Accelerating molecular modeling applications with graphics processors

Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed.     

Methods for parallel computation of SCF NMR chemical shifts by GIAO method: Efficient integral calculation,multi-Fock algorithm,and pseudodiagonalization

We implemented our gauge-including atomic orbital (GIAO) NMR chemical shielding program on a workstation cluster, using the parallel virtual machine (PVM) message-passing system. On a modest number of nodes, we achieved close to linear speedup. This program is characterized by several novel features. It uses the new integral program of Wolinski that calculates integrals in vectorized batches, increases efficiency, and simplifies parallelization. The self-consistent field (SCF) step includes a multi-Fock algorithm, i.e., the simultaneous calculation of several Fock matrices with the same integral set, increasing the efficiency of the direct SCF procedure. The SCF diagonalization step, which is difficult to parallelize, has been replaced by pseudodiagonalization. The latter, widely used in semiempirical programs, becomes important in ab initio type calculations above a certain size, because the ultimate scaling of the diagonalization step is steeper than that of integral computation. Examples of the calculation of the NMR shieldings in large systems at the SCF level are shown. Parallelization of the density functional code is underway. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 816–825, 1997     

基于高分辨质谱技术的婴幼儿食品中过敏原蛋白质的高灵敏检测

基于高效液相色谱-串联质谱(LC-MS/MS)技术,选择稳定性好、灵敏度高的特征肽段,利用平行反应监测(PRM)技术,实现了多类过敏原蛋白质的高灵敏度同时检测,并成功应用于婴幼儿食品中过敏原成分的分析。对于婴幼儿食品中蛋白质的提取,与传统的丙酮沉淀法比,采用膜上原位样品预处理方法(i-FASP)可实现更高的蛋白质提取效率和抗干扰能力。所检测的过敏原蛋白质的定量限(LOQ)最小可达到0.028 mg/L,其线性范围最宽可跨越4个数量级,且线性关系良好(相关系数R~2≥0.99)。该方法为食品中过敏原蛋白质组学快速分析提供了一种可靠的分析方法。     

Parallelizing Nonlinear Least-Squares Regression with Application to Analyses of Microalgae

Nonlinear least-squares regression is a valuable tool for gaining chemical insights into complex systems. Yet, the success of nonlinear regression as measured by residual sum of squares (RSS), correlation, and reproducibility of fit parameters strongly depends on the availability of a good initial solution. Without such, iterative algorithms quickly become trapped in an unfavorable local RSS-minimum. For determining an initial solution, a high-dimensional parameter space needs to be screened, a process that is very time-consuming but can be parallelized. Another advantage of parallelization is equally important: After determining initial solutions, the used processors can be tasked to each optimize an initial guess. Even if several of these optimizations become stuck in a shallow local RSS-minimum, other processors continue and improve the regression outcome. A software package for parallel processing-based constrained nonlinear regression (RegressionLab) has been developed, implemented, and tested on a variety of hardware configurations. As proof-of-principle, microalgae to environment interactions have been studied by infrared attenuated total reflection spectroscopy. Additionally, light microscopy has been used to monitor cell production. It is shown that spectroscopic data sets with 10,000?s of data points and >1000 nonlinear model parameters as well as imaging data with 100,000s of data points and >2000 nonlinear model parameters may now be investigated by constrained nonlinear regression. Acceleration factors of up to 8.1 have been obtained which is of high practical relevance when computations take weeks on single-processor machines. Solely using parallel processing, the RSS values may be improved up to a factor of 5.5.     

受限于两平行板间的对称星形共聚物Am Bm熔体相行为的格子自洽场理论研究

采用格子自洽场理论计算研究了受限于2个平行板间的对称星形共聚物AmBm(m=1,2,3,4,5)熔体形成的层状相结构.在给定的相互作用下(χNAB不变,χ为Flory-Huggins相互作用参数,NAB=(N?1)/m为单个聚合物分子中一对AB臂的总链节数目),针对平行板间距为体相周期的情况,系统考察了共聚物链长N和单个聚合物分子中A(或B)臂数目m对受限层结构细节及层取向的影响.由计算结果,当N或NAB不变时,受限层的归一化界面宽度随m的增大而减小.受限板为中性时,垂直层结构的单链自由能比平行层结构的低.随着板对共聚物中一种嵌段的选择作用Λ的增大,体系发生垂直层到平行层的转变,该转变为一阶相变.当m不变时,N越小,上述转变出现在越大的Λ值处,体系越容易保持垂直层结构.并且N越小,层状结构周期越小.当N或NAB不变时,m越大体系越容易保持垂直层结构.总之,星形共聚物的链长越短、臂数越多时,垂直层稳定的Λ区间越大、层状结构的界面宽度越小.这些结论可以指导刻蚀应用中对体系参数的选择.     

A parallel acquisition charged particle energy analyser using a magnetic field

A new form of charged particle energy analyser is proposed. It is broadly based on the 180° magnetic spectrograph, but is intended to detect charged particles moving out of the dispersion plane with a helical motion. The analyser has the capability to acquire charged particle energy spectra over a large energy range, similar to those acquired in Auger electron spectroscopy, ca. 2500 eV and large angular range, up to 90°, in parallel. These conditions are more favourable for surface analysis by electron spectroscopy at high vacuum, where for example an electron energy resolution of 0.2% to 0.5% is typical. Expressions showing how the landing positions of the charged particles on the detector vary as a function of energy and polar take off angle are determined as well as the conditions for optimum energy resolution at a range of polar take off angles. The equations reveal that in general, the device obtains the highest resolution at angles of revolution greater than 180°. The design is simple and could be easily put into practice using available material and technologies and be used to analyse the energies of electrons emitted from a sample placed in a scanning electron microscope. It can be made to function with a primary electron beam of any desired energy and could fit in to the small space between the sample and the end of an electron column. However, the device is difficult to retrofit into existing SEMs and ideally an SEM column needs to be designed to work in association with the analyser. The direction of the magnetic field of the analyser is coincident with the axis of the electron gun so that the primary beam is little influenced by the magnetic field and symmetry can be maintained in the primary beam electron column. Because the device is intended to acquire electron spectra in parallel, any movement of the primary beam on the sample because of a ramping field in the analyser is avoided. The field of view and the effect of the analyser upon the operation of the SEM are discussed. Spectra including elastic and Auger peaks reveal an energy resolution of ~4 eV at 900‐eV electron energy. Copyright © 2016 John Wiley & Sons, Ltd.     

A parallel radix‐4 block cyclic reduction algorithm

A conventional block cyclic reduction algorithm operates by halving the size of the linear system at each reduction step, that is, the algorithm is a radix‐2 method. An algorithm analogous to the block cyclic reduction known as the radix‐q partial solution variant of the cyclic reduction (PSCR) method allows the use of higher radix numbers and is thus more suitable for parallel architectures as it requires fever reduction steps. This paper presents an alternative and more intuitive way of deriving a radix‐4 block cyclic reduction method for systems with a coefficient matrix of the form tridiag{ ? I,D, ? I}. This is performed by modifying an existing radix‐2 block cyclic reduction method. The resulting algorithm is then parallelized by using the partial fraction technique. The parallel variant is demonstrated to be less computationally expensive when compared to the radix‐2 block cyclic reduction method in the sense that the total number of emerging subproblems is reduced. The method is also shown to be numerically stable and equivalent to the radix‐4 PSCR method. The numerical results archived correspond to the theoretical expectations. Copyright © 2013 John Wiley & Sons, Ltd.     

Scheduling deteriorating jobs with a learning effect on unrelated parallel machines

In this study we consider unrelated parallel machines scheduling problems with learning effect and deteriorating jobs, in which the actual processing time of a job is a function of joint time-dependent deterioration and position-dependent learning. The objective is to determine the jobs assigned to corresponding each machine and the corresponding optimal schedule to minimize a cost function containing total completion (waiting) time, total absolute differences in completion (waiting) times and total machine load. If the number of machines is a given constant, we show that the problems can be solved in polynomial time under the time-dependent deterioration and position-dependent learning model.     

用非精确的平行割线法求解奇异问题

奇异方程经常出现在很多实际非线性问题中,如反应扩散系统等.因此,研究奇异非线性方程的求解具有十分重要的意义.平行割线法是一种经典的求解非线性方程的迭代方法,它收敛阶较高,计算量较少.但在解决实际问题时,一方面,抽象出的数学模型与实际问题总是存在着一定的偏差,另外,在数据的计算中难免存在着一定的计算误差,所以研究用非精确的平行割线法求解非线性奇异问题具有很重要的现实意义,使得求解奇异问题具有更高的实用性和可行性.采用在平行割线法的迭代公式中加入摄动项的方法,构造出新的加速迭代格式,证明了新的迭代格式的收敛性,给出了收敛速率,得到了误差估计.     

卫星数传接收规划模型与算法研究

作为对地观测卫星任务执行的两个重要阶段之一,数传接收的规划任务是一个具有多时间窗口、多优化目标和多资源约束的NP-Hard优化问题。中继星的引入为数据全天候近实时传输提供可能,同时也为数传规划提出新的问题。本文主要完成两项工作:第一,建立风险控制的卫星数传接收规划模型;第二,阐述基于遗传禁忌的模型求解方法,进一步采用分布式并行求解策略,改善了求解算法的收敛速度和鲁棒性。最后,通过STK提供基础仿真数据,验证了本文规划模型和求解算法的有效性。