Библиотека института физики им. Л.В. Киренского СО РАН

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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Ozerskaya A. V., Zamay T. N., Kolovskaya O. S., Tokarev N. A., Belugin K. V., Chanchikova N. G., Badmaev O. N., Zamay G. S., Shchugoreva I. A., Moryachkov R. V., Zabluda V. N., Khorzhevskii V. A., Shepelevich N., Gappoev S. V., Karlova E. A., Saveleva A. S., Volzhentsev A. A., Blagodatova A. N., Lukyanenko K. A., Veprintsev D. V., Smolyarova T. E., Tomilin F. N., Zamay S. S., Silnikov V. N., Berezovski M. V., Kichkailo A. S.
Заглавие : 11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography-computed tomography
Место публикации : Mol. Ther. Nucl. Acids. - 2021. - Vol. 26. - P.1159-1172. - ISSN 21622531 (ISSN), DOI 10.1016/j.omtn.2021.10.020
Примечания : Cited References: 44
Аннотация: Identification of primary tumors and metastasis sites is an essential step in cancer diagnostics and the following treatment. Positron emission tomography-computed tomography (PET/CT) is one of the most reliable methods for scanning the whole organism for malignancies. In this work, we synthesized an 11C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer. The 11C-aptamer was applied for in vivo imaging of Ehrlich ascites carcinoma and its metastases in mice using PET/CT. The imaging experiments with the 11C-aptamer determined very small primary and secondary tumors of 3 mm2 and less. We also compared 11C imaging with the standard radiotracer, 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18F-FDG), and found better selectivity of the 11C-aptamer to metastatic lesions in the metabolically active organs than 18F-FDG. 11C radionuclide with an ultra-short (20.38 min) half-life is considered safest for PET/CT imaging and does not cause false-positive results in heart imaging. Its combination with aptamers gives us high-specificity and high-contrast imaging of cancer cells and can be applied for PET/CT-guided drug delivery in cancer therapies.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kovaleva E. A., Kuzubov A. A., Avramov P. V., Kholtobina A. S., Kuklin A. V., Tomilin F. N., Sorokin P. B.
Заглавие : A key role of tensile strain and surface termination in formation and properties of La0.7Sr0.3MnO3 composites with carbon nanotubes
Место публикации : Comput. Mater. Sci.: Elsevier, 2017. - Vol. 139. - P.125-131. - ISSN 09270256 (ISSN), DOI 10.1016/j.commatsci.2017.07.021
Примечания : Cited References: 39. - This work was supported by National Research Foundation of Republic of Korea under Grant No. NRF-2017R1A2B4004440 and the government contract of the Ministry of Education and Science of the Russian Federation to Siberian Federal University (Grant No. 16.1455.2017/PCh). The authors would like to thank Joint Supercomputer Center of RAS, Moscow; Center of Equipment for Joint Use of Siberian Federal University, Krasnoyarsk; and Information Technology Centre, Novosibirsk State University for providing the access to their supercomputers. P.B.S gratefully acknowledges the financial supports of the Ministry of Education and Science of the Russian Federation in the framework of Increase Competitiveness Program of NUST «MISiS» (No. К2-2017-001) and RFBR, according to the research project No. 16-32-60138 mol_a_dk. E.A. Kovaleva would also like to acknowledge the program of the President of Russian Federation for Leading Scientific Schools Support (Grant No. 2016 NSh-7559.2016.2).
Ключевые слова (''Своб.индексиров.''): carbon nanotubes--lsmo--interface--spin polarization
Аннотация: Atomic and electronic structure of LSMO-based composites with carbon nanotubes were studied by means of density functional theory with respect to the termination of LSMO surface. The deformation of the tubes caused by the lattice mismatch with the substrate leads to a major change in their electronic structure. The surface terminated with Mn-O layer provides much stronger interaction with carbon nanotubes than Sr-O terminated one does. The interaction with transition metal atoms is essential for spin polarization of the nanotube while no spin injection was observed for Sr-O-supported tubes. © 2017 Elsevier B.V.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Antipina L.Y., Tomilin F. N., Ovchinnikov S.G., Vysotskii E.S.
Заглавие : A quantum chemical study of the formation of 2-hydroperoxy-coelenterazine in the Ca2+-regulated photoprotein obelin
Место публикации : Journal of Structural Chemistry. - Новосибирск: Pleiades Publishing, Ltd. (Плеадес Паблишинг, Лтд), 2011. - Т. 52, № 5. - С. 870-875. - ISSN 0022-4766. - ISSN 1573-8779(eissn)
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Antipina L. Yu., Tomilin F. N., Vysotski E. S., Ovchinnikov S. G.
Заглавие : A quantum chemical study of the formation of 2-hydroperoxy-coelenterazine in the Сa2+-regulated photoprotein obelin
Место публикации : J. Struct. Chem.: Springer, 2011. - Vol. 52, Is. 5. - P.870-875. - ISSN 0022-4766
Примечания : 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).
Предметные рубрики: CALCIUM-DISCHARGED OBELIN
SEMIEMPIRICAL METHODS
1.7 ANGSTROM
OPTIMIZATION
PARAMETERS
MECHANISM
FLUORESCENCE
ELEMENTS
PROTEIN
EMITTER
Ключевые слова (''Своб.индексиров.''): 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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Artyushenko P. V., Tomilin F. N., Kuzubov A. A., Ovchinnikov S. G., Tsikalova P. E., Ovchinnikova T. M., Soukhovolsky V. G.
Заглавие : Action of the atomic and electronic structure of pheromone molecules on the effectiveness of communication in xylophagous insects
Коллективы : RFBR [13-04-00375, 16-04-00132]
Место публикации : J. Struct. Chem.: MAIK Nauka-Interperiodica / Springer, 2016. - Vol. 57, Is. 2. - P.287-293. - ISSN 0022-4766, DOI 10.1134/S0022476616020074. - ISSN 1573-8779(eISSN)
Примечания : Cited References:27. - This work was supported by RFBR projects Nos. 13-04-00375 and16-04-00132.
Предметные рубрики: Monochamus-galloprovincialis coleoptera
Density-functional theories
Beetle Ips-typographus
Pine sawyer beetle
Aggregation pheromone
Cerambycidae
Attraction
Components
Attack
Set
Ключевые слова (''Своб.индексиров.''): atomic and electronic structure--functional density methods--absorption--spectra--excited states--xylophages--pheromones
Аннотация: The B3LYD /6-31(p,d) density functional method is applied to pheromones of the forest xylophagous insects Ips typographus L., Monochamus urussovi Fisch., and Monochamus galloprovincialis Oliv. to calculate the absorption spectra and find excited states. The calculated results are used to assess the possible activity of the molecules when they are affected by solar radiation.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kolovskaya O. S., Zamay T. N., Zamay G. S., Babkin V. A., Medvedeva E. N., Neverova N. A., Kirichenko A. K., Zamay S. S., Lapin I. N., Morozov E. V., Sokolov A. Е., Narodov A. A., Fedorov D. G., Tomilin F. N., Zabluda V. N., Alekhina Yu., Lukyanenko K. A., Glazyrin Yu. E., Svetlichnyi V. A., Berezovski M. V., Kichkailo A. S.
Заглавие : Aptamer-conjugated superparamagnetic ferroarabinogalactan nanoparticles for targeted magnetodynamic therapy of cancer
Место публикации : Cancers. - 2020. - Vol. 12, Is. 1. - Ст.216. - ISSN 2072-6694 (eISSN), DOI 10.3390/cancers12010216
Примечания : Cited References: 46. - This research was funded by the Ministry of Science and Higher Education of the Russian Federation; project 0287-2019-0007
Аннотация: Nanotechnologies involving physical methods of tumor destruction using functional oligonucleotides are promising for targeted cancer therapy. Our study presents magnetodynamic therapy for selective elimination of tumor cells in vivo using DNA aptamer-functionalized magnetic nanoparticles exposed to a low frequency alternating magnetic field. We developed an enhanced targeting approach of cancer cells with aptamers and arabinogalactan. Aptamers to fibronectin (AS-14) and heat shock cognate 71 kDa protein (AS-42) facilitated the delivery of the nanoparticles to Ehrlich carcinoma cells, and arabinogalactan (AG) promoted internalization through asialoglycoprotein receptors. Specific delivery of the aptamer-modified FeAG nanoparticles to the tumor site was confirmed by magnetic resonance imaging (MRI). After the following treatment with a low frequency alternating magnetic field, AS-FeAG caused cancer cell death in vitro and tumor reduction in vivo. Histological analyses showed mechanical disruption of tumor tissues, total necrosis, cell lysis, and disruption of the extracellular matrix. The enhanced targeted magnetic theranostics with the aptamer conjugated superparamagnetic ferroarabinogalactans opens up a new venue for making biocompatible contrasting agents for MRI imaging and performing non-invasive anti-cancer therapies with a deep penetrated magnetic field.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Ivanova D., Fedorova N., Kozak V., Shubin A., Tomilin F. N.
Заглавие : Atomic and electronic structure of MAX-phase Cr2AlC studied by DFT calculations
Коллективы : International workshop on functional MAX-materials, Kirensky Institute of Physics, Siberian Federal Univercity
Место публикации : International workshop on the properties of functional MAX-materials (2nd FunMax): book of abstracts/ org. com. M. Farle [et al.]. - 2021. - P.37
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kudryavtsev, Alexander N., Krasitskaya, Vasilisa V., Efremov, Maxim K., Zangeeva, Sayana V., Rogova A. V., Tomilin F. N., Frank, Ludmila A.
Заглавие : Ca2+-triggered coelenterazine-binding protein Renilla: Expected and unexpected features
Место публикации : Int. J. Mol. Sci. - 2023. - Vol. 24, Is. 3. - Ст.2144. - ISSN 16616596 (ISSN), DOI 10.3390/ijms24032144. - ISSN 14220067 (eISSN)
Примечания : 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
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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kuzubov A. A., Eliseeva N. S., Krasnov P. O., Tomilin F. N., Fedorov A. S., Tolstaya A. V.
Заглавие : Calculating the energy of vacancies and adatoms in a hexagonal SiC monolayer
Место публикации : Russ. J. Phys. Chem. A: MAIK Nauka-Interperiodica / Springer, 2012. - Vol. 86, Is. 7. - P.1091-1095. - ISSN 0036-0244, DOI 10.1134/S0036024412070138
Примечания : Cited References: 21
Предметные рубрики: INITIO MOLECULAR-DYNAMICS
ELECTRONIC-PROPERTIES
ABSORPTION-SPECTRA
Ключевые слова (''Своб.индексиров.''): silicon carbide--defects--adatoms--density functional method
Аннотация: It is noted that the development of semiconductor SiC-electronics is prevented by a low quality of grown silicon carbide single crystals. It is found that structural defects of a substrate penetrating into an epitaxial layer upon subsequent homoepitaxial growth can considerably degrade a device's characteristics. We investigate the effect of the deformation of a hexagonal SiC monolayer on vacancy stability and material properties, and study the processes of silicon and carbon adatom migration over a surface of SiC.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Dymova M. A., Malysheva D. O., Popova V. K., Dmitrienko E. V., Endutkin A. V., Drokov D. V., Mukhanov V. S., Byvakina A. A., Kochneva G. V., Artyushenko P. V., Shchugoreva I. A., Rogova A. V., Tomilin F. N., Kichkailo A. S., Richter V. A., Kuligina E. V.
Заглавие : Characterizing aptamer interaction with the oncolytic virus VV-GMCSF-Lact
Колич.характеристики :14 с
Место публикации : Molecules. - 2024. - Vol. 29, Is. 4. - Ст.848. - ISSN 14203049 (eISSN), DOI 10.3390/molecules29040848
Примечания : Cited References: 46. - This study was supported by the Russian Science Foundation grant No. 22-64-00041, available online: https://rscf.ru/en/project/22-64-00041/ (accessed on 6 February 2024). This work was supported by the Russian state-funded project for ICBFM SB RAS (grant number 121030200173-6)
Аннотация: Aptamers are currently being investigated for their potential to improve virotherapy. They offer several advantages, including the ability to prevent the aggregation of viral particles, enhance target specificity, and protect against the neutralizing effects of antibodies. The purpose of this study was to comprehensively investigate an aptamer capable of enhancing virotherapy. This involved characterizing the previously selected aptamer for vaccinia virus (VACV), evaluating the aggregation and molecular interaction of the optimized aptamers with the recombinant oncolytic virus VV-GMCSF-Lact, and estimating their immunoshielding properties in the presence of human blood serum. We chose one optimized aptamer, NV14t_56, with the highest affinity to the virus from the pool of several truncated aptamers and built its 3D model. The NV14t_56 remained stable in human blood serum for 1 h and bound to VV-GMCSF-Lact in the micromolar range (Kd ≈ 0.35 μM). Based on dynamic light scattering data, it has been demonstrated that aptamers surround viral particles and inhibit aggregate formation. In the presence of serum, the hydrodynamic diameter (by intensity) of the aptamer–virus complex did not change. Microscale thermophoresis (MST) experiments showed that NV14t_56 binds with virus (EC50 = 1.487 × 109 PFU/mL). The analysis of the amplitudes of MST curves reveals that the components of the serum bind to the aptamer–virus complex without disrupting it. In vitro experiments demonstrated the efficacy of VV-GMCSF-Lact in conjunction with the aptamer when exposed to human blood serum in the absence of neutralizing antibodies (Nabs). Thus, NV14t_56 has the ability to inhibit virus aggregation, allowing VV-GMCSF-Lact to maintain its effectiveness throughout the storage period and subsequent use. When employing aptamers as protective agents for oncolytic viruses, the presence of neutralizing antibodies should be taken into account.
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11.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Fedorov A. S., Krasnov P. O., Visotin M. A., Tomilin F. N., Polyutov S. P., Ågren H.
Заглавие : Charge-transfer plasmons with narrow conductive molecular bridges: A quantum-classical theory
Место публикации : J. Chem. Phys. - 2019. - Vol. 150, Is. 24. - Ст.244125. - ISSN 0021-9606, DOI 10.1063/1.5131734. - ISSN 1089-7690(eISSN)
Примечания : Cited References: 56. - This study was supported by the Russian Science Foundation, Project No. 18-13-00363.
Аннотация: We analyze a new type of plasmon system arising from small metal nanoparticles linked by narrow conductive molecular bridges. In contrast to the well-known charge-transfer plasmons, the bridge in these systems consists only of a narrow conductive molecule or polymer in which the electrons move in a ballistic mode, showing quantum effects. The plasmonic system is studied by an original hybrid quantum-classical model accounting for the quantum effects, with the main parameters obtained from first-principles density functional theory simulations. We have derived a general analytical expression for the modified frequency of the plasmons and have shown that its frequency lies in the near-infrared (IR) region and strongly depends on the conductivity of the molecule, on the nanoparticle–molecule interface, and on the size of the system. As illustrated, we explored the plasmons in a system consisting of two small gold nanoparticles linked by a conjugated polyacetylene molecule terminated by sulfur atoms. It is argued that applications of this novel type of plasmon may have wide ramifications in the areas of chemical sensing and IR deep tissue imaging.
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12.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Shubin A., Olshevskaya J., Kovaleva A., Tomilin F. N.
Заглавие : Choice of the DFT functional for calculation electronic properties of (CrFe)SiC MAX phases
Коллективы : International workshop on functional MAX-materials, Kirensky Institute of Physics, Siberian Federal Univercity
Место публикации : International workshop on the properties of functional MAX-materials (2nd FunMax): book of abstracts/ org. com. M. Farle [et al.]. - 2021. - P.47
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13.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Artyushenko P. V., Mironov V. A., Morozov D. I., Shchugoreva I. A., Borbone N., Tomilin F. N., Kichkailo A. S.
Заглавие : Computational approach to design of aptamers to the receptor binding domain of sars-cov-2
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.66-67. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-66-67; Сиб. мед. обозрение
Примечания : Cited References: 5
Аннотация: The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifications in order to increase the binding with the RBD. Thus, a new aptamer Apt25 was designed. The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets.
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14.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kuzubov A. A., Kovaleva E. A., Avramov P. V., Kuklin A. V., Mikhaleva N. S., Tomilin F. N., Sakai S., Entani S., Matsumoto Y., Naramoto H.
Заглавие : Contact-induced spin polarization in BNNT(CNT)/TM (TM=Co, Ni) nanocomposites
Коллективы : Russian Scientific Fund [14-13-00139]
Место публикации : J. Appl. Phys.: American Institute of Physics, 2014. - Vol. 116, Is. 8. - Ст.084309. - ISSN 0021-8979, DOI 10.1063/1.4894157. - ISSN 1089-7550
Примечания : Cited References: 21. - This work was supported by the Russian Scientific Fund, Project No. 14-13-00139. The authors would like to thank Institute of Computational Modelling of SB RAS, Krasnoyarsk; Joint Supercomputer Center of RAS, Moscow; the HPC Research Department and Center of Equipment for Joint Use of Siberian Federal University, Krasnoyarsk; Siberian Supercomputer Center (SSCC) of SB RAS, Novosibirsk; and Laboratory of Parallel Information Technologies 21 of Research Computing Center of Moscow State University (the SKIF MSU "Chebyshev" system) for providing the access to their supercomputers.
Предметные рубрики: TOTAL-ENERGY CALCULATIONS
HEXAGONAL BORON-NITRIDE
WAVE BASIS-SET
AB-INITIO
PSEUDOPOTENTIALS
DISPERSION
NANOTUBE
NI(111)
Аннотация: The interaction between carbon and BN nanotubes (NT) and transition metal Co and Ni supports was studied using electronic structure calculations. Several configurations of interfaces were considered, and the most stable ones were used for electronic structure analysis. All NT/Co interfaces were found to be more energetically favorable than NT/Ni, and conductive carbon nanotubes demonstrate slightly stronger bonding than semiconducting ones. The presence of contact-induced spin polarization was established for all nanocomposites. It was found that the contact-induced polarization of BNNT leads to the appearance of local conductivity in the vicinity of the interface while the rest of the nanotube lattice remains to be insulating. (c) 2014 AIP Publishing LLC.
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15.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Tomilin F. N., Avramov P. V., Kuzubov A. A., Ovchinnikov S. G., Pashkov G. L.
Заглавие : Correlation of the chemical properties of carbon nanotubes with their atomic and electronic structures
Место публикации : Phys. Solid State. - 2004. - Vol. 46, Is. 6. - P.1179-1182. - ISSN 1063-7834, DOI 10.1134/1.1767264
Примечания : Cited References: 16. - This work was performed at the “Quantum-Chemical Calculations of Nanoclusters” Collective Use Center of the Krasnoyarsk Center of Science and Education in High Technology, which is supported by the Russian State Federal Program “Integration of Higher Education and Fundamental Science” (projects nos. 31 and 69) and the 6th Competition of Research Projects of Young Scientists of the Russian Academy of Sciences (project no. 155)
Аннотация: The nature of chemical bonding in carbon nanoclusters is investigated by the PM3 semiempirical quantum-chemical method. The influence of the atomic structure on the electronic characteristics and chemical properties of nanoclusters is analyzed. A sigma-pi model is proposed for the chemical bonding in nanotubes. It is shown that, in the framework of the proposed model, nanotubes are objects characterized by a small contribution of pi states to the valence band top. (C) 2004 MAIK "Nauka/Interperiodica".
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16.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Avramov P. V., Kuzubov A. A., Fedorov A. S., Sorokin P. B., Tomilin F. N., Maeda Y.
Заглавие : Density-functional theory study of the electronic structure of thin Si/SiO2 quantum nanodots and nanowires
Место публикации : Phys. Rev. B: AMERICAN PHYSICAL SOC, 2007. - Vol. 75, Is. 20. - Ст.205427. - ISSN 1098-0121, DOI 10.1103/PhysRevB.75.205427
Примечания : Cited References: 63
Предметные рубрики: ERBIUM ION LUMINESCENCE
TOTAL-ENERGY CALCULATIONS
WAVE BASIS-SET
POROUS SILICON
OPTICAL-PROPERTIES
OXIDIZED SI
SEMICONDUCTOR NANOWIRES
PHASE-TRANSFORMATIONS
NANOCRYSTALS
CONFINEMENT
Аннотация: The atomic and electronic structures of a set of proposed pentagonal thin (1.6 nm in diameter) silicon/silica quantum nanodots (QDs) and nanowires (NWs) with narrow interface, as well as parent metastable silicon structures (1.2 nm in diameter), were studied using cluster B3LYP/6-31G(*) and periodic boundary condition (PBC) plane-wave (PW) pseudopotential (PP) local-density approximation methods. The total density of states (TDOS) of the smallest quasispherical QD (Si-85) corresponds well to the PBC PW PP LDA TDOS of the crystalline silicon. The elongated SiQDs and SiNWs demonstrate the metallic nature of the electronic structure. The surface oxidized layer opens the band gap in the TDOS of the Si/SiO2 species. The top of the valence band and the bottom of conduction band of the particles are formed by the silicon core derived states. The theoretical band gap width is determined by the length of the Si/SiO2 clusters and describes the size confinement effect in the experimental photoluminescence spectra of the silica embedded nanocrystalline silicon with high accuracy.
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17.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kichkailo A. S., Narodov A. A., Komarova M. A., Zamay T. N., Zamay G. S., Kolovskaya O. S., Erakhtin E. E., Glazyrin Y. E., Veprintsev D. V., Moryachkov R. V., Zabluda V. N., Shchugoreva I., Artyushenko P., Mironov V. A., Morozov D. I., Gorbushin A. V., Khorzhevskii V. A., Koshmanova A. A., Nikolaeva E. D., Grinev I. P., Voronkovskii I. I., Grek D. S., Belugin K. V., Volzhentsev A. A., Badmaev O. N., Luzan N., Lukyanenko K. A., Peters G., Lapin I. N., Kirichenko A. K., Konarev P. V., Morozov E. V, Mironov G. G., Gargaun A., Muharemagic D., Zamay S. S., Kochkina E. V., Dymova M. A., Smolyarova T. E., Sokolov A. Е., Modestov A. A., Tokarev N. A., Shepelevich N., Ozerskaya A. V., Chanchikova N. G., Krat A. V., Zukov R. A., Bakhtina V. I., Shnyakin P. G., Shesternya P. A., Svetlichnyi V. A., Petrova M. M., Artyukhov I. P., Tomilin F. N., Berezovski, Maxim V.
Заглавие : Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells
Место публикации : Mol. Ther. - Nucleic Acids. - 2023. - Vol. 32. - P.267-288. - ISSN 21622531 (eISSN), DOI 10.1016/j.omtn.2023.03.015
Примечания : Cited References: 69. - The authors are grateful to all the patients and hospital staff participating in this research. We acknowledge the assistance of the AptamerLab LCC (www.aptamerlab.com) and personally Mr. Vasily Mezko for the aptamer 3D structure optimization and financial and technical support. The authors thank Mr. Alexey Kichkailo, Dr. Arkady B. Kogan, and Dr. Rinat G. Galeev for their general support. Mrs. Valentina L. Grigoreva, and Irina V. Gildebrand for the help with histological staining. Technical and instrumental support was provided by the Multiple-Access Center at Tomsk State University; the Krasnoyarsk Inter-District Ambulance Hospital, named after N.S. Karpovich; John L. Holmes Mass Spectrometry Facility at the University of Ottawa; Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency; Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University and Krasnoyarsk Regional Centre for Collective Use at the Federal Research Centre “KSC SB RAS”. The confocal fluorescence microscopy research was carried out with the equipment of the Tomsk Regional Core Shared Research Facilities Center of the National Research Tomsk State University. The Center was supported by the Ministry of Science and Higher Education of the Russian Federation, grant no. 075-15-2021-693 (no. 13.RFC.21.0012). Acute toxicity studies were performed in a laboratory certified for preclinical studies, Laboratory of Biological Testing, Institute of Bioorganic Chemistry named after academics M.M. Shemyakin and Y.A. Ovchinnikov Russian Academy of Sciences. The authors are grateful to the Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations. Development of the glioma tumor model in immunosuppressed mice was supported by the Russian Science Foundation grant No. 22-64-00041 (M.A.D.), https://rscf.ru/en/project/22-64-00041/. Synthesis of 11C-aptamer and PET/CT visualization was funded by the Federal Medical Biological Agency; project 122041800132-2 (A.V.O.). Aptamer selection and their clinical applications were funded by the Ministry of Healthcare of the Russian Federation; project АААА-Б19-219090690032-5 (T.N.Z.). The Ministry of Science and Higher Education of the Russian Federation project FWES-2022-0005 (A.S.K.) supported aptamer characterization, molecular modelling, and in vivo experiments. Mass spectrometry analyses, DNA sequencing, and synthesis were supported by NSERC Discovery Grant (M.V.B.). We acknowledge the European Synchrotron Radiation Facility for SAXS experiments and thank Dr. Bart Van Laer for assistance in using a beamline BM29. SAXS measurements were supported by RFBR № 18-32-00478 for young scientists (R.V.M.). The synchrotron SEC-SAXS data for Gli-55 aptamer were also collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany)
Аннотация: Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.
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18.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Poolsup S., Zaripov E., Huttmann N., Minic Z., Artyushenko P. V., Shchugoreva I. A., Tomilin F. N., Kichkailo A. S., Berezovski M. V.
Заглавие : Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics
Место публикации : Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P.731-743. - ISSN 21622531 (eISSN), DOI 10.1016/j.omtn.2023.02.010
Примечания : Cited References: 74. - M.V.B. thanks the Canadian Institutes of Health Research grant OV1-170353 for providing financial support. Molecular modeling and docking were supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. S.P. is thankful to Dr. Bob Dass, Dylan Tanner, and Dr. Degang Liu, Sartorius for generously providing excellent technical training and consumable support for binding assay on BLI, and Aldo Jordan for assisting with creating the figures. The authors also thank John L. Holmes’s mass spectrometry facility for providing access to perform nLC-MS/MS. Lastly, the authors thank the JCSS Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations
Аннотация: The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6–3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.
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19.

Вид документа : Статья из журнала
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Автор(ы) : Yakimanskiy, Anton A., Kaskevich, Ksenia I., Chulkova, Tatiana G., Krasnopeeva, Elena L., Savilov, Serguei V., Voinova, Vera V., Neumolotov, Nikolay K., Zhdanov, Andrey P., Rogova, Anastasia V., Tomilin F. N., Zhizhin, Konstantin Yu., Yakimansky, Alexander V.
Заглавие : Effect of complexation with closo-decaborate anion on photophysical properties of copolyfluorenes containing dicyanophenanthrene units in the main chain
Колич.характеристики :11 с
Место публикации : Micro. - 2023. - Vol. 3, Is. 4. - P.930-940. - ISSN 26738023 (eISSN), DOI 10.3390/micro3040063
Примечания : Cited References: 23. - This work was supported by the Russian Science Foundation, grant no. 23-43-00060
Аннотация: The functionalization of copolyfluorenes containing dicyanophenanthrene units by closo-decaborate anion is described. Target copolyfluorenes were analyzed using SEM, UV-vis, luminescence, NMR, and Fourier-transform infrared (FTIR) spectroscopy. The effect of complexation with the closo-decaborate anion on the photophysical properties was studied both experimentally and theoretically. The PL data indicate an efficient charge transfer from fluorene to the dicyanophenanthrene units coordinated to the closo-decaborate. The coordination of closo-decaborate clusters to the nitrile groups of copolyfluorenes provides an important route to new materials for sensors and light-emitting devices while, at the same time, serving as a platform for further study of the nature of boron clusters.
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20.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Ovchinnikov S. G., Antipina L. Yu., Tomilin F. N., Kuzubov A. A.
Заглавие : Effect of electron correlations on the structure of photoprotein substrates
Коллективы :
Место публикации : JETP Letters. - 2010. - Vol. 91, Is. 9. - P.490-493. - ISSN 0021-3640, DOI 10.1134/S0021364010090122
Примечания : Cited References: 14. - This work was supported by the Russian Foundation for Basic Research (project no. 07-04-00930-a), by the Presidium of the Russian Academy of Sciences (program "Molecular and Cellular Biology"), and by the Siberian Branch, Russian Academy of Sciences (project no. 2).
Предметные рубрики: ANGSTROM RESOLUTION
CRYSTAL-STRUCTURE
AEQUORIN
ENERGY
OBELIN
GAS
Аннотация: The electronic structure and total energy of various isomeric forms of coelenterazine and coelenteramide have been calculated by quantum chemistry methods both in the single-electron approximation and taking into account correlation effects. It has been shown that the inclusion of electron correlations makes it possible to obtain the structure of the coelenteramide close to the experimentally determined structure, as well as to choose the structure of the coelenterazine CLZ(1H) as the most probable isomeric form.
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