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A NUMERICAL METHOD FOR THE SIMULATION OF FREE SURFACE FLOWS OF vISCOPLASTIC FLUID IN 3D

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Journal of Computational Mathematics 2011年第6期29卷 605-622页

作者： kirill D. Nikitin Maxim A. Olshanskii kirill M. Terekhov Yuri v. vassilevski Institute of Numerical Mathematics Russian Academy of Sciences Moscow Russia Department of Mechanics and Mathematics Moscow State University Moscow Russia

In this paper we study a numerical method for the simulation of free surface flows of viscoplastic （Herschel-Bulkley） fluids. The approach is based on the level set method for capturing the free surface evolution and on locally refined and dynamically adapted octree cartesian staggered grids for the discretization of fluid and level set equations. A regu- larized model is applied to handle the non-differentiability of the constitutive relations. We consider an extension of the stable approximation of the Newtonian flow equations on staggered grid to approximate the viscoplastic model and level-set equations if the free boundary evolves and the mesh is dynamically refined or coarsened. The numerical method is first validated for a Newtonian case. In this case, the convergence of numerical solutions is observed towards experimental data when the mesh is refined. Further we compute several 3D viscoplastic Herschel-Bulkley fluid flows over incline planes for the dam-break problem. The qualitative comparison of numerical solutions is done versus experimental investigations. Another numerical example is given by computing the freely oscillating viscoplastic droplet, where the motion of fluid is driven by the surface tension forces. Altogether the considered techniques and algorithms （the level-set method, compact discretizations on dynamically adapted octree cartesian grids, regularization, and the surface tension forces approximation） result in efficient approach to modeling viscoplastic free-surface flows in possibly complex 3D geometries.

关键词： Free surface flows viscoplastic fluid Adaptive mesh refinement Oetree meshes.

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FOREWORD

Journal of Innovative Optical Health Sciences 2009年第1期2卷 I0001-I0002页

作者： Elina A.Genina kirill v.Larin valery v.Tuchin Research-Educational Institute of Optics and Biophotonics Saratov State University Saratov Russia Department of Biomedical Engineering University of Houston Houston USA Research-Educational Institute of Optics and Biophotonics Saratov State University Institute of Precise Mechanics and Control RAS Saratov Russia

Special Issue Optical Technologies in the Study of Tissues and Biological Fluids We are pleased to present this special issue of JIOHS,which focuses on optical technologies in the study of tissues and biological *** selected papers were presented during Saratov Fall Meeting—XII International School for Junior Scientists and Students on Optics,Laser Physics and Biophotonics(September 23–26,2008,Saratov,Russia)in the framework of the following workshops:“Optical Technologies in Biophysics and Medicine,”“Nanostructures and Nanoparticles,”“Microscopic and Low-Coherence Methods in Biomedical Applications,”and“Internet Biophotonics.”All eight papers in this special issue are research papers.

关键词： Junior photonics Russia

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Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

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Nano-Micro Letters 2021年第8期13卷 263-280页

作者： valery v.Prokhorov Nikolay A.Barinov kirill A.Prusakov Evgeniy v.Dubrovin Maxim D.Frank-Kamenetskii Dmitry v.Klinov Federal Research and Clinical Center of Physical-Chemical Medicine Malaya Pirogovskaya1aMoscow 119435Russian Federation A.N.Frumkin Institute of Physical Chemistry and Electrochemistry RASLeninsky prospect Moscow 199071 Russian Federation 3 Moscow Institute of Physics and TechnologyInstitutskiy per.9Dolgoprudny141700 MoscowRussian Federation Lomonosov Moscow State University Leninskie gory1-2Moscow 119991Russian Federation Department of Biomedical Engineering Boston University44 Cummington MallBoston MA02215USA

Up to now,the DNA molecule adsorbed on a surface was believed to always preserve its native *** belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been ***-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and *** argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress(>30 pNnm)inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface *** addition,the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of *** previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale *** sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force *** results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially *** underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.

关键词： DNA surface conformations Kinetic trapping Lateral stress Periodically charged surface DNA kinks

ASSESSMENT OF TISSUE OPTICAL CLEARING AS A FUNCTION OF GLUCOSE CONCENTRATION USING OPTICAL COHERENCE TOMOGRAPHY

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Journal of Innovative Optical Health Sciences 2010年第3期3卷 169-176页

作者： NARENDRAN SUDHEENDRAN MOHAMED MOHAMED MOHAMAD G.GHOSN vALERY v.TUCHIN kirill v.LARIN Department of Electrical and Computer Engineering University of Houston N308 Engineering Building 1 HoustonTX 77204USA Department of Biomedical Engineering University of Houston 2028 SERC Building HoustonTX 77204USA Department of Medicine Baylor College of Medicine HoustonTX 77030USA Institute of Optics and Biophotonics Saratov State University Saratov 410012Russia Institute of Precise Mechanics and Control of RAS Saratov 410056 Russia

One of the major challenges in imaging biological tissues using optical techniques,such as optical coherence tomography(OCT),is the lack of light penetration due to highly turbid structures within the *** clearing techniques enable the biological samples to be more optically homogeneous,allowing for deeper penetration of light into the *** study investigates the effect of optical clearing utilizing various concentrations of glucose solution(10%,30%,and 50%)on porcine skin.A gold-plated mirror was imaged beneath the tissue and percentage clearing was determined by monitoring the change in reflected light intensity from the mirror over *** ratio of percentage clearing per tissue thickness for 10%,30% and 50% glucose was determined to be 4.7±1.6%mm^(−1)(n=6),10.6±2.0%mm^(−1)(n=7)and 21.8±2.2%mm^(−1)(n=5),*** was concluded that while higher glucose concentration has the highest optical clearing effect,a suitable concentration should be chosen for the purpose of clearing,considering the osmotic stress on the tissue sample.

关键词： Glucose porcine skin percent clearing scattering coefficient optical coherence tomography

Neural network-based image reconstruction in swept-source optical coherence tomography using undersampled spectral data

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Light(Science & Applications) 2021年第9期10卷 1658-1671页

作者： Yijie Zhang Tairan Liu Manmohan Singh EgeÇetintaş Yilin Luo Yair Rivenson kirill v.Larin Aydogan Ozcan Electrical and Computer Engineering Department University of CaliforniaLos AngelesCA90095USA Department of Bioengineering University of CaliforniaLos AngelesCA90095USA California NanoSystems Institute University of CaliforniaLos AngelesCA90095USA Department of Biomedical Engineering University of HoustonHoustonTX77204USA Department of Molecular Physiology and Biophysics Baylor College of MedicineUniversity of HoustonHoustonTX77204USA Department of Surgery David Geffen School of MedicineUniversity of CaliforniaLos AngelesCA90095USA

Optical coherence tomography(OCT)is a widely used non-invasive biomedical imaging modality that can rapidly provide volumetric images of ***,we present a deep learning-based image reconstruction framework that can generate swept-source OCT(SS-OCT)images using undersampled spectral data,without any spatial aliasing *** neural network-based image reconstruction does not require any hardware changes to the optical setup and can be easily integrated with existing swept-source or spectral-domain OCT systems to reduce the amount of raw spectral data to be *** show the efficacy of this framework,we trained and blindly tested a deep neural network using mouse embryo samples imaged by an SS-OCT *** 2-fold undersampled spectral data(i.e.,640 spectral points per A-line),the trained neural network can blindly reconstruct 512 A-lines in 0.59 ms using multiple graphics-processing units(GPUs),removing spatial aliasing artifacts due to spectral undersampling,also presenting a very good match to the images of the same samples,reconstructed using the full spectral OCT data(i.e.,1280 spectral points per A-line).We also successfully demonstrate that this framework can be further extended to process 3×undersampled spectral data per A-line,with some performance degradation in the reconstructed image quality compared to 2×spectral ***,an A-line-optimized undersampling method is presented by jointly optimizing the spectral sampling locations and the corresponding image reconstruction network,which improved the overall imaging performance using less spectral data points per A-line compared to 2×or 3×spectral undersampling *** deep learning-enabled image reconstruction approach can be broadly used in various forms of spectral-domain OCT systems,helping to increase their imaging speed without sacrificing image resolution and signal-to-noise ratio.

关键词： graphics hardware image

Pulsed laser reshaping and fragmentation of upconversion nanoparticles-from hexagonal prisms to ID nanorods through“Medusa”-like structures

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Nano Research 2021年第4期14卷 1141-1148页

作者： Laszlo Sajti Denis N.Karimov vasilina v.Rocheva Nataliya A.Arkharova kirill v.Khaydukov Oleg I.Lebedev Alexey E.voloshin Alla N.Generalova Boris N.Chichkov Evgeny v.Khaydukov AIT Austrian Institute of Technology GmbH Wiener Neustadt2700Austria Federal Scientific Research Centre“Crystallography and Photonics”Russian Academy of Sciences Moscow119333Russia Laboratoire CRISMAT UMR6508CNRS-ENSIACENUniversite CaenCaen14050France Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences Moscow 117997Russia Institutfiir Quantenoptik Leibniz Universitat HannoverHannover30167Germany Center of Biomedical Engineering Institute of Molecular Medicine Sechenov First Moscow State Medical UniversityMoscow119991Russia

One dimensional(1D)nanostructures attract considerable attention,enabling a broad application owing to their unique ***,the precise mechanism of 1D morphology attainment remains a matter of *** this study,ultrafast picosecond(ps)laser-induced treatment on upconversion nanoparticles(UCNPs)is offered as a tool for 1 D-nanostructures ***,reshaping through recrystallization process and bioadaptation of initially hydrophobic(β-Na_(1.5)Y_(1.5_)F_(6):Yb^(3+),Tm^(3+)/β-Na_(1.5)Y_(1.5_)F_(6))core/shell nanoparticles by means of one-step laser treatment in water are demonstrated.“True”1D nanostructures through"Medusa^-like structures can be obtained,maintaining anti-Stokes luminescence functionalities.A matter of the one-dimensional UCNPs based on direction of energy migration processes is *** proposed laser treatment approach is suitable for fast UCNP surface modification and nano-to-nano transformation,that open unique opportunities to expand UCNP applications in industry and biomedicine.

关键词： upconversion nanoparticles fluoride crystals upconversion nanorods one-dimensional(1D)structures laser-induced reshaping

Mitogenomics clarifes the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation

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Current Zoology 2024年第5期70卷 618-630页

作者： Alexey P.Kryukov kirill A.Kryukov Kathleen Collier Bohao Fang Scott v.Edwards Laboratory of Evolutionary Zoology and Genetics Federal Scientifc Center of the East Asia Terrestrial BiodiversityRussian Academy of SciencesVladivostok 690022Russia Center for Genome Informatics Bioinformation and DDBJ CenterNational Institute of Genetics1111 YataMishima 411-8540Japan University of Alaska Museum of the North University of AlaskaFairbanksAK 99775USA Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology Harvard UniversityCambridgeMA 02138USA

Partial separation of a peripheral population may lead to its divergence and,potentially,speciation due to genetic drift followed by selection and geographic *** process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verifed *** two Nearctic allopatric species of magpies(Aves,Corvidae:Pica)serve as a good example of these *** Black-billed magpie Pica hudsonia is widely distributed in North America,whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in *** relationships with Palearctic species have been little *** obtained complete mitochondrial genomes of both Nearctic magpie species,along with the Eurasian Magpie(Pica pica)and the Oriental Magpie(Pica serica),20 mitogenomes in *** analysis reveals a basal position of ***,and *** as a sister clade to the two Nearctic *** and *** form reciprocal monophyletic subclades,showing recent divergence between and within *** data show that the Nearctic magpie lineage diverged from the common ancestor with ***,with a single migration wave via the *** the Nearctic,we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada *** amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for *** the clear phenotypic differences between *** and ***,our data,showing their reciprocal monophylies and genetic distinctness,is consistent with the two-species taxonomy.

关键词： Corvidae mitochondrial genome peripatric speciation reciprocal monophyly Sierra Nevada biogeographic barrier

Modeling of cold-temperate tree Pinus koraiensis (Pinaceae) distribution in the Asia-Pacific region: Climate change impact

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Forest Ecosystems 2022年第2期9卷 160-167页

作者： Tatyana Y.Petrenko kirill A.Korznikov Dmitry E.Kislov Nadezhda G.Belyaeva Pavel v.Krestov Botanical Garden-Institute FEB RAS Makovskogo St.142Vladivostok690024Russia Institute of Geography RAS Staromonetniy 24-4Moscow119017Russia

Background:Pinus koraiensis Siebold&Zucc.(Korean pine)is a key species of the mixed cold temperate forests of Northeast *** climate change can significantly worsen the quality of *** habitats and therefore lead to a large-scale structural and functional transformation of the East Asian mixed *** built a species distribution model(SDM)for *** using the random forest classifier–a versatile machine learning al-gorithm,to discover overlap areas of potential species occurrence in the climate condition of the Last Glacial Maximum(~21,000 year before present)and in the projected future climates(2070 year),from which possible permanent refugia for *** were ***:Using the random forest supervised learning algorithm,we developed models of the modern distribution of *** in accordance with the five selected bioclimatic variables(Kira’s warmth and coldness indices,the index of continentality,the rain precipitation index,and the snow precipitation index).In addition to current climatic conditions,we performed this analysis for the climate of the Last Glacial Maximum and for the future projected climate(2070)under scenarios RCP2.6 and *** the predictors,the rain index appears to be the most *** land area estimates with high suitability for *** was 303,785 km 2 under current climatic conditions,586,499 km 2 for the Last Glacial Maximum,and 337,573 km^(2) for the future(2070)period under the RCP2.6 scenario,and 397,764 km^(2) under the RCP8.5 ***:Most of the potential range of *** during the Last Glacial Maximum was located outside the current distribution area of the *** climatically suitable *** habitats will likely disappear in the western part of its modern *** the southern part of the range,which includes glacial refugia,the areas of continuous distribution of the *** populations since the end of the Pleistocene are expected to

关键词： Climate change Bioclimatic modeling Species distribution model Korean pine Northeast Asia

Improvement of tissue analysis and classification using optical coherence tomography combined with Raman spectroscopy

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Journal of Innovative Optical Health Sciences 2015年第4期8卷 10-19页

作者： Chih-Hao Liu Ji Qi Jing Lu Shang Wang Chen Wu Wei-Chuan Shih kirill v.Larin Department of Biomedical Engineering University of Houston 3605 Cullen Blvd. HoustonTexas 77204-5060USA Department of Electrical and Computer Engineering University of Houston 4800 Calhoun Rd. HoustonTexas 77204USA Department of Molecular Physiology and Biophysics Baylor College of Medicine One Baylor Plaza HoustonTexas 77030USA

Optical coherence tomography(OCT)provides significant advantages of high resolution(approaching the histopathology level)realtime imaging of tsess without use of contrast *** on these advantages,the microstructural features of tumors can be visualized and detected ***,it is still not clinically accepted for tumor margin delin-eation due to poor specificity and *** contrast,Raman spectroscopy(RS)can obtain tissue information at the molecular level,but does not provide real-time inaging ***,combining OCT and RS could provide *** this end,we present a tissue analysis and dassification method using both the slope of OCT intensity signal vs depth and the principle components from the RS spectrum as the indicators for tissuse *** goal of this study was to understand prediction accuracy of OCT and combined OCT/RS method for dassification of optically similar tisues and *** pilot experiments were performed on mouse kidneys,livers,and small intestines(SIs).The prediction accuracy with five-fold cross validation of the method has been evaluated by the support vector machine(SvM)*** results demonstrate that tissue characterization based on the OCT/RS method was superior compared to using OCT structural information *** combined OCT/RS method is potentially useful as a noninvasive optical biopsy technique for rapid and automatic tissue characterization during surgery.

关键词： OCT signal slope principle component analysis multi-support vector machine Raman spectra