V. E. Kurochkin's research while affiliated with State Marine Technical University and other places

Publications (88)

Article
The possibility of a wide range of adjustment of the hydrophilic-hydrophobic properties of silicon wafers is demonstrated by means of treatment with hydrofluoric acid, Caro's acid, and various concentrations of hydrogen peroxide solutions. By measuring the contact angles of wetting and calculating the total, polar, and dispersive components of the...
Article
The features of the flow potential in the electrolyte that are significant for implementing a liquid acousto-electric converter are presented. The electrochemistry of the flow potential in electrolytes is considered. The peculiarities of the process in the electrolyte solutions associated with the influence of the ion strength of the electrolyte an...
Article
The genus Xanthomonas comprises phytopathogenic bacteria which infect about 400 host species, including a wide variety of economically important plants. Xanthomonas oryzae pv. oryzicola (Fang et al., 1957) Swings et al., 1990 is the causal agent of bacterial leaf streak (BLS) being one of the most destructive bacterial diseases of rice. BLS symptom...
Article
Full-text available
The development of next-generation sequencing (NGS) technologies has made a significant contribution to the trend of reducing costs and obtaining massive sequencing data. The Institute for Analytical Instrumentation of the Russian Academy of Sciences is developing a hardware-software complex for deciphering nucleic acid sequences by the method of m...
Article
Counting the occurrence of different k-mers often causes problems of genome assembly. Analysis of the frequency distribution of k-mers makes it possible to find assembly errors in already formed contigs. Currently, in connection with the development of instrumentation for genetic analysis, there is an urgent need to develop methods for assessing th...
Article
It is shown that in an electrokinetic acoustoelectric transducer, when a constant DC electric field (pump voltage) is applied during reception of an acoustic signal, it becomes possible to retransmit the initial external acoustic field. This is due to the presence of simultaneously reverse electrokinetic phenomena in the transducer: electroosmosis...
Article
A mathematical model of an acoustoelectric transducer based on the use of the electrokinetic phenomenon of the flow potential is proposed. It is shown theoretically that the flow potential increases in proportion to the strength of the constant electric pumping field, which is confirmed experimentally. The described converter has variable sensitivi...
Article
The success of genomic sequencing is impossible without the development of information technologies and mathematical methods for data processing to establish various features in the analyzed objects (nucleic acids) and trends in their changes. The volume of experimental data in the research of the genome has grown significantly, and new methods and...
Article
Full-text available
Oligomeric diisocyanate based coatings with different contents of barium titanate (BaTiO 3 ) submicron sized particles as a ferroelectric filler are synthesized on poly(dimethylsiloxane) (PDMS) supports. The study of thus obtained coatings using confocal scanning electron microscopy allowed the characterization of their morphology and features of B...
Article
In the approximation of a thin double layer, simple dependences of the acoustic fields excited in an electrokinetic electroacoustic transducer on the velocity of the Helmholtz—Smolukhovsky osmotic movement are obtained. From the dependencies it follows that in the absence of losses, when the nonlinearity of the fluid motion equation does not yet af...
Article
Basing on the analysis of the physical features of the operation of the microphone on electrokinetic phenomena, it has been experimentally confirmed that this microphone works on a functional principle different from the principle of operation of a condenser microphone. It is shown that a microphone based on electrokinetic phenomena can increase it...
Article
A new type of microphone is proposed, one of the distinguishing features of which is a variable sensitivity, which depends on the magnitude of the constant electric pumping voltage. In addition, a matching device (mediator) has been created that allows to significantly increase the sensitivity of the microphone. In the course of experiments, a sign...
Article
Full-text available
The processes occurring during the enzymatic growth of the DNA chain in the form of elongation of the molecules, the release of pyrophosphate, proton, thermal energy, and an increase in electrical impedance, which are used in various methods of high-throughput DNA sequencing by synthesis, are briefly considered. The detection of DNA chain growth is...
Article
This review analyzes two approaches to describing the polarization of disperse systems when an alternating electric field is applied in the general case. Polarization models of Trukhan and Dukhin – Shilov are considered. As a result of this review, it follows that the most preferable model, which makes it possible to significantly increase the rate...
Article
Several decades have passed since the development of the revolutionary DNA sequencing method by Frederick Sanger and his colleagues. After the Human Genome Project, the time interval between sequencing technologies began to shrink, while the volume of scientific knowledge continued to grow exponentially. Following Sanger sequencing, considered as t...
Article
The paper considers equations describing the motion of a fluid in a porous medium under the action of an electric field in conditions of the formed turbulent mode of motion. Equations are given that describe the acoustic oscillations that occur in a fluid, the source of which can be not only an alternating, but also a constant electric field. The p...
Article
A detector of cell subpopulations developed at the Institute of Analytical Instrumentation of the Russian Academy of Sciences was used for immunophenotyping lymphocytes from healthy donors and standardized blood samples with normal and low-level cell populations. It has been shown that it is possible (provided that the modern criteria for the accur...
Article
Physical and mathematical models for describing the mechanism of operation of a new type of acoustic transducer are proposed within the linear approximation. The necessary equations and boundary conditions for describing the acoustic fields caused by electrokinetic phenomena are given. The physical model developed and the corresponding mathematical...
Article
At present, many polymerase chain reaction models have been proposed for exact quantitative estimation of the reaction results. In most models, kinetics of product accumulation and kinetics of fluorescent reporter are assumed to be identical. A model of the polymerase chain reaction is proposed to study the difference of such functions in the syste...
Article
The synthesis of unsymmetrical polymethine cyanine derivatives of f luorescent dyes is described, and their potential as a component of hybridization probes for the real-time PCR technique is first demonstrated.
Article
Fragment analysis of DNA by the capillary gel-electrophoresis method is an effective tool for studying the DNA structure, which has a large number of applications (in particular, for genetic expertise of breeds and breed samples of a number of important crops). Fragment analysis of DNA is carried out in several stages. The stage of processing of th...
Article
Full-text available
Segmented capillaries comprising two segments with different surface charges of polymer layers are prepared. One segment with a neutral surface charge is responsible for separation and another one with negatively charged surface provides the electro-osmotic flow adjustment. The average electro-osmotic flow rate is found to correlate with the length...
Article
The course of the real-time polymerase chain reaction (PCR) is determined by the temperature dependence of the kinetics of the component reactions, particularly the DNA strand hybridization. To investigate the effect of thermal processes on the reaction behavior, a mathematical model in which the variable rate constant of dissociation of “primer–si...
Article
Relationships in variation of the surface energy of polystyrene coatings on melted quartz at varied polymer concentration in solution were refined by studying the functional chemical composition and surface structure of model coatings of atactic polystyrene on quartz plates and the electromigration properties of capillary columns with polystyrene c...
Article
Full-text available
Real-time polymerase chain reaction (real-time PCR) is the main molecular genetic method used for qualitative and quantitative analysis of specific nucleic acid sequences in many areas of biomedical research. Theoretical study of pCr models allows to estimate the influence of various reaction components and parameters, and to determine the unknown...
Article
Development of methods for obtaining approximate analytical solutions of nonlinear differential equations and their systems is a rapidly developing field of mathematical physics. Earlier, an approximate solution of the simplest system of kinetic enzymatic equations for calculating dynamics of complementary strands of nucleic acids was obtained. In...
Article
Macroscopic kinetic models describing the process of polymerase chain reaction (PCR) are currently solved only by numerical methods, which hampers the development of effective software algorithms for processing the results of the reaction. This paper considers the application of the homotopy perturbation method for obtaining approximate analytical...
Article
A new noncontact method for measuring temperatures of liquids, which is based on the fluorescent probes, is proposed. The method is intended for measuring temperatures of reaction media in reactors of devices for polymerase chain reactions in real time and can be used for determining dynamic temperature parameters.
Article
The paper reviews different approaches to the mathematical analysis of polymerase chain reaction (PCR) kinetic curves. The basic principles of PCR mathematical analysis are presented. Approximation of PCR kinetic curves and PCR efficiency curves by various functions is described. Several PCR models based on chemical kinetics equations are suggested...
Article
When solving many problems in biology and med� icine, it is necessary to detect the presence of specific nucleic acid sequences in samples. For this purpose, polymerase chain reaction (PCR)—a chain enzy� matic reaction of multiplication of the analyzed DNA fragment, realized in the form of successive rounds of duplication of fragments present in th...
Article
The radiation pressure forces on a sphere with radially symmetric properties are considered as functions of the sphere size with respect to the wavelength in the quasi-standing plane wave field with a constant frequency in the presence of loss in the inclusion. It is shown that the presence of loss in the inclusion positioned in an ideal fluid medi...
Article
Currently, polymerase chain reaction (PCR) is the main moleculargenetic method used for qualitative and quantitative analysis of nucleic acid specific sequences. PCR is based on the branched chain reac� tion of replication of a doublestranded DNA frag� ment (fragment replication). The reaction is carried out by cyclically repeating two stages: (1)...
Article
An approach to calculating resonance frequencies and acoustic characteristics of ultrasonic multilayer liquid chambers bordering an air or liquid half-space and loaded to a piezoelectric emitter is proposed. The assumption on the validity of plane motion is accepted. The approach allows for obtaining comprehensive data on physical processes in the...
Article
The effect of electron beam pretreatment of fused silica glass upon its surface functional composition and possibility for subsequent immobilization of methacryloxypropyl-trimethoxysilane (MOPTMS) layer is studied using FTIR spectroscopy and adsorption of acid–base indicators. The content of Brensted acidic centers (silanol groups) on the irradiate...
Article
A method is proposed for calculating the radiation pressure forces that act on a body characterized by a given scattering amplitude and positioned in an ideal liquid in an arbitrary acoustic field. The efficiency of the method is tested by two examples: a fluid sphere in a spherical wave and a similar sphere in the field of a traveling wave with a...
Article
Let a harmonic field of a plane standing wave be formed in an ultrasonic chamber (USC) between the vertical radiator and reflector planes. Experiments show that the behavior of small grains of the same sort is strongly dependent on the grain size. The smallest grains in the node (antinode) planes do not move horizontally and descend under the actio...
Article
A analytic study has proposed a method for determining the radiation pressure in an arbitrary incident field for various complex inclusions. The attempt was to generalize an approach that the radiation pressure forces acting on an arbitrary scatterer described by a certain scattering amplitude. The study has generalized the case of longitudinal aco...
Article
A study was conducted to analyze radiation-pressure forces in a perfect liquid residing in the field of plane progressive and stationary waves that act on conglomerates produced by the cohesion of similar spherically symmetric particles, whose size was smaller than the wavelength. Researchers were able to derive the general expressions connecting t...
Article
The form, the size and the color of a fungal colony are the features which can characterize genera and species of fungi. Besides the individual properties of fungal cultures (such as the existence of circadian rhythms, the ability to produce metabolites - growth inhibitors - antibiotics, organic acids, exoenzymes, etc.) the environmental parameters...
Article
Full-text available
One of alternative methods of water disinfection is its treatment by pulsed electric discharges (PEDs). In this case, during the discharges, bacteria are destroyed by UV radiation with a significant share of energy in waves of 200-400 nm and by shock waves, which are formed at the initial stage of the discharge-column widening. This paper describes...
Chapter
We study a phenomenon of stationary pattern formation in colonies of imperfect mycelial fungi. Conditions required in order for patterns to appear and general features of spatial structures are investigated. A mathematical model is proposed for the description of this macroscopic self-organizing system. The model is demonstrated to be consistent wi...
Article
The main characteristics of pulsed discharges in water are studied, such as the discharge current, voltage drop across the discharge gap, temperature of the discharge column, and plasma conductivity, as well as compression waves and ultraviolet radiation, which are induced by the discharge. The physicochemical properties of water treated by pulsed...
Article
This paper discusses an analytical system for monitoring the amount of DNA, based on a fluorescence method for detecting the products of the polymerase chain reaction in real time. An analyzer has been developed that makes it possible to detect fluorescence simultaneously in sixteen samples on four spectral channels.
Article
At investigation of the method of water disinfection with pulsed-periodic electric discharges, established was the fact of bacteria dying not only upon water treatment but also after a long time (up to the year) in the case of secondary contamination. On the base of presented analyses results, the possible mechanisms explaining this phenomenon (nam...
Article
State-of-the-art microfluidic analytical systems are briefly surveyed. Attention is focused on the use of microchip capillary electrophoresis. The main results obtained in the development of a prototype analytical system with a laser-induced fluorescence detector for electrophoresis on a glass microfluidic chip are presented. Experimental data on e...
Article
The mechanism of antifungal action and properties of water treated by pulse electric discharges have been studied. Experiments were carried out on 3 strains of micromycetes: Ulocladium chartarum, U. consortiale, Phaeococcomyces sp. (strain Ch 49). Water treated with electrodes made of silver, titanium and steel contain high amounts of small cluster...
Article
The physical bases for analyzing the nucleotide sequence of a DNA molecule by means of capillary electrophoresis are discussed. Possible ways of increasing the throughput of the method are studied. An analysis study of schematic diagrams for the detection of nucleotides by means of laser excitation of the luminescence of primers attached to nucleot...
Article
The robust procedure of the constant signal estimation in the presence of additive noise is realized using Tsypkin's modification of the stochastic approximation method. This procedure chooses parameters of the algorithm and the initial estimate, estimates the signal, and stops the estimation as soon as a required accuracy is obtained or a failure...
Article
This paper reviews the criteria for detecting individual molecules in liquids. It focuses on the detection of individual molecules by means of capillary electrophoresis and laser fluorimetry. It discusses the main experimental limitations and obstacles that make it hard to reliably detect individual molecules. It discusses the results of tests of t...
Article
Conditions required for zone formation in colonies of imperfect mycelial fungi (Hyphomycetes) were studied. Two competitive processes are probably responsible for this phenomenon: activation of mycelial growth by substratum consumption and its inhibition by metabolite production. A mathematical model is proposed which describes properly such growth...
Article
Mathematical model of the development of the pattern of colonies is considered. The model represents the systems of defferential equations of the first order. It includes non-dimensional parameters characterizing the following features: concentration of substrate, concentration of metabolic products -growth inhibitor, mycelium and spores, radial an...
Article
Mathematical model of the development of the pattern of colonies is considered. The model represents the systems of differential equations of the first order. It includes non-dimensional parameters characterizing the following features: concentration of substrate, concentration of metabolic products--growth inhibitor, mycelium and spores, radial an...
Article
A noise-immune iterative algorithm having a relay function with a dead zone is considered. For a signal in noise that is distributed by the triangular law, the variance of the evaluation error is shown to be independent of the value of the dead zone.
Article
Portable chemosensor analyzers have been created for determining the pH in microvolumes of media (up to 5 μL) and on the surface of nonmetallic objects and to determine the concentrations of metal ions in aqueous media (Cu, Gd, Fe) from the variation of the light absorption. The main characteristics of the photometric devices are given, and the cal...
Article
Different spatial spectral dependences of the reflectance are obtained for marble from different sites. This increases the information content of the measurements and makes it possible to use the dependences as supplementary attributes in identifying the marble. Biodegradation of marble is studied on samples inoculated with melanin-containing micro...
Article
A miniature chemical sensing analyzer for the determination of pH and concentrations of metal ions has been developed. It operates on the principle of the reflection photometry of chemical sensors based on optically transparent polymers containing organic reagents. The analyzer can be used for measuring the reflection properties of color indicator...
Article
The efficiency and threshold concentration of biocides has been examined by photometric analysis of the growth of micro-organisms cultured in the laboratory. Both fungi and algae responsible for attacking museum exhibits inside and in the open air were used. The organisms were cultured on a nutrient media containing serial dilutions of biocide, and...
Chapter
The quantitative regularity of the microorganism growth at the batch cultivation in liquid media is the base for natural and outlet water biotest method. The possibility of the biosubject growth monitoring by means of the complex of devices including the 96-channel LINKEY-photometer connected with the personal computer, automatic 8-channel reagent...
Article
1. The possibility in principle of recording the results of the IHAT in wells with a parabolic bottom by the vertical photometry method in the microanalysis class was established. 2. The time from the start of setting up the tests after which it is possible to reliably record the test results without a decrease of the sensitivity of demonstrating...

Citations

... Только секвенирование всего генома теоретически может позволить такую мутацию найти. Но ДНК-паспортизация сортов и их ДНКидентификация путем полногеномного секвенирования, несмотря на его бурное развитие и удешевление [28] вряд ли в ближайшие годы станет легко доступной, дешевой и уместной, хотя бы потому что для большинства целей достаточно охарактеризовать часть генома. Лишь при наличии очень серьезной необходимости выявления всех возможных отличий (мутаций) можно (нужно) будет прибегать (в будущем) к секвенированию всего генома. ...
... The Sanger sequencing process itself predetermines the effect of a drop in quality (it is more difficult to distinguish a 700 nucleotide molecule from a 701 nucleotide molecule than 100 from 101, respectively). In this case, the final resolution is determined by both the electrophoresis parameters and the type of polymer used for separation [11]. Nevertheless, despite the variety of DNA sequencing methods developed to date, Sanger's method is preferred in studies in which it is necessary to quickly (within a few hours) decipher a genome fragment up to several hundred nucleotides in size. ...
... С их помощью проводятся WGS, WES и tNGS. Общим для разновидностей NGS является многократное прочтение каждого из исследуемых участков, обеспечивающее сравнительно высокую точность полученных данных [43]. NGS позволяет выявить непосредственно нуклеотидную последовательность заданных участков. ...
... The authors have earlier considered in [1,2] and other papers the acoustoelectric conversion based on such an electrokinetic phenomenon as electroosmosis. In [3] there was suggested an acoustoelectric conversion based on the electrokinetic phenomenon reverse to electroosmosis, i. e. flow potential that is sometimes referred to as current potential [4]. ...
... The range of zeta potentials estimated as 27 < |ζ | < 52 [mV] in Fig. 9 reasonably agree with the numerical and experimental data (Bagotsky 2005;Brant et al. 2006;Karniadakis et al. 2005;Kirby 2010;Liechty et al. 2005). This also falls within the range of 50-100 [mV] reported by Kirby and Hasselbrink (2004) for ζ-potential at silica-water interface. ...
... The authors have earlier considered in [1,2] and other papers the acoustoelectric conversion based on such an electrokinetic phenomenon as electroosmosis. In [3] there was suggested an acoustoelectric conversion based on the electrokinetic phenomenon reverse to electroosmosis, i. e. flow potential that is sometimes referred to as current potential [4]. ...
... In RT-PCR, various types of fluorogenic DNA probes are used, which are capable of increasing fluorescence when interacting with the accumulating PCR product; the fluorogenic effect is achieved as a result of the interaction of two dyes, one of which can be nonfluorescent (quencher) [5,8]. For fluorogenic probes, the relationship between the type of dye and the structure of the probe is being studied [9], new dyes are being developed [10][11][12], and probes with two residues of a fluorescent dye and/or a fluorescence quencher are being investigated [13][14][15]. The most popular dye for DNA probes is fluorescein, which is attached in the form of a carboxyl derivative at the amino group of a linker; such fluoresceinamide is abbreviated as FAM. ...
... The RT-PCR method is based on the dye fluorescent response observation during the polymerase chain reaction [4]. The obtained data are used to calculate the values of the threshold cycle Cq -a value that allows to compare samples with each other on quantitative analysis [5]. RT-PCR in its classical design is a temperature-controlled reaction and is accompanied by a cyclic two-or three-step temperature change, providing the processes of denaturation, annealing and elongation [6]. ...
... RT-PCR is one of the most relevant and popular methods of genetic analysis and is widely used in medical diagnostics and scientific research [3]. The market size of RT-PCR and digital PCR was estimated at US $ 4.47 billion in 2019 by Validated Market Research and is projected to reach US $ 8.26 billion by 2027, with CAGR from 2020 to 2027 will be 8.6%. ...
... Calculation by these methods is hindered by the tilt and vertical displacement of real plots relative to the base line, which can be explained by factors including the tem perature dependence of background fluorescence [15]. ...