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Numerical Simulations of Structural Chromosomal Instability 染色体结构不稳定性的数值模拟
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/jsfi180306
Y. Eidelman, S. Slanina, V. Pyatenko, S. Andreev
{"title":"Numerical Simulations of Structural Chromosomal Instability","authors":"Y. Eidelman, S. Slanina, V. Pyatenko, S. Andreev","doi":"10.14529/jsfi180306","DOIUrl":"https://doi.org/10.14529/jsfi180306","url":null,"abstract":"The origin of dose-response curves for radiation-induced chromosomal instability (CI) is studied using the mechanistic CI model. The model takes into account DNA damage generation and repair in the progeny of irradiated cells and cell passage through mitotic cycle. We consider the formation of DNA double-strand breaks (DSBs) de novo in the S phase, where predominantly chromatid-type aberrations are formed. Among them sister chromatid exchanges of the “isochromatid deletion” type, or “chromatid dicentrics” are of primary interest. When the cell enters mitosis, the fate of chromosomal aberrations depends on their types. Chromosomal and chromatid fragments, having entered mitosis, either are transmitted into one of the daughter cells, or are lost. A chromatid dicentric in mitosis forms an anaphase bridge. These mechanistic assumptions were used to demonstrate that the dose-response curves are closely related to the dynamic curves for CI. The principles underlying this relationship are analyzed.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"37 5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128517816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Supercomputer Simulations of Nondestructive Tomographic Imaging with Rotating Transducers 旋转换能器无损层析成像的超级计算机模拟
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/jsfi180318
S. Romanov
{"title":"Supercomputer Simulations of Nondestructive Tomographic Imaging with Rotating Transducers","authors":"S. Romanov","doi":"10.14529/jsfi180318","DOIUrl":"https://doi.org/10.14529/jsfi180318","url":null,"abstract":"A method of nondestructive ultrasound tomographic imaging employing a rotating transducer system is proposed. The rotating transducer system increases the number of emitters and detectors in a tomographic scheme by several times and makes it possible to neutralize image artifacts resulting from incomplete-data tomography. The inverse problem of tomographic reconstructing the velocity structure inside the inspected object is considered as a nonlinear coefficient inverse problem for a scalar wave equation. Scalable iterative algorithms for reconstructing the longitudinal wave velocity inside the object are discussed. The methods are based on the explicit representation for the gradient of the residual functional. The algorithms employ parallelizing the computations over emitter positions. Numerical simulations performed on the “Lomonosov-2” supercomputer showed that the tomographic methods developed can not only detect boundaries of defects, but also determine the wave velocity distribution inside the defects with high accuracy provided that both reflected and transmitted waves are registered.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128979483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Application of High Performance Computing for Comparison of Two Highly Branched Lysine Molecules of Different Topology 应用高性能计算比较两种不同拓扑结构的高支化赖氨酸分子
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/JSFI180310
I. Neelov, O. Shavykin, M. Ilyash, V. Bezrodnyi, S. Mikhtaniuk, Anna A. Marchenko, E. Fatullaev, A. A. Darinskii, F. Leermakers
{"title":"Application of High Performance Computing for Comparison of Two Highly Branched Lysine Molecules of Different Topology","authors":"I. Neelov, O. Shavykin, M. Ilyash, V. Bezrodnyi, S. Mikhtaniuk, Anna A. Marchenko, E. Fatullaev, A. A. Darinskii, F. Leermakers","doi":"10.14529/JSFI180310","DOIUrl":"https://doi.org/10.14529/JSFI180310","url":null,"abstract":"High performance computations were performed for comparison of size and other properties of big heavily charged biocompatible molecules of complex topology in water. Lysine dendrimer and short dendritic brush of the same molecular weight were studied by molecular dynamics simulation method and GROMACS software package. The size and structural properties of these two systems were compared. It was shown that dendritic brush has smaller size and more dense core than the dendrimer. Radial density profile for both molecules is not monotonous and has minimum near core of molecules. This minimum is wider and deeper for dendrimer than for dendritic brush. Thus dendrimer has larger region of low density than dendritic brush and is more suitable for use for encapsulation and delivery of hydrophobic drugs.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"PP 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126354332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Modelling of Quantum Qubit Behaviour for Future Quantum Computers 未来量子计算机中量子量子比特行为的建模
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/JSFI180308
A. Chibisov, M. Chibisova
{"title":"Modelling of Quantum Qubit Behaviour for Future Quantum Computers","authors":"A. Chibisov, M. Chibisova","doi":"10.14529/JSFI180308","DOIUrl":"https://doi.org/10.14529/JSFI180308","url":null,"abstract":"This work deals with quantum qubit modelling based on a silicon material with embedded phosphorus atoms because a future quantum computer can be built on the basis of this qubit. The building of atomic models of bulk crystalline silicon and silicene, as well as calculation of their total energies, were performed using the Quantum ESPRESSO software package, using highperformance computing (HPC). For silicon and phosphorus atoms the generalized gradient approximation (GGA) was used in terms of the spin-orbit non-collinear interaction by means of the Quantum ESPRESSO package. The equilibrium orientations of the phosphorus qubit spins and localization of the wave functions in the 2D and bulk crystalline silicon phases were theoretically investigated by means of quantum-mechanical calculations. The existence of an exchange interaction between qubits has been confirmed, which leads to a change in the wave function’s localization and spin orientation, and in the case of silicene, this interaction was stronger.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130558784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Reverse Mapping Algorithm for Multi-scale Numerical Simulation of Polylactic Acid 聚乳酸多尺度数值模拟的逆向映射算法
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/jsfi180319
M. K. Glagolev, V. Vasilevskaya
{"title":"Reverse Mapping Algorithm for Multi-scale Numerical Simulation of Polylactic Acid","authors":"M. K. Glagolev, V. Vasilevskaya","doi":"10.14529/jsfi180319","DOIUrl":"https://doi.org/10.14529/jsfi180319","url":null,"abstract":"An algorithm is proposed to convert the coarse-grained A-graft-B model of polylactic acid into the atomistic representation. In the A-graft-B model the atoms of the backbone are mapped onto A beads, which form the linear backbone of the coarse-grained macromolecule, the methyl groups are mapped onto B side pendants. The algorithm restores atomic positions based on positions of coarse-grained beads with the help of pre-defined chain fragments, called templates. The dimensions of the templates are adjusted by affine transformation to ensure coincidence of the backbone in coarse-grained and atomistic representation. The transition between coarse-grained and atomistic models conserves information about the fine structure of polymer chains. The restored configurations are suitable for further molecular-dynamic simulations. Both atomistic and coarse-grained representations require standard GROMACS software. The algorithm can be used for reverse mapping of other A-graft-B polymer models.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132859078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Parallel GPU-based Implementation of One-Way Wave Equation Migration 基于并行gpu的单向波动方程迁移实现
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/jsfi180304
A. Pleshkevich, V. Lisitsa, D. Vishnevsky, V. Levchenko, B. Moroz
{"title":"Parallel GPU-based Implementation of One-Way Wave Equation Migration","authors":"A. Pleshkevich, V. Lisitsa, D. Vishnevsky, V. Levchenko, B. Moroz","doi":"10.14529/jsfi180304","DOIUrl":"https://doi.org/10.14529/jsfi180304","url":null,"abstract":"We present an original algorithm for seismic imaging, based on the depth wavefield extrapolation by the one-way wave equation. Parallel implementation of the algorithm is based on the several levels of parallelism. The input data parallelism allows processing full coverage for some area (up to one square km); thus, data are divided into several subsets and each subset is processed by a single MPI process. The mathematical approach allows dealing with each frequency independently and treating solution layer-by-layer; thus, a set of 2D cross-sections instead of the initial 3D common-offset vector gathers are processed simultaneously. This part of the algorithm is implemented suing GPU. Next, each common-offset vector image can be stacked, processed and stored independently. As a result, we designed and implemented the parallel algorithm based on the use of CPU-GPU architecture which allows computing common-offset vector images using one-way wave equation-based amplitude preserving migration. The algorithm was used to compute seismic images from real seismic land data.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124068746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Developing Efficient Implementations of Bellman-Ford and Forward-Backward Graph Algorithms for NEC SX-ACE 在NEC SX-ACE上开发Bellman-Ford和正向向后图算法的高效实现
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/JSFI180311
I. Afanasyev, A. Antonov, D. Nikitenko, V. Voevodin, V. Voevodin, K. Komatsu, Osamu Watanabe, A. Musa, Hiroaki Kobayashi
{"title":"Developing Efficient Implementations of Bellman-Ford and Forward-Backward Graph Algorithms for NEC SX-ACE","authors":"I. Afanasyev, A. Antonov, D. Nikitenko, V. Voevodin, V. Voevodin, K. Komatsu, Osamu Watanabe, A. Musa, Hiroaki Kobayashi","doi":"10.14529/JSFI180311","DOIUrl":"https://doi.org/10.14529/JSFI180311","url":null,"abstract":"The main goal of this work is to demonstrate that the development of data-intensive appli- cations for vector systems is not only important and interesting, but is also very possible. In this paper we describe possible implementations of two fundamental graph-processing algorithms for an NEC SX-ACE vector computer: the Bellman–Ford algorithm for single source shortest paths computation and the Forward-Backward algorithm for strongly connected components detection. The proposed implementations have been developed and optimised in accordance with features and properties of the target architecture, which allowed them to achieve performance comparable to other traditional platforms, such as Intel Skylake, Intel Knight Landing or IBM Power processors.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129043876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
Simulating the Long-timescale Structural Behavior of Bacterial and Influenza Neuraminidases with Different HPC Resources 模拟不同HPC资源下细菌和流感神经氨酸酶的长时间结构行为
Supercomput. Front. Innov. Pub Date : 2018-09-01 DOI: 10.14529/jsfi180303
Yana A. Sharapova, D. Suplatov, V. Svedas
{"title":"Simulating the Long-timescale Structural Behavior of Bacterial and Influenza Neuraminidases with Different HPC Resources","authors":"Yana A. Sharapova, D. Suplatov, V. Svedas","doi":"10.14529/jsfi180303","DOIUrl":"https://doi.org/10.14529/jsfi180303","url":null,"abstract":"Understanding the conformational dynamics which affects ligand binding by Neuraminidases is needed to improve the in silico selection of novel drug candidates targeting these pathogenicity factors and to adequately estimate the efficacy of potential drugs. Conventional molecular dynamics (MD) is a powerful tool to study conformational sampling, drug-target recognition and binding, but requires significant computational effort to reach timescales relevant for biology. In this work the advances in a computer power and specialized architectures were evaluated at simulating long MD trajectories of the structural behavior of Neuraminidases. We conclude that modern GPU accelerators enable calculations at the timescales that would previously have been intractable, providing routine access to microsecond-long trajectories in a daily laboratory practice. This opens an opportunity to move away from the “static” affinity-driven strategies in drug design towards a deeper understanding of ligand-specific conformational adaptation of target sites in protein structures, leading to a better selection of efficient drug candidates in silico. However, the performance of modern GPUs is yet far behind the deeply-specialized supercomputers co-designed for MD. Further development of affordable specialized architectures is needed to move towards the much-desired millisecond timescale to simulate large proteins at a daily routine.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127550516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Generation of Multiple Turbulent Flow States for the Simulations with Ensemble Averaging 集合平均模拟中多种湍流状态的生成
Supercomput. Front. Innov. Pub Date : 2018-07-10 DOI: 10.14529/JSFI180205
B. Krasnopolsky
{"title":"Generation of Multiple Turbulent Flow States for the Simulations with Ensemble Averaging","authors":"B. Krasnopolsky","doi":"10.14529/JSFI180205","DOIUrl":"https://doi.org/10.14529/JSFI180205","url":null,"abstract":"The paper deals with the problem of improving the performance of high-fidelity incompressible turbulent flow simulations on high performance computing systems. The ensemble averaging approach, combining averaging in time together with averaging over multiple ensembles, allows to speedup the corresponding simulations by increasing the computing intensity of the numerical method (flops per byte ratio). The current paper focuses on further improvement of the proposed computational methodology, and particularly, on the optimization of procedure to generate multiple independent turbulent flow states.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130991595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scalability Evaluation of Cimmino Algorithm for Solving Linear Inequality Systems on Multiprocessors with Distributed Memory 求解线性不等式系统的Cimmino算法的可扩展性评价
Supercomput. Front. Innov. Pub Date : 2018-06-01 DOI: 10.14529/JSFI180202
L. Sokolinsky, I. Sokolinskaya
{"title":"Scalability Evaluation of Cimmino Algorithm for Solving Linear Inequality Systems on Multiprocessors with Distributed Memory","authors":"L. Sokolinsky, I. Sokolinskaya","doi":"10.14529/JSFI180202","DOIUrl":"https://doi.org/10.14529/JSFI180202","url":null,"abstract":"The paper is devoted to a scalability study of Cimmino algorithm for linear inequality systems. This algorithm belongs to the class of iterative projection algorithms. For the analytical analysis of the scalability, the BSF (Bulk Synchronous Farm) parallel computation model is used. An implementation of the Cimmino algorithm in the form of operations on lists using higher-order functions Map and Reduce is presented. An analytical estimation of the upper scalability bound of the algorithm for cluster computing systems is derived. An information about the implementation of Cimmino algorithm on lists in C++ language using the BSF program skeleton and MPI parallel programming library is given. The results of large-scale computational experiments performed on a cluster computing system are demonstrated. A conclusion about the adequacy of the analytical estimations by comparing them with the results of computational experiments is made.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121487790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
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