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Of all publications in the section: 15
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Working paper
Batsyn M.V., Kalyagin V.A., Tulyakov D. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2015. No. 91.
The Protein Structure Alignment Problem (PSAP) consists in finding the best alignment of two proteins defined by their primary structures. It finds the most similar substructure of two proteins. This problem is polynomially reducible to the Maximum Clique Problem (MCP) for the protein alignment graph. In this paper we present an efficient algorithm for the PSAP based on our recent ILS&MCS algorithm (Batsyn et al., 2014) for the MCP. To reduce the alignment problem to the MCP we follow the DAST method introduced by Malod-Dognin et al. (2010). Our main contributions include: applying the ILS heuristic to obtain a lower bound and make preprocessing of an alignment graph to reduce its size; efficient implementation of the algorithm for large but sparse alignment graphs including memory preallocation and bit representation of adjacency matrix. The computational results are provided for the popular Skolnick test set of 40 proteins and show that the suggested algorithm is more efficient than one of the fastest PSAP solvers - the ACF algorithm by Malod- Dognin et al. (2010).
Added: Oct 24, 2016
Working paper
Парусникова А. В., Брюно А. Д. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2010. № 39.
Added: Apr 18, 2012
Working paper
Ильин И. С., Заславский Г., Лавренов С. М. и др. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2013. № 6.
Added: Nov 24, 2013
Working paper
Петров А. П., Степанцов М. Е. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2014. № 100.
In this paper we consider construction and primary research of the stochastic cellular automaton based version of the "power-society" model, describing the dynamics of power distribution in a hierarchy. We herein formulate basic principles of the model and present a simulation system for numeric experiments. It is shown that most properties of the deterministic model that is a system of differential equations are inherited by the cellular automaton model, which is also shows a possibility to attract power distribution to a solution, proved to be unstable in the classical model.
Added: Dec 17, 2014
Working paper
Балашов В. А., Злотник А.А., Савенков Е. Б. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2016. № 89.
A study of the barotropic quasi-hydrodynamic system of equations for the two-phase two-component mixture involving the surface tension and stationary potential force is accomplished. Under fairly general assumptions on the Helmholtz free energy of the mixture, the~energy balance equation with non-positive energy production together with its corollary, the law of non-increasing total energy, are derived; in particular, both the isothermal and isentropic cases are covered. Under additional assumptions, the necessary and sufficient conditions for the linearized stability of constant solutions are derived (it does not take place always).   A finite-difference approximation of the problem is constructed in the 2D periodic case for a non-uniform rectangular mesh. Approximation of the capillary stress tensor is improved in the momentum balance equation thus increasing the quality of numerical solutions.   The results of numerical experiments are presented. They demonstrate the ability of the model to ensure the qualitatively correct description for the dynamics of surface effects as well as applicability of the linearized stability criterion in the original nonlinear statement.
Added: Sep 30, 2016
Working paper
Брюно А. Д., Парусникова А. В. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2010. № 72.
Added: Apr 18, 2012
Working paper
Лавренов С. М., Михайлин Д., Тучин А. Г. и др. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2013. № 68.
Added: Nov 24, 2013
Working paper
Степанцов М. Е., Гавдаева А. В., Агапова Г. И. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2011. № 73.
Added: Feb 7, 2014
Working paper
Елизарова Т. Г., Злотник А. А., Никитина О. В. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2011. № 33.
Added: Jul 5, 2012
Working paper
Тучин А. Г., Комовкин С., Лавренов С. М. и др. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2013. № 66.
Added: Nov 24, 2013
Working paper
Елизарова Т. Г., Злотник А.А., Истомина М. А. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2017. № 1.
We derive new axially symmetric stationary solutions to the barotropic Euler equations with a body force in the isentropic and isothermal cases. They are used as the initial distributions in the related non-stationary problem. Basing on a quasi-hydrodynamic approach, we perform numerical experiments on the development of small initial perturbations of the azimuthal velocity and the formation of large structures like the density "sleeves''. Splitting of the sleeves and decreasing of the gas angular momentum in the middle of the field are observed. Also the correctness of the shallow water approximation for describing the sleeve formation is confirmed. The designed algorithm is universal and allows one to perform various numerical experiments of interest in astrophysics on a personal computer.  
Added: Dec 20, 2016
Working paper
Брюно А. Д., Парусникова А. В. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2011. № 61.
Added: Apr 18, 2012
Working paper
Брюно А. Д., Парусникова А. В. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2012. № 61.
Added: Mar 24, 2013
Working paper
Брюно А. Д., Парусникова А. В. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2011. № 18.
Added: Apr 18, 2012
Working paper
Балашов В.А., Злотник А.А., Савенков Е.Б. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2017. № 91.
The paper presents a numerical algorithm for computing three-dimensional viscous compressible isothermal two-phase two-component flows with surface effects in domains of complex shape with voxel geometry. The algorithm is based on quasi-hydrodynamic regularization of the diffuse-interface model. A new improved finite-difference scheme is constructed. The method of its implementing on the domain boundary is described in detail. The simulation results are given for spreading of a drop on a substrate and displacement of a fluid by another one in a channel of complex shape.
Added: Oct 23, 2017