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Regular version of the site
Of all publications in the section: 19
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Article
Logvenkov S. A., Stein A. Biofizika. 2017. Vol. 62. No. 6. P. 926-934.

 

A general continual model of a medium composed of mechanically active cells is proposed. The medium is considered to be formed by three phases: cells, extracellular fluid, and an additional phase that is responsible for active interaction forces between cells and, for instance, may correspond to a system of protrusions that provide the development of active contractile forces. The deformation of the medium, which is identified with the deformation of the cell phase, consists of two components: elastic deformation of individual cells and cell rearrangements. The elastic deformation is associated with stresses in the cell phase. The spherical component of the stress tensor describes the nonlinear resistance of the cellular medium, which leads to the impossibility of its excessive compression. The constitutive equation for pressure in the cell phase is taken in the form of a nonlinear dependence on the volume cell density. The rearrangement of cells is considered as a flow controlled by stresses in the cell phase, active stresses, and fluid pressure. The tensor of active stresses is assumed to be spherical and nonlocally dependent on the cell density. Assuming that the process of biological tissue deformation is slow, we obtained a reduced model that neglects the elastic deformation of cells, compared to the inelastic deformation. A linear stability analysis of a spatially uniform steady-state solution was performed. The hydrostatic pressure of fluid is present among the parameters that are responsible for the loss of stability of the steady-state solution: an increase in it has a destabilizing effect owing to the action of the component of the interphase interaction force that is determined by the fluid pressure. The model we obtained can be used to describe the process of cavity formation in an initially homogeneous cell spheroid. The role of local and nonlocal mechanisms of active stress generation in the formation of cavity is investigated.

 

Added: Dec 30, 2017
Article
Sidorova A., Levashova N., Melnikova A. et al. Biofizika. 2015. Vol. 60. No. 3. P. 466-473.

The concept of active media is used as a biophysical foundation for modeling spatiotemporal self-organization in natural–anthropogenic ecosystems, appearing as establishment of regular dynamic structures with stable or unstable modes of development. Urban ecosystems are a hierarchy of interacting active media, with their nonlinearity being objectively formed owing to an extreme anthropogenic load, mismatch between the characteristic times and the evolutionary scales of the natural and anthropogenic components, as well as a complex system of positive and negative feedbacks between the constituent subsystems. The described model is purposefully simplified in order to use the Fitz–Hugh–Nagumo equation. The elaborated approach is of a general character and allows for a systematic description of spatiotemporal development of urban ecosystems as distributed dissipative systems.

Added: Dec 1, 2016
Article
Usova E., Burakov A., Shpilman A.A. Biofizika. 2010. Vol. 53. No. 6. P. 523-526.
Added: Oct 15, 2018
Article
Dmitriev A., Tverdislov V. A. Biofizika. 2006. Vol. 51. No. 4. P. 624-628.
Added: Nov 20, 2013
Article
Dmitriev A., Isaev P. P., Isaeva G. A. Biofizika. 2002. Vol. 47. No. 5. P. 864-868.
Added: Nov 21, 2013
Article
Isaeva G. A., Dmitriev A., Isaev P. P. Biofizika. 2002. Vol. 47. No. 3. P. 506-511.
Added: Nov 21, 2013
Article
Logvenkov S. A. Biofizika. 2011. No. 56(3). P. 483-489.

The continuum model of radial mass transfer in plant roots we developed previously is used for processing the nonstationary experiments aimed at the determination of the root hydraulic conductivity. It is shown that in contrast to compartmental models our model allows to describe the observed shape of the relaxation curve and to obtain segments with different relaxation times. It is found that for correctly determining the hydraulic conductivity the data processing method should be modified. A method is also proposed for estimating the extracellular to intracellular conductivity ratio.

Added: Feb 21, 2012
Article
Logvenkov S. A., Moiseeva I., Stein A. Biofizika. 2016. Vol. 61. No. 6. P. 989-995.

Invagination of epithelial sheets is an important type of morphogenetic deformation. Primary invagination during gastrulation in the sea urchin provides one of the simplest and best-studied examples. The specific mechanisms of invagination remain unclear in spite of numerous observations. The problem of plane-stress deformation of an initially circular layer exposed to a constant internal pressure is considered. Active forces developed by cells are characterized by an active moment. The rheology of a layer is described by a Maxwell-type viscoelasticity equation, which links the passive bending moment with the curvature of the layer. The presence of a passive moment threshold below which bending is purely elastic is taken into account. The active moment is defined as a function of coordinates and time that is nonzero in a certain limited region. The function is assumed to gradually increase, reach a steady state, and then decline gradually. Both constant- and alternating-sign spatial distributions of the active moment are considered. Numerical simulation showed that among all of the considered variants a realistic sequence of shapes can only be obtained if the layer is viscoelastic, there is a finite threshold for the passive bending moment, and the distribution of the active moment is of an alternating-sign type. The sign of the active moment differs between the inner and outer areas of the active region, tending to bend the sheet inward in the inner area and outward in the outer area. This study made it possible to reach several conclusions on the nature of the macroscopic organization of invagination and to outline avenues of research into the cellular mechanisms that are capable of developing the corresponding forces.

Added: Feb 14, 2017
Article
Logvenkov S. A., Stein A. Biofizika. 2015. Vol. 60. No. 6. P. 977-982.

The problem of deformation of a planar embryonic epithelium layer that is unloaded after a short period of uniaxial stretching with subsequent fixation in the stretched state for different periods of time is solved. The initial conditions for solving this problem are derived from the previously discussed problem of the uniform stretching of a tissue fragment (explant) with subsequent fixation of the obtained length. In this study we used the previously developed continuum model that describes the stress–strain state of epithelial tissue taking the parameters that characterize the shape of the cells and their stress state into account, as well as the active stresses they exert when they interact with each other. The experimentally observed continuation of the deformation of a stretched tissue after the external force has ceased to act is described theoretically as a result of active cell reactions to mechanical stress. The duration of explant fixation is shown to have a strong effect on its further elongation and on the pattern of cell activity.

Added: Feb 5, 2016
Article
Dmitriev A., Tverdislov V. A. Biofizika. 2004. Vol. 49. No. 3. P. 506-510.
Added: Nov 21, 2013
Article
Shpil'man A.A., Nadezhdina E. Biofizika. 2006. Vol. 51. No. 5. P. 880-884.
Added: Oct 15, 2018
Article
Попцова М. С., Гречишникова Д. А. Биофизика. 2017. Т. 62. № 6. С. 857-864.

Secondary RNA structures play an important role in transposition, in particular, in RNA recog- nition by transposon proteins. Previously, we found a conserved structure at the 3'-end of human transposons and proposed a hypothesis about the role of this structure in transposition. Although there is no similarity at the sequence level, the conserved position of this structure points to the fact that structural properties occur that are under positive natural selection. In this paper, the physical and geometric properties of stem-loop structures at the 3'-end of human transposons are identified and compared with properties of the structures of other genome regions. Each stem-loop structure was characterized by a set of ten characteristics: the Gibbs free energy, enthalpy, entropy, hydrophilicity, Shift, Slide, Rise, Tilt, Roll, and Twist. A model has been built using machine-learning methods, which recognizes stem-loop structures according to their physical and geo- metric characteristics with 94% accuracy. The most important parameters in the recognition model are hydrophilicity, enthalpy, Rise, and Twist. These properties of transposon structure are thought to be under positive natural selection.

Added: Oct 5, 2018
Article
Астахова Т. В., Лобанов М. Н., Поверенная И. В. и др. Биофизика. 2012. Т. 57. № 2. С. 205-211.

Verification of the PREFAB database containing golden standard protein alignments was performed. It has revealed a significant number of differences between the sequences from PREFAB and PDB databases. It was shown that, compared with the sequences given in the PDB, 575 alignments referred to a sequence with a gap; such alignments were excluded. Furthermore, compared with the PDB sequences, single substitutions or insertions were found for 440 amino acid sequences from PREFAB; these sequences were edited. SCOP domain analysis has shown that only 502 alignments in the resulting set contain sequences from the same family. Finally, eliminating duplicates, we have created a new golden standard alignment database PREFAB P based on PREFAB; the PREFAB P database contains 581 alignments.  

Added: Jul 18, 2012
Article
Астахова Т., Яковлев В., Поверенная И. В. и др. Биофизика. 2012. № 57. С. 205-211.
Added: Mar 5, 2012
Article
Логвенков С. А. Биофизика. 2011. Т. 56. № 3. С. 512-519.

The continuum model of radial mass transfer in plant roots we developed previously is used for processing the nonstationary experiments aimed at the determination of the root hydraulic conductivity. It is shown that in contrast to compartmental models our model allows to describe the observed shape of the relaxation curve and to obtain segments with different relaxation times. It is found that for correctly determining the hydraulic conductivity the data processing method should be modified. A method is also proposed for estimating the extracellular to intracellular conductivity ratio.

Added: Nov 24, 2012
Article
Исаева Г. А., Дмитриев А. В., Исаев П. П. Биофизика. 2000. Т. 45. № 6. С. 1066-1071.
Added: Nov 25, 2013
Article
Сереженков В., Калинина Е., Глазунова В.А. и др. Биофизика. 2007. Т. 52. № 5. С. 869-875.
Added: Jul 14, 2015
Article
Яковлев В. В., Ройтберг М. А. Биофизика. 2010. Т. 55. № 6. С. 965-975.

The accuracy of the global Smith–Waterman alignments and Pareto-optimal alignments depending on the degree of sequence similarity (percent of coincidence, %id, and the number of remote fragments N Gap) has been examined. An algorithm for constructing a set of three to six alignments has been developed of which the accuracy of the best alignment exceeds on the average the accuracy of the best alignment that can be constructed using the Smith–Waterman algorithm. F or weakly homologous sequences (%id 15, NG ap 20), the increase in the accuracy is on the average about 8%, with the average accuracy of the global Smith–Waterman alignments being about 38% (the accuracy was estimated on model test sets).  

Added: Oct 11, 2013