PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

Du Fort-Frankel格式及DFF-I并行格式的稳定性

 本文对抛物型方程的Du Fort-Frankel(DFF)格式以及基于该格式构造的并行差分格式(DFF-I)进行了稳定性分析。采用矩阵分析方法, 证明了其无条件(LR)稳定性, 给出了DFF格式的稳定性系数的最小值的上界估计, 结果表明其与网格比有关, 从而DFF格式并非绝对稳定。本文改进了并行差分格式(DFF-I)的稳定性分析结果, 证明了其增长矩阵的谱半径严格小于1, 从而具有长时间稳定性。数值算例验证了DFF-I格式具有空间二阶精度, 且有很好的稳定性。     

复射影空间CP~((n+p)/2)中具有2-调和的一般子流形

本文研究了复射影空间中具有2-调和的一般子流形问题.利用活动标架法,获得了这类子流形成为极小子流形的Pinching定理和Simons型积分不等式,此外还得到关于2-调和伪脐一般子流形的一个刚性定理,推广了复射影空间中具有2-调和全实子流形的一些相应结果.     

Integrating open‐source software applications to build molecular dynamics systems

Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc.     

On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

Isometric artifacts from polymerase chain reaction-massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology?

The recent introduction of polymerase chain reaction (PCR)-massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR-MPS could generate “isometric drop-ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR-MPS analyses). As expected, several well-known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology.     

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.     

ESD qualification data used as the basis for building electrostatic discharge protected areas

ESD control programs that are based on the standards IEC61340-5-1 and ANSI/ESD S20.20 are targeted to provide safer handling of electronic parts now susceptible to damage by electrostatic discharge. However, ESD failures have occurred in EPA even when all standard control methods are met. To further improve EPAs, ESD control programs should be updated to cover all known common discharge scenarios, and multiple parallel ESD source parameters should be used to assess the level of ESD risks. In addition, a reliable ESD risk assessment should be based on discharge source circuit analysis and product sensitivity tests using the real discharge waveforms found in EPA.     

基于改进DPSO算法的并行测试任务优化调度研究

并行测试以减少测试时间和降低测试成本的强大优势,已成为当前自动测试系统发展的方向。针对并行自动测试过程中,测试任务调度复杂,难以优化的问题,以PSO算法为基础,通过对问题空间编码的重新定义,并运用交叉、变异算子给出了新的粒子位置的更新公式,提出了一种改进后的DPSO算法。依据并行测试完成时间极限定理,给出了并行测试任务调度的目标函数与约束条件。以某雷达电子装备并行测试系统中三块电路板并行测试为例,对改进的DPSO算法进行了仿真验证,得到了最优调度测试序列。结果表明：与遗传算法相比,改进后的DPSO算法迭代次数更少,寻优性能更好,适用于工程应用。     

异构多核系统中跨时钟域的解决方法

随着集成电路的集成度与性能的不断发展,芯片的功耗问题已经变的十分严重,功耗带来的挑战日益突出。异构多核动态调频架构是目前研究低功耗的主流方向。SOC系统当中同一时刻只有一个处理器能够控制总线,其它处理器则处理等待状态,异构多核动态调频架构能够通过降低不控制总线的处理器频率来达到降低功耗的目的。异构多核领域的处理器和总线跨时钟域解决方案,此方案在国内属于首次提出,可以运用在异构多核动态调频(DFS)架构当中。目前手持终端设备越来越强调功耗的重要性,因此异构多核领域的处理器和总线跨时钟域解决方案将有非常好的应用前景。该方案通过在处理器和AMBA总线之间添加FIFO以及一些复杂的算法,达到消除亚稳态和正常通信的目的。最终,通过仿真发现任意调节处理器的工作频率都能满足传输协议。证明该方案能在异构多核动态调频架构中运用。