{"title":"Charge Motion along Polynucleotide Chains in a Constant Electric Field Depends on the Charge Coupling Constant with Chain Displacements","authors":"A. N. Korshunova, V. Lakhno","doi":"10.17537/2022.17.t1","DOIUrl":"https://doi.org/10.17537/2022.17.t1","url":null,"abstract":"","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87574332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The paper deals with numerical simulation of the air flow in the full human bronchial tree. In their previous studies, the authors developed an analytical model of the full human bronchial tree and a method of stage-by-stage computation of the respiratory tract. A possibility of using the proposed method for a wide range of problems of numerical simulations of the air flow in human lungs is analyzed. The following situations are considered: 1) steady inspiration (with different flow rates of air) for circular and “starry” cross sections of bronchi (“starry” cross sections models some lung pathology); 2) steady expiration; 3) unsteady inspiration; 4) precipitation of medical drug aerosol droplets in human bronchi. The results predicted by the proposed method are compared with results of other researchers and found to be in good agreement. In contrast to previous investigations, the air flow in the full (down to alveoli) bronchial tree is studied for the first time. It is shown that expiration requires a greater pressure difference (approximately by 30%) than inspiration. Numerical simulations of precipitation of medical drug aerosol droplets in the human respiratory tract show that aerosol droplets generated by a standard nebulizer do not reach the alveoli (the droplets settle down in the lower regions of the bronchi).
{"title":"Simulation of Air Motion in Human Lungs during Breathing. Dynamics of Liquid Droplet Precipitation in the Case of Medicine Drug Aerosols","authors":"A. Medvedev, P.S. Golysheva","doi":"10.17537/2021.16.422","DOIUrl":"https://doi.org/10.17537/2021.16.422","url":null,"abstract":"\u0000 The paper deals with numerical simulation of the air flow in the full human bronchial tree. In their previous studies, the authors developed an analytical model of the full human bronchial tree and a method of stage-by-stage computation of the respiratory tract. A possibility of using the proposed method for a wide range of problems of numerical simulations of the air flow in human lungs is analyzed. The following situations are considered: 1) steady inspiration (with different flow rates of air) for circular and “starry” cross sections of bronchi (“starry” cross sections models some lung pathology); 2) steady expiration; 3) unsteady inspiration; 4) precipitation of medical drug aerosol droplets in human bronchi. The results predicted by the proposed method are compared with results of other researchers and found to be in good agreement. In contrast to previous investigations, the air flow in the full (down to alveoli) bronchial tree is studied for the first time. It is shown that expiration requires a greater pressure difference (approximately by 30%) than inspiration. Numerical simulations of precipitation of medical drug aerosol droplets in the human respiratory tract show that aerosol droplets generated by a standard nebulizer do not reach the alveoli (the droplets settle down in the lower regions of the bronchi). \u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75036945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Various regimes of a charge motion along a chain in a constant electric field are investigated. This motion is simulated on the basis of the Holstein model. Earlier studies demonstrate a possibility of a uniform motion of a charge in a constant electric field over very long distances. For small values of the electric field intensity a Holstein polaron can move at a constant velocity. As the electric field intensity increases, a charge motion acquires oscillatorily character, performing Bloch oscillations. Since the charge motion depends on the whole set of the system parameters the character of the motion depends not only on the value of the electric field intensity. Therefore, the electric field intensity for which the uniform motion takes place differs for chains with different parameters. The character of the charge motion and distribution is considered in chains with different values of the constant of coupling between the charge and the displacements of the chain. We showed that the values of the electric field intensity for which the regime of a charge motion changes are different in chains with different values of the coupling constant. We also demonstrated that for one and the same value of the electric field intensity, in chains with different values of the coupling constant either a uniform motion or an oscillatory motion, or a stationary polaron can be observed.
{"title":"Charge Motion along a Polynucleotide Chains in a Constant Electric Field Depends on the Charge Coupling Constant with Chain Displacements","authors":"A. N. Korshunova, V. Lakhno","doi":"10.17537/2021.16.411","DOIUrl":"https://doi.org/10.17537/2021.16.411","url":null,"abstract":"\u0000 Various regimes of a charge motion along a chain in a constant electric field are investigated. This motion is simulated on the basis of the Holstein model. Earlier studies demonstrate a possibility of a uniform motion of a charge in a constant electric field over very long distances. For small values of the electric field intensity a Holstein polaron can move at a constant velocity. As the electric field intensity increases, a charge motion acquires oscillatorily character, performing Bloch oscillations. Since the charge motion depends on the whole set of the system parameters the character of the motion depends not only on the value of the electric field intensity. Therefore, the electric field intensity for which the uniform motion takes place differs for chains with different parameters. The character of the charge motion and distribution is considered in chains with different values of the constant of coupling between the charge and the displacements of the chain. We showed that the values of the electric field intensity for which the regime of a charge motion changes are different in chains with different values of the coupling constant. We also demonstrated that for one and the same value of the electric field intensity, in chains with different values of the coupling constant either a uniform motion or an oscillatory motion, or a stationary polaron can be observed.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77572693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The model of a three-trophic community with intraguild predation is considered. The system consists of three coupled ordinary differential equations describing the dynamics of resource, prey and predator. Models with intraguild predation are characterized by predators that feed on resource of its own prey. A number of similar models with different functional responses have been proposed. In contrast to previous works, in the present model, the predator functional response to the resource is differed from that to the prey. The model takes into account an intraspecific competition of prey to stabilize the system in resource-rich environment. Conditions of existence and local stability of non-negative solutions are established. The possibility of Hopf bifurcation around positive equilibrium with consumption rate as bifurcation parameter is studied. For the model, in the plane of the consumption and predation rates, the regions of existence and stability of boundary and internal equilibria are constructed. Numerical simulations show that the region of equilibrium coexistence of populations is increased due to the inclusion of prey self-limitation in the model. Bifurcation diagrams confirm the stabilizing effect of intraspecific competition of prey on the system dynamics in resource-rich environment.
{"title":"Coexistence of the Three Trophic Levels in a Model with Intraguild Predation and Intraspecific Competition of Prey","authors":"E. Giricheva","doi":"10.17537/2021.16.394","DOIUrl":"https://doi.org/10.17537/2021.16.394","url":null,"abstract":"\u0000 The model of a three-trophic community with intraguild predation is considered. The system consists of three coupled ordinary differential equations describing the dynamics of resource, prey and predator. Models with intraguild predation are characterized by predators that feed on resource of its own prey. A number of similar models with different functional responses have been proposed. In contrast to previous works, in the present model, the predator functional response to the resource is differed from that to the prey. The model takes into account an intraspecific competition of prey to stabilize the system in resource-rich environment. Conditions of existence and local stability of non-negative solutions are established. The possibility of Hopf bifurcation around positive equilibrium with consumption rate as bifurcation parameter is studied. For the model, in the plane of the consumption and predation rates, the regions of existence and stability of boundary and internal equilibria are constructed. Numerical simulations show that the region of equilibrium coexistence of populations is increased due to the inclusion of prey self-limitation in the model. Bifurcation diagrams confirm the stabilizing effect of intraspecific competition of prey on the system dynamics in resource-rich environment.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80839160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
E. A. Isaev, F. Doronin, A. G. Evdokimov, D. Pervukhin, Y. Rudyak, G. Rytikov, V. Kornilov, V. G. Nazarov
The need to ensure the possibility of widespread use of electronic and mobile health-saving technologies requires not only the formation of an appropriate information technology infrastructure and the development of effective algorithms for processing a large amount of personal information. Development of medical devices for recording physiological processes also involves the creation of innovative biologically compatible materials that allow sensors and medical sensors to work continuously in 24/7 mode. Taking into account the long-term positive experience of using large-capacity thermoplastics and elastomers in medical equipment, it seems promising to use the corresponding polymers as the main materials of wearable electronics for medical purposes. At the same time, to ensure the biological compatibility of the materials under discussion, it is necessary to minimize the possibility of the development of pathogenic microorganisms on surfaces in contact with living tissues. This type of pathogenic organisms (pathogens of a number of dangerous diseases – mycoses) includes some types of microscopic fungi - micromycetes (in particular, Aspergillus niger van Tiegem; Aspergillus terreus Thom; Penicillium cycopium Westling). The article examines the effect of surface modification by gas-phase fluorination on the nature and degree of development of a mixed colony of micromycetes on the surfaces of experimental samples made of several types of thermoplastics (polyvinyl chloride, polypropylene, low-density polyethylene, polyethylene terephthalate) and elastomers (butyl- and butadiene-nitrile rubbers, as well as ethylene, propylene and dicyclopentadiene copolymers). The nature and degree of development of colonies are quantitatively described using the original methodology developed earlier. The effect of fluorination on the nanotexture and chemical composition of the surface and near-surface layers of experimental samples was demonstrated using scanning electron microscopy (SEM) and IR Fourier spectroscopy (IRFS). The dynamics and efficiency of fluorination are described using a linearized hyperbolic model, the parameters of which are set by the least squares method.
{"title":"Quantitative Assessment of the Development of Micromycete Colony on the Surfaces of Polymers and Polymer Composites","authors":"E. A. Isaev, F. Doronin, A. G. Evdokimov, D. Pervukhin, Y. Rudyak, G. Rytikov, V. Kornilov, V. G. Nazarov","doi":"10.17537/2021.16.367","DOIUrl":"https://doi.org/10.17537/2021.16.367","url":null,"abstract":"\u0000The need to ensure the possibility of widespread use of electronic and mobile health-saving technologies requires not only the formation of an appropriate information technology infrastructure and the development of effective algorithms for processing a large amount of personal information. Development of medical devices for recording physiological processes also involves the creation of innovative biologically compatible materials that allow sensors and medical sensors to work continuously in 24/7 mode. Taking into account the long-term positive experience of using large-capacity thermoplastics and elastomers in medical equipment, it seems promising to use the corresponding polymers as the main materials of wearable electronics for medical purposes. At the same time, to ensure the biological compatibility of the materials under discussion, it is necessary to minimize the possibility of the development of pathogenic microorganisms on surfaces in contact with living tissues. This type of pathogenic organisms (pathogens of a number of dangerous diseases – mycoses) includes some types of microscopic fungi - micromycetes (in particular, Aspergillus niger van Tiegem; Aspergillus terreus Thom; Penicillium cycopium Westling). The article examines the effect of surface modification by gas-phase fluorination on the nature and degree of development of a mixed colony of micromycetes on the surfaces of experimental samples made of several types of thermoplastics (polyvinyl chloride, polypropylene, low-density polyethylene, polyethylene terephthalate) and elastomers (butyl- and butadiene-nitrile rubbers, as well as ethylene, propylene and dicyclopentadiene copolymers). The nature and degree of development of colonies are quantitatively described using the original methodology developed earlier. The effect of fluorination on the nanotexture and chemical composition of the surface and near-surface layers of experimental samples was demonstrated using scanning electron microscopy (SEM) and IR Fourier spectroscopy (IRFS). The dynamics and efficiency of fluorination are described using a linearized hyperbolic model, the parameters of which are set by the least squares method.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"335 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76396819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Droop's well-known model simulates phytoplankton biomass dynamics based on nutrient limitation. The defining parameter is the nutrient concentration in phytoplankton cells (cell quota). This model is modified to description of the photosynthesis processes. The effects of photosynthetically active radiation must be taken into account. At the same time, the nutritional factor remains the main one. Water temperature is considered as a controlling factor. The influence of light during photosynthesis plays a decisive role. The decisive factor is the presence of photosynthetic substances. We conventionally combine them under the name "chlorophyll". Sufficient variability in the proportion of chlorophyll in phytoplankton (chlorophyll quota) directly affects biomass production. The equation for the dynamics of chlorophyll quota is added to the Droop model. The parameters of the model depend on the concentration of nutrients, illumination and water temperature. The properties of the solutions in the model are investigated, the conditions for the existence and stability of equilibrium solutions are clarified. Complex dynamic regimes are revealed in the case of unstable equilibria. It was found that the most sensitive parameter for biomass dynamics is the minimum value of the cell quota. The dynamics of indicators for the daily cycle and the annual cycle of seasonal changes are calculated. The influence of nutrition, illumination and temperature on biomass production has been clarified. During the day, the chlorophyll quota fluctuates insignificantly due to a short period of time. The changes are noticeable at longer times for example during the season.
{"title":"Modeling of Photosynthesis Process and Assessing Of Phytoplankton Dynamics Based On Droop Model","authors":"A. Abakumov, S. Pak","doi":"10.17537/2021.16.380","DOIUrl":"https://doi.org/10.17537/2021.16.380","url":null,"abstract":"\u0000 Droop's well-known model simulates phytoplankton biomass dynamics based on nutrient limitation. The defining parameter is the nutrient concentration in phytoplankton cells (cell quota). This model is modified to description of the photosynthesis processes. The effects of photosynthetically active radiation must be taken into account. At the same time, the nutritional factor remains the main one. Water temperature is considered as a controlling factor. The influence of light during photosynthesis plays a decisive role. The decisive factor is the presence of photosynthetic substances. We conventionally combine them under the name \"chlorophyll\". Sufficient variability in the proportion of chlorophyll in phytoplankton (chlorophyll quota) directly affects biomass production. The equation for the dynamics of chlorophyll quota is added to the Droop model. The parameters of the model depend on the concentration of nutrients, illumination and water temperature. The properties of the solutions in the model are investigated, the conditions for the existence and stability of equilibrium solutions are clarified. Complex dynamic regimes are revealed in the case of unstable equilibria. It was found that the most sensitive parameter for biomass dynamics is the minimum value of the cell quota. The dynamics of indicators for the daily cycle and the annual cycle of seasonal changes are calculated. The influence of nutrition, illumination and temperature on biomass production has been clarified. During the day, the chlorophyll quota fluctuates insignificantly due to a short period of time. The changes are noticeable at longer times for example during the season.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90641925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
As part of the mathematical model of the human respiratory system, a submodel is considered for the study of the non-steady airflow with solid particles (suspended particulate matter (PM) / dust particles) and the deposition of particles of various sizes in the human nasal cavity. It is assumed that the nasal cavity is divided by the bone-cartilaginous septum into two symmetrical (relative to the nasal septum) parts; the average geometry of the right part of the human nasal cavity is considered. The inhaled air is considered as a multiphase mixture of homogeneous single-component gas and solid dust particles. The Eulerian-Lagrangian approach to modeling the motion of a multiphase mixture is used: a viscous liquid model is used to describe the motion of the carrier gas phase; the carried phase (dust particles) is modeled as separate inclusions of various sizes. The process of heating the inhaled air due to its contact with the walls is also taken into account. The features of the unsteady flow of a multiphase air mixture with dust particles were obtained using Ansys CFX for several scenarios. It has been noted that when studying the airflow in the nasal cavity, it is necessary to take into account the presence of turbulence, for which it is proposed to use the k-ω model. The velocity fields of inhaled air in the nasal cavity have been obtained; presented temperature distributions in the nasal cavity at different time points; made estimates of air heating at different temperatures of inhaled air; gave estimates of the proportion of deposited particles in the nasal cavity depending on the particle size for real machine-building production; presented trajectories of movement of suspended particles. Thus, it is shown that more than 99.7 % of particles with a diameter of more than 10 microns deposit in the human nasal cavity; as the particle diameter and mass decrease, the proportion of deposited particles decreases. Suspended particles with a size of less than 2.5 microns almost do not deposit in the nasal cavity. They can penetrate deeper into the lower airways and lungs of a person with the inhaled air and, having fibrogenic and toxic effect, can cause diseases. The results obtained are in good agreement with the results of individual studies performed by other scientists. Further development of the model involves studying airflow in the human lungs and modeling the formation of diseases caused by the harmful effects of environmental factors (including dust particles) entering the human body by inhalation.
{"title":"Mathematical Model of Airflow and Solid Particles Transport in The Human Nasal Cavity","authors":"P. Trusov, N. Zaitseva, M. Tsinker, A. Nekrasova","doi":"10.17537/2021.16.349","DOIUrl":"https://doi.org/10.17537/2021.16.349","url":null,"abstract":"\u0000As part of the mathematical model of the human respiratory system, a submodel is considered for the study of the non-steady airflow with solid particles (suspended particulate matter (PM) / dust particles) and the deposition of particles of various sizes in the human nasal cavity. It is assumed that the nasal cavity is divided by the bone-cartilaginous septum into two symmetrical (relative to the nasal septum) parts; the average geometry of the right part of the human nasal cavity is considered. The inhaled air is considered as a multiphase mixture of homogeneous single-component gas and solid dust particles. The Eulerian-Lagrangian approach to modeling the motion of a multiphase mixture is used: a viscous liquid model is used to describe the motion of the carrier gas phase; the carried phase (dust particles) is modeled as separate inclusions of various sizes. The process of heating the inhaled air due to its contact with the walls is also taken into account. The features of the unsteady flow of a multiphase air mixture with dust particles were obtained using Ansys CFX for several scenarios. It has been noted that when studying the airflow in the nasal cavity, it is necessary to take into account the presence of turbulence, for which it is proposed to use the k-ω model. The velocity fields of inhaled air in the nasal cavity have been obtained; presented temperature distributions in the nasal cavity at different time points; made estimates of air heating at different temperatures of inhaled air; gave estimates of the proportion of deposited particles in the nasal cavity depending on the particle size for real machine-building production; presented trajectories of movement of suspended particles. Thus, it is shown that more than 99.7 % of particles with a diameter of more than 10 microns deposit in the human nasal cavity; as the particle diameter and mass decrease, the proportion of deposited particles decreases. Suspended particles with a size of less than 2.5 microns almost do not deposit in the nasal cavity. They can penetrate deeper into the lower airways and lungs of a person with the inhaled air and, having fibrogenic and toxic effect, can cause diseases. The results obtained are in good agreement with the results of individual studies performed by other scientists. Further development of the model involves studying airflow in the human lungs and modeling the formation of diseases caused by the harmful effects of environmental factors (including dust particles) entering the human body by inhalation.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"57 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87106360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A one-electron model is proposed to describe a polaron on a dimerized polyacetylene lattice. Within the framework of the formulated model, the dynamics of a freely moving polaron is considered. The results obtained are compared with the many-electron model that takes into account all π-electrons of the valence band. Polaron can move at subsonic and supersonic speeds. The subsonic polaron is stable. A supersonic polaron loses stability at times ∼ 6 000 fs. A supersonic polaron has a forbidden speed range. An analytical solution to the continual approximation helps to understand the reason for the existence of forbidden speeds. The dynamics of a free polaron is similar to the dynamics of a polaron in an electric field. The proposed one-electron approximation significantly expands the possibilities of numerical simulation in comparison with the traditional many-electron model.
{"title":"Polarons on Dimerized Lattice of Polyacetilene. Continuum Approximation","authors":"T. Astakhova, G. Vinogradov","doi":"10.17537/2021.16.335","DOIUrl":"https://doi.org/10.17537/2021.16.335","url":null,"abstract":"\u0000A one-electron model is proposed to describe a polaron on a dimerized polyacetylene lattice. Within the framework of the formulated model, the dynamics of a freely moving polaron is considered. The results obtained are compared with the many-electron model that takes into account all π-electrons of the valence band. Polaron can move at subsonic and supersonic speeds. The subsonic polaron is stable. A supersonic polaron loses stability at times ∼ 6 000 fs. A supersonic polaron has a forbidden speed range. An analytical solution to the continual approximation helps to understand the reason for the existence of forbidden speeds. The dynamics of a free polaron is similar to the dynamics of a polaron in an electric field. The proposed one-electron approximation significantly expands the possibilities of numerical simulation in comparison with the traditional many-electron model. \u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88026370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
V. Efimov, K. V. Efimov, V. Kovaleva, Y. Matushkin
Any numerical series can be decomposed into principal components using singular spectral analysis. We have recently proposed a new analysis method ‒ PCA-Seq, which allows calculating numerical principal components for a sequence of elements of any type. In particular, the sequence may be composed of nucleotide base pairs or amino acid residues. Two questions inevitably arise about interpretation of the obtained principal components and about the assessment of their reliability. For interpretation of the symbolic sequence principal components, it is reasonable to evaluate their correlations with numerical characteristics of the sequence elements. To assess the significance of correlations between sequences, one should bear in mind that standard significance criteria are based on the assumption of independence of observations, which, as a rule, is not fulfilled for real sequences. The article discusses the use of an anchor bootstrap technique for these purposes also previously developed by the authors of the article. In this approach it is assumed, that points of a metric space can represent the objects. When taken together they make up some fixed structure in it, in particular, a sequence. The objects are assigned the same random integer weights as in the classical bootstrap. This is sufficient to obtain the bootstrap distribution of the correlation coefficients and assess their significance. The coding sequence of the SLC9A1 gene (synonyms APNH, NHE1, PPP1R143) were taken as an example of use the anchor bootstrap technique in the genetic sequence analysis. Significant correlations of the first principal component were revealed with the hydrophobicity/“transmembraneity” of the corresponding fragments of the amino acid sequence, the phenylalanine content in them, as well as the difference in the T- and A-content in the corresponding nucleotide fragments. Earlier a similar pattern was found by other authors for other genes. Very likely, that it is of a more general nature.
{"title":"Principal Components of Genetic Sequences: Correlations and Significance","authors":"V. Efimov, K. V. Efimov, V. Kovaleva, Y. Matushkin","doi":"10.17537/2021.16.299","DOIUrl":"https://doi.org/10.17537/2021.16.299","url":null,"abstract":"\u0000Any numerical series can be decomposed into principal components using singular spectral analysis. We have recently proposed a new analysis method ‒ PCA-Seq, which allows calculating numerical principal components for a sequence of elements of any type. In particular, the sequence may be composed of nucleotide base pairs or amino acid residues. Two questions inevitably arise about interpretation of the obtained principal components and about the assessment of their reliability. For interpretation of the symbolic sequence principal components, it is reasonable to evaluate their correlations with numerical characteristics of the sequence elements. To assess the significance of correlations between sequences, one should bear in mind that standard significance criteria are based on the assumption of independence of observations, which, as a rule, is not fulfilled for real sequences. The article discusses the use of an anchor bootstrap technique for these purposes also previously developed by the authors of the article. In this approach it is assumed, that points of a metric space can represent the objects. When taken together they make up some fixed structure in it, in particular, a sequence. The objects are assigned the same random integer weights as in the classical bootstrap. This is sufficient to obtain the bootstrap distribution of the correlation coefficients and assess their significance. The coding sequence of the SLC9A1 gene (synonyms APNH, NHE1, PPP1R143) were taken as an example of use the anchor bootstrap technique in the genetic sequence analysis. Significant correlations of the first principal component were revealed with the hydrophobicity/“transmembraneity” of the corresponding fragments of the amino acid sequence, the phenylalanine content in them, as well as the difference in the T- and A-content in the corresponding nucleotide fragments. Earlier a similar pattern was found by other authors for other genes. Very likely, that it is of a more general nature.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83639564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The genomes of large multicellular eukaryotes mainly consist of DNA that encodes not proteins, but RNAs. The unexpected discovery of approximately the same number of protein genes in Homo sapiens and Caenorhabditis elegans led to the understanding that it is not the number of proteins that determines the complexity of the development and functioning of an organism. The phenomenon of pervasive transcription of genomes is finding more and more confirmation. Data are emerging on new types of RNA that work in different cell compartments, are expressed at different stages of development, in different tissues and perform various functions. Their main purpose is fine regulation of the main cellular processes. The presence of a rich arsenal of regulators that can interact with each other and work on the principle of interchangeability determines the physiological complexity of the organism and its ability to adapt to changing environmental conditions. An overview of the currently known functional RNAs expressed in eukaryotic genomes is presented here. There is no doubt that in the near future, using high-tech transcriptome technologies, many new RNAs will be identified and characterized. But it is likely that many of the expressed transcripts do not have a function, but are an evolutionary reserve of organisms.
{"title":"Variety of Non-Coding RNAs in Eukaryotic Genomes","authors":"N. Nazipova","doi":"10.17537/2021.16.256","DOIUrl":"https://doi.org/10.17537/2021.16.256","url":null,"abstract":"\u0000The genomes of large multicellular eukaryotes mainly consist of DNA that encodes not proteins, but RNAs. The unexpected discovery of approximately the same number of protein genes in Homo sapiens and Caenorhabditis elegans led to the understanding that it is not the number of proteins that determines the complexity of the development and functioning of an organism. The phenomenon of pervasive transcription of genomes is finding more and more confirmation. Data are emerging on new types of RNA that work in different cell compartments, are expressed at different stages of development, in different tissues and perform various functions. Their main purpose is fine regulation of the main cellular processes. The presence of a rich arsenal of regulators that can interact with each other and work on the principle of interchangeability determines the physiological complexity of the organism and its ability to adapt to changing environmental conditions. An overview of the currently known functional RNAs expressed in eukaryotic genomes is presented here. There is no doubt that in the near future, using high-tech transcriptome technologies, many new RNAs will be identified and characterized. But it is likely that many of the expressed transcripts do not have a function, but are an evolutionary reserve of organisms.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"126 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74180461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：