MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

We present the software package MO VI PAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MO VI PAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, MO VI PAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 (S)‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 3₁₀‐helical analogs. © 2012 Wiley Periodicals, Inc.     

绿色建筑项目管理综合均衡优化研究

绿色建筑凭借其诸多优点,已然成为我国未来建筑发展的新方向,而对绿色建筑的工期、成本和功能进行全面系统研究并进行综合均衡优化,对于促进绿色建筑的发展具有深远影响.在描述各工程活动的成本和持续时间之间、功能和持续时间之间的非线性关系基础上,运用多属性效用函数理论构建了绿色建筑项目的功能一工期一成本综合均衡优化模型,并用遗传算法进行求解,可以得到最佳均衡解.最后通过一个实例验证了优化模型具有良好的科学性和实用性.     

Modern information technologies in construction of kinetic models for reactions of metal complex catalysis

For detailed study of complex chemical reactions mechanisms experiment is conducted for selected private reactions. This causes a problem of kinetic parameters getting—the same set of rate constants must describe both public and private reaction stages, and also a general mechanism. In this paper, solution of this problem for a reaction of olefins hydroalumination is proposed. To optimize the computational process a methodology of parallelization is elaborated. On the base of parallel computations, a kinetic model for the reaction assigned is constructed, and on its base, the physical and chemical conclusions about reaction mechanism are done.     

Several Jordan-algebraic aspects of optimization†

We describe some concepts from the theory of Euclidean Jordan algebras and their use in optimization theory. This includes: primal-dual algorithms, optimality conditions, convexity of spectral functions, proof of some inequalities and a Jordan-algebraic version of Horn–Schur theorem     

Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities

The influence of the total number of cores, the number of cores dedicated to Particle mesh Ewald (PME) calculation and the choice of single vs. double precision on the performance of molecular dynamic (MD) simulations in the size of 70,000 to 1.7 million of atoms was analyzed on three different high‐performance computing facilities employing GROMACS 4 by running about 6000 benchmark simulations. Small and medium sized systems scaled linear up to 64 and 128 cores, respectively. Systems with half a million to 1.2 million atoms scaled linear up to 256 cores. The best performance was achieved by dedicating 25% of the total number of cores to PME calculation. Double precision calculations lowered the performance by 30–50%. A database for collecting information about MD simulations and the achieved performance was created and is freely available online and allows the fast estimation of the performance that can be expected in similar environments. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Parallel implementation of γ‐point pseudopotential plane‐wave DFT with exact exchange

Semi‐local functionals commonly used in density functional theory (DFT) studies of solids usually fail to reproduce localized states such as trapped holes, polarons, excitons, and solitons. This failure is ascribed to self‐interaction which creates a Coulomb barrier to localization. Pragmatic approaches in which the exchange correlation functionals are augmented with small amount of exact exchange (hybrid‐DFT, e.g., B3LYP and PBE0) have shown to promise in rectifying this type of failure, as well as producing more accurate band gaps and reaction barriers. The evaluation of exact exchange is challenging for large, solid state systems with periodic boundary conditions, especially when plane‐wave basis sets are used. We have developed parallel algorithms for implementing exact exchange into pseudopotential plane‐wave DFT program and we have implemented them in the NWChem program package. The technique developed can readily be employed in Γ‐point plane‐wave DFT programs. Furthermore, atomic forces and stresses are straightforward to implement, making it applicable to both confined and extended systems, as well as to Car‐Parrinello ab initio molecular dynamic simulations. This method has been applied to several systems for which conventional DFT methods do not work well, including calculations for band gaps in oxides and the electronic structure of a charge trapped state in the Fe(II) containing mica, annite. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.     

Noninvasive prenatal paternity testing by maternal plasma DNA sequencing in twin pregnancies

SNPs, combined with massively parallel sequencing technology, have proven applicability in noninvasive prenatal paternity testing (NIPPT) for singleton pregnancies in our previous research, using circulating cell-free DNA in maternal plasma. However, the feasibility of NIPPT in twin pregnancies has remained uncertain. As a pilot study, we developed a practical method to noninvasively determine the paternity of twin pregnancies by maternal plasma DNA sequencing based on a massively parallel sequencing platform. Blood samples were collected from 15 pregnant women (twin pregnancies at 9–18 weeks of gestation). Parental DNA and maternal plasma cell-free DNA were analyzed with custom-designed probes covering 5226 polymorphic SNP loci. A mathematical model for data interpretation was established, including the zygosity determination and paternity index calculations. Each plasma sample was independently tested against the alleged father and 90 unrelated males. As a result, the zygosity in each twin case was correctly determined, prior to paternity analysis. Further, the correct biological father was successfully identified, and the paternity of all 90 unrelated males was excluded in each case. Our study demonstrates that NIPPT can be performed for twin pregnancies. This finding may contribute to development in NIPPT and diagnosis of certain genetic diseases.     

图形处理器并行计算用于离子发动机粒子模拟

 为了研究离子发动机羽流对航天器的影响,采用质点网格-蒙特卡罗碰撞方法对离子发动机羽流中的交换电荷离子进行了模拟。利用计算设备统一架构技术,开发出一套基于图形处理器的并行粒子模拟程序。随机数生成采用并行MT19937伪随机数生成器算法,电场方程使用完全近似存储格式的代数多重网格法求解。r-z轴对称坐标系中,在z=0 m处获得的电流密度均值为4.5×10^-5 A/m²,图形处理器所得结果与中央处理器模拟结果吻合。在16核心的NVIDIA GeForce 9400 GT图形显示卡上,取得相对于Intel Core 2 E6300中央处理器4.5~10.0倍的加速比。     

强光电离团簇并行数值模拟

 为研究强激光电离氢原子团簇,在理论上采用1维氢原子团簇的经典粒子动力学模型,结合粒子对(PP)算法及粒子模拟（PIC）方法,采用自行搭建的9节点并行集群系统,利用消息传递接口（MPI)与OpenMP混合编程模型进行了并行数值模拟计算,获得了较为理想的计算加速比。并且引入了弛豫时间参数,有效地处理了粒子间的碰撞过程,在极大简化计算量的同时,保留了物理本质。所得模拟结果与已有的实验结果符合较好,表明该并行计算模型是稳定、可行的。