Hydroxyapatite (Ca5(PO4)3 OH) (HAp) is a crystalline structure and composition analogue to calcified tissues of vertebrates. The biomedical significance of HAp is its bioactivity – HAp ceramics leads to the formation of new bone on their surface. HAp properties are ascribed to the characteristic surface structure of HAp, while the detailed mechanism is still unknown. Modeling and computation of HAp molecular nanostructures, exploration of the possible mechanisms of its surface charging (polarization), based on proton transfer, and the discussion of the adhesion properties of HAp nanoparticles and ceramics are the aim of the work.

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In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector–scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization.

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DFT (VASP) and semi-empirical (HyperChem) calculations for the L-and D-chiral diphenylalanine (L-FF and D-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. The results obtained show that after optimization, the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like-cluster obtained after optimization inside L-FF and D-FF PNT and total L-FF and D-FF PNT with embedded water/ice cluster are discussed.

О р д е н а Л е н и н а ИНСТИТУТ ПРИКЛАДНОЙ МАТЕМАТИКИ имени М.В. Келдыша Р о с с и й с к о й а к а д е м и и н а у к С.В. Филиппов Программная платформа Blender как среда моделирования объектов и процессов естественно-научных дисциплин Москва -2018 Филиппов С.В. Программная платформа Blender как среда моделирования объектов и процессов естественно-научных дисциплинДано вводное описание Blender Python API, необходимое для численного моделирования в среде открытой программной платформы трёхмерного моделирования, анимации и рендеринга -Blender. Рассмотрены базовые методы 3D-моделирования объектов исследований на примере построения динамических молекулярных моделей и моделей фрагмента дна Северного Ледовитого океана по расчётным и внешним (экспериментальным) данным, представленным как численно, так и в форме графических изображений. Приведены примеры программ на языке Python, демонстрирующие основные методы работы с базовыми данными. Описана комплексная задача по созданию аналитической визуализации динамической молекулярной модели бета-2 адренорецептора по данным молекулярно-динамического исследования.Ключевые слова: 3D, моделирование, аналитическая визуализация, Blender, Python, API, бета-2 адренорецептор, молекулярная динамика. Blender software platform as an environment for modeling objects and processes of science disciplinesAn introductory description of the Blender Python API is given, which is necessary for numerical simulation in the open source software platform of three-dimensional modeling, animation and rendering -Blender. The basic methods of 3D-modeling of research objects are considered on the example of building dynamic molecular models and models of the ocean bed fragment of the Arctic Ocean using calculated and external (experimental) data presented both numerically and in the form of graphic images. Examples of programs in the Python language are given, demonstrating the basic methods of working with basic data. The complex task of creating analytical visualization of the dynamic molecular model of the beta-2 adrenoreceptor according to the data of molecular dynamics research is described.

<p><strong>Abstract.</strong> We present results of the first phase of an ongoing project to create a system for three-dimensional (3D) geomorphometric modeling of the Arctic Ocean submarine topography. In this phase, we developed a testing, lowresolution desktop version of the system. We utilized a small, 5-km gridded digital elevation model (DEM) extracted from the International Bathymetric Chart of the Arctic Ocean (IBCAO) version 3.0. From the smoothed DEM, we derived digital models of several morphometric variables: horizontal, vertical, minimal, and maximal curvatures, catchment and dispersive areas, as well as topographic and stream power indices. To construct and visualize 3D morphometric models, we applied an original approach for 3D terrain modeling in the environment of the Blender package, free and open-source software. Finally, we present a series of 3D morphometric models with perspective views from the Atlantic, Eurasia, the Pacific, and North America. The experiment showed that the approach is efficient and can be used for creating next, desktop and web versions of the system for visualizing 3D morphometric models of higher resolutions.</p>