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A quantum chemical study of the formation of 2-hydroperoxy-coelenterazine in the Сa2+-regulated photoprotein obelin / L. Y. Antipina [et al.] // J. Struct. Chem. - 2011. - Vol. 52, Is. 5. - P. 870-875. - Cited References: 19. - The work was supported by RFBR (07-04-00930-a), the "Molecular and Cell Biology" Program of the Presidium of the Russian Academy of Sciences, and the Program of the Siberian Division of the Russian Academy of Sciences (project No. 2) within the implementation of the Federal Targeted Program "Scientific and Scientific Pedagogical Personnel of Innovative Russia, 2010" (P333 and P213). . - ISSN 0022-4766

РУБ Chemistry, Inorganic & Nuclear + Chemistry, Physical
Рубрики:
CALCIUM-DISCHARGED OBELIN
   SEMIEMPIRICAL METHODS
   1.7 ANGSTROM
   OPTIMIZATION
   PARAMETERS
   MECHANISM
   FLUORESCENCE
   ELEMENTS
   PROTEIN
   EMITTER
Кл.слова (ненормированные):
coelenterazine -- 2-hydroperoxy-coelenterazine -- Obelia longissima -- Renilla muelleri
Аннотация: The Ca2+-regulated photoprotein obelin determines the luminescence of the marine hydroid Obelia longissima. Bioluminescence is initiated by calcium and appears as a result of the oxidative decarboxylation related to the coelenterazine substrate. The luciferase of the luminescent marine coral Renilla muelleri (RM) also uses coelenterazine as a substrate. However, three proteins are involved in the in vivo bioluminescence of these animals: luciferase, green fluorescent protein, and Ca2+-regulated coelenterazine-binding protein (CBP). In fact, CBP that contains one strongly bound coelenterazine molecule is the RM luciferase substrate in the in vivo bioluminescent reaction. Coelenterazine becomes available for oxygen and the reaction with luciferase only after binding CBP with calcium ions. Unlike Ca2+-regulated photoproteins, the coelenterazine molecule is not activated by oxygen in the CBP molecule. In this work, by means of quantum chemical methods the behavior of substrates in these proteins is analyzed. It is shown that coelenterazine can form different tautomers: CLZ(2H) and CLZ(7H). The formation of 2-hydroperoxy-coelenterazine is studied. According to the obtained data, these proteins use different forms of the substrates for the reaction. In obelin, the substrate is in the CLZ(2H) form that affords hydrogen peroxide. In RM, coelenterazine is in the CLZ(7H) form, and therefore, CBP is not activated by oxygen.

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Держатели документа:
Russian Acad Sci, LV Kirensky Phys Inst, Siberian Div, Krasnoyarsk, Russia
Russian Acad Sci, Inst Biophys, Siberian Div, Krasnoyarsk, Russia
MF Reshetnev Siberian State Aerosp Univ, Krasnoyarsk, Russia

Доп.точки доступа:
Antipina, L. Yu.; Tomilin, F. N.; Томилин, Феликс Николаевич; Vysotski, E. S.; Высоцкий, Евгений Степанович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич
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    Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method / D. G. Fedorov [et al.] // Chem. Phys. Lett. - 2009. - Vol. 477, Is. 1-3. - P. 169-175, DOI 10.1016/j.cplett.2009.06.072. - Cited Reference Count: 49. - Гранты: We thank Professor M. Suenaga of Kyushu University for continuing his development of the modeling software FACIO and its FMO interface. D. G. F. and K. K. were supported by the a Grant-in- Aid for Scientific Research (JSPS, Japan) and the Next Generation SuperComputing Project, Nanoscience Program (MEXT, Japan). J.H.J. was supported by a Skou Fellowship from the Danish Research Agency (Forskningsradet for Natur og Univers). - Финансирующая организация: JSPS, Japan; Next Generation SuperComputing Project; MEXT, Japan; Danish Research Agency . - JUL 28. - ISSN 0009-2614
Рубрики:
DENSITY-FUNCTIONAL THEORY
   GEOMETRY OPTIMIZATIONS
   SEMICONDUCTOR NANOWIRES
   SILICON NANOWIRES
   METHOD FMO
   ENERGY
   SURFACES
   RECONSTRUCTION
   CHEMISTRY
   PROTEINS
Кл.слова (ненормированные):
Energy gradients -- Fragment molecular orbital methods -- Future applications -- Geometry optimization -- Numerical criteria -- Silicon Nanowires -- Molecular modeling -- Molecular orbitals
Аннотация: We have developed and implemented the analytic energy gradient for the bond detachment scheme in the fragment molecular orbital method (FMO) suitable to describe solids, and applied it to the geometry optimization of a silicon nanowire at several levels of theory. In addition, we have examined in detail the effects of the particular choice of the fragmentation upon the accuracy and introduced a number of numerical criteria to characterize the errors. The established route is expected to provide guidance for future applications of FMO to surfaces, solids and nanosystems. (C) 2009 Elsevier B. V. All rights reserved.

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Держатели документа:
Natl Inst Adv Ind Sci & Technol, RICS, Tsukuba, Ibaraki 3058568, Japan
SB RAS, LV Kirensky Phys Inst, Krasnoyarsk 660036, Russia
Siberian Fed Univ, Krasnoyarsk 660041, Russia
Univ Copenhagen, Dept Chem, DK-2100 Copenhagen, Denmark
Kyoto Univ, Grad Sch Pharmaceut Sci, Sakyo Ku, Kyoto 6068501, Japan

Доп.точки доступа:
Fedorov, D.G.; Kitaura, K.; Avramov, P. V.; Аврамов, Павел Вениаминович; Jensen, J.H.
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Aplesnin, S. S.
Effect of bond fluctuations on the transport properties of manganites and nickelates / S. S. Aplesnin // J. Exp. Theor. Phys. - 2007. - Vol. 104, Is. 5. - P. 766-774, DOI 10.1134/S1063776107050111. - Cited References: 26 . - ISSN 1063-7761

РУБ Physics, Multidisciplinary
Рубрики:
NEUTRON-DIFFRACTION
   CHARGE DISPROPORTIONATION
   ELECTRONIC-STRUCTURE
   MAGNETIC ORDER
   TRANSITIONS
   PEROVSKITES
   PRNIO3
   GAP
Кл.слова (ненормированные):
Crystal structure -- Manganites -- Optimization -- Thermal conductivity -- Thermal effects -- Bond fluctuations -- Nickelates -- Orthorhombic crystal structure -- Nickel compounds
Аннотация: For the manganites RMnO(3) (R = La, Pr, Nd), a mechanism is proposed to explain the anomalous temperature dependences of the kinetic coefficients, resistivity, and thermoelectric power during the transition from the pseudocubic O to the orthorhombic O' crystal structure. The contributions of the bending and stretching modes of the octahedron to the formation of thermal-conductivity maxima and to the deviation from the linear dependence of ln(rho/T) on 1/T at low temperatures have been estimated. In nickelates, the metal-insulator transition is caused by lattice-polaron pinning by the stretching mode of the octahedron, and the low-temperature anomaly of the thermal conductivity is related to electron scattering by the bending mode of the octahedron.

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Держатели документа:
Russian Acad Sci, LV Kirensky Phys Inst, Krasnoyarsk 660036, Russia
Reshetnev Siberian State Aerosp Univ, Krasnoyarsk 660014, Russia
ИФ СО РАН
Kirensky Institute of Physics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Reshetnev Siberian State Aerospace University, Krasnoyarsk, 660014, Russian Federation

Доп.точки доступа:
Аплеснин, Сергей Степанович
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    Bulgakov, E. N.
    Q-factor optimization in dielectric oligomers / E. N. Bulgakov, D. N. Maksimov // Phys. Rev. A. - 2019. - Vol. 100, Is. 3. - Ст. 033830, DOI 10.1103/PhysRevA.100.033830. - Cited References: 43. - This work was supported by the Ministry of Higher Education and Science of the Russian Federation (State Contract No. 3.1845.2017/4.6). . - ISSN 2469-9926. - ISSN 2469-9934
   Перевод заглавия: Оптимизация добротности в диэлектрических олигомерах

РУБ Optics + Physics, Atomic, Molecular & Chemical
Рубрики:
FOURIER MODAL METHOD
   PHOTONIC CRYSTAL
   BOUND-STATES
   ENHANCEMENT
Аннотация: In this paper we propose an optimization procedure for quality-factor (Q-factor) enhancement in dielectric oligomers. The oligomers are introduced as linear periodic chains of dielectric elements the individual Q factors of which are optimized via multipolar conversion in an avoided crossing of two resonant eigenfrequencies. It is demonstrated that when such dielectric elements are assembled into an infinite periodic array the coupling between individual resonances gives rise to an in-Γ optical bound state in the continuum (BIC) unprotected by symmetry. By setting up the oligomers of finite numbers of dielectric elements we observe high quality resonances which occur as traces of the infinite array band structure. The resulting high quality resonances exhibit light localization spots of a few squared wavelengths with Q factors Q ˃10 4. The localization is provided by similarity of the field pattern to that of the BIC with the losses at the edges of the array suppressed due to an almost flat BIC host band. The scaling law of the Q factor against the dielectric permittivity is derived.

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Держатели документа:
Reshetnev Siberian State Univ Sci & Technol, Krasnoyarsk 660037, Russia.
RAS, Kirensky Inst Phys, Fed Res Ctr KSC SB, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Krasnoyarsk 660041, Russia.

Доп.точки доступа:
Maksimov, D. N.; Максимов, Дмитрий Николаевич; Булгаков, Евгений Николаевич; Ministry of Higher Education and Science of the Russian FederationMinistry of Education and Science, Russian Federation [3.1845.2017/4.6]
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Efficiency comparison of the optimization methods that are used to design microwave filters [Text] / V. V. Tyurnev // Materials digest of the VUIth International Scientific and Practical conference "Space and time - coordinate system of human develop-ment", Kiev, August 25 - September 1. - 2011. - P75-76

Доп.точки доступа:
Tyurnev, V.V.; "Space and time - coordinate system of human develop-ment", International Scientific and Practical conference(2011 ; Aug. 25 - Sep. 1 ; Kiev)
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Fedorov, A. S.
Optimization of the calculations of the electronic structure of carbon nanotubes / A. S. Fedorov, P. B. Sorokin // Phys. Solid State. - 2005. - Vol. 47, Is. 11. - P. 2196-2202, DOI 10.1134/1.2131167. - Cited References: 19 . - ISSN 1063-7834

РУБ Physics, Condensed Matter
Рубрики:
MOLECULAR-DYNAMICS
ELASTIC PROPERTIES
TUBES
Аннотация: A method is proposed for calculating the electronic structure and physical properties (in particular, Young's modulus) of nanotubes, including single-walled carbon nanotubes. This method explicitly accounts for the periodic boundary conditions for the geometric structure of nanotubes and makes it possible to decrease considerably (by a factor of 10-10(3)) the time needed to calculate the electronic structure with minimum error. In essence, the proposed method consists in changing the geometry of the structure by partitioning nanotubes into sectors with the introduction of the appropriate boundary conditions. As a result, it becomes possible to reduce substantially the size of the unit cell of the nanotube in two dimensions, so that the number of atoms in a new unit cell of the modified nanotube is smaller than the number of atoms in the initial unit cell by a factor equal to an integral number. A decrease in the unit cell size and the corresponding decrease in the number of atoms provide a means for drastically reducing the computational time, which, in turn, substantially decreases with an increase in the degree of partition, especially for nanotubes with large diameters. The results of the calculations performed for carbon and non-carbon (boron nitride) nanotubes demonstrate that the electronic structures, densities of states, and Young's moduli determined within the proposed approach differ insignificantly from those obtained by conventional computational methods. (c) 2005 Pleiades Publishing, Inc.

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Держатели документа:
Russian Acad Sci, Kirensky Phys Inst, Siberian Div, Krasnoyarsk 660036, Russia
ИФ СО РАН
Kirensky Institute of Physics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Sorokin, P. B.; Федоров, Александр Семенович
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    Machine learning methods in assessing the effect of mixture composition on the physical and mechanical characteristics of road concrete / I. G. Endzhievskaya, A. S. Endzhievskiy, M. A. Galkin, M. S. Molokeev // J. Build. Eng. - 2023. - Vol. 76. - Ст. 107248, DOI 10.1016/j.jobe.2023.107248. - Cited References: 17. - The work was carried out within the framework of the Strategic Academic Leadership Program "Priority-2030" for the Siberian Federal University. The research in field of Machine Learning application was supported by the Tyumen Oblast Government, as part of the West-Siberian Interregional Science and Education Center’s project No. 89-DON (3) . - ISSN 2352-7102
   Перевод заглавия: Методы машинного обучения в оценке влияния состава смеси на физико-механические характеристики дорожного бетона
Кл.слова (ненормированные):
Concrete optimization -- Random forest -- Decision tree -- Machine learning -- Сement concrete roads
Аннотация: Current manuscript presents a study on the use of 48 experimental data points containing parameters of concrete production technological process and its properties, such as strength, density, and bending strength. It was revealed that temporal characteristics, specifically - compressive strength at the age of 3, 7, 28 days, R3, R7, and R28, are significantly correlated with each other, indicating that only one characteristic, such as R28 or Rfl 28, is sufficient for prediction. The absence of multiple correlations between parameters and properties suggests that linear regression analysis may not be accurate. Therefore, the use of Machine Learning is optimal; specifically Random Forest method is preferable due to ease of use and minimum hyperparameters for tuning. Low prediction errors (?1–11%) for 30% of the test data, as determined by the cross-validation method, confirm a relationship between the experimental parameters and the concrete properties. The most important parameters for achieving high values of compressive and bending strengths, R28 and Rfl 28, were identified, namely: air-entraining additives, granite crushed stone consisting of a mixture of fractions 5–20 mm, crushed stone derived from gravel of high strength grains of large fractions 10–20 mm. To obtain explanatory model, another Machine Learning method, that was used, called Decision Tree. The model showed that a high amount of crushed stone 10–20 mm from gravel, more than 212 (kg per 1 m3 of concrete mix), leads to a higher number of strong grains with smooth, rounded surface, thereby, reducing the bending strength of concrete. However, a large concentration of crushed stone mix fractions of 5–20 mm from granite, more than 537 (kg per 1 m3 of concrete mix), leads to the maximum roughness, which makes a significant contribution to the increased strength of concrete due to the adhesion of the matrix and aggregates to each other.

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Держатели документа:
Siberian Federal University, Svobodny Ave., 79, Krasnoyarsk, 660041, Russia
Laboratory of Theory and Optimization of Chemical and Technological Processes, University of Tyumen, Tyumen, 625003, Russia
Laboratory of Crystal Physics, Kirensky Institute of Physics SB RAS, Krasnoyarsk, 660036, Russia

Доп.точки доступа:
Endzhievskaya, I. G.; Endzhievskiy, A. S.; Galkin, M. A.; Molokeev, M. S.; Молокеев, Максим Сергеевич
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Magnetic nanoparticles in borate glasses: Identification and sizing / I. S. Edelman [et al.] // International Conference on Optimization of Electrical and Electronic Equipment (OPTIM 2014) : IEEE Computer Society, 2014. - P. 95-104, DOI 10.1109/OPTIM.2014.6850939. - Cited References: 60 . - ISBN 978-1-4799-5183-3
Рубрики:
Engineering, Electrical and Electronic
Кл.слова (ненормированные):
SUPERPARAMAGNETIC RESONANCE -- FERROMAGNETIC-RESONANCE -- FERRITE NANOPARTICLES -- OXIDE NANOPARTICLES -- FARADAY-ROTATION -- CERAMICS -- IRON -- CRYSTALLIZATION -- ANISOTROPY -- PARTICLES
Аннотация: Heat treatment of borate glasses co-doped with low contents of iron and larger radius elements: Dy, Tb, Gd, Ho, Er, Y and Bi results in formation of magnetic nanoparticles, radically changing their physical properties. Transmission electron microscopy and synchrotron radiation-based techniques: XRD, EXAFS, XANES and SAXS, show a broad distribution of nanoparticle sizes with characteristic depending on the treatment regime; a crystalline structure of these nanoparticles is detected in heat treated samples. Magnetic circular dichroism (MCD) studies of samples subjected to heat treatment as well as of maghemite, magnetite and iron garnet allow to unambiguously assigning the nanoparticle structure to maghemite. Different features observed in the MCD spectra are related to different electron transitions in Fe3+ ions gathered in the nanoparticles. Variable-temperature electron magnetic resonance (EMR) studies confirm the formation of magnetic nanoparticles and the identification of their nature. Computer simulations of the EMR spectra corroborate the broad distribution of nanoparticle sizes found by 'direct' techniques. © 2014 IEEE.

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Доп.точки доступа:
Edelman, I. S.; Эдельман, Ирина Самсоновна; Ivanova, O. S.; Иванова, Оксана Станиславовна; Zubavichus, Y.; Trofimova, N. N.; Zaikovskiy, V. I.; Artemenko, A.; Curely, J.; Kliava, J.; Russian Foundation for Basic Research; Russian Foundation for Basic Research; International Conference on Optimization of Electrical and Electronic Equipmen (22 May - 24 May 2014 ; Bran, Romania)
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Miniature suspended-substrate bandpass filter / B. A. Belyaev [et al.] // Prog. Electromagn. Res. C. - 2010. - Vol. 15. - P219-231, DOI 10.2528/PIERC10070604 . - ISSN 1937-8718
Кл.слова (ненормированные):
Attenuation poles -- Narrow band filter -- Optimization method -- Pass-band edge -- Resonator filters -- Strip conductors -- Stripline structures -- Microwave filters -- Resonators -- Strip telecommunication lines -- Bandpass filters
Аннотация: A new quasi-lumped suspended-substrate stripline structure admitting implementation of miniature highly selective narrowband filters is studied. Appreciable improvement of the device selectivity is achieved with supplementary strip conductors introduced between the resonators, which induce attenuation poles near both passband edges. Furthermore, these supplementary conductors reducing the coupling between the resonators allow diminishing the interresonator spacing and the total size. A four-resonator filter is synthesized using the intelligence optimization method. Experimental results of the manufactured filter are presented.

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Держатели документа:
Kirensky Institute of Physics, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russian Federation
Institute of Engineering Physics and Radio Electronics, Siberian Federal University, Krasnoyarsk 660074, Russian Federation

Доп.точки доступа:
Belyaev, B. A.; Беляев, Борис Афанасьевич; Лексиков, Александр Александрович; Leksikov, A. A.; Tyurnev, V. V.; Тюрнев, Владимир Вениаминович; Serzhantov, A. M.; Сержантов, Алексей Михайлович
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10.

Nanoparticle shape optimization for Tamm-plasmon-polariton-based organic solar cells in the visible spectral range / R. G. Bikbaev, S. Y. Vetrov, I. V. Timofeev, V. F. Shabanov // Photonics. - 2022. - Vol. 9, Is. 11. - Ст. 786, DOI 10.3390/photonics9110786. - Cited References: 28. - The reported study was funded by a grant of the President of the Russian Federation №MK-46.2021.1.2 . - ISSN 2304-6732
Кл.слова (ненормированные):
photonic crystal -- Tamm plasmon polariton -- organic solar cell
Аннотация: The effect of the shape of the nanoparticles and the polarization of incident light on the surface current density and the efficiency of an organic solar cell based on the Tamm plasmon polariton is investigated. In the cases of both elongated and flattened nanoparticles, it is shown that the efficiency of such a solar cell is increased when the electric field vector is parallel to the largest axis of the spheroid.

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation

Доп.точки доступа:
Bikbaev, R. G.; Бикбаев, Рашид Гельмединович; Vetrov, S. Y.; Timofeev, I. V.; Тимофеев, Иван Владимирович; Shabanov, V. F.; Шабанов, Василий Филиппович
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