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    Anomalous mechanical materials squeezing three-dimensional volume compressibility into one dimension / X. Jiang, M. S. Molokeev, L. Dong [et al.] // Nat. Commun. - 2020. - Vol. 11, Is. 1. - Ст. 5593, DOI 10.1038/s41467-020-19219-5. - Cited References: 49. - The authors acknowledge Zhuohong Yin for useful discussions and the experimental time provided by the 4W2 beam line of Beijing Synchrotron Radiation Facility (BSRF). This work was supported by the National Scientific Foundations of China (Grants 51702330, 11974360, 51872297, 51890864, 21975132, and 21991143), the Youth Innovation Promotion Association in CAS (Grant 2017035 for X.J.), Young Elite Scientist Sponsorship Program by CAST (YESS), and Fujian Institute of Innovation (FJCXY18010201) in CAS . - ISSN 2041-1723
   Перевод заглавия: Аномальные механические материалы, преобразующие трехмерную объемную сжимаемость в одномерную
Кл.слова (ненормированные):
high pressure -- mechanical property -- one-dimensional modeling -- precision -- pressure effect -- stress-strain relationship -- three-dimensional modeling
Аннотация: Anomalous mechanical materials, with counterintuitive stress-strain responding behaviors, have emerged as novel type of functional materials with highly enhanced performances. Here we demonstrate that the materials with coexisting negative, zero and positive linear compressibilities can squeeze three-dimensional volume compressibility into one dimension, and provide a general and effective way to precisely stabilize the transmission processes under high pressure. We propose a “corrugated-graphite-like” structural model and discover lithium metaborate (LiBO2) to be the first material with such a mechanical behavior. The capability to keep the flux density stability under pressure in LiBO2 is at least two orders higher than that in conventional materials. Our study opens a way to the design and search of ultrastable transmission materials under extreme conditions.

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Держатели документа:
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
Laboratory of Crystal Physics, Kirensky Institute of Physics, SB RAS, Krasnoyarsk, 660036, Russian Federation
Department of Physics, Far Eastern State Transport University, Khabarovsk, 680021, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Wuhan National Laboratory for Optoelectronics and School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, China
Laboratory of Space Astronomy and Technology, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
University of Chinese Academy of Sciences, Beijing, 100049, China
Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
School of Materials Science and Engineering; TKL of Metal and Molecule-Based Material Chemistry, Nankai University, Tianjin, 300350, China

Доп.точки доступа:
Jiang, X.; Molokeev, M. S.; Молокеев, Максим Сергеевич; Dong, L.; Dong, Z.; Wang, N.; Kang, L.; Li, X.; Li, Y.; Tian, C.; Peng, S.; Li, W.; Lin, Z.
}
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    Simulation of fullerene formation in a carbon-helium plasma / P. V. Novikov, I. V. Osipova, G. N. Churilov, A. I. Dudnik // Fuller. Nanotub. Carbon Nanostruct. - 2021. - Vol. 29, Is. 5. - P. 337-342, DOI 10.1080/1536383X.2020.1842738. - Cited References: 22 . - ISSN 1536-383X
   Перевод заглавия: Моделирование образования фуллерена в углеродно-гелиевой плазме
Кл.слова (ненормированные):
Fullerene formation -- kinetic model -- carbon clusters -- Kinetic modeling -- Fullerenes
Аннотация: A kinetic model of fullerene formation in the carbon-helium plasma of an arc discharge was proposed. In the model, in addition to the coagulation of carbon clusters, the cluster isomerization and their cooling with a buffer gas were taken into account. The simulation results of the fullerene formation are in qualitatively agreement with the experimental data, i.e., the fraction of higher fullerenes increases at high pressures in the fullerene mixture.

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Держатели документа:
Krasnoyarsk Institute of Railway Transport, Krasnoyarsk, Russian Federation
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Novikov, P. V.; Osipova, I. V.; Осипова, Ирина Владимировна; Churilov, G. N.; Чурилов, Григорий Николаевич; Dudnik, A. I.; Дудник, Александр Иванович
}
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Iron silicides formation on Si (100) and (111) surfaces through theoretical modeling of sputtering and annealing / I. V. Chepkasov, V. S. Baidyshev, E. V. Sukhanova [et al.] // Appl. Surf. Sci. - 2020. - Vol. 527. - Ст. 146736, DOI 10.1016/j.apsusc.2020.146736. - Cited References: 67. - We thank Dr. Ivan Tarasov for fruitful discussions. The research is carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University and resources of the Center for the Information and Computing of Novosibirsk State University. The molecular dynamics study of sputtering and annealing iron silicides was supported by the Russian Science Foundation, project no. 16-13-00060-П. All quantum-chemical calculations were supported by Ministry of Education and Science of the Russian Federation in the framework of Increase Competitiveness Program of NUST “MISiS” (No. K2-2020-009) . - ISSN 0169-4332
Кл.слова (ненормированные):
Fe3Si -- Epitaxial films -- Sputtering -- Annealing -- MD simulation
Аннотация: The iron silicides formation during epitaxial film grown process on the (100) and (111) silicon surfaces were investigated using molecular dynamics (MD). The iron and silicon atom deposition rate and silicon substrate temperature influence on the formed iron silicide structure and stoichiometric composition were studied in detail. During the growth of iron silicide crystal structure significant diffusion of the substrate atoms into the forming BCC core occurs, this intensifies with the substrate temperature increase, and the ratio of substrate atoms inside the Fe3Si phase reaches nearly 12%. The BCC structure formation is less active on the (100) surface, and at the temperatures as low as 26 °C and 300 °C the iron silicide crystal phase does not form at all. However, with the temperature increase or the deposition rate decrease, the crystal structure formation processes occur more actively in both cases of (100) and (111) surfaces. Thus, the effect of the deposition rate decrease is identical to the temperature growth. It was shown that the formation of the structured B2 phase of iron silicide in buffer layer between the film and the substrate leads to the inhibition of the mutual diffusion of iron and silicon atoms.

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Держатели документа:
Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow, 121205, Russian Federation
Katanov Khakas State University, 90 Lenin pr., Abakan, 655017, Russian Federation
Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russian Federation
Emanuel Institute of Biochemical Physics RAS, Moscow, 199339, Russian Federation
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 50/38 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, 660041, Russian Federation
EK-MFA, Dept. of Nanostructures, Budapest, Hungary
National University of Science and Technology MISiS, 4 Leninskiy pr., Moscow, 119049, Russian Federation
Plekhanov Russian University of Economics, 36 Stremyanny per., Moscow, 199339, Russian Federation

Доп.точки доступа:
Chepkasov, I. V.; Baidyshev, V. S.; Sukhanova, E. V.; Visotin, M. A.; Высотин, Максим Александрович; Sule, P.; Popov, Z. I.
}
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    Полевое тестирование метода картографического моделирования влагозапасов поверхностного слоя почвенного покрова, основанного на данных радарной съёмки Sentinel-1 и цифровой модели рельефа / А. М. Зейлигер, K. V. Muzalevskiy, Е. В. Зинченко [и др.] // Соврем. проблемы дистанц. зондир. Земли из космоса. - 2020. - Т. 17, № 4. - С. 113-128, DOI 10.21046/2070-7401-2020-17-4-113-128. - Библиогр.: 32 . - ISSN 2070-7401. - ISSN 2411-0280
   Перевод заглавия: Field testing of the cartographic modeling of soil water content of the surface layer of soil cover based on Sentinel-1 radar survey and digital elevation model
Кл.слова (ненормированные):
почвенный покров -- влажность почвы -- точечные данные -- растровые данные -- гранулометрический состав -- шероховатость земной поверхности -- цифровая модель местности -- БПЛА -- радарная съёмка -- Sentinel-1 -- обратное радарное рассеяние -- нейронные сети -- диэлектрическая модель почвы -- Soil cover -- Soil moisture -- Raster data -- Particle size distribution -- Surface roughness -- Digital terrain model -- UAV -- Radar imaging -- Sentinel-1 -- Radar backscatter -- Neural networks -- Dielectric soil model
Аннотация: Влагосодержание поверхностного слоя почвенного покрова (ВПС ПП) является одним из ключевых параметров, используемых для количественного описания гидрологического состояния поверхности почвы, а также при оценке доступности почвенной влаги растительному покрову. Поскольку коэффициент обратного радарного рассеяния чувствителен к влажности почвы, в настоящей работе применялись данные Sentinel-1 для картирования влажности почвы с высоким пространственным разрешением с целью отображения пространственных и временных закономерностей распределения почвенной влаги на уровне поля в практике управления почвенными и водными ресурсами. Прямые измерения ВПС ПП толщиной 5 см были реализованы в результате проведённого полевого мониторинга на экспериментальном участке, расположенном на территории Всероссийского научно-исследовательского института орошаемого земледелия (пос. Водный, Волгоградская обл.). В заданных координатах на тестовом участке были отобраны соответствующие почвенные образцы, влагосодержание которых было определено с использованием термостатно-весового метода. В результате создан первый точечный слой геоданных ВПС ПП. По данным радарной съёмки Sentinel-1 была выполнена оценка ВПС ПП для того же пространственного экстента экспериментального участка. Значения растрового набора значений влажности почвы по данным дистанционного зондирования (ВПС ПП-ДЗЗ) в пределах границ экспериментального участка были рассчитаны по данным радарной съёмки Sentinel-1. Эти расчёты основаны на оценке отражательной способности почвы, полученной методом нейронной сети, и дальнейшего решения обратной задачи с использованием диэлектрической модели, учитывающей содержание глинистой фракции почвы тестового участка. В ходе тренировки нейронной сети использовались входные данные коэффициентов обратного радарного рассеяния, измеренные Sentinel-1 на согласованной вертикальной и перекрёстной поляризации, и выходное значение отражательной способности почвы, оценённое на основе точечного слоя геоданных ВПС ПП и диэлектрической модели. Ортотрансформация снимка Sentinel-1 осуществлялась с использованием цифровой модели рельефа (ЦМР), созданной в результате стереосъёмки, выполненной с использованием беспилотного летательного аппарата Phantom 4 Pro. В результате сравнения наборов геоданных ВПС ПП и ВПС ПП-ДЗЗ, полученных в ходе полевого мониторинга и дистанционного зондирования соответственно, были оценены значения коэффициента детерминации (0,948) и стандартного отклонения (2,04 %). Этот результат подтверждает удовлетворительную линейную корреляцию между наборами ВПС ПП и ВПС ПП-ДЗЗ. Сравнение двух полученных точечных слоёв геоданных ВПС ПП указывает на удовлетворительное воспроизведение первого набора вторым. Такой вывод получен в результате наземного мониторинга и картографического моделирования, выполненного с помощью разработанного метода с использованием данных радарной съёмки Sentinel-1 и характеристик ЦМР. Результаты исследования позволяют сделать вывод, что разработанный метод может рассматриваться в качестве научной и методологической основы новой технологии картографического мониторинга ВПС ПП, которая рассматривается в настоящее время в качестве одной из основных базовых характеристик для использования в точном орошаемом земледелии.
The surface moisture content (SMC) is one of the key parameters, which is used for the quantitative description of soil hydrological state as well as the estimation of soil water availability to vegetation canopy. Since the radar backscattering coefficient is sensitive to SMC, in this investigation Sentinel-1 data was used for soil moisture mapping with a high spatial resolution, based on which the spatial and temporal patterns of soil moisture distribution at field level was mapped for implementing in the management of soil and water resources. Direct measurements of SMC in a layer thickness of 5 cm were carried out during field monitoring at an experimental test site, located on the territory of the All-Russian Scientific Research Institute of Irrigated Agriculture (Vodny village, Volgograd region). In the given coordinates on the test site, soil samples were taken, the moisture content of which was determined using the thermostat-weight method. As a result, the first point georeferenced layer of SMC was created. At the same time, the estimation of SMC based on Sentinel-1 radar observations was performed for the same spatial extent of the test site. The raster set of SMC within the boundaries of the test site was calculated from the Sentinel-1 remote sensing (RS) observations. This layer will be named SMC-RS. These calculations were based on the assessment of soil reflectivity obtained by neural network (NN) method and the further solution of the inverse problem using a dielectric model, which takes into account the soil clay content at the test site. During the training of the NN, backscatter coefficients measured by Sentinel-1 at co- and cross-polarization were used as input data. As the output data of the NN, the value of soil reflectivity, which was estimated based on point georeferenced layer of SMC and a dielectric model were used. Terrain correction of Sentinel-1 image was carried out using a digital elevation model (DEM), created by Phantom 4 Pro unmanned aerial vehicle as the result of stereo photography. As a result of comparing the georeferenced data sets SMC and SMC-RS obtained during field monitoring and remote sensing, respectively, the following values of determination coefficient (0.948) and standard deviation (2.04 %) were estimated. This result confirms a satisfactory linear correlation between both data sets. The comparison of the two layers of point georeferenced data sets indicates that the first set is well correlated by the second. This conclusion was obtained as the result of ground monitoring and cartographic modelling carried out using the developed method, Sentinel-1 observation and DEM. The developed method can be considered as the scientific and methodological basis of the new technology for the cartographic monitoring of SMC, which is currently treated as one of the main basic characteristics to be used in precision irrigated agriculture. © 2020 Space Research Institute of the Russian Academy of Sciences. All rights reserved.

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Держатели документа:
Российский государственный аграрный университет ― МСХА имени К. А. Тимирязева, Москва, Россия
Институт физики им. Л.В. Киренского СО РАН, Красноярск, Россия
Всероссийский научно-исследовательский институт орошаемого земледелия, Волгоград, Россия

Доп.точки доступа:
Зейлигер, А. М.; Muzalevskiy, K. V.; Музалевский, Константин Викторович; Зинченко, Е. В.; Ермолаева, О. С.; Мелихов, В. В.
}
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Modeling of Electronic Spectra of Ionic Forms of Eosin and Erythrosin / A. V. Rogova, F. N. Tomilin, M. A. Gerasimova, E. A. Slyusareva // Russ. Phys. J. - 2020. - Vol. 63, Is. 8. - P. 1417-1423, DOI 10.1007/s11182-020-02186-1. - Cited References: 17 . - ISSN 1064-8887
Кл.слова (ненормированные):
eosin -- erythrosin -- ionic forms -- non-stationary density functional theory TD-DFT -- B3LYP -- polarized continuum model -- electronic spectra -- absorption -- fluorescence
Аннотация: Multistage dissociation of fluoroscein dyes, widely used in biological labeling, yields a variety of ionic and tautomeric forms in a wide range of pH values. In contrast to well-studied absorption spectra, the emission spectra are not quite readily interpreted due to their strong overlapping and proton transfer in electronically excited states. The least studied are the fluorescent properties of eosin and erythrosin dyes containing heavy atoms (Br, I), in which the characteristics of the dianionic form only are reliably determined. In the framework of the density functional theory using the B3LYP-functional including nonequilibrium solvation, the geometries of the series of ionic forms of eosin and erythrosin in the ground and excited states are found, and the electronic spectra are calculated. Based on the identified linear regression of the calculated and experimental data for the earlier resolved electronic spectra, for the first time, the emission spectrum maxima of the monoanionic, neutral quinoid, and cationic forms of the dyes are determined. The spectral peculiarities (Stokes shifts) are discussed in terms of variation of the molecule and ion geometries in the ground and excited states.

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Публикация на русском языке Моделирование электронных спектров ионных форм эозина и эритрозина [Текст] / А. В. Рогова, Ф. Н. Томилин, М. А. Герасимова, Е. А. Слюсарева // Изв. вузов. Физика. - 2020. - Т. 63 № 8. - С. 115-121

Держатели документа:
Siberian Federal University, Krasnoyarsk, Russian Federation
Kirenskii Institute of Physics of the Siberian Branch of the Russian Academy of Sciences – Division of the Federal Research Center, Krasnoyarsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Rogova, A. V.; Tomilin, F. N.; Томилин, Феликс Николаевич; Gerasimova, M. A.; Slyusareva, E. A.
}
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Modeling optical properties of plant epicuticular wax / E. Bukhanov, Y. Gurevich, M. Krakhalev, D. Shabanov // Proceedings of ITNT 2020 - 6th IEEE International Conference on Information Technology and Nanotechnology : Institute of Electrical and Electronics Engineers Inc., 2020. - Ст. 9253272DOI 10.1109/ITNT49337.2020.9253272. - Cited References: 39
Кл.слова (ненормированные):
photonic crystal -- epicuticular wax -- density of photon states -- fluorescence
Аннотация: Wax is found on the leaves almost of all plants. Its physicochemical and protective properties are widely discussed in the scientific literature. In the presented work, the influence of the structure of wax on the optical properties in wheat leaves and needles of blue spruce has been revealed for the first time. Long-period ordering was established. The structural elements are nanotubes up to several microns in length and about 150 nm in diameter. The paper presents the influence of a long-period structure on the optical properties and local characteristics of light waves, including the transmission spectrum, the density of photon states, as well as fluorescence spectra and polarization microscopy. Using modern mathematical tools, the main spectral and optical characteristics were calculated using the example of the wax cover of blue spruce and glaucas wheat. Based on calculations that establish the relationship between the structural, spectral and optical properties, the influence of wax structures on the process of photosynthesis was revealed.

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Держатели документа:
Kirensky Institute of Physics Sb Ras, Krasnoyarsk, Russian Federation
Frc Ksc Sb Ras, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Bukhanov, E. R.; Буханов, Евгений Романович; Gurevich, Y.; Krakhalev, M. N.; Крахалев, Михаил Николаевич; Shabanov, D. A.; Шабанов, Дмитрий Александрович; IEEE International Conference on Information Technology and Nanotechnology(6th ; 26 - 29 May 2020 ; Samara, Russian Federation)
}
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Kolovsky, A. R.
Open Fermi-Hubbard model: Landauer's versus master equation approaches / A. R. Kolovsky // Phys. Rev. B. - 2020. - Vol. 102, Is. 17. - Ст. 174310, DOI 10.1103/PhysRevB.102.174310. - Cited References: 22. - The author acknowledges discussions with D. N. Maksimov and financial support of Russian Science Foundation (RU) through Grant No. 19-12-00167 . - ISSN 2469-9950
Кл.слова (ненормированные):
Relaxation processes -- Fermi particles -- Landauer formalisms -- Master equations -- Non equilibrium -- Quantum transport -- Quasimomentum -- Rate of relaxation -- Simple modeling
Аннотация: We introduce a simple model for the quantum transport of Fermi particles between two contacts connected by a lead. It generalizes the Landauer formalism by explicitly taking into account the relaxation processes in the contacts. We calculate the contact resistance and nonequilibrium quasimomentum distribution of the carriers in the lead and show that they strongly depend on the rate of relaxation processes.

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Держатели документа:
Kirensky Institute of Physics, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation

Доп.точки доступа:
Коловский, Андрей Радиевич
}
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    Bukhanov, E. R.
    Modeling an optical properties of plant epiticular wax / E.R. Bukhanov, Y.L. Gurevich, D.A. Shabanov // Информационные технологии и нанотехнологии (ИТНТ-2020) : сб трудов. - 2020. - P224-231. - Библиогр.: 38
   Перевод заглавия: Моделирование оптических свойств эпитикулярного воска растений
Аннотация: Wax is found on the leaves almost of all plants. Its physicochemical and protective properties are widely discussed in the scientific literature. In the presented work, the influence of the structure of wax on the optical properties in wheat leaves and needles of blue spruce has been revealed for the first time. Long-period ordering was established. The structural elements are nanotubes up to several microns in length and about 150 nm in diameter. The paper presents the influence of a long-period structure on the optical properties and local characteristics of light waves, including the transmission spectrum, the density of photon states, as well as fluorescence spectra and polarization microscopy. Using modern mathematical tools, the main spectral and optical characteristics were calculated using the example of the wax cover of blue spruce and glaucas wheat. Based on calculations that establish the relationship between the structural, spectral and optical properties, the influence of wax structures on the process of photosynthesis was revealed.

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Доп.точки доступа:
Gurevich, Юрий Леонидович; Shabanov, D. A.; Шабанов, Дмитрий Александрович; Буханов, Евгений Романович; "Информационные технологии и нанотехнологии", Международная конференция и молодежная школа(6 ; 2020 ; ; Самара (on-line)); Самарский национальный исследовательский университет им. акад. С.П. Королева; Институт систем обработки изображений РАН
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Collective resonances in hybrid photonic-plasmonic nanostructures / A. E. Ershov, R. G. Bikbaev, I. L. Rasskazov [et al.] // J. Phys.: Conf. Ser. - 2020. - Vol. 1461, Is. 1. - Ст. 012046DOI 10.1088/1742-6596/1461/1/012046. - Cited References: 11. - The reported study was funded by Russian Foundation for Basic Research, Government of Krasnoyarsk Territory, Krasnoyarsk Regional Fund of Science (Grant No. 18-42-240013); A.E. thanks the grant of the President of Russian Federation (agreement 075-15-2019-676)
Кл.слова (ненормированные):
Hybrid systems -- Plasmonics -- Time domain analysis -- 1-D photonic crystal -- Defect layers -- Nanodisks -- Periodic arrays -- Plasmonic nanostructures -- Rayleigh anomalies -- Spectral position -- Theoretical modeling -- Finite difference time domain method
Аннотация: We present the theoretical model to predict the spectral position of Rayleigh anomalies emerged in hybrid system consisting of periodic array of plasmonic nanodisks embeded into the middle of defect layer of 1D photonic crystal (PhC). The spectral positions of these new emerged Rayleigh anomalies agree well with the results of exact simulations with Finite-Difference Time-Domain (FDTD) method.

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Держатели документа:
Institute of Computational Modeling SB RAS, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Siberian State University of Science and Technology, Krasnoyarsk, 660014, Russian Federation
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation
Institute of Optics, University of Rochester, Rochester, NY 14627, United States

Доп.точки доступа:
Ershov, A. E.; Bikbaev, R. G.; Бикбаев, Рашид Гельмединович; Rasskazov, I. L.; Gerasimov, V. S.; Timofeev, I. V.; Тимофеев, Иван Владимирович; Polyutov, S. P.; Karpov, S. V.; Карпов, Сергей Васильевич; International Conference on Metamaterials and Nanophotonics(4th ; 15 - 19 July 2019 ; St. Petersburg, Russian Federation)
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10.

Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation / F. N. Tomilin [et al.] // Anal. Bioanal. Chem. - 2019. - Vol. 411, Is. 25. - P. 6723-6732, DOI 10.1007/s00216-019-02045-0. - Cited References: 51. - Authors are grateful to Ana Gargaun for English grammar correction. This work was funded in parts by the Ministry of Science and Higher Education of the Russian Federation; project 0287-2019-0007 the Council of the President of the Russian Federation for Support of Young Scientists and Leading Scientific Schools (project no. SP-938.2015.5) and the grant of KSAI “Krasnoyarsk Regional Fund of Supporting Scientific and Technological Activities” for M.P., the internship “The study of the stacking of the secondary structure of DNA aptamers to thrombin” for R.M. . - ISSN 1618-2642
Кл.слова (ненормированные):
Aptamer -- Thrombin -- Three-dimensional structure -- Small-angle X-ray scattering -- Molecular modeling
Аннотация: Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule’s electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids. [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC Siberian Branch Russian Academy of Sciences, 50/38 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, 660041, Russian Federation
Federal Research Center “Krasnoyarsk Science Center” Siberian Branch of the Russian Academy of Sciences, 50 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
NRC Kurchatov Institute, 1, Academic Kurchatov Square, Moscow, 123182, Russian Federation
A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, Moscow, 119992, Russian Federation
Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk, 660022, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada

Доп.точки доступа:
Tomilin, F. N.; Томилин, Феликс Николаевич; Moryachkov, R.; Морячков, Роман Владимирович; Shchugoreva, I.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G.; Platunov, M. S.; Платунов, Михаил Сергеевич; Spiridonova, V.; Melnichuk, A.; Atrokhova, A.; Zamay, S. S.; Замай, С. С.; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Zamay, G. S.; Замай, Галина Сергеевна; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zamay, T. N.; Замай, Т. Н.; Berezovski, M. V.; Kichkailo, A. S.
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