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Search Results: 1 - 10 of 2533 matches for " Andrey Alekseenko "
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Evaluation of CDK6 and p16/INK4a-Derived Peptides Interaction  [PDF]
Andrey Kazennov, Andrey Alekseenko, Vladimir Bozhenko, Tatiana Kulinich, Nikolay Shuvalov, Yaroslav Kholodov
Computational Molecular Bioscience (CMB) , 2013, DOI: 10.4236/cmb.2013.33007
Abstract:  The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling method. The SASA implicit solvent model was used for simulation, which was accelerated using NVIDIA GPUs.
Molecular mechanisms, thermodynamics, and dissociation kinetics of knob-hole interactions in fibrin
Olga Kononova,Rustem I. Litvinov,Artem Zhmurov,Andrey Alekseenko,Chai-Ho Cheng,Silvi Agarwal,Kenneth A. Marx,John W. Weisel,Valeri Barsegov
Quantitative Biology , 2015, DOI: 10.1074/jbc.M113.472365
Abstract: Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs 'A' and 'B' in the central nodule of fibrin monomer to complementary holes 'a' and 'b' in the beta- and gamma-nodules, respectively, of another monomer. We characterized the A:a and B:b knob-hole interactions under varying solution conditions using Molecular Dynamics simulations of the structural models of fibrin(ogen) fragment D complexed with synthetic peptides GPRP (knob 'A' mimetic) and GHRP (knob 'B' mimetic). The strength of A:a and B:b knob-hole complexes was roughly equal, decreasing with pulling force; yet, the dissociation kinetics were sensitive to variations in acidity (pH=5-7) and temperature (T=25-37 C). There were similar structural changes in holes 'a' and 'b' during forced dissociation of the knob-hole complexes: elongation of loop I, stretching of interior region, and translocation of the moveable flap. The disruption of the knob-hole interactions was not an "all-or-none" transition, as it occurred through distinct two-step or single-step pathways with or without intermediate states. The knob-hole bonds were stronger, tighter, and more brittle at pH=7 than at pH=5. The B:b knob-hole bonds were weaker, looser, and more compliant than the A:a knob-hole bonds at pH=7, but stronger, tighter, and less compliant at pH=5. Surprisingly, the knob-hole bonds were stronger, not weaker, at elevated temperature (T=37 C) compared to T=25 C due to the helix-to-coil transition in loop I, which helps stabilize the bonds. These results provide detailed qualitative and quantitative characteristics underlying the most significant non-covalent interactions involved in fibrin polymerization.
Constraint-Preserving Boundary Conditions for the Linearized Baumgarte-Shapiro-Shibata-Nakamura Formulation
Alexander M. Alekseenko
Abstract and Applied Analysis , 2008, DOI: 10.1155/2008/742040
Abstract: We derive two sets of explicit homogeneous algebraic constraint-preserving boundary conditions for the second-order in time reduction of the linearized Baumgarte-Shapiro-Shibata-Nakamura (BSSN) system. Our second-order reduction involves components of the linearized extrinsic curvature only. An initial-boundary value problem for the original linearized BSSN system is formulated andthe existence of the solution is proved using the properties of the reduced system. A treatment is proposed for the full nonlinear BSSN system to construct constraint-preserving boundary conditions without invoking the second order in time reduction. Energy estimates on the principal part of the BSSN system (which is first order in temporal and second order in spatial derivatives) are obtained. Generalizations to the case of nonhomogeneous boundary data are proposed.
Constraint preserving boundary conditions for the linearized BSSN formulation
Alexander M. Alekseenko
Physics , 2004,
Abstract: We derive two sets of explicit algebraic constraint preserving boundary conditions for the linearized BSSN system. The approach can be generalized to inhomogeneous differential and evolution conditions, the examples of which are given. The proposed conditions are justified by an energy estimate on the original BSSN variables.
Well-Posed Initial-Boundary Value Problem for a Constrained Evolution System and Radiation-Controlling Constraint-Preserving Boundary Conditions
Alexander M. Alekseenko
Physics , 2006,
Abstract: A well-posed initial-boundary value problem is formulated for the model problem of the vector wave equation subject to the divergence-free constraint. Existence, uniqueness and stability of the solution is proved by reduction to a system evolving the constraint quantity statically, i.e., the second time derivative of the constraint quantity is zero. A new set of radiation-controlling constraint-preserving boundary conditions is constructed for the free evolution problem. Comparison between the new conditions and the standard constraint-preserving boundary conditions is made using the Fourier-Laplace analysis and the power series decomposition in time. The new boundary conditions satisfy the Kreiss condition and are free from the ill-posed modes growing polynomially in time.
Deterministic Solution of the Boltzmann Equation Using Discontinuous Galerkin Discretizations in Velocity Space
Alexander Alekseenko,Eswar Josyula
Physics , 2013, DOI: 10.1016/j.jcp.2014.03.031
Abstract: We present a new deterministic approach for the solution of the Boltzmann kinetic equation based on nodal discontinuous Galerkin (DG) discretizations in velocity space. In the new approach the collision operator has the form of a bilinear operator with pre-computed kernel; its evaluation requires $O(n^5)$ operations at every point of the phase space where $n$ is the number of degrees of freedom in one velocity dimension. The method is generalized to any molecular potential. Results of numerical simulations are presented for the problem of spatially homogeneous relaxation for the hard spheres potential. Comparison with the method of Direct Simulation Monte Carlo (DSMC) showed excellent agreement.
An Electrostatic Catastrophe Machine as an Attosecond Pulse Generator  [PDF]
Andrey Gitin
Optics and Photonics Journal (OPJ) , 2014, DOI: 10.4236/opj.2014.412034
Abstract: The generation of an attosecond pulse in the ultraviolet range is described in the terms of the catastrophe theory. A simple criterion of tunneling is proposed. The criterion allows constructing the quasiclassical model of the generator of attosecond laser pulses based on the interaction of an electric field of extremely powerful femtosecond pulse with the valence electron in the potential well of the gas atom.
Unified Theory of Force Fields (Electromagnetic and Gravitational)  [PDF]
Chaykin Andrey
World Journal of Condensed Matter Physics (WJCMP) , 2017, DOI: 10.4236/wjcmp.2017.71003
Abstract: In this paper, the superfluid substance is described by the same equations of the electromagnetic field and the gravitational field. The gravitational mass is sufficiently considered as the gravitational charge, having the same dimensions as electric charge.
The Influence of Leadership Art on Modern Enterprise Management  [PDF]
Dryamin Andrey
Open Journal of Business and Management (OJBM) , 2019, DOI: 10.4236/ojbm.2019.72067
Abstract: In today’s society, the rapid development of the knowledge-based economy puts forward new requirements for the leadership of enterprises: improving the ideas of employees and enterprises, improving leadership art has become extremely important content for the leadership management model in this new era. Leadership art is the content and performance of the leadership style. The correct use of leadership art is very important for the whole enterprise. It can not only effectively improve the efficiency of the enterprise, but also promote the common development of the company and employees. However, how to make the successful use of leadership art in enterprises has become an urgent problem to be solved. In this article, two or more existing situations are studied to determine their similarities and differences, the background, development, current conditions and environmental interactions of one or more individuals, groups, communities, businesses or institutions is observed, recorded and analyzed for stages of patterns in relation to internal and external influences. This article will briefly discuss the influence of leadership art on modern enterprise management.
New first-order formulation for the Einstein equations
A. M. Alekseenko,D. N. Arnold
Physics , 2002, DOI: 10.1103/PhysRevD.68.064013
Abstract: We derive a new first-order formulation for Einstein's equations which involves fewer unknowns than other first-order formulations that have been proposed. The new formulation is based on the 3+1 decomposition with arbitrary lapse and shift. In the reduction to first order form only 8 particular combinations of the 18 first derivatives of the spatial metric are introduced. In the case of linearization about Minkowski space, the new formulation consists of symmetric hyperbolic system in 14 unknowns, namely the components of the extrinsic curvature perturbation and the 8 new variables, from whose solution the metric perturbation can be computed by integration.
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