Autonomous forward inference via DNA computing

Recent studies direct the researchers into building DNA computing machines with intelligence, which is measured by three main points: autonomous, programmable and able to learn and adapt. Logical inference plays an important role in programmable information processing or computing. Here we present a new method to perform autonomous molecular forward inference for expert system. A novel repetitive recognition site (RRS) technique is invented to design rule-molecules in knowledge base. The inference engine runs autonomously by digesting the rule-molecule, using a Class IIB restriction enzyme PpiI. Concentration model has been built to show the feasibility of the inference process under ideal chemical reaction conditions. Moreover, we extend to implement a triggering communication between molecular automata, as a further application of the RRS technique in our model.     

An autonomous molecular computer for logical control of gene expression

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems. Recently, simple molecular-scale autonomous programmable computers were demonstrated allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for 'logical' control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug.     

普适计算对我国IT行业的挑战

普适计算是正在发展的一种新的计算模式，硬件技术、软件技术、通讯技术、网络技术等是普适计算发展和普及的关键技术．我国在普适计算时代面临着巨大机遇和挑战，所以应积极研发具有自主知识产权的普适计算技术，加大开发普适计算市场的力度．     

A Novel Processor Scheduling Schema in Programmable Router Based on Queue Length Thresholds

Programmable router may execute computing tasks except for forwarding IP packets. How to schedule the CPU in the programmable router is an important issue that needs to be solved. In this paper, the authors establish general software architecture of programmable router firstly. Based on this architecture, authors present a novel CPU scheduling algorithm based on queue length thresholds. We model this algorithm using stochastic Petri nets. The analytic results show that this scheduling algorithm can guarantee the requirements of computing of best-effort flows and QoS flows in prograrmmable router at the same time.     

DNA计算研究的新进展

DNA计算(DNA computing)是伴随着分子生物学的兴起和发展而出现的．作为一种全新的算法，DNA计算显示了其进行复杂运算的可行性．该文介绍DNA计算的机理，探讨了目前DNA计算的研究进展，并介绍了表面固定的生物计算和由输入DNA分子同时提供数据和燃料的生物分子自动机．     

Linearly programmed DNA-based molecular computer operated on magnetic particle surface in test-tube

The postgenomic era has seen an emergence of new applications of DNA manipulation technologies, including DNA-based molecular computing. Surface DNA computing has already been reported in a number of studies that,however, all employ different mechanisms other than automaton functions. Here we describe a programmable DNA surface-computing device as a Turing machine-like finite automaton. The laboratory automaton is primarily composed of DNA (inputs, output-detectors, transition molecules as software), DNA manipulating enzymes and buffer system that solve artificial computational problems autonomously. When fluoresceins were labeled in the 5‘ end of (-) strand of the input molecule, direct observation of all reaction intermediates along the time scale was made so that the dynamic process of DNA computing could be conveniently visualized. The features of this study are: (i) achievement of finite automaton functions by linearly programmed DNA computer operated on magnetic particle surface and (ii)direct detection of all DNA computing intermediates by capiilary electrophoresis. Since DNA computing has the massive parallelism and feasibility for automation, this achievement sets a basis for large-scale implications of DNA computing for functional genomics in the near future.     

二安替比林甲烷共振瑞利散射法测定硫酸葡聚糖钠

采用共振瑞利散射法研究了二安替比林甲烷与硫酸葡聚糖钠的相互作用及其分析应用．在pH为10．0的Britton—Robinson缓冲溶液中,二安替比林甲烷与硫酸葡聚糖钠结合后共振瑞利散射急剧增强,最大散射峰在352nm处．研究了此反应体系的最佳实验条件以及共振瑞利散射光谱的特征,在最佳条件下,共振瑞利散射信号的增强与硫酸葡聚糖钠的浓度在0．05～1．5μg·mL。范围内成正比,检出限为17．0ng·mL^-1,该法用于痕量硫酸葡聚糖钠的测定,灵敏,简便．     

催化剂分子设计专家系统推理机的设计

承接前文关于催化剂分子设计专家系统的数据库与知识库的建造．详细沦述了本系统推理机的设计与实现．针对特定催化领域的知识体系，初步建立起相应的推理机制，主要包括对合适的知识推理技术的采用和推理的搜索、控制策略的选择确定．     

生产函数模型中参数的Minimax估计及应用

 生产函数模型中参数的估计问题是生产函数建模和统计推断的重要环节,也是用于测算科技进步的重要手段.在实际问题中,由于数据的原因,用传统的最小二乘估计得到的结果与实际解释会产生较大的偏差.文章介绍有效利用先验信息进行模型参数估计的Minimax估计方法,并给出了一种迭代算法,同时通过实例进行了分析和说明.     

Neural network computation with DNA strand displacement cascades

The impressive capabilities of the mammalian brain--ranging from perception, pattern recognition and memory formation to decision making and motor activity control--have inspired their re-creation in a wide range of artificial intelligence systems for applications such as face recognition, anomaly detection, medical diagnosis and robotic vehicle control. Yet before neuron-based brains evolved, complex biomolecular circuits provided individual cells with the 'intelligent' behaviour required for survival. However, the study of how molecules can 'think' has not produced an equal variety of computational models and applications of artificial chemical systems. Although biomolecular systems have been hypothesized to carry out neural-network-like computations in vivo and the synthesis of artificial chemical analogues has been proposed theoretically, experimental work has so far fallen short of fully implementing even a single neuron. Here, building on the richness of DNA computing and strand displacement circuitry, we show how molecular systems can exhibit autonomous brain-like behaviours. Using a simple DNA gate architecture that allows experimental scale-up of multilayer digital circuits, we systematically transform arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades that function as small neural networks. Our approach even allows us to implement a Hopfield associative memory with four fully connected artificial neurons that, after training in silico, remembers four single-stranded DNA patterns and recalls the most similar one when presented with an incomplete pattern. Our results suggest that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment.     

An SNP map of the human genome generated by reduced representation shotgun sequencing

Most genomic variation is attributable to single nucleotide polymorphisms (SNPs), which therefore offer the highest resolution for tracking disease genes and population history. It has been proposed that a dense map of 30,000-500,000 SNPs can be used to scan the human genome for haplotypes associated with common diseases. Here we describe a simple but powerful method, called reduced representation shotgun (RRS) sequencing, for creating SNP maps. RRS re-samples specific subsets of the genome from several individuals, and compares the resulting sequences using a highly accurate SNP detection algorithm. The method can be extended by alignment to available genome sequence, increasing the yield of SNPs and providing map positions. These methods are being used by The SNP Consortium, an international collaboration of academic centres, pharmaceutical companies and a private foundation, to discover and release at least 300,000 human SNPs. We have discovered 47,172 human SNPs by RRS, and in total the Consortium has identified 148,459 SNPs. More broadly, RRS facilitates the rapid, inexpensive construction of SNP maps in biomedically and agriculturally important species. SNPs discovered by RRS also offer unique advantages for large-scale genotyping.     

Programmable and autonomous computing machine made of biomolecules.

Devices that convert information from one form into another according to a definite procedure are known as automata. One such hypothetical device is the universal Turing machine, which stimulated work leading to the development of modern computers. The Turing machine and its special cases, including finite automata, operate by scanning a data tape, whose striking analogy to information-encoding biopolymers inspired several designs for molecular DNA computers. Laboratory-scale computing using DNA and human-assisted protocols has been demonstrated, but the realization of computing devices operating autonomously on the molecular scale remains rare. Here we describe a programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously. The automaton's hardware consists of a restriction nuclease and ligase, the software and input are encoded by double-stranded DNA, and programming amounts to choosing appropriate software molecules. Upon mixing solutions containing these components, the automaton processes the input molecule via a cascade of restriction, hybridization and ligation cycles, producing a detectable output molecule that encodes the automaton's final state, and thus the computational result. In our implementation 1012 automata sharing the same software run independently and in parallel on inputs (which could, in principle, be distinct) in 120 microl solution at room temperature at a combined rate of 109 transitions per second with a transition fidelity greater than 99.8%, consuming less than 10-10 W.     

A Novel Forensic Computing Model

0 IntroductionOWith the rapid development of society informatization,information society has arrived. While computer andcomputer networktechniques are being widely used,commit-ting cri mes on computers or using computers committingcri mes has been more and more rampant . Such cri mes treatcomputers as targets of tools ,and pri marily happen throughnetworks . They are seriously harmto national security andsocial stability,against the legal rights of citizens ,legiti matesand all other organiza…     

Multisim 11在可编程逻辑设计实验教学中的应用

介绍了Mu ltisim 11仿真软件的最新功能和特点,提出将其应用于可编程逻辑设计实验教学中。通过交通灯仿真电路实例证明,利用该软件可以进行可编程逻辑电路设计,并从一个可编程逻辑器件(PLD)原理图中导出原始VHDL语言,还可以将这个VDHL文件下载到现场可编程门阵列(FPGA)硬件中,从而简化通过仿真学习到的理论与真实实现的过渡。实践证明,该软件能够帮助学生理解可编程逻辑器件的工作原理,掌握可编程逻辑器件的设计和测试方法,提高自主学习的兴趣,有利于创新人才的培养,对可编程逻辑设计实验教学改革起到了积极作用。     

云计算环境下移动大数据合理分流方法研究

采用传统方法对移动大数据进行分流时,结果不合理,对不同处理器的分流均衡性较差。为此,提出一种新的移动大数据合理分流方法。给出云计算环境下移动大数据分流平台整体结构,在云计算环境中每个可编程交换机上安装移动大数据分流单元。将移动大数据分流问题转换成求解最优解问题,通过状态反馈实现分流。将优化分解方法与拉格朗日乘法结合在一起完成分布式计算,获取移动大数据在链路上的均衡分流模型。采用交换机分流单元获取云计算环境下网络的分流状态,求出此时收益函数的偏导数,将两者相加获取最终分流结果。对移动大数据分流延迟进行分析。实验结果表明,所提方法能够保证分流均衡性和合理性。     

基于条件谓词逻辑的可信计算形式化分析

随着可信计算应用的不断发展,针对可信计算的形式化分析理论将成为可信计算领域研究的热点。在深入研究可信计算相关技术、信任链建立和信任传递过程影响因素的基础上,提出了基于条件谓词逻辑的可信计算形式化分析方法。通过定义不同的谓词和推演规则,并在谓词逻辑中添加可信性的影响因素作为约束条件,实现对可信计算信任模型的形式化验证。利用提出的方法举例对可信计算平台安全引导过程进行了分析,并且根据分析结果提出了委托受限的安全引导过程。结果表明,基于条件谓词逻辑的形式化验证方法,能够清晰、有效的实现对可信计算信任模型的形式化分析,为可信计算应用模型的设计和完善提供参考。形式化方法的提出,对于丰富可信计算信任评估理论,促进可信计算应用发展具有一定的意义。     

溴酚蓝共振瑞利散射光谱法测定痕量阳离子表面活性剂

在盐酸介质中,溴酚蓝(BromophenolBlue,BPB)和3种阳离子表面活性剂本身的RRS强度均很弱,但当它们依靠静电引力和疏水作用力相结合形成离子缔合物后,则可观察到共振瑞利散射强度急剧增强.考察了适宜的反应条件,影响因素及共振瑞利散射强度与阳离子表面活性剂浓度之间的关系,提出了用共振瑞利散射技术测定痕量阳离子表面活性剂的方法.方法的灵敏度高,检出限可达到纳克级,其中溴酚蓝-溴化十六烷基吡啶体系的灵敏度最高,其检出限可达3 1ng/mL,并且具有较好的选择性和较高的稳定性,用于合成水样和环境水样中阳离子表面活性剂的测定,结果令人满意.     

共振瑞利散射法测定核酸探针的发展及应用

共振瑞利散射（RRS）技术以其高灵敏度、高选择性、操作简便等优点广泛应用于核酸的研究及测定。该方法中,探针的应用与发展对于核酸的测定有至关重要的影响。综述近十几年来应用于该方法中的探针发展情况及其在测定核酸中的应用进展,并对今后的发展趋势作了展望。     

DNA粘接计算模型及其应用

DNA计算是应用分子生物技术进行计算的新方法。应用形式语言及自动机理论技术研究DNA计算理论,有利于推动理论计算科学的发展。本文根据DNA分子的结构及特点给出了DNA分子的形式化描述,介绍了DNA粘接计算模型的文法结构和计算能力,并应用DNA计算方法求解3-SAT问题。     

一个稳定的基于网络坐标的多业务有偿服务P2P体系结构

提出一个稳定的基于网络坐标多业务有偿服务P2P体系结构即CIPS-P2P,使用网络坐标来提高距离敏感型应用的性能,引进信誉度和金钱点数来保证PC机实现盈利,同时保持系统的稳定性.提出用户可编程机制来方便终端用户发展新业务,该机制与金钱点数机制协同作用,驱动节点更新和改进服务.并论述了基于这一体系结构两个应用,即文件共享服务和中小规模网络计算.