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81.
Fast determination of neighboring atoms is an essential step in molecular dynamics simulations or Monte Carlo computations, and there exists a variety of algorithms to efficiently compute neighbor lists. However, most of these algorithms are general, and not specifically designed for a given type of application. As a result, although their average performance is satisfactory, they might be inappropriate in some specific application domains. In this article, we study the case of detecting neighbors between large rigid molecules, which has applications in, e.g., rigid body molecular docking, Monte Carlo simulations of molecular self-assembly or diffusion, and rigid body molecular dynamics simulations. More precisely, we compare the traditional grid-based algorithm to a series of hierarchy-based algorithms that use bounding volumes to rapidly eliminate large groups of irrelevant pairs of atoms during the neighbor search. We compare the performance of these algorithms based on several parameters: the size of the molecules, the average distance between them, the cutoff distance, as well as the type of bounding volume used in the culling hierarchy (AABB, OBB, wrapped, or layered spheres). We demonstrate that for relatively large systems (> 100,000 atoms) the algorithm based on the hierarchy of wrapped spheres shows the best results and the traditional grid-based algorithm gives the worst timings. For small systems, however, the grid-based algorithm and the one based on the wrapped sphere hierarchy are beneficial. 相似文献
82.
83.
Gonnet P 《Journal of computational chemistry》2007,28(2):570-573
Cell lists are ubiquitous in molecular dynamics simulations--be it for the direct computation of short-range inter-atomic potentials, the short-range direct part of a long-range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary interparticle distance calculations. In this paper, an algorithm is presented which reduces the number of spurious distance calculations by first sorting the particles along the cell pair axis and then only interacting two particles if their distance along the axis is smaller than the cutoff distance of the interaction. This approach is shown to be more efficient than the conventional approach and similar approaches using smaller cells. 相似文献
84.
85.
在深海远程正交频分复用(Orthogonal Frequency Division Multiplexing,OFDM)水声通信中,信道时延较长,导致信道频率选择性衰落严重,传统的压缩感知信道估计算法性能大幅下降。为此,本文利用深海远程信道在一定时间内具有相关性并呈较稳定簇状分布的特点,在分布式压缩感知信道估计中引入簇区域信息,进行簇约束的多数据块联合稀疏信道估计,提出一种簇约束的分布式压缩感知信道估计方法,并在深海开展了定点远程水声通信实验进行验证,实验结果表明,与传统的分布式压缩感知信道估计算法相比,本方法的能够降低50%左右的误码率。 相似文献
86.
组合优化问题的定义[1]是定义1问题XYZ是指:对于每一个π(1)-集合S,从其诸π(2)-子集合中找出π(3)-(优)集合S*.本文直接从它出发,§§2-5讨论诸π(i)-集合(i=1,2,3)的某基本特性(property),公理(pos-tulate),或者特殊情形(particularcase).列出了一个清单PPP,叫做特性清单.它远非完善,但已经可以用来讨论不少问题.§6起简单地讨论若干个子清单,所对应的问题类,并讨论求解它们的一些方法. 相似文献
87.
H. D. Baecker 《BIT Numerical Mathematics》1970,10(4):405-414
The implications of the heap, reference variables and global generators in ALGOL 68 are examined and some notes on possible implementation mechanisms are presented. In particular the use or simulation of hardware with segment addressing facilities is discussed. 相似文献
88.
A.V. Nikitin S.N. Mikhailenko N.N. Filippov I. Morino R. Kumazawa 《Journal of Quantitative Spectroscopy & Radiative Transfer》2010,111(15):2211-2224
A methane spectral line list for the 5550-6236 cm−1 range with the intensity cut off 4×10−26 cm/molecule at 296 K is presented. The line list is based on new extensive measurements of methane spectral line parameters performed at different temperatures and pressures of methane and buffer gases N2, O2 and air. This spectral line list is prepared in HITRAN-2008 format and contains the following spectral line parameters of about 11,000 lines: position, intensity, energy for lower state (where possible), air-broadening and air-shifting coefficients, exponent of temperature dependence of air-broadening coefficient and self-broadening coefficient. 相似文献
89.
Sergei V. Shirin 《Journal of Quantitative Spectroscopy & Radiative Transfer》2008,109(4):549-558
A line list for D2 16O isotopologue of water molecule was calculated in the region 0-16,000 cm−1 with energy levels up to J=30. Variational calculations are based on the semi-theoretical potential energy surface obtained by morphing ab initio potential using the experimental energy levels of D2 16O. For energy levels with J=0, 2, 5 and 10, the standard deviation of the fit is 0.023 cm−1. This line list should make an excellent starting point for spectroscopic modeling and analysis of D2O rovibrational spectra. 相似文献
90.
The study compares the effect of incorporation of three different groups of anti-hyperlipidemic drugs, namely niacin, simvastatin, and fenofibrate on the phase profile of liposomal membranes of dipalmitoylphosphatidylcholine (DPPC). The fluorescence anisotropy studies, using 1,6-diphenyl-1,3,5-hexatriene as fluorescent probe, have shown that the lipophilic molecule fenofibrate changes phase behavior of DPPC liposomal membrane to a greater extent compared to the changes produced by amphiphilic simvastatin and hydrophilic niacin. This variation in effect can be attributed to the nature of the drug molecules and hence their location in different parts of the liposomal membrane. We have also calculated the changes in van’t Hoff enthalpy values in all these three cases and observed that these values decreased with increase in drug concentrations in the case of simvastatin but for fenofibrate and niacin the effect is completely the reverse. In order to get a better insight, the fraction of motionally restricted lipid molecules has been calculated. 相似文献