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Chemical visualization of asphaltenes aggregation processes studied in situ with ATR-FTIR spectroscopic imaging and NMR imaging / A. A. Gabrienko [et al.] // J. Phys. Chem. C. - 2015. - Vol. 119, Is. 5. - P. 2646-2660, DOI 10.1021/jp511891f. - Cited References:78. - This research was performed under the UNIHEAT project. The authors wish to acknowledge the Skolkovo Foundation and BP for financial support. The authors thank BP for providing samples of crude oil . - ISSN 1932-7447

РУБ Chemistry, Physical + Nanoscience & Nanotechnology + Materials Science, Multidisciplinary
Рубрики:
MEXICAN CRUDE OILS
   X-RAY-DIFFRACTION
   INFRARED-SPECTROSCOPY
   PETROLEUM ASPHALTENES
   MOLECULAR-DYNAMICS
   VARIABLE SELECTION
   ORGANIC-SOLVENTS
   LIGHT-SCATTERING
   N-HEPTANE
   NEAR-IR
Аннотация: Crude oil phase behavior and asphaltene precipitation have been studied by two complementary chemical imaging methods for the first time. ATR-FTIR spectroscopic imaging approach has revealed the chemical composition of agglomerated and precipitated asphaltenes upon dilution with a flocculant. Asphaltenes, containing oxygen and nitrogen heteroatomic functional groups, have been detected to be least stable. Aromatic abundant asphaltenes have been observed to have relatively high solubility in crude oil/heptane blends. NMR imaging approach, capable of imaging in the bulk of crude oil samples, has demonstrated that n-heptane causes aggregation which can lead to the stable suspension or to the sedimentation followed by the formation of deposits, depending on flocculant concentration. These processes have been monitored for small and large amounts of heptane added to crude oil. The data obtained by ATR-FTIR spectroscopic imaging and NMR imaging have been correlated to propose a possible link between the chemical structure of asphaltenes and a mechanism of the formation of deposits.

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Держатели документа:
Univ London Imperial Coll Sci Technol & Med, Dept Chem Engn, London SW7 2AZ, England.
Russian Acad Sci, Siberian Branch, Boreskov Inst Catalysis, Novosibirsk 630090, Russia.
Russian Acad Sci, Siberian Branch, Inst Chem & Chem Technol, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Siberian Branch, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.
UNICAT Ltd, Novosibirsk 630090, Russia.
BP Prod North Amer Inc, Refining & Logist Technol, Naperville, IL 60563 USA.
Novosibirsk State Univ, Novosibirsk 630090, Russia.

Доп.точки доступа:
Gabrienko, A. A.; Morozov, E. V.; Морозов, Евгений Владимирович; Subramani, V.; Martyanov, O. N.; Kazarian, S. G.; Skolkovo Foundation; BP
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Gorban, A.
Codon usage trajectories and 7-cluster structure of 143 complete bacterial genornic sequences / A. . Gorban, T. . Popova, A. . Zinovyev // Physica A. - 2005. - Vol. 353. - P. 365-387, DOI 10.1016/j.physa.2005.01.043. - Cited References: 46 . - ISSN 0378-4371

РУБ Physics, Multidisciplinary
Рубрики:
DNA-BASE COMPOSITION
   ASYMMETRIC SUBSTITUTION PATTERNS
   PROTEIN-CODING REGIONS
   MICROBIAL GENOMES
   GENE IDENTIFICATION
   MARKOV-MODELS
   G+C CONTENT
   BIAS
   PREDICTION
   SELECTION
Кл.слова (ненормированные):
genome -- cluster -- codon usage -- correlations -- entropy -- mean field -- Cluster -- Codon usage -- Correlations -- Entropy -- Genome -- Mean field -- Approximation theory -- Correlation methods -- Database systems -- Entropy -- Functions -- Genes -- Mathematical models -- Clusters -- Codon usage -- Genomes -- Mean field -- Bacteria
Аннотация: Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic "pure" types of this model, observed in nature: "parallel triangles", "perpendicular triangles", degenerated case and the flower-like type. Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes. We show that codon us-age of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/similar to zinovyev/7clusters. (c) 2005 Elsevier B.V. All rights reserved.

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Держатели документа:
Univ Leicester, Dept Math, Leicester LE1 7RH, Leics, England
RAS, SB, Inst Computat Modelling, Krasnoyarsk, Russia
Bures Sur Yvette & Bioinformat Serv Inst Curie, Inst Hautes Etudes Sci, Paris, France
ИВМ СО РАН
Department of Mathematics, University of Leicester, Leicester, University Road, Leicester LE1 7RH, United Kingdom
Institute of Computational Modelling, SB RAS, Krasnoyarsk, Russian Federation
Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette and Bioinformatics Service of Institut Curie, Paris, France

Доп.точки доступа:
Popova, T.; Zinovyev, A.
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Breaking of the Selection Rules for Optical Transitions in the Dielectric PrFe3(BO3)(4) Crystal by a Praseodymium-Iron Exchange Interaction / M. N. Popova [et al.] // Phys. Rev. Lett. - 2009. - Vol. 102, Is. 18. - Ст. 187403, DOI 10.1103/PhysRevLett.102.187403. - Cited References: 26. - This work was supported in part by the RFBR under Grants No. 07-02-01185 and No. 07-02-00704 and by the Russian Academy of Sciences under the Programs for Basic Research. . - ISSN 0031-9007

РУБ Physics, Multidisciplinary
Рубрики:
SINGLE-CRYSTAL
   GDFE3(BO3)(4)
   PHASE
   DYFE3(BO3)(4)
   SPECTRUM
   LINES
Кл.слова (ненормированные):
Magnetic ordering temperatures -- Optical spectrum -- Order parameters -- Point symmetries -- Selection rules -- Exchange interactions -- Neon -- Praseodymium -- Single crystals -- Crystal symmetry
Аннотация: We report on the emergence of new lines in the optical spectrum of the PrFe3(BO3)(4) single crystal at the magnetic ordering temperature. The transitions between singlet crystal-field sublevels of Pr3+ ion with the same transformational properties, strictly forbidden for the trigonal D-3 point symmetry of this ion in PrFe3(BO3)(4), appear below the Neel temperature and grow in intensity as a square of the order parameter. We show that the phenomenon originates from the mixing of wave functions of different Pr3+ sublevels by the Pr-Fe exchange interaction.

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Держатели документа:
[Popova, M. N.
Stanislavchuk, T. N.] Russian Acad Sci, Inst Spect, Troitsk 142190, Moscow Region, Russia
[Malkin, B. Z.] Kazan VI Lenin State Univ, Kazan 420008, Russia
[Bezmaternykh, L. N.] Russian Acad Sci, LV Kirensky Phys Inst, Siberian Branch, Krasnoyarsk 660036, Russia
ИФ СО РАН
Institute of Spectroscopy, Russian Academy of Sciences, 142190 Troitsk, Moscow region, Russian Federation
Kazan State University, 420008 Kazan, Russian Federation
L.V. Kirensky Institute of Physics, Siberian Branch, RAS, 660036 Krasnoyarsk, Russian Federation

Доп.точки доступа:
Popova, M. N.; Stanislavchuk, T. N.; Malkin, B. Z.; Bezmaternykh, L. N.; Безматерных, Леонард Николаевич; RFBR [07-02-01185, 07-02-00704]; Russian Academy of Sciences
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Selection of DNA aptamers for breast cancer / G. S. Zamay, I. V. Belyanina, A. S. Zamay [et al.] // Biochem. Mosc.-Suppl. Ser. B-Biomed. Chem. - 2016. - Vol. 10, Is. 2. - P. 158-164, DOI 10.1134/S1990750816020128. - Cited References:23 . - ISSN 1990-7508. - ISSN 1990-7516

РУБ Biochemistry & Molecular Biology
Рубрики:
BIOMARKERS
MORTALITY
PATTERNS
Кл.слова (ненормированные):
SELEX -- DNA aptamers -- oligonucleotides -- breast cancer
Аннотация: A method of selection of DNA aptamers to breast tumor tissue based on the use of postoperative material has been developed. Breast cancer tissues were used as the positive target; the negative targets included benign tumor tissue, adjacent healthy tissues, breast tissues from mastopathy patients, and also tissues of other types of malignant tumors. During selection a pool of DNA aptamers demonstrating selective binding to breast cancer cells and tissues and insignificant binding to breast benign tissues has been obtained. These DNA aptamers can be used for identification of protein markers, breast cancer diagnostics, and targeted delivery of anticancer drugs.

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Публикация на русском языке Селекция ДНК-аптамеров для диагностики рака молочной железы [Текст] / Г. С. Замай [и др.] // Биомедицинская химия. - Москва : Научно-исследовательский институт биомедицинской химии им. В.Н. Ореховича, 2016. - Т. 62 № 4. - С. 411-417

Держатели документа:
Kirensky Inst Phys, Krasnoyarsk, Russia.
Voino Yasenetski Krasnoyarsk State Med Univ, Ul Partizana Zheleznyaka 1, Krasnoyarsk 660022, Russia.
KKRCCC, Krasnoyarsk, Russia

Доп.точки доступа:
Zamay, G. S.; Замай, Г. С.; Belyanina, I. V.; Zamay, A. S.; Замай, Анна Сергеевна; Komarova, M. A.; Krat, A. V.; Eremina, E. N.; Zukov, R. A.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zamay, T. N.; Замай, Т. Н.
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    Temperature and Eu2+-doping induced phase selection in NaAlSiO4 polymorphs and the controlled yellow/blue emission / M. Zhao [et al.] // Chem. Mater. - 2017. - Vol. 29, Is. 15. - P. 6552-6559, DOI 10.1021/acs.chemmater.7b02548. - Cited References: 48. - The present work was supported by the National Natural Science Foundation of China (Grants 91622125 and 51572023 and 11574003), Natural Science Foundations of Beijing (2172036), and Fundamental Research Funds for the Central Universities (FRF-TP-16-002A3). L.N. acknowledges the support from the Special and Excellent Research Fund of Anhui Normal University. . - ISSN 0897-4756
   Перевод заглавия: Фазовый переход индуцированный температурой и допированием Eu2+ в NaAlSiO4, и контролируемое излучение желтого/голубого света
Кл.слова (ненормированные):
Chemical modification -- Coordination reactions -- Europium -- Light emitting diodes -- Photoluminescence -- Functional properties -- High color rendering index -- Local coordination structures -- Near ultraviolet excitations -- Structural transformation -- Synthesis temperatures -- Temperature dependent -- White light emitting diodes -- Density functional theory
Аннотация: The union of temperature-dependent phase transition and relating structural transformation via modification of chemical compositions is of fundamental importance for the discovery of new materials or their functional properties optimization. Herein, the synthesis temperature and Eu2+-doping content induced phase selection and variations of the local structures in nepheline, low-carnegieite and high-carnegieite types of NaAlSiO4 polymorphs were studied in detail. The luminescence of Eu2+ in low-carnegieite and nepheline phases shows blue (460 nm) and yellow (540 nm) broad-band emissions, respectively, under near-ultraviolet excitation. The photoluminescence evolution can be triggered by the different synthesis temperatures in relation to the Eu2+-doping concentration, as corroborated by density functional theory calculations on the local coordination structures and corresponding mechanical stabilities in terms of the Debye temperature. The fabricated white light-emitting diode device with high color rendering index demonstrates that the multicolor phosphors from one system provides a new gateway for the photoluminescence tuning. © 2017 American Chemical Society.

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Держатели документа:
Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Sciences and Engineering, University of Science and Technology Beijing, Beijing, China
Laboratory of Crystal Physics, Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation
Department of Physics, Far Eastern State Transport University, Khabarovsk, Russian Federation
Anhui Key Laboratory of Optoelectronic Materials Science and Technology, Department of Physics, Anhui Normal University, Wuhu, Anhui, China

Доп.точки доступа:
Zhao, M.; Xia, Z.; Molokeev, M. S.; Молокеев, Максим Сергеевич; Ning, L.; Liu, Q.
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Core-hole localization and ultra-fast dissociation in SF6 / V. Ekholm, G. S. Chiuzbaian, C. Sathe [et al.] // J. Phys. B. - 2020. - Vol. 53, Is. 18. - Ст. 185101, DOI 10.1088/1361-6455/aba204. - Cited References: 36. - This work was supported by the Swedish Research Council (VR). The calculations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC). FG acknowledges support within the Russian Science Foundation (Project No. 16-12-10109) . - ISSN 0953-4075. - ISSN 1361-6455

РУБ Optics + Physics, Atomic, Molecular & Chemical
Рубрики:
X-RAY-EMISSION
   SYMMETRY-BREAKING
   AB-INITIO
   SPECTROSCOPY
   SPECTRA
Кл.слова (ненормированные):
SF6 -- resonant inelastic x-ray scattering -- symmetry selection rules -- ultrafast dynamics -- vibronic couplings
Аннотация: Resonant inelastic x-ray scattering spectra excited at the fluorine K resonances of SF6 have been recorded. While a small but significant propensity for electronically parity-allowed transitions is found, the observation of parity-forbidden electronic transitions is attributed to vibronic coupling that breaks the global inversion symmetry of the electronic wavefunction and localizes the core hole. The dependence of the scattering cross section on the polarization of the incident radiation and the scattering angle is interpreted in terms of local π/σ symmetry around the S–F bond. This symmetry selectivity prevails during the dissociation that occurs during the scattering process.

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Держатели документа:
Lund Univ, MAX IV Lab, Box 118, SE-22100 Lund, Sweden.
Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.
Sorbonne Univ, F-75005 Paris, France.
CNRS, LCPMR, F-75005 Paris, France.
Synchrotron SOLEIL, LOrme Merisiers, BP 48, F-91192 Gif Sur Yvette, France.
Ctr Nacl Pesquisa Energia & Mat CNPEM, BR-10000 Campinas, Brazil.
Royal Inst Technol, Sch Biotechnol, Theoret Chem & Biol, S-10691 Stockholm, Sweden.
Siberian Fed Univ, Krasnoyarsk 660041, Russia.
Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.
Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.

Доп.точки доступа:
Ekholm, V.; Chiuzbaian, G. S.; Sathe, C.; Nicolaou, A.; Guarise, M.; Simon, M.; Jaouen, N.; Luning, J.; Hague, C. F.; Gel'mukhanov, F.; Гельмуханов, Фарис Хафизович; Odelius, M.; Bjorneholm, O.; Rubensson, J-E; Swedish Research Council (VR)Swedish Research Council; Russian Science FoundationRussian Science Foundation (RSF) [16-12-10109]
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Computational approach to design of aptamers to the receptor binding domain of sars-cov-2 / P. V. Artyushenko, V. A. Mironov, D. I. Morozov [et al.] // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 66-67 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-66-67. - Cited References: 5 . - ISSN 1819-9496
Кл.слова (ненормированные):
selection -- aptamer -- receptor-binding domain -- SARS-CoV-2
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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Держатели документа:
Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Lomonosov Moscow State University, Moscow, 119991, Russian Federation
University of Jyvaskyla, Jyvaskyla, 40014, Finland
University of Naples Federico II, Naples, 80138, Italy
Kirensky Institute of Physics KSC SB RAS, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Artyushenko, P. V.; Mironov, V. A.; Morozov, D. I.; Shchugoreva, I. A.; Borbone, N.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.

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Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics / S. Poolsup, E. Zaripov, N. Huttmann [et al.] // Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P. 731-743, DOI 10.1016/j.omtn.2023.02.010. - 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 . - ISSN 2162-2531
Кл.слова (ненормированные):
MT: Oligonucleotides: Diagnostics and Biosensors -- COVID-19 diagnosis -- SARS-CoV-2 nucleocapsid detection -- label-free optical aptasensor -- aptamer selection -- biolayer interferometry -- binding motif identification
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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Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Poolsup, S.; Zaripov, E.; Huttmann, N.; Minic, Z.; Artyushenko, P. V.; Shchugoreva, I. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.; Berezovski, M. V.
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