Biocomputing Based on DNA Strand Displacement Reactions

The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.     

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.     

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。     

基于AltiVec技术的PowerPC处理器矢量运算性能测试

基于AltiVec技术的PowerPC处理器,在很多嵌入式信号处理领域已经取代传统的DSP处理器成为信号处理器件的首选。为了评估基于AltiVec技术的PowerPC处理器的矢量运算性能和信号处理能力,选取MPC8641D处理器为硬件测试平台,采用符合VSIPL标准的VSI/Pro Core矢量库和ixlibsav矢量库,通过测试复乘和FFT典型算法不同类型的运算时间,对AltiVec处理单元的矢量运算性能进行了测试评估。通过对测试结果的分析,基于AltiVec技术的PowerPC处理器具备强大的矢量运算处理性能,可以满足嵌入式数字信号处理技术对高性能处理器的需求。     

基于AHP权重和灰色服务器负载预测的云计算On-line迁移策略

为了克服云计算环境下由于实时用户任务的不确定性到来和服务器性能差异而导致的云计算环境的负载不均衡问题,提出了一种AHP权重获取和灰度算法预测服务器负载的云计算on-line虚拟机迁移策略。首先,设计了基于AHP和灰色服务器预测的虚拟机on-line迁移模型,提出了采用AHP获取虚拟机各资源需求权重,然后,采用灰色模型预测下一时刻的服务器负载,采用此权值向量与各无需迁移的服务器的空闲资源向量进行加权得到加权和,将具有最小加权和的物理服务器作为迁移的目标宿主机。最后,定义了基于AHP权重和灰色服务器负载预测的云计算on-line迁移算法。在CloudSim环境下进行实验,结果表明文中的迁移策略使得云计算在响应用户任务时,具有任务失败次数少、SLA违约率低和迁移成功率高的优点,同时与其它方法相比,具有负载均衡程度高的优点,具有较强的可行性。     

基于云环境的分布式软件接口自动化测试

软件测试是保证软件质量,提供可靠服务的重要技术手段。目前基于Web Service的分布式软件越来越多,其测试技术手段也越来越受到关注。Web Service的分布性和多样性使手工测试变得非常低效,因而需要不断提高Web Service测试的自动化程度。另外,云计算因其计算成本低、可伸缩性强的特点为自动化测试提供了新的支持环境。本文结合Web Service的测试需求,首次提出了基于云环境的Web Service接口自动化测试的技术框架,分析了框架内原子Web Service、组合Web Service测试的关键技术,并研发了基于CloudStack云平台的自动化测试的原型系统。实验结果表明,本文所提出的基于云平台的WebService自动化测试方案可行且提高了测试效率。     

A local parallel superconvergence method for the incompressible flow by coarsening projection

In this article, we investigate a local parallel superconvergence method by coarsening projection for the incompressible Stokes flow. The method is a combination of the local superconvergence technique and the given framework of local parallel method. For the smooth subdomains, the local superconvergence method is applied in a higher order finite dimensional space corresponding to an appropriate coarse mesh on interior domain. Moreover, a useful and flexible local parallel method is designed to obtain the local parallel superconvergence results of presented method, which offset theoretical limitation of the model without the smoothness of the exact solution and a priori regularity of the underlying problem over the whole domain. © 2014 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 31: 1209–1223, 2015     

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.     

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.     

Intracellular Entropy‐Driven Multi‐Bit DNA Computing for Tumor Progression Discrimination

Tumor progressions such as metastasis are complicated events that involve abnormal expression of different miRNAs and enzymes. Monitoring these biomolecules in live cells with computational DNA nanotechnology may enable discrimination of tumor progression via digital outputs. Herein, we report intracellular entropy‐driven multivalent DNA circuits to implement multi‐bit computing for simultaneous analysis of intracellular telomerase and microRNAs including miR‐21 and miR‐31. These three biomolecules can trigger respective DNA strand displacement recycling reactions for signal amplification. They are visualized by fluorescence imaging, and their signal outputs are encoded as multi‐bit binary codes for different cell types. The results can discriminate non‐tumorigenic, malignant and metastatic breast cells as well as respective tumors. This DNA computing circuit is further performed in a microfluidic chip to differentiate rare co‐cultured cells, which holds a potential for the analysis of clinical samples.