[Текст] : статья / М.Г. Садовский и др. // Int. conf. on Bioinformatics. - p. 78
Доп.точки доступа:
Темлякова, Е.А.; Sadovskii V.M.
Труды сотрудников ИВМ СО РАН
w10=
Найдено документов в текущей БД: 41
Periodicity in Triplet Distribution over Genomes
[Текст] : статья / Е.Ю. Бушмелев и др. // Int. conf. on Bioinformatics. - 2011. - p. 65
Доп.точки доступа:
Садовский, Михаил Георгиевич; Sadovskii M.G.
Доп.точки доступа:
Садовский, Михаил Георгиевич; Sadovskii M.G.
System Biology on Mitochondrion Genomes
[Text] : статья / M.G. Sadovskii, N.A. Zaitseva, Yu.A. Putintseva // Proceedings of The Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies. - 2011. - p. 61-66
. - ISBN 978-1-61208-007-9
Полный текст
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zaitseva, N.A.; Putintseva, Yu.A.; Путинцева Ю.А.; Садовский, Михаил Георгиевич
Полный текст
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zaitseva, N.A.; Putintseva, Yu.A.; Путинцева Ю.А.; Садовский, Михаил Георгиевич
Constructing the integral OLAP-model for scientific activities based on FCA
/ T. Penkova, A. Korobko // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2013. - Vol. 7828 LNAI: 16th International Conference on Knowledge Engineering, Machine Learning and Lattice Computing with Applications, KES 2012 (10 September 2012 through 12 September 2012, San Sebastian. - P163-170, DOI 10.1007/978-3-642-37343-5_17
. -
Кл.слова (ненормированные):
Formal concept analysis -- Integral OLAP-model -- On-line analytical processing -- Analytical decisions -- Data accessibility -- Expert knowledge -- Integral OLAP-model -- Multidimensional cube -- Multidimensional data -- On-line analytical processing -- Scientific activity -- Analytical models -- Decision making -- Formal concept analysis -- Information analysis -- Knowledge engineering -- Learning systems -- Models -- Data handling
Аннотация: In this paper an original approach to analytical decision making support based on on-line analytical processing of multidimensional data is suggested. According to Dr. Codd's rules, the effectiveness of data analysis significantly depends on the data accessibility and transparency of an analytical model of domain. The method of constructing a conceptual OLAP-model as an integral analytical model of the domain is proposed. The method is illustrated by the example of the scientific activities domain. The integral analytical model includes all possible combinations of analyzed objects and gives them the opportunity to be manipulated ad-hoc. The suggested method consists in a formal concept analysis of measures and dimensions based on an expert knowledge about the structure of analyzing objects and their comparability. As a result, conceptual OLAP-model is represented as a concept lattice of multidimensional cubes. Concept lattice features allow the decision maker to discover the nonstandard analytical dependencies on the set of all actual measures and dimensions of the scientific activities domain. Conceptual OLAP-model implementation allows user makes better decisions based on on-line analytical processing of the scientific activity indicators. В© 2013 Springer-Verlag.
Scopus
Доп.точки доступа:
Penkova, T.; Пенькова, Татьяна Геннадьевна; Korobko, A.; Коробко, Анна Владимировна
Кл.слова (ненормированные):
Formal concept analysis -- Integral OLAP-model -- On-line analytical processing -- Analytical decisions -- Data accessibility -- Expert knowledge -- Integral OLAP-model -- Multidimensional cube -- Multidimensional data -- On-line analytical processing -- Scientific activity -- Analytical models -- Decision making -- Formal concept analysis -- Information analysis -- Knowledge engineering -- Learning systems -- Models -- Data handling
Аннотация: In this paper an original approach to analytical decision making support based on on-line analytical processing of multidimensional data is suggested. According to Dr. Codd's rules, the effectiveness of data analysis significantly depends on the data accessibility and transparency of an analytical model of domain. The method of constructing a conceptual OLAP-model as an integral analytical model of the domain is proposed. The method is illustrated by the example of the scientific activities domain. The integral analytical model includes all possible combinations of analyzed objects and gives them the opportunity to be manipulated ad-hoc. The suggested method consists in a formal concept analysis of measures and dimensions based on an expert knowledge about the structure of analyzing objects and their comparability. As a result, conceptual OLAP-model is represented as a concept lattice of multidimensional cubes. Concept lattice features allow the decision maker to discover the nonstandard analytical dependencies on the set of all actual measures and dimensions of the scientific activities domain. Conceptual OLAP-model implementation allows user makes better decisions based on on-line analytical processing of the scientific activity indicators. В© 2013 Springer-Verlag.
Scopus
Доп.точки доступа:
Penkova, T.; Пенькова, Татьяна Геннадьевна; Korobko, A.; Коробко, Анна Владимировна
On validation of the SIgMA.CA pedestrian dynamics model with bottleneck flow
/ E.Kirik, T.Vitova // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2012. - Vol. 7495 LNCS: 10th International Conference on Cellular Automata for Research and Industry, ACRI 2012 (24 September 2012 through 27 September 2012, Santorini Island. - pp. 719-727, DOI 10.1007/978-3-642-33350-7-74
. -
Кл.слова (ненормированные):
(specific) flow rate -- bottleneck -- cellular automata -- pedestrian dynamics -- transition probabilities -- bottleneck -- Flow byes -- Initial density -- Model parameters -- Pedestrian dynamics -- Pedestrian movement -- Stochastic cellular automata -- Transition probabilities -- Cellular automata -- Dynamics -- Flow rate -- Industrial research -- Automata theory
Аннотация: In this paper a connection of a width of a bottleneck and unidirectional virtual people flow by the SIgMA.CA pedestrian movement model (stochastic Cellular Automata model) is investigated. Specific and full flow rates for different model parameters, initial densities, and bottleneck width are presented and discussed. В© 2012 Springer-Verlag Berlin Heidelberg.
Scopus
Доп.точки доступа:
Kirik, E.; Кирик, Екатерина Сергеевна; Vitova, T.
Кл.слова (ненормированные):
(specific) flow rate -- bottleneck -- cellular automata -- pedestrian dynamics -- transition probabilities -- bottleneck -- Flow byes -- Initial density -- Model parameters -- Pedestrian dynamics -- Pedestrian movement -- Stochastic cellular automata -- Transition probabilities -- Cellular automata -- Dynamics -- Flow rate -- Industrial research -- Automata theory
Аннотация: In this paper a connection of a width of a bottleneck and unidirectional virtual people flow by the SIgMA.CA pedestrian movement model (stochastic Cellular Automata model) is investigated. Specific and full flow rates for different model parameters, initial densities, and bottleneck width are presented and discussed. В© 2012 Springer-Verlag Berlin Heidelberg.
Scopus
Доп.точки доступа:
Kirik, E.; Кирик, Екатерина Сергеевна; Vitova, T.
Numerical solution of dynamic problems in block media with thin interlayers on supercomputers with GPUs
/ M. Varygina // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2013. - Vol. 8236 LNCS: 5th International Conference on Numerical Analysis and Applications, NAA 2012 (15 June 2013 through 20 June 2013, Lozenetz. - P517-523, DOI 10.1007/978-3-642-41515-9_59
. -
Аннотация: Parallel computational algorithms for the modeling of dynamic interaction of elastic blocks through thin viscoelastic interlayers in structurally inhomogeneous media such as rock are worked out. Numerical algorithms are based on monotonous grid- characteristic schemes with the balanced number of time steps in layers and interlayers. The numerical results to demonstrate qualitative characteristics of wave propagation in materials with microstructure are shown. В© 2013 Springer-Verlag.
Scopus,
Полный текст
Доп.точки доступа:
Варыгина, Мария Петровна
Аннотация: Parallel computational algorithms for the modeling of dynamic interaction of elastic blocks through thin viscoelastic interlayers in structurally inhomogeneous media such as rock are worked out. Numerical algorithms are based on monotonous grid- characteristic schemes with the balanced number of time steps in layers and interlayers. The numerical results to demonstrate qualitative characteristics of wave propagation in materials with microstructure are shown. В© 2013 Springer-Verlag.
Scopus,
Полный текст
Доп.точки доступа:
Варыгина, Мария Петровна
Parallel program systems for problems of the dynamics of elastic-plastic and granular media
/ O. V. Sadovskaya // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2013. - Vol. 8236 LNCS: 5th International Conference on Numerical Analysis and Applications, NAA 2012 (15 June 2013 through 20 June 2013, Lozenetz. - P471-478, DOI 10.1007/978-3-642-41515-9_53
. -
Кл.слова (ненормированные):
Cosserat continuum -- Dynamics -- elasticity -- granular medium -- parallel computational algorithm -- plasticity -- shock-capturing method
Аннотация: Parallel program systems for numerical solution of 2D and 3D problems of the dynamics of deformable media with constitutive relationships of rather general form on the basis of universal mathematical model describing small strains of elastic, elastic-plastic and granular materials are worked out. Computational algorithm is based on the splitting methods with respect to physical processes and spatial variables. Some computations of dynamic problems with and without taking into account the moment properties of a material were performed on clusters. В© 2013 Springer-Verlag.
Scopus,
Полный текст
Держатели документа:
Institute of Computational Modeling SB RAS, Akademgorodok 50/44, 660036 Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovskaya, O.V.; Садовская, Оксана Викторовна
Кл.слова (ненормированные):
Cosserat continuum -- Dynamics -- elasticity -- granular medium -- parallel computational algorithm -- plasticity -- shock-capturing method
Аннотация: Parallel program systems for numerical solution of 2D and 3D problems of the dynamics of deformable media with constitutive relationships of rather general form on the basis of universal mathematical model describing small strains of elastic, elastic-plastic and granular materials are worked out. Computational algorithm is based on the splitting methods with respect to physical processes and spatial variables. Some computations of dynamic problems with and without taking into account the moment properties of a material were performed on clusters. В© 2013 Springer-Verlag.
Scopus,
Полный текст
Держатели документа:
Institute of Computational Modeling SB RAS, Akademgorodok 50/44, 660036 Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovskaya, O.V.; Садовская, Оксана Викторовна
Some new approaches to solving Navier-Stokes equations for viscous heat-conducting gas
/ V. V. Shaydurov, G. I. Shchepanovskaya, M. V. Yakubovich // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2013. - Vol. 8236 LNCS: 5th International Conference on Numerical Analysis and Applications, NAA 2012 (15 June 2013 through 20 June 2013, Lozenetz. - P122-131, DOI 10.1007/978-3-642-41515-9_11
. -
Кл.слова (ненормированные):
finite element method -- Navier-Stokes equations -- numerical modeling -- trajectories -- viscous heat-conducting gas
Аннотация: The algorithm for numerical solving the Navier-Stokes equations for two-dimensional motion for viscous heat-conducting gas is proposed. The discretization of equations is performed by a combination of a special version of the trajectory method for a substantial derivative and the finite element method with piecewise bilinear basis functions for other terms. The results of numerical studies of the structure of a supersonic flow in a plane channel with an obstacle for a wide range of Mach numbers and Reynolds numbers are presented. Velocity and pressure fields are investigated, and the vortex structure of flow is studied in the circulation area of the obstacle. В© 2013 Springer-Verlag.
Scopus
Держатели документа:
Institute of Computational Modeling, Siberian Branch, Russian Academy of Science, Krasnoyarsk, Russian Federation
Beihang University, Beijing, China
Доп.точки доступа:
Shaydurov, V.V.; Shchepanovskaya, G.I.; Yakubovich, M.V.
Кл.слова (ненормированные):
finite element method -- Navier-Stokes equations -- numerical modeling -- trajectories -- viscous heat-conducting gas
Аннотация: The algorithm for numerical solving the Navier-Stokes equations for two-dimensional motion for viscous heat-conducting gas is proposed. The discretization of equations is performed by a combination of a special version of the trajectory method for a substantial derivative and the finite element method with piecewise bilinear basis functions for other terms. The results of numerical studies of the structure of a supersonic flow in a plane channel with an obstacle for a wide range of Mach numbers and Reynolds numbers are presented. Velocity and pressure fields are investigated, and the vortex structure of flow is studied in the circulation area of the obstacle. В© 2013 Springer-Verlag.
Scopus
Держатели документа:
Institute of Computational Modeling, Siberian Branch, Russian Academy of Science, Krasnoyarsk, Russian Federation
Beihang University, Beijing, China
Доп.точки доступа:
Shaydurov, V.V.; Shchepanovskaya, G.I.; Yakubovich, M.V.
On thermodynamically consistent formulations of dynamic models of deformable media and their numerical implementation
/ V. M. Sadovskii // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2013. - Vol. 8236 LNCS: 5th International Conference on Numerical Analysis and Applications, NAA 2012 (15 June 2013 through 20 June 2013, Lozenetz. - P479-486, DOI 10.1007/978-3-642-41515-9_54
. -
Кл.слова (ненормированные):
computational algorithm -- discontinuous solution -- Dynamics -- elasticity -- granular medium -- plastic shock wave -- variational inequality
Аннотация: Mathematical models of the dynamics of elastic-plastic and granular media are formulated as variational inequalities for hyperbolic operators with one-sided constraints describing the transition of a material in plastic state. On this basis a priori integral estimates are constructed in characteristic cones of operators, from which follows the uniqueness and continuous dependence on initial data of solutions of the Cauchy problem and of the boundary-value problems with dissipative boundary conditions. With the help of an integral generalization of variational inequalities the relationships of strong discontinuity in dynamic models of elastic-plastic and granular media are obtained, whose analysis allows us to calculate velocities of shock waves and to construct discontinuous solutions. Original algorithms of solution correction are developed which can be considered as a realization of the splitting method with respect to physical processes. В© 2013 Springer-Verlag.
Scopus,
Полный текст
Доп.точки доступа:
Sadovskii, V.M.; Садовский, Владимир Михайлович
Кл.слова (ненормированные):
computational algorithm -- discontinuous solution -- Dynamics -- elasticity -- granular medium -- plastic shock wave -- variational inequality
Аннотация: Mathematical models of the dynamics of elastic-plastic and granular media are formulated as variational inequalities for hyperbolic operators with one-sided constraints describing the transition of a material in plastic state. On this basis a priori integral estimates are constructed in characteristic cones of operators, from which follows the uniqueness and continuous dependence on initial data of solutions of the Cauchy problem and of the boundary-value problems with dissipative boundary conditions. With the help of an integral generalization of variational inequalities the relationships of strong discontinuity in dynamic models of elastic-plastic and granular media are obtained, whose analysis allows us to calculate velocities of shock waves and to construct discontinuous solutions. Original algorithms of solution correction are developed which can be considered as a realization of the splitting method with respect to physical processes. В© 2013 Springer-Verlag.
Scopus,
Полный текст
Доп.точки доступа:
Sadovskii, V.M.; Садовский, Владимир Михайлович
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
[Text] : статья / A. Zinovyev [et al.] // Bioinformatics. - 2008. - Vol. 24, Iss. 6. - p. 876-877DOI 10.1093/bioinformatics/btm553
. -
Аннотация: BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured BioPAX editor and a method of ‘interfaces’ for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databases. In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format. BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others.
Полный текст на сайте журнала
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel
Аннотация: BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured BioPAX editor and a method of ‘interfaces’ for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databases. In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format. BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others.
Полный текст на сайте журнала
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel
Method of wellbeing estimation in territory management
/ T. Penkova // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2014. - Vol. 8582 LNCS, Is. PART 4. - P. 57-68, DOI 10.1007/978-3-319-09147-1_5
. -
Кл.слова (ненормированные):
Decision making support -- Territory management -- Wellbeing estimation -- Fuzzy logic -- Semantics -- Decision making support -- Index values -- Semantic interpretation -- Territory managements -- Wellbeing -- Decision making
Аннотация: This paper presents the new technique of territory wellbeing estimation based on creation of a geographically-oriented wellbeing standard and estimation of the territory wellbeing level. The author proposes a method of wellbeing level estimation that provides the calculation of territory wellbeing index taking into account various aspects of vital activity and semantic interpretation of index values using fuzzy logic. The practical result of the work is an implementation of suggested solutions for social monitoring of the territory. © 2014 Springer International Publishing.
Scopus
Держатели документа:
Institute of Computational Modelling SB RAS, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Penkova, T.; Пенькова, Татьяна Геннадьевна
Кл.слова (ненормированные):
Decision making support -- Territory management -- Wellbeing estimation -- Fuzzy logic -- Semantics -- Decision making support -- Index values -- Semantic interpretation -- Territory managements -- Wellbeing -- Decision making
Аннотация: This paper presents the new technique of territory wellbeing estimation based on creation of a geographically-oriented wellbeing standard and estimation of the territory wellbeing level. The author proposes a method of wellbeing level estimation that provides the calculation of territory wellbeing index taking into account various aspects of vital activity and semantic interpretation of index values using fuzzy logic. The practical result of the work is an implementation of suggested solutions for social monitoring of the territory. © 2014 Springer International Publishing.
Scopus
Держатели документа:
Institute of Computational Modelling SB RAS, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Penkova, T.; Пенькова, Татьяна Геннадьевна
Cellular Automata Pedestrian Movement Model SIgMA.CA: Model Parameters as an Instrument to Regulate Movement Regimes
/ E. Kirik, T. Vitova // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2014. - Vol. 8751: Cellular Automata: 11th International Conference on Cellular Automata for Research and Industry . - P501-507DOI 10.1007/978-3-319-11520-7
. -
Аннотация: In the paper a connection of model parameters with movement regimes in different geometrical conditions are considered for the cellular automata floor field pedestrian movement model SIgMA.CA. Evacuation time is considered as measure of influence.
Доп.точки доступа:
Vitova, T.; Витова, Татьяна Брониславовна; Кирик, Екатерина Сергеевна
Аннотация: In the paper a connection of model parameters with movement regimes in different geometrical conditions are considered for the cellular automata floor field pedestrian movement model SIgMA.CA. Evacuation time is considered as measure of influence.
Доп.точки доступа:
Vitova, T.; Витова, Татьяна Брониславовна; Кирик, Екатерина Сергеевна
Strong inhomogeneity in triplet distribution alongside a genome
/ M. Sadovsky, X. Nikitina // (15 April 2015 through 17 April 2015. - 2015. - Vol. 9044. - P248-255
. -
Кл.слова (ненормированные):
Inhomogeneity -- Longest gap -- Order -- Periodicity -- Track -- Bioinformatics -- Biomedical engineering -- Mammals -- Inhomogeneities -- Longest gap -- Order -- Periodicity -- Track -- Genes
Аннотация: The distribution of triplets alongside a genome is studied.We explored the distribution to the nearest neighbour, that is the pattern where two triplets are fixed, and the distance is determined from the former to the latter so that the second triplet takes place nowhere inside the observed gap surrounded with the couple of the given triplets. The distribution differs strongly, for different organisms. Yeast and bacteria seem to have rather smooth pattern, while mammalia and other higher eukaryotes exhibit very complex patterns with long-range correlations in the triplet distribution. © Springer International Publishing Switzerland 2015.
Scopus
Держатели документа:
Institute of computational modelling of SB RASAkademgorodok, Krasnoyarsk, Russian Federation
ИВМ СО РАН
Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Nikitina, X.
Кл.слова (ненормированные):
Inhomogeneity -- Longest gap -- Order -- Periodicity -- Track -- Bioinformatics -- Biomedical engineering -- Mammals -- Inhomogeneities -- Longest gap -- Order -- Periodicity -- Track -- Genes
Аннотация: The distribution of triplets alongside a genome is studied.We explored the distribution to the nearest neighbour, that is the pattern where two triplets are fixed, and the distance is determined from the former to the latter so that the second triplet takes place nowhere inside the observed gap surrounded with the couple of the given triplets. The distribution differs strongly, for different organisms. Yeast and bacteria seem to have rather smooth pattern, while mammalia and other higher eukaryotes exhibit very complex patterns with long-range correlations in the triplet distribution. © Springer International Publishing Switzerland 2015.
Scopus
Держатели документа:
Institute of computational modelling of SB RASAkademgorodok, Krasnoyarsk, Russian Federation
ИВМ СО РАН
Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Nikitina, X.
Genome structure of organelles strongly relates to taxonomy of bearers
/ M. Sadovsky [et al.] // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2015. - Vol. 9043: 3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015; Granada; Spain; 15 April 2015 through 17 April 2015; Code 125929. - P481-490
. -
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Morphology -- Order -- Similitude -- Synchrony -- Triplet -- Bioinformatics -- Biology -- Biomedical engineering -- Morphology -- Taxonomies -- Cluster -- Evolution -- Frequency -- Order -- Similitude -- Synchrony -- Triplet -- Genes
Аннотация: We studied the relations between the triplet frequency dictionaries of organelle genome, and the phylogeny of their bearers. The clusters in 63-dimensional space were identified through K-means, and the clade composition of those clusters has been investigated. Very high regularity in genomes distribution among the clusters was found, in terms of taxonomy. The strong synchrony in evolution of nuclear and organelle genomes manifests through this correlation: the proximity in frequency space was determined over the organelle genomes, while the proximity in taxonomy was determined morphologically. Similar effect is also found in the ensembles of other (say, yeast) genomes. © Springer International Publishing Switzerland 2015.
Scopus
Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Putintseva, Y.; Chernyshova, A.; Fedotova, V.
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Morphology -- Order -- Similitude -- Synchrony -- Triplet -- Bioinformatics -- Biology -- Biomedical engineering -- Morphology -- Taxonomies -- Cluster -- Evolution -- Frequency -- Order -- Similitude -- Synchrony -- Triplet -- Genes
Аннотация: We studied the relations between the triplet frequency dictionaries of organelle genome, and the phylogeny of their bearers. The clusters in 63-dimensional space were identified through K-means, and the clade composition of those clusters has been investigated. Very high regularity in genomes distribution among the clusters was found, in terms of taxonomy. The strong synchrony in evolution of nuclear and organelle genomes manifests through this correlation: the proximity in frequency space was determined over the organelle genomes, while the proximity in taxonomy was determined morphologically. Similar effect is also found in the ensembles of other (say, yeast) genomes. © Springer International Publishing Switzerland 2015.
Scopus
Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Putintseva, Y.; Chernyshova, A.; Fedotova, V.
Numerical modeling of a block medium as an orthotropic cosserat continuum
/ O. V. Sadovskaya, V. M. Sadovskii, M. A. Pokhabova // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2015. - Vol. 9045: 6th International Conference on Finite Difference Methods, FDM 2014; Lozenetz; Bulgaria; 18 June 2014 through 23 June 2014; Code 156479. - P340-347, DOI 10.1007/978-3-319-20239-6_37
. -
Кл.слова (ненормированные):
Block medium -- Cosserat continuum -- Dynamics -- Elasticity -- Parallel computational algorithm -- Shock-capturing method -- Computation theory -- Continuum mechanics -- Dynamics -- Elastic waves -- Elasticity -- Finite difference method -- Wave propagation -- Block medium -- Computational algorithm -- Cosserat continuum -- Couple-stress continuum -- Elastic wave velocity -- Mechanical parameters -- Piecewise-homogeneous model -- Shock-capturing method -- Algorithms
Аннотация: Based on the equations of the dynamics of a piecewisehomogeneous elastic material, parallel computational algorithms are developed to simulate the process of stress and strain wave propagation in a medium consisting of a large number of blocks, interacting through compliant interlayers. For the description of waves in a block medium with thick interlayers the orthotropic couple-stress continuum theory, taking into account the symmetry of elastic properties relative to the coordinate planes, can be applied. By comparing the elastic wave velocities in the framework of piecewise-homogeneous model and continuum model, the simple method is obtained to estimate mechanical parameters of an orthotropic Cosserat continuum, modeling a block medium. In two-dimensional formulation of the orthotropic model, the computational algorithm and the program system are worked out for the analysis of propagation of elastic waves. The comparison showed good qualitative agreement between the results of computations of waves, caused by localized impulses, by the model of a block medium with compliant interlayers and the model of an orthotropic Cosserat continuum. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modeling SB RAS, Akademgorodok 50/44, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovskii, V. M.; Садовский, Владимир Михайлович; Pokhabova, M. A.; Похабова М.А.; Садовская, Оксана Викторовна
Кл.слова (ненормированные):
Block medium -- Cosserat continuum -- Dynamics -- Elasticity -- Parallel computational algorithm -- Shock-capturing method -- Computation theory -- Continuum mechanics -- Dynamics -- Elastic waves -- Elasticity -- Finite difference method -- Wave propagation -- Block medium -- Computational algorithm -- Cosserat continuum -- Couple-stress continuum -- Elastic wave velocity -- Mechanical parameters -- Piecewise-homogeneous model -- Shock-capturing method -- Algorithms
Аннотация: Based on the equations of the dynamics of a piecewisehomogeneous elastic material, parallel computational algorithms are developed to simulate the process of stress and strain wave propagation in a medium consisting of a large number of blocks, interacting through compliant interlayers. For the description of waves in a block medium with thick interlayers the orthotropic couple-stress continuum theory, taking into account the symmetry of elastic properties relative to the coordinate planes, can be applied. By comparing the elastic wave velocities in the framework of piecewise-homogeneous model and continuum model, the simple method is obtained to estimate mechanical parameters of an orthotropic Cosserat continuum, modeling a block medium. In two-dimensional formulation of the orthotropic model, the computational algorithm and the program system are worked out for the analysis of propagation of elastic waves. The comparison showed good qualitative agreement between the results of computations of waves, caused by localized impulses, by the model of a block medium with compliant interlayers and the model of an orthotropic Cosserat continuum. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modeling SB RAS, Akademgorodok 50/44, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovskii, V. M.; Садовский, Владимир Михайлович; Pokhabova, M. A.; Похабова М.А.; Садовская, Оксана Викторовна
Computational algorithm for modeling viscoelastic waves in the Kelvin-Voigt medium
/ V. M. Sadovskii // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) . - 2015. - Vol. 9045: 6th International Conference on Finite Difference Methods, FDM 2014; Lozenetz; Bulgaria; 18 June 2014 through 23 June 2014; Code 156479. - P348-355, DOI 10.1007/978-3-319-20239-6_38
. -
Кл.слова (ненормированные):
Computational algorithm -- Dissipative difference scheme -- Viscoelasticity -- Wave motion -- Algorithms -- Approximation theory -- Computation theory -- Numerical methods -- One dimensional -- Problem solving -- Surface waves -- Viscoelasticity -- Approximation methods -- Computational algorithm -- Difference schemes -- Dissipative properties -- Finite difference scheme -- One dimensional problems -- Two-dimensional problem -- Wave motions -- Finite difference method
Аннотация: Numerical algorithm for solving dynamic problems of the theory of viscoelastic medium of Kelvin-Voigt is worked out on the basis of Ivanov’s method of constructing finite difference schemes with prescribed dissipative properties. In one-dimensional problem the results of computations are compared with the exact solution, describing the propagation of plane monochromatic waves. When solving two-dimensional problems, the total approximation method based on the splitting of the system with respect to the spatial variables is applied. The algorithm is tested on solving the problem of traveling surface waves. For illustration of the method, the numerical solution of Lamb’s problem about instantaneous action of concentrated force on the boundary of a half-plane is represented in viscoelastic formulation. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modeling SB RAS, Akademgorodok 50/44, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Садовский, Владимир Михайлович
Кл.слова (ненормированные):
Computational algorithm -- Dissipative difference scheme -- Viscoelasticity -- Wave motion -- Algorithms -- Approximation theory -- Computation theory -- Numerical methods -- One dimensional -- Problem solving -- Surface waves -- Viscoelasticity -- Approximation methods -- Computational algorithm -- Difference schemes -- Dissipative properties -- Finite difference scheme -- One dimensional problems -- Two-dimensional problem -- Wave motions -- Finite difference method
Аннотация: Numerical algorithm for solving dynamic problems of the theory of viscoelastic medium of Kelvin-Voigt is worked out on the basis of Ivanov’s method of constructing finite difference schemes with prescribed dissipative properties. In one-dimensional problem the results of computations are compared with the exact solution, describing the propagation of plane monochromatic waves. When solving two-dimensional problems, the total approximation method based on the splitting of the system with respect to the spatial variables is applied. The algorithm is tested on solving the problem of traveling surface waves. For illustration of the method, the numerical solution of Lamb’s problem about instantaneous action of concentrated force on the boundary of a half-plane is represented in viscoelastic formulation. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modeling SB RAS, Akademgorodok 50/44, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Садовский, Владимир Михайлович
Effectiveness of the parallel implementation of the FEM for the problem of the surface waves propagation
/ E. Karepova, E. Dementyeva // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) . - 2015. - Vol. 9045: 6th International Conference on Finite Difference Methods, FDM 2014; Lozenetz; Bulgaria; 18 June 2014 through 23 June 2014; Code 156479. - P233-240, DOI 10.1007/978-3-319-20239-6_24
. -
Кл.слова (ненормированные):
Data assimilation problem -- Finite element method and high performance computation -- Algorithms -- Application programming interfaces (API) -- Computation theory -- Equations of motion -- Finite difference method -- Numerical methods -- Surface waves -- Boundary function problems -- Data assimilation -- High performance computation -- Numerical solution -- Parallel implementations -- Parallel technology -- Shallow water equations -- Finite element method
Аннотация: In this paper effectiveness of several parallel implementations of the finite element method is investigated for an algorithm of a numerical solution of the boundary function problem for the shallow water equations. The parallel technologies MPI, OpenMP and MPI+OpenMP are used. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modelling of SB RAS, Siberian Federal University, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Dementyeva, E.V.; Дементьева, Екатерина Васильевна; Карепова, Евгения Дмитриевна
Кл.слова (ненормированные):
Data assimilation problem -- Finite element method and high performance computation -- Algorithms -- Application programming interfaces (API) -- Computation theory -- Equations of motion -- Finite difference method -- Numerical methods -- Surface waves -- Boundary function problems -- Data assimilation -- High performance computation -- Numerical solution -- Parallel implementations -- Parallel technology -- Shallow water equations -- Finite element method
Аннотация: In this paper effectiveness of several parallel implementations of the finite element method is investigated for an algorithm of a numerical solution of the boundary function problem for the shallow water equations. The parallel technologies MPI, OpenMP and MPI+OpenMP are used. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modelling of SB RAS, Siberian Federal University, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Dementyeva, E.V.; Дементьева, Екатерина Васильевна; Карепова, Евгения Дмитриевна
Superconvergence of some linear and quadratic functionals for higher-order finite elements
/ V. V. Shaydurov, T. Xu // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) . - 2015. - Vol. 9045: 6th International Conference on Finite Difference Methods, FDM 2014; Lozenetz; Bulgaria; 18 June 2014 through 23 June 2014; Code 156479. - P84-95, DOI 10.1007/978-3-319-20239-6_8
. -
Кл.слова (ненормированные):
Bogner-Fox-Schmit element -- Convergence order -- Dual problems -- Finite element method -- Hermite finite elements -- Output functional -- Finite difference method -- Poisson equation -- Bogner-Fox-Schmit element -- Convergence order -- Dual problem -- Hermite finite elements -- Output functional -- Finite element method
Аннотация: This paper deals with the calculation of linear and quadratic functionals of approximate solutions obtained by the finite element method. It is shown that under certain conditions the output functionals of an approximate solution are computed with higher order of accuracy than that of the solution itself. These abstract results are illustrated by two numerical examples for the Poisson equation. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modeling of Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Beihang University, Beijing, China
Доп.точки доступа:
Xu, T.; Шайдуров, Владимир Викторович
Кл.слова (ненормированные):
Bogner-Fox-Schmit element -- Convergence order -- Dual problems -- Finite element method -- Hermite finite elements -- Output functional -- Finite difference method -- Poisson equation -- Bogner-Fox-Schmit element -- Convergence order -- Dual problem -- Hermite finite elements -- Output functional -- Finite element method
Аннотация: This paper deals with the calculation of linear and quadratic functionals of approximate solutions obtained by the finite element method. It is shown that under certain conditions the output functionals of an approximate solution are computed with higher order of accuracy than that of the solution itself. These abstract results are illustrated by two numerical examples for the Poisson equation. © Springer International Publishing Switzerland 2015.
Scopus,
WOS
Держатели документа:
Institute of Computational Modeling of Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Beihang University, Beijing, China
Доп.точки доступа:
Xu, T.; Шайдуров, Владимир Викторович
On the evacuation module sigmaeva based on a discrete-continuous pedestrian dynamics model
/ E. Kirik, A. Malyshev, M. Senashova // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2016. - Vol. 9574: 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015; Krakow; Poland; 6 September 2015 through 9 September 2015; Code 173429. - P539-549, DOI 10.1007/978-3-319-32152-3_50
. -
Кл.слова (ненормированные):
Discrete-continuous approach -- Evacuation modeling -- Fundamental diagram -- Pedestrian dynamics model -- Artificial intelligence -- Computer science -- Computers -- Computational aspects -- Continuous approach -- Continuous modeling -- Continuous models -- Continuous spaces -- Evacuation modeling -- Fundamental diagram -- Pedestrian dynamics -- Dynamics
Аннотация: The discrete-continuous model is a novel contribution to mathematical modeling of pedestrian dynamics. This model is of individual type; people (particles) move in a continuous space, – in this sense the model is continuous. But the number of directions for the particles to move is limited, – in this sense the model is discrete. The model is realized in the computer evacuation module SigmaEva. This article is focused on a presenting of the model and computational aspects and the model is discussed in respect with discrete and continuous models. © Springer International Publishing Switzerland 2016.
Scopus,
Смотреть статью,
WOS
Держатели документа:
Institute of Computational Modelling SB RAS, Akademgorodok 50/44, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Kirik, E.; Malyshev, A.; Senashova, M.
Кл.слова (ненормированные):
Discrete-continuous approach -- Evacuation modeling -- Fundamental diagram -- Pedestrian dynamics model -- Artificial intelligence -- Computer science -- Computers -- Computational aspects -- Continuous approach -- Continuous modeling -- Continuous models -- Continuous spaces -- Evacuation modeling -- Fundamental diagram -- Pedestrian dynamics -- Dynamics
Аннотация: The discrete-continuous model is a novel contribution to mathematical modeling of pedestrian dynamics. This model is of individual type; people (particles) move in a continuous space, – in this sense the model is continuous. But the number of directions for the particles to move is limited, – in this sense the model is discrete. The model is realized in the computer evacuation module SigmaEva. This article is focused on a presenting of the model and computational aspects and the model is discussed in respect with discrete and continuous models. © Springer International Publishing Switzerland 2016.
Scopus,
Смотреть статью,
WOS
Держатели документа:
Institute of Computational Modelling SB RAS, Akademgorodok 50/44, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Kirik, E.; Malyshev, A.; Senashova, M.
De novo assembly and cluster analysis of Siberian Larch transcriptome and genome
/ M. Sadovsky [et al.] // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2016. - Vol. 9656: 4th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016; Granada; Spain; 20 April 2016 through 22 April 2016; Code 173369. - P455-464, DOI 10.1007/978-3-319-31744-1_41
. -
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Order -- Triplet -- Bioinformatics -- Biomedical engineering -- Genes -- Cluster -- Evolution -- Frequency -- Order -- Triplet -- Cluster analysis
Аннотация: We studied Siberian Larch (Larix Sibirica) transcriptome making de novo assembly and cluster analysis of contigs frequency dictionaries. Also, some preliminary results of similar study of the larch genome are present. It was found that the larch transcriptome yields a number of unexpected symmetries in the statistical and combinatorial properties of the entities. © Springer International Publishing Switzerland 2016.
Scopus,
Смотреть статью,
WOS
Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovsky, M.; Putintseva, Y.; Birukov, V.; Novikova, S.; Krutovsky, K.
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Order -- Triplet -- Bioinformatics -- Biomedical engineering -- Genes -- Cluster -- Evolution -- Frequency -- Order -- Triplet -- Cluster analysis
Аннотация: We studied Siberian Larch (Larix Sibirica) transcriptome making de novo assembly and cluster analysis of contigs frequency dictionaries. Also, some preliminary results of similar study of the larch genome are present. It was found that the larch transcriptome yields a number of unexpected symmetries in the statistical and combinatorial properties of the entities. © Springer International Publishing Switzerland 2016.
Scopus,
Смотреть статью,
WOS
Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovsky, M.; Putintseva, Y.; Birukov, V.; Novikova, S.; Krutovsky, K.