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Quantum Chemistry Research of Interaction between 3D-Transition Metal Ions and a Defective Graphene on the Supercomputer Base 三维过渡金属离子与缺陷石墨烯在超级计算机上相互作用的量子化学研究
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180314
N. Khokhriakov, S. Melchor
Quantum chemistry research is presented in the article, and it concerns the interaction within the complexes formed by the defective graphene clusters and ions of 3d-transition metals V,Cr,Mn, Fe,Co,Ni,Cu. The charges of all regarded ions were +1. All calculations were made at UDFT B3LYP/6-31G level of theory with the BSSE error taken into account. The strongest interaction with the defective clusters is observed in the case of Co+ ion. At the same time, this ion has demonstrated rather weak interaction with the defect-free graphene. Thus, the presence of Co+ in the reaction media increases probability of defect formation with the further forming of short nanotubes and curved carbon clusters with complex topology of their own.
本文介绍了量子化学研究,它涉及由缺陷石墨烯簇和三维过渡金属V,Cr,Mn, Fe,Co,Ni,Cu离子形成的配合物内部的相互作用。所有离子的电荷均为+1。所有计算均在UDFT B3LYP/6-31G理论水平上进行,并考虑了BSSE误差。Co+离子与缺陷团簇的相互作用最强。同时,该离子与无缺陷石墨烯的相互作用较弱。因此,Co+在反应介质中的存在增加了缺陷形成的可能性,从而进一步形成具有复杂拓扑结构的短纳米管和弯曲碳团簇。
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引用次数: 0
Supercomputer Simulation of MATIS-H Problem MATIS-H问题的超级计算机模拟
Pub Date : 2018-09-01 DOI: 10.14529/JSFI180324
M. A. Zaitsev, V. M. Goloviznin, S. A. Karabasov
A supercomputer simulation of the benchmark MATiS-H problem is considered. A highresolution CABARET code is applied for solving Navier-Stokes equations in the framework of the Monotonically Integrated LES approach for the MATiS-H problem. The code is based on a generalisation of low-dissipative, low-dispersive and non-oscillatory CABARET scheme to hybrid topology meshes in the supercomputing framework. The solutions for the time-averaged fields are reported. These show a relatively small sensitivity to the grid density. Comparison with the experiment data available is provided.
考虑了基准MATiS-H问题的超级计算机模拟。采用高分辨率的CABARET编码,在单调积分的LES方法框架下求解求解MATiS-H问题的Navier-Stokes方程。该代码基于将低耗散、低色散和非振荡CABARET方案推广到超级计算框架中的混合拓扑网格。报告了时间平均字段的解。这些显示相对较小的灵敏度网格密度。并与现有实验数据进行了比较。
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引用次数: 0
Supercomputer Docking: Investigation of Low Energy Minima of Protein-Ligand Complexes 超级计算机对接:蛋白质-配体复合物低能最小值的研究
Pub Date : 2018-09-01 DOI: 10.14529/JSFI180326
D. Kutov, A. Sulimov, V. Sulimov
It is shown that the global energy minimum of a protein-ligand complex, when the energy is calculated by the PM7 quantum-chemical semiempirical method with the COSMO implicit solvent model, can be determined as follows. First, the low energy minima are found by a docking program when the protein-ligand energy is calculated with the MMFF94 force field in vacuum. Second, energies of all these minima are recalculated with the PM7 method and the COSMO implicit solvent model. Third, among these recalculated energies the minimal energy is determined and the respective minimum is the global energy minimum when the energy is calculated with the PM7 method and the COSMO implicit solvent model. The optimal width of the spectrum of low energy minima found with MMFF94 in vacuum is determined to perform minimal quantity of quantum-chemical recalculations. The proposed approach allows to perform docking in solvent with the quantum-chemical method and to increase the docking positioning accuracy.
结果表明,用PM7量子化学半经验方法和COSMO隐式溶剂模型计算蛋白质-配体复合物的整体能量最小值可确定为:首先,利用真空条件下MMFF94力场计算蛋白质-配体能量时,通过对接程序找到了低能量最小值;其次,用PM7方法和COSMO隐式溶剂模型重新计算了所有这些极小值的能量。第三,在这些重新计算的能量中,确定了最小能量,并且各自的最小值为PM7方法和COSMO隐式溶剂模型计算能量时的全局能量最小值。确定了MMFF94在真空中发现的低能极小值的最佳谱宽,以进行最少量的量子化学重新计算。该方法可以利用量子化学方法在溶剂中进行对接,提高对接定位精度。
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引用次数: 10
Supercomputer Technologies as a Tool for High-resolution Atmospheric Modelling towards the Climatological Timescales 超级计算机技术作为气候时间尺度高分辨率大气模拟的工具
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180320
V. Platonov, M. Varentsov
Estimation of the recent and future climate changes is the most important challenge in the modern Earth sciences. Numerical climate models are an essential tool in this field of research. However, modelling results are highly sensitive to the spatial resolution of the model. The most of the climate change studies utilize the global atmospheric models with a grid cell size of tens of kilometres or more. High-resolution mesoscale models are much more detailed, but require significantly more computational resources. Applications of such high-resolution models in climate studies are usually limited by regional simulations and by relatively short timespan. In this paper we consider the experience of the long-term regional climate studies based on the mesoscale modelling. On the examples of urban climate studies and extreme wind assessments, we demonstrate the principle advantage of long-term high-resolution simulations, which were carried out on the modern supercomputers.
对近期和未来气候变化的估计是现代地球科学中最重要的挑战。数值气候模式是这一研究领域的重要工具。然而,模拟结果对模型的空间分辨率高度敏感。大多数气候变化研究利用网格单元大小为数十公里或更大的全球大气模式。高分辨率中尺度模式更加详细,但需要更多的计算资源。这种高分辨率模式在气候研究中的应用通常受到区域模拟和相对较短时间跨度的限制。本文讨论了基于中尺度模式的长期区域气候研究的经验。以城市气候研究和极端风评估为例,我们展示了在现代超级计算机上进行的长期高分辨率模拟的主要优势。
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引用次数: 3
Supercomputer Simulations in Design of Ultrasound Tomography Devices 超声断层扫描设备设计中的超级计算机模拟
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180321
A. Goncharsky, S. Seryozhnikov
The paper considers the use of supercomputers in design of medical ultrasound tomography devices. The mathematical models describing the wave propagation in ultrasound tomography should take into account such physical phenomena as diffraction, multiple scattering, and so on. The inverse problem of wave tomography is posed as a coefficient inverse problem with respect to the wave propagation velocity and the absorption factor. Numerous simulations made it possible to determine the optimal parameters of an ultrasound tomograph in order to obtain a spatial resolution of 1.5 mm suitable for early-stage breast cancer diagnosis. The developed methods were tested both on model problems and on real data obtained at the experimental test bench for tomographic studies. The computations were performed on GPU devices of Lomonosov-2 supercomputer at Lomonosov Moscow State University.
本文探讨了超级计算机在医用超声成像设备设计中的应用。描述超声层析成像中波传播的数学模型应考虑到衍射、多次散射等物理现象。将波层析成像反问题提出为关于波传播速度和吸收因子的系数反问题。为了获得适合早期乳腺癌诊断的1.5 mm的空间分辨率,大量的模拟使确定超声层析成像的最佳参数成为可能。所开发的方法在模型问题和在层析研究的实验测试台上获得的实际数据上进行了测试。计算在莫斯科国立罗蒙诺索夫大学的罗蒙诺索夫-2超级计算机的GPU设备上进行。
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引用次数: 1
High-performance Computational Modeling of Chromosome Structure 染色体结构的高性能计算建模
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180305
Y. Eidelman, S. Slanina, O. A. Gusev, S. Andreev
We present a polymer modeling approach to generate the ensemble of 3D chromosome conformations at different time points of mitosis-interphase transition. Dynamics of structure during mitosis-G1 transition indicates quick and slow stages of chromosome shape alterations. At intermediate and late time scale the changes in chromosome compaction are small. To assess time dependence of contact map establishment during G1 we calculate contact maps at different times after mitotic decondensation. We demonstrate that the patterns of contacts observed soon after mitotic decondensation remain similar during G1. Whole contact map for mouse chromosome 18 at late G1 time correlates with the experimental chromosome conformation capture data. The simulations reproduce the main experimental findings, contact map persistence during G1 as well as specific pattern of long-range interactions in interphase chromosome. Our results suggest that spatial compartmentalization of an interphase chromosome is driven by interactions between different types of megabase sized chromatin domains during the formation of globular chromosome state at the end of mitotis to G1 transition.
我们提出了一种聚合物建模方法来生成在有丝分裂-期间过渡的不同时间点的三维染色体构象集合。有丝分裂- g1过渡期间的结构动力学表明染色体形状改变的快速和缓慢阶段。在中后期,染色体压实的变化很小。为了评估G1期间接触图谱建立的时间依赖性,我们计算了有丝分裂去浓缩后不同时间的接触图谱。我们证明,在有丝分裂去浓缩后不久观察到的接触模式在G1期间保持相似。G1后期小鼠18号染色体的全接触图谱与实验染色体构象捕获数据相关。模拟重现了主要的实验结果,G1期间接触图的持久性以及间期染色体远程相互作用的特定模式。我们的研究结果表明,间期染色体的空间区隔是由不同类型的大碱基大小的染色质结构域之间的相互作用驱动的,在有丝分裂结束时形成球状染色体状态到G1过渡。
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引用次数: 0
Applications of High Performance Computing: Born-Oppenheimer Molecular Dynamics of Complex Formation in Aqueous Solutions 高性能计算的应用:Born-Oppenheimer水溶液中复杂形成的分子动力学
Pub Date : 2018-09-01 DOI: 10.14529/jsfi180312
M. Khrenova, D. Kapusta, I. V. Babchuk, Yulia I. Meteleshko
The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 10 times for Cs and Na ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.
超级计算机技术的进步促进了计算化学方法及其应用的发展,特别是从头算势的分子动力学模拟。这些新方法可以解决重要的化学和技术问题。特别是,溶剂萃取和分离技术被广泛用于减少放射性废物的数量,特别是存在于液相中的放射性铯同位素。我们证明了Cs和Na离子在碱阳离子和杯[4]芳烃之间的结合常数的计算值相差10倍,这与实验值吻合得很好。我们报告了929个原子组成的模型系统的基准计算结果,该模型是用具有经验色散校正D3的gga型泛函PBE和高斯函数与具有Goedecker-Teter-Hutter伪势的平面波DZVP的组合基在密度泛函理论近似中描述的。我们证明,如果在Lomonosov-2超级计算机上节点数量为16,计算效率将下降到一半左右。
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引用次数: 4
High-performance Full-atomistic Simulation of Optical Thin Films 光学薄膜的高性能全原子模拟
Pub Date : 2018-09-01 DOI: 10.14529/JSFI180325
F. Grigoriev, V. Sulimov, A. Tikhonravov
The experimental study of the dependence of thin film properties on the deposition conditions may be still a great challenge. Today the progress in high performance computing allows one to perform the investigation of these dependencies on the atomistic level using the classical molecular dynamics (MD) simulation. In the present work the computational cost and efficiency of classical full-atomistic simulation of thin film deposition process using the Lonmonosov-2 supercomputer facilities is discussed. It is demonstrated that using 512 computational cores of the Lomonosov-2 supercomputer ensures the simulation of thin film cluster with technologically meaningful thickness of an optical film. Because of a relatively slow growth of the simulation time with the increase of film thickness we guess that simulations clusters with thicknesses that are several times higher than the currently achieved thicknesses about one hundred nanometers is quite realistic if the number of available computational cores will be increased up to several thousands.
沉积条件对薄膜性能影响的实验研究仍然是一个巨大的挑战。今天,高性能计算的进步使人们能够使用经典分子动力学(MD)模拟在原子水平上对这些依赖关系进行研究。本文讨论了利用lonmonsov -2超级计算机设备进行薄膜沉积过程经典全原子模拟的计算成本和效率。结果表明,使用Lomonosov-2超级计算机的512个计算核可以保证薄膜簇的模拟具有技术意义的光学薄膜厚度。由于随着膜厚的增加,模拟时间的增长相对缓慢,我们推测,如果可用的计算核心数量增加到几千个,那么厚度比目前达到的厚度(约100纳米)高几倍的模拟簇是相当现实的。
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引用次数: 1
Recent Progress on Supercomputer Modelling of High-Speed Rarefied Gas Flows Using Kinetic Equations 用动力学方程模拟高速稀薄气体流动的超级计算机研究进展
Pub Date : 2018-09-01 DOI: 10.14529/JSFI180322
A. Frolova, V. Titarev
Numerical solution of the Boltzmann equation for stationary high-speed flows around complex three-dimensional bodies is an extremely difficult computational problem. This is because of high dimension of the equation and lack of efficient implicit methods for the calculation of the collision integral on arbitrary non-uniform velocity grids. Therefore, the use of the so-called model (approximate) kinetic equations appears to be more appropriate and attractive. This article uses the numerical methodology recently developed by the second author which includes an implicit method for solving the approximating kinetic equation of E.M. Shakhov (S-model) on arbitrary unstructured grids in both velocity and physical spaces. Since most of model equations have a well-known drawback associated with the velocityindependent collision frequency it is important to determine the deviations of solutions of these equations from the solution of the complete Boltzmann equation or DSMC for high-speed gas flows. Our recent comparison of the DSMC and S-model solutions for monatomic gases with a soft interaction potential shows good agreement of surface coefficients of the pressure, heat transfer and friction, which are most important for industrial applications. In this paper, we compare the solution of model equations and the Boltzmann equation for the problem of supersonic gas flow around a cylinder when molecules interact according to the law of hard spheres. Since this law of molecular interaction is the most rigid, the difference in solutions can show the maximum error that can be obtained by using model equations instead of the exact Boltzmann equation in such problems. Our high-fidelity computations show that the use of model kinetic equations with adaptation in phase space is very promising for industrial applications.
绕复杂三维物体的静止高速流动的玻尔兹曼方程的数值解是一个极其困难的计算问题。这是由于方程的高维数和缺乏有效的隐式方法来计算任意非匀速网格上的碰撞积分。因此,使用所谓的模型(近似)动力学方程显得更为合适和有吸引力。本文采用第二作者最近开发的数值方法,其中包括一种隐式方法,用于在速度和物理空间中求解任意非结构网格上的Shakhov (s模型)近似动力学方程。由于大多数模型方程都有与速度无关的碰撞频率相关的众所周知的缺点,因此确定这些方程的解与完全玻尔兹曼方程或DSMC的解的偏差对于高速气体流动是很重要的。我们最近对具有软相互作用势的单原子气体的DSMC和s模型解进行了比较,结果表明压力、传热和摩擦的表面系数非常一致,这对于工业应用是最重要的。本文比较了分子按硬球定律相互作用时超声速气体绕圆柱体流动问题的模型方程和玻尔兹曼方程的解。由于这种分子相互作用的规律是最严格的,所以解的差异可以显示在这类问题中使用模型方程而不是精确玻尔兹曼方程所能得到的最大误差。我们的高保真计算表明,在相空间中使用具有自适应的模型动力学方程非常有希望用于工业应用。
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引用次数: 7
Analysis of the Effect of Dispersion Forces on the Dielectric Film Properties Using Parallel Computing 用并行计算分析色散力对介质薄膜性能的影响
Pub Date : 2018-09-01 DOI: 10.14529/JSFI180313
K. A. Emelyanenko, L. Boinovich, A. Emelyanenko
The paper presents the analysis of dispersion forces effect on local properties in thin free films. Using a Coupled Fluctuated Dipole Method with developed methods for numerical calculations of dielectric properties, the films with different lateral sizes and thicknesses were studied. In particular, the molecular polarizabilities at different distance from the film interface were analyzed. It was shown that dispersion interaction between the molecules, even for the case of nonpolar liquid with weak intermolecular interactions, causes a notable variation in dielectric properties of thin film, which is associated with the boundary layer formation. This variation, in turn, causes a strong dependence of polarizability accuracy on the cut-off radius. It is demonstrated that parallel computing algorithms can be effectively applied for obtaining the reliable data on properties of liquids in wetting films and boundary layers even under resource-imposed constraint on the size of ensemble of molecules to be handled in the numerical studies.
本文分析了色散力对自由薄膜局部特性的影响。采用耦合波动偶极子法和已发展的介电性能数值计算方法,对不同横向尺寸和厚度的薄膜进行了研究。特别分析了分子在离膜界面不同距离处的极化特性。结果表明,分子间的色散相互作用,即使是非极性液体的弱分子间相互作用,也会引起薄膜介电性能的显著变化,这种变化与边界层的形成有关。这种变化,反过来,导致极化精度对截止半径的强烈依赖。结果表明,并行计算算法可以有效地应用于获得湿膜和边界层中液体性质的可靠数据,即使在数值研究中要处理的分子系综的大小受到资源限制的情况下。
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引用次数: 2
期刊
Supercomput. Front. Innov.
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