31 results match your criteria: "Institute of Computational Modeling[Affiliation]"
J Chem Phys
February 2024
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk, Russia.
Golden nanoparticle dimers connected by conjugated molecular linkers 1,2-bis(2-pyridyl)ethylene are produced. The formation of stable dimers with 22 nm diameter nanoparticles is confirmed by transmission electron microphotography. The possibility of charge transfer through the linkers between the particles in the dimers is shown by the density functional theory calculations.
View Article and Find Full Text PDFJ Chem Phys
January 2024
International Research Center of Spectroscopy and Quantum Chemistry, Siberian Federal University, 660041 Krasnoyarsk, Russia.
Metal nanoparticle (NP) complexes lying on a single-layer graphene surface are studied with a developed original hybrid quantum-classical theory using the Finite Element Method (FEM) that is computationally cheap. Our theory is based on the motivated assumption that the carrier charge density in the doped graphene does not vary significantly during the plasmon oscillations. Charge transfer plasmon (CTP) frequencies, eigenvectors, quality factors, energy loss in the NPs and in graphene, and the absorption power are aspects that are theoretically studied and numerically calculated.
View Article and Find Full Text PDFMembranes (Basel)
April 2023
Membrane Institute, Kuban State University, 149 Stavropolskaya St., 350040 Krasnodar, Russia.
The entrance of even a small amount of phosphorus compounds into natural waters leads to global problems that require the use of modern purification technologies. This paper presents the results of testing a hybrid electrobaromembrane (EBM) method for the selective separation of Cl (always present in phosphorus-containing waters) and HPO anions. Separated ions of the same charge sign move in an electric field through the pores of a nanoporous membrane to the corresponding electrode, while a commensurate counter-convective flow in the pores is created by a pressure drop across the membrane.
View Article and Find Full Text PDFPhilos Trans A Math Phys Eng Sci
April 2023
Institute of Mathematics and Information Technologies, Altai State University, Barnaul, Russia.
The right choice of the appropriate mathematical model is crucial for evaluating the physical plausibility of modelling results. The issue of the correct application of the classical Boussinesq approximation for studying the heat and mass transfer in fluidic systems with a deformable boundary is a subject of scientific discussions despite the good agreement of numerous theoretical and numerical results obtained within the convection models based on the Oberbeck-Boussinesq equations with the data of physical experiments and observations. A comparative analysis of the results of numerical simulations in the framework of two-sided models based on the Navier-Stokes equations, and their Boussinesq approximation, is performed in the context of a convection problem in a locally heated two-phase system with a deformable interface.
View Article and Find Full Text PDFIntegr Environ Assess Manag
July 2023
Institute of Computational Modeling Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia.
The watershed management approach is an efficient tool for organizing and implementing natural resource management at the regional and interregional levels. Statistical processing of watershed information contributes to a comprehensive assessment of the environment of the river watersheds at different hierarchical levels. The purpose of this work is to use spatial analysis and data simulation for assessing the state of ecosystems in hydrologically defined geographical areas such as watersheds.
View Article and Find Full Text PDFJ Math Anal Appl
October 2022
Institute of Computational Mathematics and Mathematical Geophysics of SB RAS, 6 Ac. Lavrentieva ave., 630090, Novosibirsk, Russia.
The paper presents one of the possible approaches to pandemic spread modeling. The proposed model is based on the mean-field control inside separate groups of population, namely, suspectable (S), infected (I), removed (R) and cross-immune (C) ones. The numerical algorithm to solve this problem ensures conservation of the total population mass during timeline.
View Article and Find Full Text PDFFront Mol Biosci
February 2022
Laboratory of Advanced Methods for High-Dimensional Data Analysis, Lobachevsky University, Nizhniy Novgorod, Russia.
Cell cycle is a biological process underlying the existence and propagation of life in time and space. It has been an object for mathematical modeling for long, with several alternative mechanistic modeling principles suggested, describing in more or less details the known molecular mechanisms. Recently, cell cycle has been investigated at single cell level in snapshots of unsynchronized cell populations, exploiting the new methods for transcriptomic and proteomic molecular profiling.
View Article and Find Full Text PDFNanoscale
January 2022
International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, Krasnoyarsk, 660041, Russia.
The dependence of plasmon resonance excitations in ultrafine (3-7 nm) gold nanoparticles on heating and melting is investigated. An integrated approach is adopted, where molecular dynamics simulations of the spatial and temporal development of the atoms constituting the nanoparticles generate trajectories out of which system conformations are sampled and extracted for calculations of plasmonic excitation cross sections which then are averaged over the sample configurations for the final result. The calculations of the plasmonic excitations, which take into account the temperature- and size-dependent relaxation of the plasmons, are carried out with a newly developed Extended Discrete Interaction Model (Ex-DIM) and complemented by multilayered Mie theory.
View Article and Find Full Text PDFZh Nevrol Psikhiatr Im S S Korsakova
January 2021
Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia.
Objective: To study tremor and olfactory dysfunction in patients with Parkinson's disease (PD), patients with essential tremor and healthy people for the differential diagnosis and to verify the hypothesis on the inverse dependence between tremor and olfactory dysfunction.
Material And Methods: Olfactory dysfunction was studied in 45 patients with PD, 40 patients with essential tremor and 64 healthy controls. Tremor was studied in 90 people, including 30 controls and 30 patients with PD and essential tremor.
BMC Genomics
September 2020
Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.
Background: Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family).
View Article and Find Full Text PDFPhys Chem Chem Phys
June 2020
Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, SE-10691, Sweden. and Federal Siberian Research Clinical Centre under FMBA of Russia, 26 Krasnoyarsk, Kolomenskaya, 660037, Russia and College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China.
Using the extended discrete interaction model and Mie theory, we investigate the tunability of the optical polarizability of small metallic nano-shells. We show that the spectral positions of symmetric and antisymmetric dipolar plasmon resonances vary with the ratio of particle radius to hole radius in a manner similar to one predicted for uniform metallic nano-shells using a semiclassical approach of two coupled harmonic oscillators. We show that, according to the extended discrete interaction model, the dipolar plasmon resonances are also present for nano-shells in the 2-13 nm size region and show the same functional dependence seen for larger nano-shells.
View Article and Find Full Text PDFJ Chem Phys
January 2020
International Tomography Center, Siberian Branch, Russian Academy of Sciences, Institutskaya Str. 3a, Novosibirsk 630090, Russia.
Magnetic Field Effects (MFEs) on the recombination of radicals, which diffuse on an infinite plane, are studied theoretically. The case of spin-selective diffusion-controlled recombination of Radical Pairs (RPs) starting from a random spin state is considered assuming uniform initial distribution of the radicals. In this situation, reaction kinetics is described by a time-dependent rate coefficient K(t), which tends to zero at long times.
View Article and Find Full Text PDFJ Phys Chem Lett
April 2019
Rome International Center for Materials Science Superstripes (RICMASS), Via dei Sabelli 119A , 00185 Rome , Italy.
Local and fast structural probes using synchrotron radiation have shown nanoscale striped puddles and nanoscale phase separation in doped perovskites. It is known that the striped phases in doped perovskites are due to competing interactions involving charge, spin, and lattice degrees of freedom. In this work, we show that two different stripes can be represented as a superposition of a pair of stripes, U(θ ) or D(θ ), characterized by perovskite tilts where one of the pair is rotated in relation to the other partner by an angle Δθ = π/2.
View Article and Find Full Text PDFBiomedical applications of magnetic nanoparticles under the influence of a magnetic field have been proved useful beyond expectations in cancer therapy. Magnetic nanoparticles are effective heat mediators, drug nanocarriers, and contrast agents; various strategies have been suggested to selectively target tumor cancer cells. Our study presents magnetodynamic nanotherapy using DNA aptamer-functionalized 50 nm gold-coated magnetic nanoparticles exposed to a low frequency alternating magnetic field for selective elimination of tumor cells .
View Article and Find Full Text PDFNucleic Acid Ther
April 2017
1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk, Russia .
Magnetomechanical cell disruption using nano- and microsized structures is a promising biomedical technology used for noninvasive elimination of diseased cells. It applies alternating magnetic field (AMF) for ferromagnetic microdisks making them oscillate and causing cell membrane disruption with cell death followed by apoptosis. In this study, we functionalized the magnetic microdisks with cell-binding DNA aptamers and guided the microdisks to recognize cancerous cells in a mouse tumor in vivo.
View Article and Find Full Text PDFJ Chem Phys
August 2015
International Tomography Center, Siberian Branch, Russian Academy of Sciences, Institutskaya St. 3a, Novosibirsk 630090, Russia.
In this work, we treat spin-selective recombination of a geminate radical pair (RP) in a spherical "microreactor," i.e., of a RP confined in a micelle, vesicle, or liposome.
View Article and Find Full Text PDFPhys Rev E Stat Nonlin Soft Matter Phys
November 2009
Institute of Computational Modeling, Russian Academy of Sciences, Krasnoyarsk, Russia.
Laser cooling and crystallization of electron-ion plasma is studied using the Brownian dynamics simulation technique and taking into consideration the interaction of ions with the electron subsystem. It has been shown that the nonlinear dependence of laser friction force on the velocity of ions has to be taken into account in order to simulate in an adequate manner the cooling dynamics and obtain a correct estimate for minimum temperatures. It has been found that times required for formation of an ordered ionic structure can be much longer than the typical plasma cooling time.
View Article and Find Full Text PDFDokl Biochem Biophys
February 2008
Institute of Computational Modeling, Siberian Branch of the Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russia.
Dokl Biol Sci
June 2007
Institute of Computational Modeling, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, Russia.
Phys Rev E Stat Nonlin Soft Matter Phys
December 2006
Institute of Computational Modeling SB RAS, Krasnoyarsk, 660036, Russia.
Long nonlinear two-dimensional traveling waves on a film driven by laminar gas flow are investigated numerically via solving Navier-Stokes equations. The evolution of their shape, amplitude, and speed with increasing Reynolds number is studied. The existence of solitary waves is demonstrated.
View Article and Find Full Text PDFMicrobiol Res
May 2008
LTD Territory-oriented information systems, Institute of Computational Modeling, off.501-1, Russian Academy of Sciences, Siberian Branch, Akademgorodok 50, Krasnoyarsk 660036, Russian Federation.
Resistance to Ampicillin and Kanamycin displayed by heterotrophic bacteria isolated in Summer and in Spring from the littoral and the central parts of Lake Shira (a therapeutic lake in the Khakasia Republic, Russia) has been investigated. It has been found that in Summer, human and animal microflora featuring multiple antibiotic resistance (to Ampicillin and Kanamycin) predominates in all the studied stations of the littoral zone of the lake. In Spring, concentrations of bacteria featuring multiple antibiotic resistance decrease significantly and bacteria sensitive to antibiotics predominate in the lake.
View Article and Find Full Text PDFDokl Biol Sci
August 2006
Institute of Computational Modeling, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk.
In Silico Biol
November 2005
Institute of Computational Modeling, Russian Academy of Science, Russia.
Coding information is the main source of heterogeneity (non-randomness) in the sequences of microbial genomes. The heterogeneity corresponds to a cluster structure in triplet distributions of relatively short genomic fragments (200-400 bp). We found a universal 7-cluster structure in microbial genomic sequences and explained its properties.
View Article and Find Full Text PDFBioorg Khim
September 2004
Institute of Computational Modeling, Kirenskii Institute of Physics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036 Russia.
The atomic and electronic structures of heme complexes with His, Gly, and Cys residues (Heme-His, Heme-Gly, and Heme-Cys) in the fifth coordination position of the Fe atom and with oxygen and nitrogen oxide molecules in the sixth Fe position were studied by the semiempirical quantum-chemical method PM3. A comparative analysis of internuclear distances showed that the strength of chemical bonding between the ligand molecules (oxygen and nitrogen oxide) is greater for Heme-Cys than for Heme-His and Heme-Gly complexes. Consequently, the strengthening of the chemical bond of the oxygen (or nitrogen oxide) molecule with Heme-Cys substantially weakens the chemical bond in the ligand molecule.
View Article and Find Full Text PDFMikrobiologiia
July 2004
Institute of Computational Modeling, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036 Russia.
The effect of mineral particulate matter on the population of bacterioplankton, its aggregation, and productive characteristics was studied in model experiments with different concentrations of particulate kaolin and the same concentration of organic substance (sodium humate). It was found that the presence of mineral particulate matter stimulated the aggregation of bacterioplankton, improved bacterial production, and extended the productive period of bacterioplankton. The integral specific production of aggregated bacterioplankton was higher than that of free-swimming bacterioplankton.
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