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Lakhno V.D.,Institute of Mathematical Problems of Biology | Fialko N.S.,Institute of Mathematical Problems of Biology
Mathematical Biology and Bioinformatics | Year: 2015

We considered two ways of finding the free energy, using thermodynamic equilibrium characteristics, which are calculated by direct computational experiments. The results of calculations are described for homogeneous nucleotide dimers AA, GG and TT. Both of these methods yield similar results for biologically relevant temperatures. © 2015.


Lunina N.L.,Institute of Mathematical Problems of Biology | Petrova T.E.,Institute of Mathematical Problems of Biology | Urzhumtsev A.G.,Institute Of Genetique Et Biologie Moleculaire Et Cellulaire | Urzhumtsev A.G.,University of Lorraine | Lunin V.Y.,Institute of Mathematical Problems of Biology
Mathematical Biology and Bioinformatics | Year: 2015

Advances in the methodology of the X-ray diffraction experiments leads to a possibility to register the rays scattered by large isolated biological particles (viruses and individual cells) but not only by crystalline samples. The experiment with an isolated particle provides researchers with the intensities of the scattered rays for the continuous spectrum of scattering vectors. Such experiment gives much more experimental data than an experiment with a crystalline sample where the information is limited to a set of Bragg reflections. This opens up additional opportunities in solving underlying problem of X-ray crystallography, namely, calculating phase values for the scattered waves needed to restore the structure of the object under study. In practice, the original continuous diffraction pattern is sampled, reduced to the values at grid points in the space of scattering vectors (in the reciprocal space). The sampling step determines the amount of the information involved in solving the phase problem and the complexity of the necessary calculations. In this paper, we investigate the effect of the sampling step on the accuracy of the phase problem solution obtained by the method proposed earlier by the authors. It is shown that an expected improvement of the accuracy of the solution with the reducing the sampling step continues even after crossing the Nyquist limit defined as the inverse of the double size of the object under study. © 2015.


Matveeva O.V.,Biopolymer Design LLC | Matveeva O.V.,RAS Engelhardt Institute of Molecular Biology | Nechipurenko Y.D.,RAS Engelhardt Institute of Molecular Biology | Riabenko E.,Moscow Institute of Physics and Technology | And 4 more authors.
Bioinformatics | Year: 2016

Motivation: Target-specific hybridization depends on oligo-probe characteristics that improve hybridization specificity and minimize genome-wide cross-hybridization. Interplay between specific hybridization and genome-wide cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design and in data analysis. Results: In this study, we defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization. A microarray database, derived from the Genomic Comparison Hybridization (GCH) experiment and performed using the Affymetrix platform, contains two different types of probes. The first type of oligo-probes does not have a specific target on the genome and their hybridization signals are derived from genome-wide cross-hybridization alone. The second type includes oligonucleotides that have a specific target on the genomic DNA and their signals are derived from specific and cross-hybridization components combined together in a total signal. A comparative analysis of hybridization specificity of oligo-probes, as well as their nucleotide sequences and thermodynamic features was performed on the database. The comparison has revealed that hybridization specificity was negatively affected by low stability of the fully-paired oligo-target duplex, stable probe self-folding, G-rich content, including GGG motifs, low sequence complexity and nucleotide composition symmetry. Conclusion: Filtering out the probes with defined 'negative' characteristics significantly increases specific hybridization and dramatically decreasing genome-wide cross-hybridization. Selected oligo-probes have two times higher hybridization specificity on average, compared to the probes that were filtered from the analysis by applying suggested cutoff thresholds to the described parameters. A new approach for efficient oligo-probe design is described in our study. © 2016 The Author 2016. Published by Oxford University Press. All rights reserved.


Hudzinskyy D.,TU Eindhoven | Hudzinskyy D.,Dutch Polymer Institute | Lyulin A.V.,TU Eindhoven | Baljon A.R.C.,San Diego State University | And 2 more authors.
Macromolecules | Year: 2011

We have performed molecular dynamics simulations to explore the influence of confinement on the glass-transition temperature Tg for supported atactic-polystyrene (aPS) thin films of different thickness (1-10 nm) and different strengths of attraction to the substrate (0.1-3.0 kcal/mol). The aPS films have been equilibrated in a melt at 540 K and further cooled down with a constant cooling velocity of 0.01 K/ps below Tg to room temperature, 300 K. On the basis of the density measurements, we have defined three different (substrate, middle, and surface) layers for each film. We found that the monomers close to the surface and in the substrate layer are partially oriented, which leads to more effective monomer packing. For the whole film the average density-based Tg value remains almost constant for films down to 2 nm thickness, where the middle layer vanishes. For the middle layer itself T g does not depend on the total film thickness, while an increase up to 70 K is measured for the substrate layer depending on the strength of attraction to the actual substrate. The surface layer remains liquidlike in the whole temperature range (300-540 K). We claim that the redistribution of mass in the three film layers may explain the change with film thickness of the average Tg, if the latter is determined from linear fits of the average glass and melt densities. © 2011 American Chemical Society.


Baljon A.R.C.,San Diego State University | Williams S.,San Diego State University | Balabaev N.K.,Institute of Mathematical Problems of Biology | Paans F.,TU Eindhoven | And 3 more authors.
Journal of Polymer Science, Part B: Polymer Physics | Year: 2010

In this article, we investigate the glass transition in polystyrene melts and free-standing ultra-thin films by means of large-scale computer simulations. The transition temperatures are obtained from static (density) and dynamic (diffusion and orientational relaxation) measurements. As it turns out, the glass transition temperature of a 3 nm thin film is ∼60 °K lower than that of the bulk. Local orientational mobility of the phenyl bonds is studied with the help of Legendre polynomials of the second-order P2(t). The α and β relaxation times are obtained from the spectral density of P2(t). Our simulations reveal that interfaces affect α and β relaxation processes differently. The β relaxation rate is faster in the center of the film than near a free surface; for the α relaxation rate, an opposite trend is observed. © 2010 Wiley Periodicals, Inc.


Seyedhosseini E.,University of Aveiro | Ivanov M.,University of Aveiro | Bystrov V.,University of Aveiro | Bystrov V.,Institute of Mathematical Problems of Biology | And 8 more authors.
Crystal Growth and Design | Year: 2014

Glycine is the simplest amino acid and one of the basic and important elements in biology, as it serves as a building block for proteins. The interest in this material has recently arisen from its useful functional properties, such as its high value of nonlinear optical susceptibility and ferroelectricity. Three polymorphic forms with different physical properties are possible in glycine, the most useful β-polymorph being much less stable than the other two. In this work, we could grow stable microcrystals of β-glycine using a (111)Pt/SiO2/Si substrate as a template. The effects of the solution concentration and Pt-assisted nucleation on the crystal growth and phase evolution were evaluated using X-ray diffraction analysis and Raman spectroscopy. A second harmonic generation (SHG) method confirmed that the 2-fold symmetry is preserved in as-grown crystals, thus reflecting the expected P21 symmetry of the β-phase. Spontaneous polarization direction is found to be parallel to the monoclinic [010] axis and directed along the crystal length. These data are confirmed by computational molecular modeling. Optical measurements revealed also relatively high values of the nonlinear optical susceptibility (50% greater than in the z-cut quartz). The potential use of stable β-glycine crystals in nonlinear optical applications is discussed. © 2014 American Chemical Society.


Heredia A.,University of Aveiro | Bdikin I.,University of Aveiro | Kopyl S.,University of Aveiro | Mishina E.,Moscow State Institute of Radioengineering | And 7 more authors.
Journal of Physics D: Applied Physics | Year: 2010

Diphenylalanine (FF) peptide nanotubes (PNTs) represent a unique class of self-assembled functional biomaterials owing to a wide range of useful properties including nanostructural variability, mechanical rigidity and chemical stability. In addition, strong piezoelectric activity has recently been observed paving the way to their use as nanoscale sensors and actuators. In this work, we fabricated both horizontal and vertical FF PNTs and examined their optical second harmonic generation and local piezoresponse as a function of temperature. The measurements show a gradual decrease in polarization with increasing temperature accompanied by an irreversible phase transition into another crystalline phase at about 140-150 °C. The results are corroborated by the molecular dynamic simulations predicting an order-disorder phase transition into a centrosymmetric (possibly, orthorhombic) phase with antiparallel polarization orientation in neighbouring FF rings. Partial piezoresponse hysteresis indicates incomplete polarization switching due to the high coercive field in FF PNTs. © 2010 IOP Publishing Ltd.


Gevorkyan V.E.,Southern Federal University | Paramonova E.V.,Institute of Mathematical Problems of Biology | Avakyan L.A.,Southern Federal University | Bystrov V.S.,Institute of Mathematical Problems of Biology
Mathematical Biology and Bioinformatics | Year: 2015

In this paper, molecular models are used to investigate and analyze the structure and polarization of polyvinylidene fluoride (PVDF) and poly(vinylidene fluoride-trifluoroethylene) (P(VDF-TrFE)) Langmuir-Blodgett (LB) nanofilms, depending on the structure and composition of the monomers of their polymer and copolymer chains. Quantum-mechanical calculations and modeling, as well as molecular dynamics (MD) simulations based on semi-empirical quantum-chemical methods (such as PM3), show that the energy of the studied PVDF and P (VDF-TrFE) molecular structures, and their polarization switching proceed by homogeneous switching mechanism in the framework of the phenomenological theory of Landau-Ginzburg-Devonshire (LGD) in the linear approximation of low values of the electric field. The magnitude of the resulting critical coercive field is within the EC ~ 0.5. 2.0 GV/m, which is consistent with experimental data. It is also found that the uniform polarization switching mechanism of the polymer chains PVDF and P (VDF-TrFE) is due to the quantum properties of the molecular orbitals of the electron subsystem: the applied electric field induces a gradual shift of the electron "clouds" density (electron polarizability), which in turn causes a gradual shift of the nuclear cores, in accordance with the principle of minimum total energy of the system, and this leads eventually, when it reaches a critical point (bifurcation) - to overturn of the entire chain and a sharp decrease in the total energy of the total system to its energetically more favorable state. This is clearly seen in both the polarization hysteresis loops, and the total energy changes. In this case, the turnover chain time, obtained by molecular dynamics within semi-empirical quantum-chemical PM3 approach in a limited Hartree-Fock approximation, when approaching this critical point, increases sharply, tending to infinity, which corresponds to the theory of LGD.


Poltev V.I.,Autonomous University of Puebla | Poltev V.I.,Institute of Theoretical and Experimental Physics | Rodriguez E.,Autonomous University of Puebla | Grokhlina T.I.,Institute of Mathematical Problems of Biology | And 2 more authors.
International Journal of Quantum Chemistry | Year: 2010

To understand the molecular basis of the principal biological action of the caffeine (CAF), the molecular mechanics calculations of possible complexes between CAF and the fragments of human A1 adenosine receptor were performed. The fragments were selected after considerations of the CAF molecular structure and its possible interactions, as well as after an analysis of the extensive bibliography on the structure, biological role, site-directed mutagenesis, and the modeling of the adenosine receptors. The minimum energy configurations of these complexes were obtained using two different computer programs with different force fields. The most favorable configurations correspond to the formation of two hydrogen bonds between the CAF molecule and hydrophilic amino acid residues of the fragments of transmembrane domains of the receptor. These configurations are supposed to contribute to CAF blocking of the adenosine receptors. They will be used later for the construction of model CAF complexes with two transmembrane domains simultaneously. © 2009 Wiley Periodicals, Inc.


Astakhova T.V.,Institute of Mathematical Problems of Biology | Roytberg M.A.,Moscow Institute of Physics and Technology | Tsitovich I.I.,Moscow Institute of Physics and Technology | Yakovlev V.V.,Institute of Mathematical Problems of Biology
Mathematical Biology and Bioinformatics | Year: 2014

The regularities in distribution of intron lengths for genomes of 17 species belonging to different taxa (insects, fish, amphibians, reptiles, birds, mammals) were studied. It is shown that the fraction of introns with phase 1 increases with the length of the intron. It was also shown that short and long introns tend to form series. For example, the proportion of short (long) introns that follow short (long) introns is considerably higher than the proportion of short (long) introns in a genome. These patterns are shown for all considered genomes. © 2014 Astakhova T.V., Roytberg M.A., Tsitovich I.I., Yakovlev V.V.

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