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Electronic Structure of p-Type La1-xMx2+MnO3 Manganites in the Ferromagnetic and Paramagnetic Phases in the LDA plus GTB Approach / V. A. Gavrichkov [et al.] // J. Exp. Theor. Phys. - 2011. - Vol. 112, Is. 5. - P. 860-876, DOI 10.1134/S1063776111030101. - Cited References: 47. - This study was supported financially by integration project no. 40 of the Ural and Siberian Branches of the Russian Academy of Sciences, the program "Strong Electron Correlations" of the Russian Academy of Sciences, and the Russian Foundation for Basic Research (project no. 10-02-00251-a). . - ISSN 1063-7761

РУБ Physics, Multidisciplinary
Рубрики:
DOUBLE-EXCHANGE
   COLOSSAL MAGNETORESISTANCE
   THIN-FILMS
   PHYSICS
   LA1-XSRXMNO3
   RESISTIVITY
   SEPARATION
   TRANSPORT
   MODEL
Кл.слова (ненормированные):
Complex structure -- Cubic materials -- Ferromagnetic phase -- Half metals -- Jahn Teller effect -- Metal properties -- Metal types -- Orbitals -- P-type -- Paramagnetic phase -- Paramagnetic phasis -- Quasi particles -- Spectral intensity -- Spin projections -- Strong electron correlations -- Barium -- Density functional theory -- Electron correlations -- Electron density measurement -- Electronic properties -- Electronic structure -- Fermi level -- Ferromagnetic materials -- Ferromagnetism -- Manganese oxide -- Manganites -- Paramagnetic materials -- Paramagnetism -- Valence bands -- Lanthanum
Аннотация: The band structure, spectral intensity, and position of the Fermi level in doped p-type La1-xMx2+ MnO3 manganites (M = Sr, Ca, Ba) is analyzed using the LDA + GBT method for calculating the electronic structure of systems with strong electron correlations, taking into account antiferro-orbital ordering and using the Kugel-Khomskii ideas and real spin S = 2. The results of the ferromagnetic phase reproduce the state of a spin half-metal with 100% spin polarization at T = 0, when the spectrum is of the metal type for a quasiparticle with one spin projection and of the dielectric type for the other. It is found that the valence band becomes approximately three times narrower upon a transition to the paramagnetic phase. For the paramagnetic phase, metal properties are observed because the Fermi level is located in the valence band for any nonzero x. The dielectrization effect at the Curie temperature is possible and must be accompanied by filling of d(x) orbitals upon doping. The effect itself is associated with strong electron correlations, and a complex structure of the top of the valence band is due to the Jahn-Teller effect in cubic materials. DOI: 10.1134/S1063776111030101

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Публикация на русском языке Электронная структура манганитов La[1-x]M[x]2+MnO[3] p-типа в ферромагнитной и парамагнитной фазах в рамках LDA+GTB-подхода [Текст] / В. А. Гавричков [и др.] // Журнал экспериментальной и теоретической физики. - 2011. - Т. 139 Вып. 5. - С. 983-1000

Держатели документа:
[Gavrichkov, V. A.
Ovchinnikov, S. G.] Russian Acad Sci, Siberian Branch, LV Kirensky Phys Inst, Krasnoyarsk 660036, Russia
[Gavrichkov, V. A.
Ovchinnikov, S. G.] Siberian Fed Univ, Krasnoyarsk 660041, Russia
[Nekrasov, I. A.] Russian Acad Sci, Ural Branch, Inst Electrophys, Ekaterinburg 620016, Russia
[Pchelkina, Z. V.] Russian Acad Sci, Ural Branch, Inst Met Phys, Ekaterinburg 620990, Russia
ИФ СО РАН
Siberian Branch, Kirensky Institute of Physics, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Ural Branch, Institute of Electrophysics, Russian Academy of Sciences, Yekaterinburg, 620016, Russian Federation
Ural Branch, Institute of Metal Physics, Russian Academy of Sciences, Yekaterinburg, 620990, Russian Federation

Доп.точки доступа:
Gavrichkov, V. A.; Гавричков, Владимир Александрович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Nekrasov, I. A.; Pchelkina, Z. V.
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Ovchinnikov, S. G.
Effect of interlayer tunneling on the electronic structure of bilayer cuprates and quantum phase transitions in carrier concentration and high magnetic field / S. G. Ovchinnikov, I. A. Makarov, E. I. Shneyder // J. Exp. Theor. Phys. - 2011. - Vol. 112, Is. 2. - P. 288-302, DOI 10.1134/S106377611005119X. - Cited References: 64. - This study was supported financially by the program "Quantum Physics of Condensed Media" of the Presidium of the Russian Academy of Sciences (project no. 5.7), the integration projects of the Siberian Branch and the Ural Division of the Russian Academy of Sciences (project no. 40), the Russian Foundation for Basic Research (project no. 09-02-00127), the President of the Russian Federation (grant no. MK-1683.2010.2), and the Federal Target Program P891. . - ISSN 1063-7761

РУБ Physics, Multidisciplinary
Рубрики:
T-J MODEL
   HIGH-TEMPERATURE SUPERCONDUCTORS
   DIMENSIONAL HUBBARD-MODEL
   FERMI-SURFACE
   COPPER OXIDES
   GROUND-STATE
   CUO2 PLANES
   SPECTRUM
   BAND
   NMR
Кл.слова (ненормированные):
Antibonding -- Bi-layer -- Bilayer cuprates -- Complex sequences -- Cuprates -- Doping levels -- External magnetic field -- Field magnitude -- Hartree-Fock approximations -- High magnetic fields -- Lifshitz transition -- Main effect -- Orbitals -- Perturbation theory -- Quantum phase transitions -- Quantum transitions -- Single-layer structure -- Theoretical study -- Unit cells -- Carrier concentration -- Copper compounds -- Density functional theory -- Electronic properties -- Electronic structure -- Hartree approximation -- Magnetic fields -- Perturbation techniques -- Phase transitions -- Surface structure -- Quantum theory
Аннотация: We present a theoretical study of the electronic structure of bilayer HTSC cuprates and its evolution under doping and in a high magnetic field. Analysis is based on the t-t'-taEuro(3)-J* model in the generalized Hartree-Fock approximation. Possibility of tunneling between CuO2 layers is taken into account in the form of a nonzero integral of hopping between the orbitals of adjacent planes and is included in the scheme of the cluster form of perturbation theory. The main effect of the coupling between two CuO2 layers in a unit cell is the bilayer splitting manifested in the presence of antibonding and bonding bands formed by a combination of identical bands of the layers themselves. A change in the doping level induces reconstruction of the band structure and the Fermi surface, which gives rise to a number of quantum phase transitions. A high external magnetic field leads to a fundamentally different form of electronic structure. Quantum phase transitions in the field are observed not only under doping, but also upon a variation of the field magnitude. Because of tunneling between the layers, quantum transitions are also split; as a result, a more complex sequence of the Lifshitz transitions than in single-layer structures is observed.

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Публикация на русском языке Овчинников, Сергей Геннадьевич. Влияние межслойного туннелирования на электронную структуру двухслойных купратов и квантовые фазовые переходы по концентрации носителей и сильному магнитному полю [Текст] / С. Г. Овчинников, И. А. Макаров, Е. И. Шнейдер // Журнал экспериментальной и теоретической физики. - 2011. - Т. 139 Вып. 2. - С. 334-350

Держатели документа:
[Ovchinnikov, S. G.
Makarov, I. A.
Shneyder, E. I.] Russian Acad Sci, LV Kirensky Phys Inst, Siberian Branch, Krasnoyarsk 660036, Russia
[Ovchinnikov, S. G.
Shneyder, E. I.] Reshetnev Siberian State Aerosp Univ, Krasnoyarsk 660014, Russia
ИФ СО РАН
Kirensky Institute of Physics, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russian Federation
Reshetnev Siberian State Aerospace University, Krasnoyarsk 660014, Russian Federation

Доп.точки доступа:
Makarov, I. A.; Макаров, Илья Анатольевич; Shneyder, E. I.; Шнейдер, Елена Игоревна; Овчинников, Сергей Геннадьевич
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Aplesnin, S. S.
Magnetic structures upon ordering of e(g) orbitals in a square lattice / S. S. Aplesnin, A. I. Moskvin // J. Phys.: Condens. Matter. - 2008. - Vol. 20, Is. 32. - Ст. 325202, DOI 10.1088/0953-8984/20/32/325202. - Cited References: 11 . - ISSN 0953-8984

РУБ Physics, Condensed Matter
Рубрики:
HEISENBERG-ANTIFERROMAGNET
S=1/2
PHASE
Кл.слова (ненормированные):
Crystallography -- Exchange mechanisms -- Magnetic structure
Аннотация: The exchange mechanism effect on the ordering of electrons on e(g) orbitals in a two-dimensional Heisenberg model with exchange anisotropy for a S = 1/2 spin is determined. The regions of existence of long-range quasi-one- and two-dimensional antiferromagnetic order with the special exchange topology are calculated by a quantum Monte Carlo method. The Neel temperature and quantum reduction of spin on site for an antiferromagnet with the stripe structure is estimated as a function of exchange anisotropy.

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Держатели документа:
[Aplesnin, S. S.] Russian Acad Sci, Siberian Branch, LV Kirensky Phys Inst, Krasnoyarsk 660036, Russia
[Moskvin, A. I.] MF Reshetneva Aircosm Siberian State Univ, Krasnoyarsk 660014, Russia
ИФ СО РАН
L. V. Kirenskii Institute of Physics, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
M. F. Reshetneva Aircosmic Siberian State University, Krasnoyarsk, 660014, Russian Federation

Доп.точки доступа:
Moskvin, A. I.; Аплеснин, Сергей Степанович
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Dominance of many-body effects over the one-electron mechanism for band structure doping dependence in Nd2-xCexCuO4: the LDA + GTB approach / M. M. Korshunov [et al.] // J. Phys.: Condens. Matter. - 2007. - Vol. 19, Is. 48. - Ст. 486203, DOI 10.1088/0953-8984/19/48/486203. - Cited References: 36 . - ISSN 0953-8984

РУБ Physics, Condensed Matter
Рубрики:
NARROW ENERGY BANDS
   HUBBARD-MODEL
   SUPERCONDUCTORS
   DENSITY
   TEMPERATURE
   ORBITALS
   WAVE
Кл.слова (ненормированные):
Antiferromagnetism -- Band structure -- Correlation methods -- Crystal structure -- Local density approximation -- Superconducting materials -- Electronic correlations -- Fermionic quasiparticles -- Neodymium compounds
Аннотация: In the present work we report band structure calculations for the high-temperature superconductor Nd2-xCexCuO4 in the regime of strong electronic correlations within an LDA + GTB method, which combines the local density approximation (LDA) and the generalized tight-binding method (GTB). The two mechanisms of band structure doping dependence were taken into account. Namely, the one-electron mechanism provided by the doping dependence of the crystal structure, and the many-body mechanism provided by the strong renormalization of the fermionic quasiparticles due to the large on-site Coulomb repulsion. We have shown that, in the antiferromagnetic and in the strongly correlated paramagnetic phases of the underdoped cuprates, the main contribution to the doping evolution of the band structure and Fermi surface comes from the many-body mechanism.

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Держатели документа:
[Korshunov, M. M.
Gavrichkov, V. A.
Ovchinnikov, S. G.] Russian Acad Sci, LV Kirensky Phys Inst, Siberian Branch, R-660036 Krasnoyarsk, Russia
[Korshunov, M. M.] Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany
[Nekrasov, I. A.
Kokorina, E. E.] Russian Acad Sci, Inst Electrophys, R-620016 Ekaterinburg, Russia
[Pchelkina, Z. V.] Russian Acad Sci, Inst Met Phys, Ural Div, R-620041 Ekaterinburg, Russia
ИФ СО РАН
L V Kirensky Institute of Physics, Siberian Branch, Russian Academy of Sciences, 660036 Krasnoyarsk, Russian Federation
Max-Planck-Institut fur Physik Komplexer Systeme, D-01187 Dresden, Germany
Institute of Electrophysics, Russian Academy of Sciences, Ural Division, Amundsena 106, 620016 Yekaterinburg, Russian Federation
Institute of Metal Physics, Russian Academy of Sciences-Ural Division, GSP-170, 620041 Yekaterinburg, Russian Federation

Доп.точки доступа:
Korshunov, M. M.; Коршунов, Максим Михайлович; Gavrichkov, V. A.; Гавричков, Владимир Александрович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Nekrasov, I. A.; Kokorina, E. E.; Pchelkina, Z. V.
}
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Effective parameters of the band dispersion in n-type high-T-c superconductors / M. M. Korshunov [et al.] // Physica C. - 2004. - Vol. 402, Is. 4. - P. 365-370, DOI 10.1016/j.physc.2003.10.017. - Cited References: 32 . - ISSN 0921-4534

РУБ Physics, Applied
Рубрики:
DOPED CUPRATE SUPERCONDUCTORS
   TIGHT-BINDING METHOD
   QUASI-PARTICLES
   COPPER OXIDES
   LA2-XSRXCUO4
   SYMMETRY
   MODEL
   EVOLUTION
   ORDER
Кл.слова (ненормированные):
high-T-c superconductivity -- electronic correlations -- electron-doped cuprates -- Electron-doped cuprates -- Electronic correlations -- High-Tc superconductivity -- Approximation theory -- Atomic physics -- Band structure -- Binding energy -- Charge transfer -- Correlation methods -- Doping (additives) -- Electronic structure -- Hamiltonians -- Mathematical models -- Mathematical operators -- Oxide superconductors -- Perturbation techniques -- Photoelectron spectroscopy -- Atomic orbitals -- Conduction band -- Electron doped cuprates -- Electron spins -- Valence band -- High temperature superconductors
Аннотация: The electronic structure of electron-doped cuprates is discussed in the regions of small and optimal doping. For optimal doping we obtain the parameters from a simple tight-binding analysis by fitting ARPES data, and for small doping we study the band structure by the generalized tight-binding method that takes strong electronic correlations into account explicitly. This method has also reproduced well the ARPES data for small doping. The effective low-energy Hamiltonian is the t-t'-J model with hopping parameters t and t'. We compare both methods and find very good agreement for the value of t while t' is different because it is caused by the different contribution of the short-range spin correlations. (C) 2003 Elsevier B.V. All rights reserved.

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Держатели документа:
Free Univ Berlin, Inst Theoret Phys, D-14195 Berlin, Germany
Russian Acad Sci, LV Kirensky Phys Inst, Siberian Branch, Krasnoyarsk 660036, Russia
ИФ СО РАН
L.V. Kirensky Institute of Physics, Siberian Branch, Russian Academy of Science, Krasnoyarsk 660036, Russian Federation
Inst. fur Theoretische Physik, Freie Universitat Berlin, Arnimallee 14, D-14195 Berlin, Germany

Доп.точки доступа:
Korshunov, M. M.; Коршунов, Максим Михайлович; Gavrichkov, V. A.; Гавричков, Владимир Александрович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Manske, D.; Eremin, I.
}
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Structure- and interaction-based design of anti-SARS-CoV-2 Aptamers / V. Mironov, I. A. Shchugoreva, P. V. Artyushenko [et al.] // Chem. - Eur. J. - 2022. - Vol. 28, Is. 12. - Ст. e202104481, DOI 10.1002/chem.202104481. - Cited References: 85. - The authors are grateful to JCSS Joint Super Computer Center of the Russian Academy of Sciences – Branch of Federal State Institution “Scientific Research Institute for System Analysis of the Russian Academy of Sciences” for providing supercomputers for computer simulations. The authors thank the RSC Group (www.rscgroup.ru) and personally Mr. Oleg Gorbachev for the constant support and establishment of “The Good Hope Net Project” (www.thegoodhope.net) multifunctional non-profit anti-CoVID research project. The authors also thank the Helicon Company (www.helicon.ru) and personally Olesya Kucenko, Alexander Kolobov, Leonid Klimov for instrumental support and help with conducting fluorescence polarization assays, which were performed on a demo instrument Clariostar Plus microplate reader (BMG LABTECH, Germany). We thank Dr. Yong-Zhen Zhang for providing the genome sequence of 2019-nCoV and Dr. Xinquan Wang for providing the crystal structure of the binding domain of the SARS-2 Spike protein. The authors are grateful to Aptamerlab LCC financial support (www.aptamerlab.com). Y.A.’s work at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, under contract DE-AC02-06CH11357. The work of D.M. and G.G. has been done as part of the BioExcel CoE (www.bioexcel.eu), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. D.M. and G.G. also thank the CSC-IT center in Espoo, Finland, as well as PRACE for awarding access to resource Curie-Rome based in France at GENCI. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043). A.B.’s and N.K.’s work was supported by the Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS). V. deF. G.C., N.B and G.O. are grateful to FISR2020 _00177 Shield, Italian Ministry of Education and Research, for funding. GC is grateful to the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement: cONCReTE 872391; PRISAR2 872860. Use of the 13 A BioSAXS beamtime at the Taiwan Photon Source is acknowledged. The work of M.V.B was funded by the Canadian Institutes of Health Research grant OV1-170353. SAXS measurements and PIEDA analyses were funded by the Russian Science Foundation (project No 21-73-20240 for A.S.K.) . - ISSN 0947-6539. - ISSN 1521-3765

РУБ Chemistry, Multidisciplinary
Рубрики:
BIOLOGICAL MACROMOLECULES
   SOLUTION SCATTERING
   BINDING
   SPIKE
Кл.слова (ненормированные):
aptamers -- fragment molecular orbitals method -- molecular dynamics -- SARS-CoV-2 -- SAXS
Аннотация: Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

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Держатели документа:
Lomonosov Moscow State Univ, Dept Chem, Moscow 119991, Russia.
Kyungpook Natl Univ, Dept Chem, Daegu 702701, South Korea.
Fed Res Ctr KSC SB RAS, Lab Digital Controlled Drugs & Theranost, Krasnoyarsk 660036, Russia.
Natl Tsing Hua Univ, Dept Chem Engn, Hsinchu 30013, Taiwan.
Siberian Fed Univ, Sch Nonferrous Met & Mat Sci, Krasnoyarsk 660041, Russia.
IRCCS Neuromed Ist Neurol Mediterraneo Pozzilli, Via Atinense 18, I-86077 Pozzilli, Italy.
Krasnoyarsk State Med Univ, Lab Biomol & Med Technol, Krasnoyarsk 660022, Russia.
Univ Jyvaskyla, Nanosci Ctr, Jyvaskyla 40014, Finland.
Univ Jyvaskyla, Dept Chem, Jyvaskyla 40014, Finland.
Univ Naples Federico II, Dept Pharm, I-80138 Naples, Italy.
Univ Naples Federico II, Dept Mol Med & Med Biotechnol, I-80131 Naples, Italy.
Kirensky Inst Phys, Lab Phys Magnet Phenomena, Krasnoyarsk 660012, Russia.
Siberian Fed Univ, Sch Fundamental Biol & Biotechnol, Krasnoyarsk 660041, Russia.
Xiamen Univ, Coll Chem & Chem Engn, Dept Chem Biol, Xiamen 361005, Peoples R China.
State Res Ctr Virol & Biotechnol Vector, Koltsov 630559, Russia.
NRC Kurchatov Inst, Moscow 117259, Russia.
Russian Acad Sci, Siberian Branch, Inst Chem Biol & Fundamental Med, Novosibirsk 630090, Russia.
Russian Acad Sci, Res Ctr Biotechnol, AN Bach Inst Biochem, Lab Immunobiochem, Moscow 119071, Russia.
Tomsk State Univ, Lab Adv Mat & Technol, Tomsk 634050, Russia.
Altai State Univ, Barnaul 656049, Russia.
Fed Res Ctr KSC SB RAS, Dept Mol Elect, Krasnoyarsk 660036, Russia.
Krasnoyarsk State Med Univ, Dept Infect Dis & Epidemiol, Krasnoyarsk 660022, Russia.
Natl Pingtung Univ, Dept Appl Chem, Pingtung 900391, Taiwan.
Natl Synchrotron Radiat Res Ctr, Hsinchu Sci Pk, Hsinchu 30076, Taiwan.
Res Natl Council CNR, Inst Genet & Biomed Res IRGB, I-09042 Milan, Italy.
Shanghai Jiao Tong Univ, Sch Med, Renji Hosp, Inst Mol Med, Shanghai 200127, Peoples R China.
Natl Inst Adv Ind Sci & Technol, Res Ctr Computat Design Adv Funct Mat, Tsukuba, Ibaraki 3058560, Japan.
Hunan Univ, Coll Chem & Chem Engn, Changsha 410082, Hunan, Peoples R China.
Argonne Natl Lab, Computat Sci Div, Lemont, IL 60439 USA.
Dept Chem & Biomol Sci, Ottawa, ON K1N 6N5, Canada.

Доп.точки доступа:
Mironov, Vladimir; Shchugoreva, I. A.; Artyushenko, P. V.; Артюшенко, Полина Владимировна; Morozov, D. I.; Морозов, Дмитрий И.; Borbone, N.; Oliviero, G.; Zamay, T. N.; Замай, Т. Н.; Moryachkov, R. V.; Морячков, Роман Владимирович; Kolovskaya, .; Коловская О. С.; Lukyanenko, K. A.; Лукьяненко Кирилл А.; Song, Y. L.; Merkuleva, I. A.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G.; Koroleva, L. S.; Veprintsev, D. V.; Glazyrin, Y. E.; Volosnikova, E. A.; Belenkaya, S. V.; Esina, T. I.; Isaeva, A. A.; Nesmeyanova, .; Shanshin, D. V.; Berlina, A. N.; Komova, N. S.; Svetlichnyi, V. A.; Silnikov, V. N.; Shcherbakov, D. N.; Zamay, G. S.; Замай, Галина Сергеевна; Zamay, S. S.; Замай, С. С.; Smolyarova, T. E.; Смолярова, Татьяна Евгеньевна; Tikhonova, E. P.; Chen, U. S.; Jeng, G.; Condorelli, V.; Franciscis, G.; Groenhof, C. Y.; Yang, A. A.; Moskovsky, D. G.; Fedorov, F. N.; Tomilin, F. N.; Томилин, Феликс Николаевич; Tan, Y.; Alexeev, M. V.; Berezovski, A. S.; Kichkailo, A.S.; Aptamerlab LCC; U.S. Department of Energy, Office of ScienceUnited States Department of Energy (DOE) [DE-AC02-06CH11357]; European UnionEuropean Commission [H2020-INFRAEDI-02-2018-823830, H2020-EINFRA-2015-1-675728, 872391, PRISAR2 872860]; CSC-IT center in Espoo, Finland; PRACE; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [19-03-00043]; Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS); Italian Ministry of Education and ResearchMinistry of Education, Universities and Research (MIUR) [FISR2020 _00177]; Canadian Institutes of Health ResearchCanadian Institutes of Health Research (CIHR) [OV1-170353]; Russian Science FoundationRussian Science Foundation (RSF) [21-73-20240]
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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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Ca2+-triggered coelenterazine-binding protein Renilla: Expected and unexpected features / A. N. Kudryavtsev, V. V. Krasitskaya, M. K. Efremov [et al.] // Int. J. Mol. Sci. - 2023. - Vol. 24, Is. 3. - Ст. 2144, DOI 10.3390/ijms24032144. - Cited References: 24. - This research was supported by the state budget allocated to the fundamental research at the Russian Academy of Sciences, project No. 0287-2022-0002 and the Interagency Supercomputer Center of the Russian Academy of Sciences, MVS-100K and MVS-10P . - ISSN 1661-6596. - ISSN 1422-0067
Кл.слова (ненормированные):
Ca2+-triggered coelenterazine-binding protein -- coelenterazine -- furimazine -- luciferase NanoLuc -- B3LYP -- TDDFT -- fragmented molecular orbitals method -- DFTB3
Аннотация: Ca2+-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay. In search of a similar substrate form for the luciferase NanoLuc, a furimazine-apoCBP complex was prepared and verified against furimazine, coelenterazine, and CBP. Furimazine-apoCBP is relatively stable in solution and in a frozen or lyophilized state, but as distinct from CBP, its bioluminescence reaction with NanoLuc is independent of Ca2+. NanoLuc turned out to utilize all the four substrates under consideration. The pairs of CBP-NanoLuc and coelenterazine-NanoLuc generate bioluminescence with close efficiency. As for furimazine-apoCBP-NanoLuc pair, the efficiency with which it generates bioluminescence is almost twice lower than that of the furimazine-NanoLuc. The integral signal of the CBP-NanoLuc pair is only 22% lower than that of furimazine-NanoLuc. Thus, along with furimazine as the most effective NanoLuc substrate, CBP can also be recommended as a substrate for in vitro analytical application in view of its water solubility, stability, and Ca2+-triggering “character”.

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Держатели документа:
Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
Kirensky Institute of Physics, Federal Research Center “Krasnoyarsk Science Center SB”, 660036 Krasnoyarsk, Russia

Доп.точки доступа:
Kudryavtsev, Alexander N.; Krasitskaya, Vasilisa V.; Efremov, Maxim K.; Zangeeva, Sayana V.; Rogova, A. V.; Рогова, Анастасия Владимировна; Tomilin, F. N.; Томилин, Феликс Николаевич; Frank, Ludmila A.
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