicularly to the center of the hexameric unit. This central mass is presumed to be the stalk that connects V1 with the membrane domain (V(O)) in the intact V1V(O)-ATPase. In comparison, the shape of the F1 ATPase from E. coli possesses a quasi-3-fold symmetry over the major part of the enzyme. The overall asymmetry of the structure is given by a stem, assumed to include the central stalk subunits. The features of the V1 and F1 ATPase reveal structural homologies and diversities of the key components of the complexes.

Animals↗
PubMed1998

Evidence for a major structural change in Escherichia coli chorismate synthase induced by flavin and substrate binding.

Chorismate synthase (EC 4.6.1.4) catalyses the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) into chorismate, and requires reduced FMN as a cofactor. The enzyme can bind first oxidized FMN and then EPSP to form a stable ternary complex which does not undergo turnover. This complex can be considered to be a model of the ternary complex between enzyme, EPSP and reduced FMN immediately before catalysis commences. It is shown that the binding of oxidized FMN and EPSP to chorismate synthase affects the properties and structure of the protein. Changes in small-angle X-ray scattering data, decreased susceptibility to tryptic digestion and altered Fourier-transform (FT)-IR spectra provide the first strong evidence for major structural changes in the protein. The tetrameric enzyme undergoes correlated screw movements leading to a more overall compact shape, with no change in oligomerization state. The changes in the FT-IR spectrum appear to reflect changes in the environment of the secondary-structural elements rather than alterations in their distribution, because the far-UV CD spectrum changes very little. Changes in the mobility of the protein during non-denaturing PAGE indicate that the ternary complex may exhibit less conformational flexibility than the apoprotein. Increased enzyme solubility and decreased tryptophan fluorescence are discussed in the light of the observed structural changes. The secondary structure of the enzyme was investigated using far-UV CD spectroscopy, and the tertiary structure was predicted to be an alpha-beta-barrel using discrete state-space modelling.

Circular Dichroism↗
PubMed1998

Escherichia coli SecA shape and dimensions.

SecA shape and conformational flexibility in solution were studied by small angle X-ray scattering. Dimeric SecA is a very elongated molecule, 15 nm long and 8 nm wide. SecA is therefore four times as long as the membrane is wide. The two globular protomers are distinctly separated and share limited surface of intermolecular contacts. ATP, ADP or adenylyl-imidodiphosphate (AMP-PNP) binding does not alter the SecA radius of gyration. A SecA mutant that catalyzes multiple rounds of ATP hydrolysis does not undergo conformational changes detectable by small angle X-ray scattering (SAXS). We conclude that SecA conformational alterations observed biochemically during nucleotide interaction are only small-scale and localized. The ramifications of these findings on SecA/SecYEG interaction are discussed.

Adenosine Diphosphate↗
PubMed1998

Small-angle X-ray solution-scattering studies on ligand-induced subunit interactions of the thiamine diphosphate dependent enzyme pyruvate decarboxylase from different organisms.

The quaternary structures of the thiamine diphosphate dependent enzyme pyruvate decarboxylase (EC 4.1.1.1) from the recombinant wild type of Saccharomycescerevisiae and Zymomonas mobilis and from germinating Pisum sativum seeds were examined by X-ray solution scattering. The dependence of the subunit association equilibrium on the pH and the presence of the cofactors thiamine diphosphate and magnesium ions were compared, and the differences between the catalytic properties of the different enzymes are discussed. The influence of amino acid substitutions at the cofactor binding site of the enzyme from Saccharomyces cerevisiae (E51 is substituted by Q or A and G413 by W) on the subunit association was examined. Low-resolution models of the P. sativum, Z.mobilis, and S. cerevisiae enzymes were evaluated ab initio from the scattering data. The enzyme from the bacterium and yeast appear as a dimer of dimers, whereas the plant enzyme is an octamer formed by two tetramers arranged side-by-side. The shape of the S. cerevisiae enzyme agrees well with the atomic structure in the crystal but suggests that the dimers in the latter should be tilted by approximately 10 degrees. The resulting modification of the atomic structure also yields a significantly better fit to the experimental solution scattering data than that calculated form the original crystallographic model.

Bacterial Proteins↗
PubMed1997

Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. I. Invariants and validation of electron microscopy models.

Solutions of selectively deuterated 70 S Escherichia coli ribosomes and of free 30 S and 50 S subunits were studied by neutron scattering using contrast variation. The integrity of the partially deuterated particles was controlled by parallel X-ray measurements. Integral parameters of the entire ribosome, of its subunits and of the protein and rRNA moieties were evaluated. The data allow an experimental validation of the two most recent electron microscopy reconstructions of the 70 S ribosome presented by the groups of J. Frank (Albany) and of M. van Heel & R. Brimacombe (Berlin). For each reconstruction, integral parameters and theoretical scattering curves from the 70 S and its subunits were calculated and compared with the experimental data. Although neither of the two models yields a comprehensive agreement with the experimental data, Frank's model provides a better fit. For the 50 S subunit of van Heel & Brimacombe's model the fit with the experimental data improves significantly when the internal channels and tunnels are filled up. The poorer fit of the latter model is thus caused by its "sponge"-like structure which may partly be due to an enhancement of high frequency contributions in some of the steps of the three-dimensional image reconstruction. It seems therefore unlikely that the ribosome has a "sponge"-like structure with a pronounced network of channels.

Deuterium↗
PubMed1997

Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. II. A model of the ribosome and its RNA at 3.5 nm resolution.

Selectively deuterated 70 S E. coli ribosomes and isolated 30 S and 50 S subunits were analyzed by X-ray and neutron solution scattering. The resulting contrast variation data set (42 curves in total) was proven to be consistent in describing the ribosome as a four-phase system composed of the protein and rRNA moieties of both subunits. This data set thus provides ten times more information than a single scattering curve. A solid body four-phase model of the 70 S ribosome at low resolution was built from the envelope functions of the 30 S and 50 S subunits and of those of the corresponding RNA moieties. The four envelopes were parameterized at a resolution of 3.5 nm using spherical harmonics and taking into account interface layers between the phases. The initial approximation for the envelopes of the subunits was taken from electron microscopic data presented recently by J. Frank and co-workers (Albany); the rRNA envelopes were initially approximated by spheres. The optimization and the refinement of the model proceeded by non-linear least squares minimization fitting the available experimental data. The refined envelopes of the subunits differ by about 10% from the starting approximation and the shape of the final 70 S model lies between the outer envelopes of the models by Frank and by M. von Heel & R. Brimacombe (Berlin). The rRNA moiety in the 30 S subunit is more anisometric than the subunit itself, whereas the rRNA of the 50 S subunit forms a compact core. The rRNAs protrude to the surfaces of the subunits and occupy approximately 30 to 40% of the corresponding surface areas. X-ray scattering curves of the two main functional elongation 70 S complexes (pre- and post-translocational) differ only marginally from those of the non-programmed ribosomes, suggesting that the low resolution four-phase model is also valid for the elongating 70 S ribosome.

Escherichia coli↗