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Simulation of properties of composite materials reinforced by carbon nanotubes using perceptron complexes
Computer Research and Modeling, 2015, v. 7, no. 2, pp. 253-262Views (last year): 2. Citations: 1 (RSCI).Use of algorithms based on neural networks can be inefficient for small amounts of experimental data. Authors consider a solution of this problem in the context of modelling of properties of ceramic composite materials reinforced with carbon nanotubes using perceptron complex. This approach allowed us to obtain a mathematical description of the object of study with a minimal amount of input data (the amount of necessary experimental samples decreased 2–3.3 times). Authors considered different versions of perceptron complex structures. They found that the most appropriate structure has perceptron complex with breakthrough of two input variables. The relative error was only 6%. The selected perceptron complex was shown to be effective for predicting the properties of ceramic composites. The relative errors for output components were 0.3%, 4.2%, 0.4%, 2.9%, and 11.8%.
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Molecular dynamics assessment of the mechanical properties of fibrillar actin
Computer Research and Modeling, 2022, v. 14, no. 5, pp. 1081-1092Actin is a conserved structural protein that is expressed in all eukaryotic cells. When polymerized, it forms long filaments of fibrillar actin, or F-actin, which are involved in the formation of the cytoskeleton, in muscle contraction and its regulation, and in many other processes. The dynamic and mechanical properties of actin are important for interaction with other proteins and the realization of its numerous functions in the cell. We performed 204.8 ns long molecular dynamics (MD) simulations of an actin filament segment consisting of 24 monomers in the absence and the presence of MgADP at 300 K in the presence of a solvent and at physiological ionic strength using the AMBER99SBILDN and CHARMM36 force fields in the GROMACS software environment, using modern structural models as the initial structure obtained by high-resolution cryoelectron microscopy. MD calculations have shown that the stationary regime of fluctuations in the structure of the F-actin long segment is developed 80–100 ns after the start of the MD trajectory. Based on the results of MD calculations, the main parameters of the actin helix and its bending, longitudinal, and torsional stiffness were estimated using a section of the calculation model that is far enough away from its ends. The estimated subunit axial (2.72–2.75 nm) and angular (165–168◦) translation of the F-actin helix, its bending (2.8–4.7 · 10−26 N·m2), longitudinal (36–47·10−9 N), and torsional (2.6–3.1·10−26 N·m2) stiffness are in good agreement with the results of the most reliable experiments. The results of MD calculations have shown that modern structural models of F-actin make it possible to accurately describe its dynamics and mechanical properties, provided that computational models contain a sufficiently large number of monomers, modern force fields, and relatively long MD trajectories are used. The inclusion of actin partner proteins, in particular, tropomyosin and troponin, in the MD model can help to understand the molecular mechanisms of such important processes as the regulation of muscle contraction.
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International Interdisciplinary Conference "Mathematics. Computing. Education"