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 共查询到19条相似文献,搜索用时 125 毫秒
1.
DNA分子计算的工作原理是对生物系统进行编码,以生物化学反应为基础,利用生物技术实现生物系统的状态转移来推进计算过程.2001年以色列的Yaakov Benenson等人在基于DNA计算的发卡模型实现了具有状态转移功能的分子有限状态自动机,国内则有利用DNA计算的方法构造可编程分子下推存储器的相关研究.该存储器基于分子自动机的原理,能按一定逻辑进行自组装,是一种纳米尺度的生物存储机构.文中首先通过在分子有限自动机上扩展一个分子下推存储器从而获得了一种简单的分子下推自动机,并基于该下推自动机提出了一类语言的分子自动机解法.接着提出了两种改进的分子下推自动机的模型,通过增加模型复杂度,分别解决了基本型分子下推自动机存在输人字符串限制和输入分子形式不统一的问题.计算理论表明,该种下推自动机的计算能力超过了已有的有限自动机.  相似文献   

2.
基于自组装模型的最大团问题DNA计算算法   总被引:1,自引:0,他引:1  
DNA计算在解决NP完全问题时,有着传统图灵机无法比拟的优势.但是随着DNA计算研究的不断深入,传统DNA计算模型显现出杂交错误率和生化操作复杂性过高的缺点.如何提高DNA计算结果的准确性在DNA计算研究中日显重要.针对NP完全的最大团问题,引入DNA自组装模型,提出了一种求解最大团问题的DNA计算算法.算法通过减少实验的操作步骤数,以降低生化解的错误率,给出了DNA分子的编码方案及结果检测的实验方法.算法设计的tiles种类为(O)(n+|E|),生化操作复杂性为(o)(1),其中n为图的顶点数,|E|为边数.与求解最大团问题的其他DNA算法的对比分析表明,本算法不仅明显提高了生化解的准确性,且算法的生化实验复杂度低,具有良好的实验操作性.  相似文献   

3.
DNA自组装的可满足性问题模型   总被引:1,自引:0,他引:1  
DNA自组装技术在DNA计算和纳米技术领域都发挥着极其重要的作用,许多小规模NP完全问题都可以通过自组装模型得以解决.文中以可满足问题为模型,通过构造范式中变量的特殊补链,使其与初始数据库中初始DNA链发生杂交反应,形成发夹结构,利用形成发夹结构的DNA链与没形成发夹结构的DNA链长度不同的特点,通过凝胶电泳将这些带发夹的DNA链提取出来;然后加入与这些特殊补链完全互补的DNA链,在一定温度下,通过碱基互补配对原则,发夹结构又将被重新打开.该模型充分利用了DNA分子间的自组装能力,在计算过程中只需要用到凝胶电泳操作,在一定程度上大大减少了因生物操作过多而引起的各种实验误差.  相似文献   

4.
压电基因传感器是一种新型的生物传感器,它把压电传感器的灵敏性和DNA杂交反应相结合.与传统的基因检测技术相比,它具有结构简单、无需标记、检测时间短、检测信号易处理等特点.将它用于分子运算,与常规的DNA芯片相比,它的检测结果更易于进行自动化处理,因此便于构建大规模的分子运算机器.文中在压电基因传感器和新兴学科DNA计算的基础上,给出了解决0-1规划问题新的DNA计算方法,并指出以前两种基于表面DNA计算在解决这一问题时的不足.与以往的DNA计算方法相比其输出的是电信号,因此具有操作易自动化、识别解更方便和高信息量的优点.与使用常规DNA芯片的表面DNA计算相比,使用压电基因传感器进行DNA计算可以克服可行解识别困难的问题.压电基因传感器技术有望成为新的分子运算工具,可作为构建自动化的DNA计算机的基础.  相似文献   

5.
DNA计算因其优异的计算能力已经成为当前研究热点,DNA逻辑计算模型是DNA计算体系与运算实现的重要依托。按应用技术将现有DNA逻辑计算模型进行分类:基于链置换的DNA逻辑计算模型、基于核酶的DNA逻辑计算模型、基于G-quadruplex的DNA逻辑计算模型、基于DNA自组装的逻辑计算模型、基于其他分子技术和分子材料的DNA逻辑计算模型。首先阐述了DNA逻辑计算的研究背景和研究目的以及现阶段在生物分子检测、疾病诊断、多因素分析和生物成像等领域的应用并简述其相关概念;然后梳理各DNA逻辑计算模型的研究历史和现状,分析各类逻辑计算模型所应用的分子操控技术和分子材料以及优缺点和应用前景;最后归纳总结DNA逻辑计算领域当前研究热点和发展前景,为未来提出全新的计算方式奠定基础,为信息、医疗等领域提供更好的服务。  相似文献   

6.
文中提出了一种基于硅芯片集成自组装磁珠颗粒的新型DNA光电检测系统,该系统利用普通照射光源及光电二极管进行光电信号转换,通过比较DNA杂交反应前后的光电流值,来识别DNA杂交信号.该系统是一种首次将磁珠和光电二极管相结合的新型DNA杂交检测系统,具有成本低廉、快速检测及高精度的特点.这种检测方法不需要信号增强步骤,就能够有效区分DNA单碱基错配及完全杂交的情况;由于采用了磁珠颗粒,易于在DNA计算中删除问题的非解.文中给出了求解图的最小顶点覆盖问题DNA计算模型实例,该实例证实了文中所提出的检测系统较传统检测系统具有明显的优势,有利于实现DNA计算机检测系统中解的自动化检测.  相似文献   

7.
求解0-1规划问题的DNA计算模型(英文)   总被引:1,自引:0,他引:1  
DNA计算是以DNA分子作为数据的一种新型计算模式.在DNA计算中首要面对的问题是编码问题.文中提出了一种双编码方法,利用这种编码方法可以使得在DNA计算的读解过程类似于DNA测序过程,容易实现自动化操作.基于该编码方法所建立的DNA计算模型可用于求解0-1规划问题,只需4次PCR反应即可读取问题的可行解.与其他DNA计算模型相比,该模型具有操作简单、易于实现的优点.  相似文献   

8.
近年来,随着生物计算和量子计算研究的深入,多值逻辑电路的各种实现成为一个热门的研究方向.发夹结构是DNA分子一种特殊杂交方式的产物,具有结果稳定、特异性强的优点.本文首次提出了一种利用DNA分子来实现多值逻辑电路的方法,用DNA分子的多发夹结构来表示三值逻辑的值,并给出"与"运算和"或"运算的计算模型,该模型适合应用于大规模的多值逻辑电路.  相似文献   

9.
自组装DNA计算在解决NP问题,尤其在破译密码系统方面,具有传统计算机无法比拟的优势.文中提出了一种用自组装DNA计算破译NTRU公钥密码系统的方法.针对NTRU密码系统的特点,采用DNA瓦片编码信息,借助于瓦片间的粘性末端进行自组装,给出了求解多项式卷积运算的实现方案.在此基础上,通过引入非确定性的指派瓦片,提出了一种破译NTRU系统的非确定性算法.通过创建数以亿计的参与计算的DNA瓦片,该算法可以并行地测试每个可能的密钥,以高概率地输出正确密钥.该方法最大的优点是充分利用了DNA瓦片具有的海量存储能力、生化反应的巨大并行性以及组装的自发有序性.理论分析表明,该方法具有一定的可行性.  相似文献   

10.
DNA计算机研究的重要内容是关于如何减少DNA计算机在求解大型难解问题中以问题输入纯指数增长的DNA链数。本文将分治策略应用于背包问题的DNA分子计算中,提出了一种新的DNA计算机求解背包问题的算法。背包问题的算法由咒位并行减法器、咒位数据搜索器和其他的4个子算法组成。  相似文献   

11.
基于DNA计算自组装模型的Diffie-Hellman算法破译(英文)   总被引:1,自引:0,他引:1  
DNA自组装计算模型是近年来引人关注的计算模型,已有基于自组装模型的二进制加法、乘法以及有限域中的加法和乘法的讨论.文中利用DNA自组装模型设计的模乘系统,实现了素数P的本原根g连续乘方后模p的数的排列,从而可以在线性时间内求解离散对数,为破译Diffie—Hellman密钥交换算法提供了新的生物方法.该模乘系统使用了Θ(p)种自组装类型,组装的时间复杂度为Θ(p-1).系统最后组装结果提取出报告链后,经过PCR和凝胶电泳读取离散对数结果.该模型扩展了DNA自组装计算模型的应用,为求取离散对数提供了新思路.  相似文献   

12.
Fractal patterns represent an important classof aperiodic arrangements. Generating fractalstructures by self-assembly is a majorchallenge for nanotechnology. The specificityof DNA sticky-ended interactions and thewell-behaved structural nature of DNAparallelogram motifs has previously led to aprotocol that appears likely to be capable ofproducing fractal constructions [A. Carbone andN.C. Seeman, A route to fractal DNAassembly, Natural Computing 1,469–480, 2002]. That protocol dependson gluing the set of tiles with special `gluetiles' to produce the fractal structure. It ispossible to develop a fractal-assembly protocolthat does not require the participation ofgluing components. When designed with similarDNA parallelogram motifs, the protocol involvessixteen specific tiles, sixteen closely relatedtiles, and a series of protecting groups thatare designed to be removed by the introductionof specific strands into the solution. Onenovel aspect of the construction on thetheoretical level is the interplay of bothgeometry and coding in tile design. A secondfeature, related to the implementation, is thenotion of generalized protecting groups.  相似文献   

13.
自组装DNA计算在破译密码系统方面,具有传统计算机无法比拟的优势。采用DNA分子瓦编码信息,借助于分子瓦之间的粘性末端进行自组装,通过引入非确定性的指派型分子瓦,提出了用自组装DNA计算破译EIGamal公钥密码系统的非确定性算法。通过创建数以亿计的参与计算的DNA分子瓦,该算法可以并行地以高概率地破译EIGamal公钥密码系统。  相似文献   

14.
It is shown that the (infinite) tiling problem by Wang tiles is undecidable even if the given tile set is deterministic by all four corners, i.e. a tile is uniquely determined by the colors of any two adjacent edges. The reduction is done from the Turing machine halting problem and uses the aperiodic tile set of Kari and Papasoglu.  相似文献   

15.
Towards a re-programmable DNA computer   总被引:2,自引:0,他引:2  
Microreactors lend themselves to a relatively simple implementation of DNA computing. Not only is the design of the DNA library critical for the success of the system but also the architecture of the microfluidic structure. Microreactors can be configured as Boolean operators. This paper will show that biomolecular computing can be performed with elementary building blocks, analogous to electronic logic gates. These logical operations will be performed using negative selection. Furthermore, an alternative bead barrier is introduced which can render the computer re-programmable and shows an principle architecture for selection and analysis.  相似文献   

16.
Winfree’s pioneering work led the foundations in the area of error-reduction in algorithmic self-assembly (Winfree and Bekbolatov in DNA Based Computers 9, LNCS, vol. 2943, pp. 126–144, [2004]), but the construction resulted in increase of the size of assembly. Reif et al. (Nanotechnol. Sci. Comput. 79–103, [2006]) contributed further in this area with compact error-resilient schemes that maintained the original size of the assemblies, but required certain restrictions on the Boolean functions to be used in the algorithmic self-assembly. It is a critical challenge to improve these compact error resilient schemes to incorporate arbitrary Boolean functions, and to determine how far these prior results can be extended under different degrees of restrictions on the Boolean functions. In this work we present a considerably more complete theory of compact error-resilient schemes for algorithmic self-assembly in two and three dimensions. In our error model, ε is defined to be the probability that there is a mismatch between the neighboring sides of two juxtaposed tiles and they still stay together in the equilibrium. This probability is independent of any other match or mismatch and hence we term this probabilistic model as the independent error model. In our model all the error analysis is performed under the assumption of kinetic equilibrium. First we consider two-dimensional algorithmic self-assembly. We present an error correction scheme for reduction of errors from ε to ε 2 for arbitrary Boolean functions in two dimensional algorithmic self-assembly. Then we characterize the class of Boolean functions for which the error can be reduced from ε to ε 3, and present an error correction scheme that achieves this reduction. Then we prove ultimate limits on certain classes of compact error resilient schemes: in particular we show that they can not provide reduction of errors from ε to ε 4 is for any Boolean functions. Further, we develop the first provable compact error resilience schemes for three dimensional tiling self-assemblies. We also extend the work of Winfree on self-healing in two-dimensional self-assembly (Winfree in Nanotechnol. Sci. Comput. 55–78, [2006]) to obtain a self-healing tile set for three-dimensional self-assembly.  相似文献   

17.
The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a set of coloured tiles that, starting from a bordering seed structure, self-assembles to a given rectangular colour pattern. The task of finding minimum-size tile sets is known to be NP-hard. We explore several complete and incomplete search techniques for finding minimal, or at least small, tile sets and also assess the reliability of the solutions obtained according to the kinetic Tile Assembly Model.  相似文献   

18.
Many different constructions of proofreading tile sets have been proposed in the literature to reduce the effect of deviations from ideal behaviour of the dynamics of the molecular tile self-assembly process. In this paper, we consider the effect on the tile assembly process of a different kind of non-ideality, namely, imperfections in the tiles themselves. We assume a scenario in which some small proportion of the tiles in a tile set are “malformed”. We study, through simulations, the effect of such malformed tiles on the self-assembly process within the kinetic Tile Assembly Model (kTAM). Our simulation results show that some tile set constructions show greater error-resilience in the presence of malformed tiles than others. For example, the 2- and 3-way overlay compact proofreading tile sets of Reif et al. (DNA Computing 10, Lecture Notes in Computer Science, vol 3384. Springer, 2005) are able to handle malformed tiles quite well. On the other hand, the snaked proofreading tile set of Chen and Goel (DNA Computing 10, Lecture Notes in Computer Science, vol 3384. Springer, 2005) fails to form even moderately sized tile assemblies when malformed tiles are present. We show how the Chen–Goel construction may be modified to yield new snaked proofreading tile sets that are resilient not only to errors intrinsic to the assembly process, but also to errors caused by malformed tiles.  相似文献   

19.
This paper presents an agent-based model of the emergence and evolution of a language system for Boolean coordination. The model assumes the agents have cognitive capacities for invention, adoption, abstraction, repair and adaptation, a common lexicon for basic concepts, and the ability to construct complex concepts using recursive combinations of basic concepts and logical operations such as negation, conjunction or disjunction. It also supposes the agents initially have neither a lexicon for logical operations nor the ability to express logical combinations of basic concepts through language. The results of the experiments we have performed show that a language system for Boolean coordination emerges as a result of a process of self-organisation of the agents’ linguistic interactions when these agents adapt their preferences for vocabulary, syntactic categories and word order to those they observe are used more often by other agents. Such a language system allows the unambiguous communication of higher-order logic terms representing logical combinations of basic properties with non-trivial recursive structure, and it can be reliably transmitted across generations according to the results of our experiments. Furthermore, the conceptual and linguistic systems, and simplification and repair operations of the agent-based model proposed are more general than those defined in previous works, because they not only allow the simulation of the emergence and evolution of a language system for the Boolean coordination of basic properties, but also for the Boolean coordination of higher-order logic terms of any Boolean type which can represent the meaning of nouns, sentences, verbs, adjectives, adverbs, prepositions, prepositional phrases and subexpressions not traditionally analysed as forming constituents, using linguistic devices such as syntactic categories, word order and function words.  相似文献   

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