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Mechanical properties of eukaryotic cells play an important role in life cycle conditions and in the development of pathological processes. In this paper we discuss the problem of parameters identification and verification of viscoelastic constitutive models based on force spectroscopy data of living cells. It is proposed to use one-dimensional continuous wavelet transform to calculate the relaxation function. Analytical calculations and the results of numerical simulation are given, which allow to obtain relaxation functions similar to each other on the basis of experimentally determined force curves and theoretical stress-strain relationships using wavelet differentiation algorithms. Test examples demonstrating correctness of software implementation of the proposed algorithms are analyzed. The cell models are considered, on the example of which the application of the proposed procedure of identification and verification of their parameters is demonstrated. Among them are a structural-mechanical model with parallel connected fractional elements, which is currently the most adequate in terms of compliance with atomic force microscopy data of a wide class of cells, and a new statistical-thermodynamic model, which is not inferior in descriptive capabilities to models with fractional derivatives, but has a clearer physical meaning. For the statistical-thermodynamic model, the procedure of its construction is described in detail, which includes the following. Introduction of a structural variable, the order parameter, to describe the orientation properties of the cell cytoskeleton. Setting and solving the statistical problem for the ensemble of actin filaments of a representative cell volume with respect to this variable. Establishment of the type of free energy depending on the order parameter, temperature and external load. It is also proposed to use an oriented-viscous-elastic body as a model of a representative element of the cell. Following the theory of linear thermodynamics, evolutionary equations describing the mechanical behavior of the representative volume of the cell are obtained, which satisfy the basic thermodynamic laws. The problem of optimizing the parameters of the statisticalthermodynamic model of the cell, which can be compared both with experimental data and with the results of simulations based on other mathematical models, is also posed and solved. The viscoelastic characteristics of cells are determined on the basis of comparison with literature data.

The transition from α-helices to β-strands under external mechanical force in fibrin molecule containing coiled-coils is studied and free energy landscape is resolved. The detailed theoretical modeling of each stage of coiled-coils fragment pulling process was performed. The plots of force (F) as a function of molecule expansion (X) for two symmetrical fibrin coiled-coils (each ∼17 nm in length) show three distinct modes of mechanical behaviour: (1) linear (elastic) mode when coiled-coils behave like entropic springs (F<100−125 pN and X<7−8 nm), (2) viscous (plastic) mode when molecule resistance force does not increase with increase in elongation length (F≈150 pN and X≈10−35 nm) and (3) nonlinear mode (F>175−200 pN and X>40−50 nm). In linear mode the coiled-coils unwind at 2π radian angle, but no structural transition occurs. Viscous mode is characterized by the phase transition from the triple α-spirals to three-stranded parallel β-sheet. The critical tension of α-helices is 0.25 nm per turn, and the characteristic energy change is equal to 4.9 kcal/mol. Changes in internal energy Δu, entropy Δs and force capacity c_f per one helical turn for phase transition were also computed. The observed dynamic behavior of α-helices and phase transition from α-helices to β-sheets under tension might represent a universal mechanism of regulation of fibrillar protein structures subject to mechanical stresses due to biological forces.

Virtual machines are usually associated with an ability to create them on demand by calling web services, then these machines are used to deliver resident services to their clients; however, providing clients with an ability to run an arbitrary programme on the newly created machines is beyond their power. Such kind of usage is useful in a high performance computing environment where most of the resources are consumed by batch programmes and not by daemons or services. In this case a cluster of virtual machines is created on demand to run a distributed or parallel programme and to save its output to a network attached storage. Upon completion this cluster is destroyed and resources are released. With certain modifications this approach can be extended to interactively deliver computational resources to the user thus providing virtual desktop as a service. Experiments show that the process of creating virtual clusters on demand can be made efficient in both cases.

Laminar-turbulent transition is the subject of an active research related to improvement of economic efficiency of air vehicles, because in the turbulent boundary layer drag increases, which leads to higher fuel consumption. One of the directions of such research is the search for efficient methods, that can be used to find the position of the transition in space. Using this information about laminar-turbulent transition location when designing an aircraft, engineers can predict its performance and profitability at the initial stages of the project. Traditionally, $e^N$ method is applied to find the coordinates of a laminar-turbulent transition. It is a well known approach in industry. However, despite its widespread use, this method has a number of significant drawbacks, since it relies on parallel flow assumption, which limits the scenarios for its application, and also requires computationally expensive calculations in a wide range of frequencies and wave numbers. Alternatively, flow analysis can be done by using Dynamic Mode Decomposition, which allows one to analyze flow disturbances using flow data directly. Since Dynamic Mode Decomposition is a dimensionality reduction method, the number of computations can be dramatically reduced. Furthermore, usage of Dynamic Mode Decomposition expands the applicability of the whole method, due to the absence of assumptions about the parallel flow in its derivation.

The presented study proposes an approach to finding the location of a laminar-turbulent transition using the Dynamic Mode Decomposition method. The essence of this approach is to divide the boundary layer region into sets of subregions, for each of which the transition point is independently calculated, using Dynamic Mode Decomposition for flow analysis, after which the results are averaged to produce the final result. This approach is validated by laminar-turbulent transition predictions of subsonic and supersonic flows over a 2D flat plate with zero pressure gradient. The results demonstrate the fundamental applicability and high accuracy of the described method in a wide range of conditions. The study focuses on comparison with the $e^N$ method and proves the advantages of the proposed approach. It is shown that usage of Dynamic Mode Decomposition leads to significantly faster execution due to less intensive computations, while the accuracy is comparable to the such of the solution obtained with the $e^N$ method. This indicates the prospects for using the described approach in a real world applications.

Processing of large amounts of data often consists of several steps, e.g. pre- and post-processing stages, which are executed sequentially with data written to disk after each step, however, when pre-processing stage for each task is different the more efficient way of processing data is to construct a pipeline which streams data from one stage to another. In a more general case some processing stages can be factored into several parallel subordinate stages thus forming a distributed pipeline where each stage can have multiple inputs and multiple outputs. Such processing pattern emerges in a problem of classification of wave energy spectra based on analytic approximations which can extract different wave systems and their parameters (e.g. wave system type, mean wave direction) from spectrum. Distributed pipeline approach achieves good performance compared to conventional “sequential-stage” processing.

The approach to build territorial distributed storage system for high performance computing environment of UB RAS is presented. The storage system is based on the dCache middleware from the European Middleware Initiative project. The first milestone of distributed storage system implementation includes the data centers at the two UB RAS Regions: Yekaterinburg and Perm.

This work is devoted to molecular dynamic modeling of the thermal impact processes on the metal sample consisting of nickel atoms. For the solution of this problem, a continuous mathematical model on the basis of the classical Newton mechanics equations has been used; a numerical method based on the Verlet scheme has been chosen; a parallel algorithm has been offered, and its realization within the MPI and OpenMP technologies has been executed. By means of the developed parallel program, the investigation of thermodynamic equilibrium of nickel atoms’ system under the conditions of heating a sample to desired temperature has been executed. In numerical experiments both optimum parameters of calculation procedure and physical parameters of analyzed process have been defined. The obtained numerical results are well corresponding to known theoretical and experimental data.

The paper presents a software system aimed at finding best (in some sense) parameters of an algorithm. The system handles both discrete and continuous parameters and employs massive parallelism offered by public clouds. The paper presents an overview of the system, a method to measure algorithm's performance in the cloud and numerical results of system's use on several problem sets.

Efficiency and completeness of the numerical simulation in oceanography and hydrometeorology are entirely determined by algorithmic features of the construction of an interactive computer simulations in the scale of the oceans with adaptive coated closed seas and coastal waters refined mathematical models, with the possibility of specifying software parallelization calculations near the concrete — the protected areas of the sea coast. An important component of the research is continuous graphical visualization techniques in the course of calculations, including those undertaken in parallel processes with shared RAM or test points on the external media. The results of computational experiments are used in the description of hydrodynamic processes near the coast, which is important in keeping the organization of sea control services and forecasting marine hazards.

The decomposition algorithms provide approaches to deal with NP-hardness in solving discrete optimization problems (DOPs). In this article one of the promising ways to exploit sparse matrices — local elimination algorithm in parallel interpretation (LEAP) are demonstrated. That is a graph-based structural decomposition algorithm, which allows to compute a solution in stages such that each of them uses results from previous stages. At the same time LEAP heavily depends on elimination ordering which actually provides solving stages. Also paper considers tree- and block-parallel for LEAP and required realization process of it comparison of a several heuristics for obtaining a better elimination order and shows how is related graph structure, elimination ordering and solving time.