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Numerical Simulations of Structural Chromosomal Instability 染色体结构不稳定性的数值模拟
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180306
Y. Eidelman, S. Slanina, V. Pyatenko, S. Andreev
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.
利用机制CI模型研究了辐射诱导的染色体不稳定性(CI)的剂量-反应曲线的起源。该模型考虑了辐照细胞后代DNA损伤的产生和修复以及细胞在有丝分裂周期中的传代。我们考虑在S期重新形成DNA双链断裂(DSBs),其中主要形成染色单体型畸变。其中,姐妹染色单体交换的“等染色单体缺失”类型,或“染色单体双中心”是主要的兴趣。当细胞进入有丝分裂时,染色体畸变的命运取决于它们的类型。进入有丝分裂的染色体和染色单体碎片,要么传递到其中一个子细胞中,要么丢失。染色单体在有丝分裂中形成一个后期桥。这些机制假设被用来证明剂量-响应曲线与CI的动态曲线密切相关。分析了这种关系背后的原理。
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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
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180318
S. Romanov
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.
提出了一种利用旋转换能器系统进行无损超声层析成像的方法。旋转换能器系统将层析成像方案中的发射器和检测器的数量增加了几倍,并且可以消除由不完整数据层析成像引起的图像伪影。层析成像重建被测物体内部速度结构的反问题被认为是一个标量波动方程的非线性系数反问题。讨论了用于重建物体内部纵波速度的可扩展迭代算法。该方法基于残差泛函梯度的显式表示。该算法采用对发射器位置的并行计算。在“Lomonosov-2”超级计算机上进行的数值模拟表明,所开发的层析成像方法不仅可以检测缺陷的边界,而且在同时记录反射波和透射波的情况下,可以高精度地确定缺陷内部的波速分布。
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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
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
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.
对水中具有复杂拓扑结构的大型重电荷生物相容性分子的大小和其他性质进行了高性能计算。采用分子动力学模拟方法和GROMACS软件包对相同分子量的赖氨酸树突和短树突刷进行了研究。比较了两种体系的尺寸和结构性能。结果表明,树枝状电刷比树枝状聚合物具有更小的尺寸和更致密的芯。两种分子的径向密度分布都不是单调的,在分子核心附近具有最小值。树突刷的最小值比树突刷的更宽更深。因此,树突比树突刷具有更大的低密度区域,更适合用于疏水药物的包封和递送。
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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
Pub Date : 2018-09-01 DOI: 10.14529/JSFI180308
A. Chibisov, M. Chibisova
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.
这项工作涉及基于嵌入磷原子的硅材料的量子量子比特建模,因为未来的量子计算机可以建立在这个量子比特的基础上。采用高性能计算(HPC)技术,利用Quantum ESPRESSO软件包建立了块状晶体硅和硅烯的原子模型,并计算了它们的总能量。对于硅原子和磷原子,利用量子ESPRESSO包对自旋-轨道非共线相互作用进行了广义梯度近似(GGA)。通过量子力学计算,从理论上研究了磷量子比特自旋的平衡取向和波函数在二维和块状晶体硅相中的局域性。量子比特之间存在交换相互作用,这导致波函数的定位和自旋方向发生变化,并且在硅烯的情况下,这种相互作用更强。
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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
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180319
M. K. Glagolev, V. Vasilevskaya
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.
提出了一种将聚乳酸粗粒度a -接枝- b模型转换为原子表示的算法。在A-接枝-B模型中,主链的原子被映射到A珠上,形成粗粒大分子的线性主链,甲基被映射到B侧垂坠上。该算法在预先定义的链片段(称为模板)的帮助下,根据粗粒度珠子的位置恢复原子位置。模板的尺寸通过仿射变换来调整,以确保在粗粒度和原子表示中骨架的一致性。粗粒度模型和原子模型之间的转换保存了有关聚合物链精细结构的信息。恢复的构型适合于进一步的分子动力学模拟。原子表示和粗粒度表示都需要标准的GROMACS软件。该算法可用于其他a -接枝- b聚合物模型的反向映射。
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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
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180304
A. Pleshkevich, V. Lisitsa, D. Vishnevsky, V. Levchenko, B. Moroz
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.
基于单向波动方程的深度波场外推,提出了一种新颖的地震成像算法。该算法的并行实现是基于几个层次的并行性。输入数据的并行性允许处理某些区域(最多一平方公里)的全覆盖;因此,数据被分成几个子集,每个子集由单个MPI进程处理。数学方法允许独立处理每个频率,并逐层处理解决方案;因此,同时处理一组2D横截面而不是初始的3D共偏移矢量集。这部分算法是在GPU上实现的。接下来,每个共偏移矢量图像可以单独堆叠、处理和存储。因此,我们设计并实现了基于CPU-GPU架构的并行算法,该算法允许使用基于单向波方程的保幅偏移来计算共偏移矢量图像。将该算法应用于实际地震地表数据的地震图像计算。
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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
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
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.
这项工作的主要目标是证明矢量系统的数据密集型应用的发展不仅是重要和有趣的,而且是非常可能的。在本文中,我们描述了NEC SX-ACE矢量计算机的两种基本图形处理算法的可能实现:用于单源最短路径计算的Bellman-Ford算法和用于强连接组件检测的Forward-Backward算法。提议的实现已经根据目标架构的特性和属性进行了开发和优化,这使得它们能够达到与其他传统平台(如英特尔Skylake,英特尔Knight Landing或IBM Power处理器)相当的性能。
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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
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180303
Yana A. Sharapova, D. Suplatov, V. Svedas
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.
了解影响神经氨酸酶结合配体的构象动力学,有助于改进针对这些致病因子的新型候选药物的计算机筛选,并充分评估潜在药物的疗效。传统分子动力学(MD)是研究构象采样、药物靶标识别和结合的有力工具,但需要大量的计算工作才能达到与生物学相关的时间尺度。在这项工作中,评估了计算机能力和专门架构在模拟神经氨酸酶结构行为的长MD轨迹方面的进展。我们得出的结论是,现代GPU加速器能够在以前难以处理的时间尺度上进行计算,在日常实验室实践中提供对微秒长的轨迹的常规访问。这为从药物设计中的“静态”亲和驱动策略转向更深入地了解蛋白质结构中靶位点的配体特异性构象适应提供了机会,从而更好地选择有效的硅候选药物。然而,现代gpu的性能仍然远远落后于为MD共同设计的深度专业超级计算机。需要进一步开发负担得起的专业架构,以实现人们渴望的毫秒时间尺度,以模拟日常生活中的大型蛋白质。
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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
Pub Date : 2018-07-10 DOI: 10.14529/JSFI180205
B. Krasnopolsky
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.
本文研究了在高性能计算系统上提高高保真不可压缩湍流模拟性能的问题。集成平均方法将时间平均与多个集成平均相结合,可以通过增加数值方法的计算强度(每字节的flop比)来加速相应的模拟。本文的重点是进一步改进所提出的计算方法,特别是对产生多个独立湍流状态的过程进行优化。
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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
Pub Date : 2018-06-01 DOI: 10.14529/JSFI180202
L. Sokolinsky, I. Sokolinskaya
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.
本文主要研究线性不等式系统的Cimmino算法的可扩展性。该算法属于迭代投影算法。对于可扩展性的分析分析,采用了BSF (Bulk Synchronous Farm)并行计算模型。给出了一种使用高阶函数Map和Reduce对列表进行操作的Cimmino算法的实现。给出了该算法适用于集群计算系统的可扩展性上限的解析估计。给出了利用BSF程序框架和MPI并行编程库在c++语言中实现列表上的Cimmino算法的信息。在集群计算系统上进行的大规模计算实验结果进行了验证。通过与计算实验结果的比较,得出了分析估计的充分性结论。
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引用次数: 6
期刊
Supercomput. Front. Innov.
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