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M V Fedorov

Publications and source records attributed to M V Fedorov.

11 recordsLinked to original sources
PubMed2006

Side chain dynamics and alternative hydrogen bonding in the mechanism of protein thermostabilization.

To elucidate the mechanism of protein thermostabilization, the thermodynamic properties of small monomeric proteins from mesophilic and thermophilic organisms have been analyzed. Molecular dynamics simulations were employed in the study of dynamic features of charged and polar side chains of amino acid residues. The basic conclusion has been made: surface charged and polar side chains with high conformational mobility can form alternative hydrogen bonded (H-bonded) donor-acceptor pairs. The correlation between the quantitative content of alternative H-bonds per residue and the temperature of maximal thermostability of proteins has been found. The proposed mechanism of protein thermostabilization suggests continuous disruption of the primary H-bonds and formation of alternative ones, which maintain constant the enthalpy value in the native state and prevent a rapid increase of the conformational entropy with the rising temperature. The analysis of the results show that the more residues located in the N- and C-terminal regions and in the extended loops that are capable of forming alternative longer-range H-bonded pairs, the higher the protein thermostability.

Computer Simulation↗
PubMed2005

Observation of nonspreading wave packets in an imaginary potential.

We propose and experimentally demonstrate a method to prepare a nonspreading atomic wave packet. Our technique relies on a spatially modulated absorption constantly chiseling away from an initially broad de Broglie wave. The resulting contraction is balanced by dispersion due to Heisenberg's uncertainty principle. This quantum evolution results in the formation of a nonspreading wave packet of Gaussian form with a spatially quadratic phase. Experimentally, we confirm these predictions by observing the evolution of the momentum distribution. Moreover, by employing interferometric techniques, we measure the predicted quadratic phase across the wave packet. Nonspreading wave packets of this kind also exist in two space dimensions and we can control their amplitude and phase using optical elements.

Journal Article↗
PubMed2004

Wavelet treatment of the intrachain correlation functions of homopolymers in dilute solutions.

Discrete wavelets are applied to the parametrization of the intrachain two-point correlation functions of homopolymers in dilute solutions obtained from Monte Carlo simulations. Several orthogonal and biorthogonal basis sets have been investigated for use in the truncated wavelet approximation. The quality of the approximation has been assessed by calculation of the scaling exponents obtained from the des Cloizeaux ansatz for the correlation functions of homopolymers with different connectivities in a good solvent. The resulting exponents are in better agreement with those from recent renormalization group calculations as compared to the data without the wavelet denoising. We also discuss how the wavelet treatment improves the quality of data for correlation functions from simulations of homopolymers at varied solvent conditions and of heteropolymers.

Journal Article↗
PubMed2004

Wavelet treatment of structure and thermodynamics of simple liquids.

A new algorithm is developed to solve integral equations for simple liquids. The algorithm is based on the discrete wavelet transform of radial distribution functions. The Coifman 2 basis set is employed for the wavelet treatment. To solve integral equations we have applied the combined scheme in which the coarse part of the solution is calculated by wavelets, while the fine part by the direct iterations. Tests on the PY and HNC approximations have indicated that the proposed procedure is more effective than the conventional method based on the hybrid algorithm. Possibilities for application of the method to molecular liquids and mixed quantum-classical systems are discussed.

Journal Article↗
PubMed2003

Wavelet treatment of radial distribution functions of solutes.

Discrete wavelets are applied to parametrize the radial distribution functions of hydrated ions and hydrophobic solutes. The data on radial distribution functions are derived from the integral equation theory and neutron scattering experiment. The Coifman and the discrete Meyer basis sets are used for the wavelet approximation. The quality of the approximation is verified by calculations of the solvation energy, the coordination number, and the change in chemical potential of solutes.

Journal Article↗
PubMed2002

Delay-dependent amplification of a probe pulse via stimulated Rayleigh scattering.

Stimulated Rayleigh scattering of pump and probe light pulses of close carrier frequencies is considered. A nonzero time delay between the two pulses is shown to give rise to amplification of the delayed (probe) pulse accompanied by attenuation of the pump, both on resonance and off resonance. In either case, phase-matching effects are shown to provide a sufficiently large gain, which can exceed significantly direct one-photon absorption losses.

Journal Article↗
PubMedDate not supplied

[Correlation of fine structures of distributions of amplitudes of a photomultiplier dark current fluctuations with the Earth rotations about its axis].

The fine structures of distributions of photomultiplier dark current fluctuations measured in two laboratories 2000 km distant from other: in the international Institute of Biophysics (Neuss, Germany) and in the Moscow State University (Moscow, Russia) were compared. It is shown that similar forms of appropriate histograms are apparently more often realized at both locations at the same local time. This confirms the previous conclusion that the fine structure of distributions correlates with rotation of the Earth about its axis.

Earth, Planet↗
PubMedDate not supplied

[Comparison of forms of "unfit histograms" by a wavelet transform method].

Two methods checking changes in time of histogram patterns were investigated. These methods are relied on discrete wavelet transform. The result is that in the some cases these methods can more effectively to examine latency in the behavior of histograms form constructed by on overlapping short segments of experimental data.

Alpha Particles↗
PubMedDate not supplied

[Regular changes in histogram forms in physical measurements and mathematical modeling].

A study of macroscopic fluctuations for objects separated by large distances confirmed the conclusion drawn earlier that, if the objects being measured are in different time zones, the increase in the probability of occurrence of histograms of similar form corresponds to the difference in the local time at the points of measurement. It was also found that, upon realization of pseudo-random sequences of numbers in mathematical generators, sequences of histograms very similar to those in real physical series can be realized. This suggests the presence of previously unknown regularities, both physical and mathematical, in sequences traditionally considered as absolutely random.

Alpha Particles↗
PubMedDate not supplied

[The study of autowave mechanisms of electrocardiogram variability during high frequency arrhythmias: mathematical modeling data].

High-frequency cardiac arrhythmias are very dangerous, as they quite often lead to sudden death. These high-frequency arrhythmias are frequently produced by rotating autowaves. In the given work, the dynamics of a rotating three-dimensional excitation scroll wave and the influence of this dynamics on the variability of model electrocardiograms (ECGs) were simulated with the use of the Aliev--Panfilov model for both homogeneous and heterogeneous excitable media. Model ECGs were obtained by summing up local membrane potentials, while ECG variability was estimated numerically through the normalized variability analysis. In the homogeneous medium, the stability of the scroll wave to its filament perturbations was shown to be dependent both on the excitability of the medium and tension of the filament, while in the heterogeneous medium, the scroll was shown to be unstable. It was shown that the scroll wave dynamics affects essentially the variability of the model ECGs, and the ECG variability increases as the excitation threshold value grows. It was found that, at some parameters of the excitable medium, the variability of ECGs in the homogeneous medium is higher than in the heterogeneous medium.

Arrhythmias, Cardiac↗