Труды сотрудников ИВМ СО РАН

[Electronic resource]. - Electronic data
. - Режим доступа: http://icm.krasn.ru/refextra.php?id=2102. - Электрон. версия печ. публикации : научное издание / Gorban A.N. Zinovyev A.Y. - Electronic data // Institut des Hautes Etudes Scientifiques Preprint. IHES M/01/36. - 2001
   Перевод заглавия: Визуализация данных с помощью метода упругих карт и его приложения в геномике, экономике и социологии
Аннотация: Technology of data visualization and data modeling is suggested. The basic of the technology is original idea of elastic net and methods of its construction and application. A short review of relevant methods has been made. The methods proposed are illustrated by applying them to the real biological, economical, sociological datasets and to some model data distributions.

http://icm.krasn.ru/refextra.php?id=2102


Доп.точки доступа:
Zinovyev, A.Y.; Зиновьев, Андрей Юрьевич; Горбань, Александр Николаевич

[Text] : монография / E. A. Novikov, Yu. V. Shornikov, B. U. Uatay ; Kazakh-British Technical University. - Almaty : KBTU, 2010. - 157 p. : il. - Библиогр.: с. 144. - ISBN 978-601-269-009-5 : Б. ц.

УДК

519.6

ББК В14

Аннотация: This monograph covers the problem of modeling of numerical methods for solving of Cauchy problem for stiff systems of ordinary differential equations. Particular attention will be paid to notion and classification of hybrid systems. Capabilities of instrumental environment of computerizedanalysis for hybrid systems will be described. This book is intended for individuals who are involved in modeling of physical, chemical, biological and other processes


Доп.точки доступа:
Shornikov, Yu.V.; Шорников Ю.В.; Uatay, B.U.; Новиков, Евгений Александрович
Свободных экз. нет

[Text] / K.V. Purtov [et al.] // Nanoscale Res. Lett. - 2010. - Vol. 5, Is. 3. - pp. 631-636, DOI 10.1007/s11671-010-9526-0. - Cited References: 24. - This work was supported by the Program # 27 for Basic Research of the Presidium of RAS (project 3.6.3). . - ISSN 1931-7573РУБ Nanoscience & Nanotechnology + Materials Science, Multidisciplinary + Physics, Applied

Аннотация: Surface of detonation nanodiamonds was functionalized for the covalent attachment of immunoglobulin, and simultaneously bovine serum albumin and Rabbit Anti-Mouse Antibody. The nanodiamond-IgG(I125) and RAM-nanodiamond-BSA(I125) complexes are stable in blood serum and the immobilized proteins retain their biological activity. It was shown that the RAM-nanodiamond-BSA(I125) complex is able to bind to the target antigen immobilized on the Sepharose 6B matrix through antibody-antigen interaction. The idea can be extended to use nanodiamonds as carriers for delivery of bioactive substances (i.e., drugs) to various targets in vivo.


Доп.точки доступа:
Purtov, K.V.; Petunin, A.I.; Burov, A.E.; Буров, Андрей Ефимович; Puzyr, A.P.; Bondar, V.S.

[Text] / A.Zinovyev [et al.] // BMC Syst. Biol. - 2010. - Vol. 4. - Ст. 13, DOI 10.1186/1752-0509-4-13. - Cited References: 66. - We acknowledge support from Agence Nationale de la Recherche (project ANR-08-SYSC-003 CALAMAR) and from the Projet Incitatif Collaboratif "Bioinformatics and Biostatistics of Cancer" at Institut Curie. AZ and EB are members of the team "Systems Biology of Cancer" Equipe labellis'ee par la Ligue Nationale Contre le Cancer. This work was supported by the European Commission Sixth Framework Programme Integrated Project SIROCCO contract number LSHG-CT-2006-037900. We thank Vitaly Volpert and Laurence Calzone for inspiring and useful discussions. . - ISSN 1752-0509РУБ Mathematical & Computational Biology

Аннотация: Background: Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple mechanisms. It remains unclear what mechanisms of microRNA action are the most dominant: moreover, many experimental reports deliver controversial messages on what is the concrete mechanism actually observed in the experiment. Nissan and Parker have recently demonstrated that it might be impossible to distinguish alternative biological hypotheses using the steady state data on the rate of protein synthesis. For their analysis they used two simple kinetic models of protein translation. Results: In contrary to the study by Nissan and Parker, we show that dynamical data allow discriminating some of the mechanisms of microRNA action. We demonstrate this using the same models as developed by Nissan and Parker for the sake of comparison but the methods developed (asymptotology of biochemical networks) can be used for other models. We formulate a hypothesis that the effect of microRNA action is measurable and observable only if it affects the dominant system (generalization of the limiting step notion for complex networks) of the protein translation machinery. The dominant system can vary in different experimental conditions that can partially explain the existing controversy of some of the experimental data. Conclusions: Our analysis of the transient protein translation dynamics shows that it gives enough information to verify or reject a hypothesis about a particular molecular mechanism of microRNA action on protein translation. For multiscale systems only that action of microRNA is distinguishable which affects the parameters of dominant system (critical parameters), or changes the dominant system itself. Dominant systems generalize and further develop the old and very popular idea of limiting step. Algorithms for identifying dominant systems in multiscale kinetic models are straightforward but not trivial and depend only on the ordering of the model parameters but not on their concrete values. Asymptotic approach to kinetic models allows putting in order diverse experimental observations in complex situations when many alternative hypotheses co-exist.


Доп.точки доступа:
Zinovyev, A.; Morozova, N.; Nonne, N.; Barillot, E.; Harel-Bellan, A.; Gorban, A.N.; Горбань, Александр Николаевич

[Текст] : статья / K. A. Kourshakova, M. Yu. Senashova // Journal of Siberian Federal University. Mathematics & Physics = Журнал Сибирского федерального университета. Математика и физика. - 2008. - Т. 1, № 3. - С. 284-289
Аннотация: A population changes model of spatial distributed two-species consocietum is considered. Species react as a "predator-prey" system. Each species occupies two states. Migrations lead to the problem of a net reproduction maximization. The basic model and its three reflexive modifications are considered.

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Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44

Доп.точки доступа:
Senashova, M.Yu.; Сенашова, Мария Юрьевна

[Text] : статья / L. Calzone [et al.] // Molecular Systems Biology. - 2008. - Vol. 4. - p. 174-178DOI 10.1038/msb.2008.7 . -
Аннотация: We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large‐scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher‐level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.

Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44

Доп.точки доступа:
Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Radvanyi, François; Barillot, Emmanuel

[Text] / N. Shaparev, N. Astafiev // Int. J. Sustain. Dev. World Ecol. - 2008. - Vol. 15, Is. 6. - P574-583, DOI 10.3843/SusDev.15.6:9. - Cited References: 23. - The work was carried out with financial support from the RFBR-KRFS project (No. 07-05-96802) and a grant from the Russian Federation President for leading scientific schools (SS3428.2006.9). . - ISSN 1350-4509РУБ Ecology

Аннотация: A system of sustainable water management is suggested. This includes natural water production; acceptable sanitary-epidemiological water state; conservation and maintenance of biological water diversity; development of socioeconomic functions of water management; and instruments for water policy to conserve sustainable management of water consumption and protect consumers from injurious water effects. The developed system was applied to analyse the situation in the Yenisei River basin (Russia). Analysis in the basin showed that it is currently unsustainable: the share of purified water has not increased; water cost per unit production is high; the quality of water in the Yenisei River is still characterised as 'polluted'; some people in the basin drink water containing injurious substances; and both purification facilities and water supply systems are in an unsatisfactory state. Hence, the financing of hydrological work is currently inadequate.


Доп.точки доступа:
Astafiev, N.; Шапарев, Николай Якимович

[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.

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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

[Text] : статья / A. N. Gorban, S. Petrovskii // Mathematical Medicine and Biology. - 2011. - Vol. 28, Iss. 2. - p. 85-88DOI 10.1093/imammb/dqr003 . -
Аннотация: A brief introduction into the interdisciplinary field of collective dynamics is given, followed by an overview of ‘Mathematical Models of Collective Dynamics in Biology and Evolution’ (University of Leicester, 11–13 May 2009).

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Доп.точки доступа:
Petrovskii, Sergei; Горбань, Александр Николаевич

[Text] / N. M. Mineeva, L. A. Shchur // Water Resour. - 2014. - Vol. 41, Is. 2. - P. 188-195, DOI 10.1134/S0097807814020109. - Cited References: 39 . - ISSN 0097-8078. - ISSN 1608-344XРУБ Water Resources

Аннотация: The relationship between plankton primary production and the geographic latitude suggests the dependence of biological productivity of water bodies on natural climatic conditions. Comparative analysis of the key factors governing phytoplankton productivity in the Volga and Yenisei rivers was made to reveal this relationship; these rivers represent two large river systems which extend in meridional direction, pass through various natural climatic zones, and differ in aquatic life habitats.

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Держатели документа:
[Mineeva, N. M.] Russian Acad Sci, Papanin Inst Biol Inland Waters, Yaroslavl Oblast 152742, Russia
[Shchur, L. A.] Russian Acad Sci, Siberian Branch, Inst Computat Modeling, Krasnoyarsk 660036, Russia
ИВМ СО РАН

Доп.точки доступа:
Mineeva, N.M.; Shchur, L.A.; Щур, Людмила Александровна

/ M. V. Panchenko [et al.] // Proceedings of SPIE - The International Society for Optical Engineering. - 2014. - Vol. 9292: 20th International Symposium on Atmospheric and Ocean Optics: Atmospheric Physics (23 June 2014 through 27 June 2014, ) Conference code: 110711. - Ст. 92922Y, DOI 10.1117/12.2075391 . -
Аннотация: We study the effect of physical, chemical and biological processes on gas exchange of CO2 in the air-water system in Lake Baikal. Photosynthesis of aquatic biota is known to play a crucial role in changing the concentration of carbon dioxide in the water. Fluorescent methods are considered to be of high performance in problems of determining quantitative characteristics of biomass, however they require preliminary calibration directly for a specific type of plankton. In the pelagic zone of Lake Baikal the species composition, quantitative and spatial distribution of phytoplankton are characterized by strong spatial and temporal variability. Therefore, the fluorescent devices calibration on a single reference does not provide acceptable accuracy of quantitative assessment of the biomass. The results discussed in the paper were obtained by shipboard measurements during the Baikal campaign of 2010-2011. Correlation between the biomass in 25-meter water layer and the integral value of the fluorescent signal in this layer was obtained for calibration. The report discusses the advantages and disadvantages of the chosen methods and the results of retrieval of the vertical profiles of the biomass for stations in the pelagic zone of Lake Baikal in spring for the 2010-2011 biennium.

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Держатели документа:
Institute of Atmospheric Optics, Siberian Branch, Russian Academy of SciencesTomsk, Russian Federation
Limnological Institute, Siberian Branch, Russian Academy of SciencesIrkutsk, Russian Federation
Institute of Computational Modeling, Siberian Branch, Russian Academy of SciencesKrasnoyarsk, Russian Federation

Доп.точки доступа:
Panchenko, M.V.; Sakirko, M.V.; Usoltseva, M.V.; Popovskaya, G.I.; Domysheva, V.M.; Shimaraev, M.N.; Zavoruev, V.V.; Pestunov, D.A.

/ A. Shevyrgonov, G. Vysotskaya, E. Shevyrgonov // Advances in Space Research. - 2002. - Vol. 30, Is. 11. - P. 2541-2546, DOI 10.1016/S0273-1177(02)80334-9 . - ISSN 0273-1177
Аннотация: The work presents long-standing CZCS-satellite-based data about spatial distribution of anomalies in chlorophyll concentration and temperature of the ocean. An anomaly criterion is proposed. Maps of Atlantic ocean areas with elevated probability of anomalies are given. Properties of anomalous zones in different parts of the Atlantic ocean are discussed. Satellite-based maps of anomaly coefficients for chlorophyll concentration and temperature in the Atlantic ocean have been shown to feature substantial differences, the zones of elevated anomaly of chlorophyll concentration and temperature - to be close only in the vicinity of the Amazon outflow into the Atlantic ocean. Along with fundamental knowledge about dynamics of biological phenomena in the ocean the methods described may be used to reveal deviations due to anthropogenic impact. The methods presented may be used to process SeaWiFS prograna data. The data derived may be used to analyze long-standing time series to estimate randomness of cunent changes. В©2002 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

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Доп.точки доступа:
Shevyrgonov, A.; Vysotskaya, G.; Высоцкая, Галина Степановна; Shevyrgonov, E.

/ A. Shevyrnogov [et al.] // Advances in Space Research. - 2000. - Vol. 26, Is. 7. - P. 1169-1172, DOI 10.1016/S0273-1177(99)01142-4 . - ISSN 0273-1177
Аннотация: Deep insight into types of vegetation variability provided by AVHRR space scanner images of vegetation index spatial distribution helps reveal impact of land surface changes on environment. The Institute of Computational Modeling SB RAS has developed nonparametric algorithms of automatic to classify and recognize patterns of these images which helped to reveal: (1) major variability types (generally connected); (2) areas belonging to small classes, which can be used to reveal deviations from 'normal' (e.g., forest fires, etc.); (3) deviation from a certain type of dynamics indicative of changes in condition of plants, which can be used to diagnose pathology at early stages; (4) impact of economical activities on vegetation in Norilsk area. The authors provide biological interpretation of the satellite data. Computer-animated dynamics and color maps are presented. Nonparametric algorithms of an automatic classification and pattern recognition were provided by the Institute of Computational Modeling SB RAS. (C) 2000 COSPAR. Published by Elsevier Science Ltd.

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Доп.точки доступа:
Shevyrnogov, A.; Vysotskaya, G.; Высоцкая, Галина Степановна; Sidko, A.; Dunaev, K.

/ M. G. Sadovskii, M. Y. Senashova // J. Appl. Ind. Math. - 2014. - Vol. 8, Is. 3. - P375-384, DOI 10.1134/S1990478914030107 . - ISSN 1990-4789
Аннотация: Under study is some model of a spatially distributed two-species population. The species interact according to the predator-prey pattern. Each species is distributed over two stations. The migration of individuals between the stations are purposeful and maximize the breeding coefficient for each species. In addition, each species pursues its reflexive strategy of behavior to determine the optimal migration flow. © 2014 Pleiades Publishing, Ltd.

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Держатели документа:
Institute of Computer Modeling, Akademgorodok, d. 50, str. 44, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Sadovskii, M.G.; Садовский, Михаил Георгиевич; Senashova, M.Y.; Сенашова, Мария Юрьевна

/ L. A. Kompaniets, T. V. Iakubailik // International Multidisciplinary Scientific GeoConference Surveying Geology and Mining Ecology Management, SGEM. - 2015. - Vol. 2: 15th International Multidisciplinary Scientific Geoconference and EXPO, SGEM 2015 (18 June 2015 through 24 June 2015, ) Conference code: 153969, Is. 3. - P635-642 . -
Аннотация: To understand the mechanisms of formation of water quality it is necessary to study both biological and chemical properties of a lake as well as its hydro regime. For many years researchers have focused on the study of chemistry and biology of Lake Shira (situated in Siberia), but a detailed investigation of its hydro regime has become possible only recently with the development of modern measuring instruments. Using the latest generation of measuring devices we have obtained the hydrophysical characteristics of the stratified salt lake in situ (air and water temperature, wind strength and direction, water velocity). Relationships between the measured data have allowed us to analyze the flow in the lake as a whole, thus outlining the problem of determining lake ecological status in the period under observation. © SGEM2014.

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Держатели документа:
ICM SB RAS, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Yakubaylik, T.V.; Якубайлик, Татьяна Валерьевна; Компаниец, Лидия Алексеевна

[Текст] : статья / Н. И. Волкова [и др.] // Вопросы рыболовства. - 2012. - Т. 13, № 2-50. - С. 250-262 . - ISSN 0234-2774
   Перевод заглавия: BIOLOGICAL PRODUCTIVITY AND STRUCTURE OF ICHTHYOFAUNA OF LAKES IN TODZHINSKAYA HOLLOWS (REPUBLIC TYVA)
Аннотация: В результате исследований, проведенных в июле 2009 г. на озерах Тоджинской котловины (Республика Тыва) дана оценка состояния фитопланктона, зоопланктона, зообентоса, определены их количественные и продукционные показатели (численность, биомасса, продукция), рассчитана рыбопродуктивность озер с учетом кормовой базы. Приведены видовой и размерно-возрастной состав уловов, данные по питанию рыб.
The research was conducted on the Todzha depressions lakes in 2009. Quantitative and qualitative indexes (abundance, biomass, production) of phytoplankton, zooplankton and zoobenthos were estimated. Fish capacity of these lakes was calculated inclusive of food reserve. Species of fishes, their structure, age, dimension, food spectrum are presented.

РИНЦ

Держатели документа:
Институт вычислительного моделирования Сибирского отделения Российской академии наук
Научно-исследовательский институт экологии рыбохозяйственных водоемов

Доп.точки доступа:
Волкова, Нина Ивановна; Volkova N.Y.; Михалева, Татьяна Владимировна; Michaleva T.V.; Поляева, Ксения Викторовна; Polyaeva K.V.; Щур, Людмила Александровна; Schure L.A.

[Текст] : статья / Е. О. Кутумова [и др.] // Математическая биология и биоинформатика. - 2012. - Т. 7, № 2. - С. 572-588 . - ISSN 1994-6538
   Перевод заглавия: The Application of Model Reduction Methods to the Construction of the Composite Model of Apoptotic Pathways
Аннотация: В работе предлагается новый подход для объединения математических моделей биологических систем на основе их редукции. Данный подход описан на примере двух моделей апоптоза, рассматривающих про- и антиапоптотические (активация NF-?B) пути рецептора СD95.
We propose a new approach to composition of mathematical models of biological systems, based on their reduction. This approach has been tested on the example of two apoptosis models describing pro- and anti-apoptotic (activation of NF-?B) pathways of CD95.

РИНЦ

Держатели документа:
Институт вычислительного моделирования СО РАН
Institut Curie
Институт цитологии и генетики СО РАН
Конструкторско-технологический институт вычислительной техники СО РАН
ООО “Институт системной биологии”

Доп.точки доступа:
Кутумова, Елена Олеговна; Kutumova Elena O.; Зиновьев, Андрей Юрьевич; Zinovyev A.Y.; Шарипов, Руслан Нильевич; Sharipov Ruslan N.; Колпаков, Федор Анатольевич; Kolpakov Fedor A.

[Text] / L. A. Kompaniets, T. V. Iakubailik // WATER RESOURCES, FOREST, MARINE AND OCEAN ECOSYSTEMS, SGEM 2015, VOL II : STEF92 TECHNOLOGY LTD, 2015. - 15th International Multidisciplinary Scientific Geoconference (SGEM) (JUN 18-24, 2015, Albena, BULGARIA). - P635-641. - (International Multidisciplinary Scientific GeoConference-SGEM). - Cited References:6 . -
Аннотация: To understand the mechanisms of formation of water quality it is necessary to study both biological and chemical properties of a lake as well as its hydro regime. For many years researchers have focused on the study of chemistry and biology of Lake Shira (situated in Siberia), but a detailed investigation of its hydro regime has become possible only recently with the development of modern measuring instruments. Using the latest generation of measuring devices we have obtained the hydrophysical characteristics of the stratified salt lake in situ (air and water temperature, wind strength and direction, water velocity). Relationships between the measured data have allowed us to analyze the flow in the lake as a whole, thus outlining the problem of determining lake ecological status in the period under observation.

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Держатели документа:
ICM SB RAS, Krasnoyarsk, Russia.

Доп.точки доступа:
Kompaniets, Lidiya A.; Компаниец, Лидия Алексеевна; Iakubailik, Tatiana V.; Якубайлик, Татьяна Валерьевна

/ S. P. Tsarev, M. G. Sadovsky // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2016. - Vol. 9702: 3rd International Conference on Algorithms for Computational Biology, AlCoB 2016; Trujillo; Spain; 21 June 2016 through 22 June 2016; Code 177079. - P171-182, DOI 10.1007/978-3-319-38827-4_14 . -
Аннотация: A new method to identify all sufficiently long repeating nucleotide substrings in one or several DNA sequences is proposed. The method based on a specific gauge applied to DNA sequences that guarantees identification of the repeating substrings. The method allows the matching substrings to contain a given level of errors. The gauge is based on the development of a heavily sparse dictionary of repeats, thus drastically accelerating the search procedure. Some biological applications illustrate the method. © Springer International Publishing Switzerland 2016.

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Держатели документа:
Siberian Federal University, Kirenskogo, 26, Krasnoyarsk, Russian Federation
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Tsarev, S. P.; Sadovsky, M. G.

/ P. V. Postnikova // Proceedings of SPIE - The International Society for Optical Engineering : SPIE, 2016. - Vol. 10035: 22nd International Symposium on Atmospheric and Ocean Optics: Atmospheric Physics (30 June 2016 through 3 July 2016, ) Conference code: 125266, DOI 10.1117/12.2248511 . -
Аннотация: The seasonal variability of hydrooptical and fluorescent characteristics from the coastal waters of the Yenisei river have been studied. The work was estimated chlorophyll content, photosynthetic activity, concentration dissolved organic matter (DOM) and mineral component. The data have been obtained from series of regular observations in the coastal waters of Krasnoyarsk during 2012 - 2014. During year the chlorophyll "a" concentration and mineralization varied 2 times for warm and cold seasons. Regression analysis revealed relationship between coefficient synthetic activity and concentration of chlorophyll "a". © 2016 SPIE.

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Держатели документа:
Institute of Computational Modelling, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Postnikova, P. V.