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pepgrep:A Tool for Peptide MS/MS Pattern Matching

Genomics, Proteomics & Bioinformatics 2013年第2期11卷 127-132页

作者： igor Chernukhin School of Biological Sciences University of Essex

Typically, detection of protein sequences in collision-induced dissociation （CID） tandem MS （MS2） dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search （PDS） engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a com- pact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 finger- print for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to- MS2 scoring algorithm, pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications （PTMs） into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface （API） or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity puri- fication techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http：//***：8080/data/download/pepgrep- ***.

关键词： Collision-induced dissociation Tandem MSTandem MS Protein database search Peptide identification

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Shapes of the fastest fish and optimal underwater and floating hulls

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Theoretical & Applied Mechanics Letters 2022年第6期12卷 403-408页

作者： igor Nesteruk Institute of Hydromechanics National Academy of Sciences of UkraineNational Technical University of Ukraine“Igor Sikorsky Kyiv Polytechnic Institute”Ukraine

A streamlined shape of the best swimmers removes the boundary-layer separation and ensures a laminar flow *** fastest fish have a very sharp convex nose(rostrum),the purpose of which remains *** bodies of revolution similar to their shapes are analyzed in steady underwater and floating *** sources and sinks were located on the axis of symmetry and above the water surface to estimate the pressure on the body and the vertical velocities on the water *** was shown that the flow patterns on a special shaped body with concave nose has no stagnation points and ensure small values of the water surface *** fact allow diminishing the maximum pressure on the surface and wave *** shapes with the sharp concave nose and negative pressure gradients on their surface could be parts of the low drag underwater and floating hulls.

关键词： Drag reduction Wave drag Ship hulls optimization Unseparated shapes Water locomotion

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Analytical model of 2D leakoff in waterflood-induced fractures

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Journal of Rock Mechanics and Geotechnical Engineering 2023年第7期15卷 1713-1733页

作者： igor Reznikov Dimitry Chuprakov Ilmir Bekerov Schlumberger Moscow Research MoscowRussia

Waterflood-induced fractures,also known as self-induced fractures,spontaneously form at injection wells during *** fractures propagate long distances through rock,allowing injected fluids to travel far away from a well,both within and outside the flooding ***,the me-chanics of waterflood-induced fracture propagation is similar to that of hydraulic fractures,which are intentionally created for reservoir *** models developed for hydraulic fractures can also be applied to waterflood-induced ***,waterflood-induced fractures are typically pumped with much larger volumes of water or brine and grow much longer in *** a result,fluid leakoff from waterflood fractures into the formation is more extensive and two-dimensional(2D),a characteristic that is often ignored in a majority of modern fracturing simulators,making their appli-cation to waterflood fractures *** this work,we revisit the problem of leakoff for long-growing waterflood-induced fractures and develop a new analytical model for fluid leakoff that provides improved predictions of fracture geometry and can be easily implemented in fracturing *** incorporate the developed solution into the classical Perkins-Kern-Nordgren(PKN)model of fracture growth,which shows that the choice of the Carter or a 2D leakoff model greatly impacts fracture ge-ometry at large *** conducted parametric study shows while a toughness-dominated regime af-fects fracture evolution,most of fracture lifetime occurs in a viscosity-and-leakoff-dominated *** also develop an asymptotic solution for a leakoff profile in the limiting case of 2D leakoff domination(~~M and~~K).Finally,we study 3D fracture growth and out-of-zone injection with three layers and a complex structure of *** study shows that ignoring the 2D leakoff during simulation results in a significant overestimation of fracture geometry *** present work,thus,plays an impor

关键词： Waterflooding Leakoff Analytical model Hydraulic fracturing Two-dimensional flow

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Dynamical behavior of a mobile system with two degrees of freedom near the resonance

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Acta Mechanica Sinica 2011年第1期27卷 7-17页

作者： Klaus Zimmermann igor Zeidis Faculty of Mechanical Engineering Technische Universitaet Ilmenau

The design of mobile robots that can move without wheels or legs is an important engineering and technological ***-propelling mechanisms consisting of a body that has contact with a rough surface and moveable internal masses are *** models of such systems are presented in this ***,a model of a vibration driven robot that moves along a rough horizontal plane with isotropic dry friction is *** is shown that by changing the off-resonance frequency detuning in sign,one can control the direction of motion of the *** addition,a locomotion system which moves in an environment with anisotropic viscous friction is *** all models,the method of averaging to obtain an algebraic equation for the steady-state＂average＂velocity of the system is used. Prototypes were constructed to compare the theoretical results with experimental ones.

关键词： Dynamics Friction Resonance Vibrationdriven systems

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Release the iron: does the infection of magnetotactic bacteria by phages play a role in making iron available in aquatic environments?

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Journal of Oceanology and Limnology 2021年第6期39卷 2063-2069页

作者： igor TAVEIRA Dennis ABAZYLINSKI Fernanda ABREU Instituto de Microbiologia Paulo de Góes Departamento de Microbiologia GeralUniversidade Federal do Rio de JaneiroRio de Janeiro 21941-902Brazil School of Life Sciences University of Nevada at Las VegasLas Vegas 94720USA

Magnetotactic bacteria(MTB)are ubiquitous prokaryotes that orient along magnetic field lines due to magnetosomes’biomineralization within the *** structures are ferrimagnetic organelles that impart a magnetic moment to the *** succeed in producing magnetosomes,MTB accumulate iron in(i)cytoplasm;(ⅱ)magnetosomes;and(ⅲ)nearby the *** has already been estimated that a single MTB has an iron content of 10 to 100-fold higher than Escherichia *** are the most abundant entity in oceans and are known for controlling nutrient flow such as carbon and nitrogen by viral shunt and *** current work addresses the putative role of phages that infect MTB on the iron biogeochemical *** phage infection in MTB hosts cause a biogenic iron fertilization-like event in localized microenvironments?Are phages critical players in driving magnetosome biomineralization genes(BGs)horizontal transfer?Further investigation of those events,including frequency of occurrence,is necessary to fully comprehend MTB’s effect on iron cycling in aqueous environments.

关键词： horizontal gene transfer iron biogeochemical cycle magnetotactic bacteria magnetosome biomineralization genes phages

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Output feedback control with disturbancecompensation in nonlinear MIMO systems undermeasurement noises

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Journal of Control and Decision 2022年第1期9卷 35-44页

作者： igor Furtat Pavel Gushchin Institute for Problems of Mechanical Engineering of the Russian Academy of Sciences(IPME RAS) St.-PetersburgRussia

A novel output feedback control law with disturbance compensation for nonlinear multiinputmulti-output (MIMO) time-invariant systems under measurement noises is proposed. Thedesigned control law, based on the noise and disturbance estimations, ensures the accuracy insteady state depending on the disturbance, only one component of noise vector and its firstderivatives. Therefore, the proposed algorithm is efficient under noises with large *** conditions in terms of linear matrix inequalities (LMIs) provide a practical exponentialstability of the closed-loop system. The simulations illustrate an efficiency of the proposedmethod compared with some existing ones.

关键词： Nonlinear system disturbance measurement noise compensation S-procedure LMI

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Quasi-Lagrangian Acceleration of Eulerian Methods

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Communications in Computational Physics 2009年第9期6卷 743-757页

作者： igor Kliakhandler Alexander Kurganov Department of Mathematical Sciences Michigan Technological UniversityHoughtonMI 49931USA Mathematics Department Tulane UniversityNew OrleansLA 70118USA

We present a simple and efficient strategy for the acceleration of explicit Eulerian methods for multidimensional hyperbolic systems of conservation *** strategy is based on the Galilean invariance of dynamic equations and optimization of the reference frame,in which the equations are numerically *** optimal reference frame moves(locally in time)with the average characteristic speed of the system,and,in this sense,the resulting method is *** leads to the acceleration of the numerical computations thanks to the optimal CFL condition and automatic adjustment of the computational domain to the evolving part of the *** show that our quasi-Lagrangian acceleration procedure may also reduce the numerical dissipation of the underlying Eulerian *** leads to a significantly enhanced resolution,especially in the supersonic *** demonstrate a great potential of the proposed method on a number of numerical examples.

关键词： Eulerian methods quasi-Lagrangian method finite volume methods Galilean invariance

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Modeling of Ice-Water Phase Change in Horizontal Annulus Using Modified Enthalpy Method

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Advances in Applied Mathematics and Mechanics 2011年第3期3卷 354-369页

作者： Esad Tombarevic igor Vusanovic Faculty of Mechanical Engineering University of MontenegroCetinjski put bb81000 PodgoricaMontenegro

Phase change in ice-water systems in the geometry of horizontal cylindrical annulus with constant inner wall temperature and adiabatic outer wall is modeled with an enthalpy-based mixture *** and melting phenomena under different temperature conditions are analyzed through a sequence of numerical *** the case of freezing of water,the importance of convection and conduction as well as the influence of cold pipe temperature on time for the complete solidification are *** for the case of melting of ice,the influence of the inner pipe wall temperature on the shape of the ice-water interface,the flow and temperature fields in the liquid,the heat transfer coefficients and the rate of melting are *** results of numerical calculations point to good qualitative agreement with the available experimental and other numerical results.

关键词： Phase change solidification melting enthalpy model fixed grid annulus

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Inhaled nicotine replacement therapy

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Asian Journal of Pharmaceutical Sciences 2015年第6期10卷 472-480页

作者： David Cipolla igor Gonda Aradigm Corp 3929 Point EdenWayHaywardCA 94545USA

There are a large number of smokers who want to quit smoking but have failed in their attempts to do so,with many having been unsuccessful at quitting multiple times over their *** existing marketed nicotine replacement therapies(NRT)have only marginal effectiveness and none provide a comparable physiological response to that derived from cigarette smoking;that is,rapid absorption of nicotine from the lung leading to peak levels of nicotine in the bloodstream to target the receptors in the ***,existing NRTs produce a slower and delayed rise in nicotine blood levels which is less effective at reducing the craving *** data for electronic cigarettes show that they typically deliver nicotine with a profile closer to that for nicotine patches,with a slow rise that can take 30–60 min,or longer,to reach the same peak nicotine concentration that is produced in less than 3 min from a single cigarette.A number of attempts have been made to develop an inhaled product which would deliver the nicotine through the lung and mimic the physiological response from smoking,but many of them produced intolerable aversive reactions or delivered an ineffective *** paper discusses examples of the potential for the recent inhaled nicotine products in development to be effective as NRTs,but is not meant to be a comprehensive review.

关键词： Nicotine Smoking cessation Inhalation delivery AERx system Staccato Voke inhaler

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Determining effects of impact loading on residual strength of fiber-metal laminates with grid-characteristic numerical method

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Chinese Journal of Aeronautics 2021年第7期34卷 1-12页

作者： Katerina BEKLEMYSHEVA Vasily GOLUBEV igor PETROV Alexey VASYUKOV Moscow Institute of Physics and Technology DolgoprudniyRussia

The Grid-Characteristic numerical Method(GCM)that is quite common in solving aero and hydrodynamic problems can also be applied for mechanics of *** allows to implement complex border and contact conditions,including the non-reflecting border and the destructible *** this conditions are very important for the precise and effective modeling of LowVelocity Impacts(LVI)on fiber and Fiber-Metal Laminates(FML)and the resulting Barely Visible Impact Damage(BVID)that influences the residual strength of a composite aircraft *** is the type of damage that is not visible by the naked eye and can be hardly detected by a standard ultrasound equipment that is used for regular *** can appear during any weak impacts like bird strike or *** its influence on the residual strength of the part is very important to define the priorities of development of ultrasound *** this paper,the GCM was applied for a full cycle of loading of an FML aircraft cover *** FML consisted of a Carbon Fiber Reinforced Polymer(CFRP)and a single titanium layer on the upper *** cycle of loading in a single calculation consisted of an LVI caused by a small striker and a comparatively slow compressive in-plane ***-dimensional patterns of velocity and stress distributions over the time of calculation are *** patterns,obtained via the Hashin failure criterion are given and analyzed.

关键词： Fiber-metal laminate Grid-characteristic method Low-velocity impact Numerical modeling Residual strength

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