DNA分子计算模型

The field of practical DNA computing opened in 1994 with Adleman's paper,in which a laboratory experi-ment involving DNA molecules was used to solve a small instance of the Hamiltonian Path problem. The characteris-tic of this computation is its powerful ability in parallelism,its huge storage and high energy efficiency. This paper mainly introduces the principles of DNA computing and the sticker computing model.     

Symmetric-key cryptosystem with DNA technology

DNA cryptography is a new field which has emerged with progress in the research of DNA computing. In our study, a symmetric-key cryptosystem was designed by applying a modern DNA biotechnology, microarray, into cryptographic technologies. This is referred to as DNA symmetric-key cryptosystem (DNASC). In DNASC, both encryption and decryption keys are formed by DNA probes, while its ciphertext is embedded in a specially designed DNA chip (microarray). The security of this system is mainly rooted in difficult biology processes and problems, rather than conventional computing technology, thus it is unaffected by changes from the attack of the coming quantum computer. The encryption process is a fabrication of a specially designed DNA chip and the decryption process is the DNA hybridization. In DNASC, billions of DNA probes are hybridized and identified at the same time, thus the decryption process is conducted in a massive, parallel way. The great potential in vast parallelism computation and the extraordinary information density of DNA are displayed in DNASC to some degree.     

构造类型论与计算机程序设计

Recent years,in the area of computer programming language theories,automated deduction,and more generalized area of logic and computing,a lot of systems based on constructive type theory are used widely to design type system for computer programming languages,to do formal system develpment and verification,and to be used as foundation of mathematics and computing.constructive type theory provides computer scientists with a framework to combine logic and computer program design in an elegant and flexible way.In this paper,the evolvement of constructive type theory is first introduced.The several foundations of type theory are then discussed,together with analysis of the relationships between them.The relation between constructive type theory and computer programming is explored in-depth.In the last,Martin Lof‘‘‘‘s intuitionistic type theory is used as an example to demonstrate how to do program development and verification in the same formal system.     

Peer To Peer计算技术的应用领域与典型问题讨论

With the rapid development of computer networks there are more and more resources involoved in it,such as CPU cycles,PC‘‘s disk space and network bandwidth.Many people believe that peer to peer computing can harness these disruptive powers.In this paper we describe the applied fields,research issues and typical problems in peer to peer computing.     

计算机科学与技术方法论

In this paper,two documents of “Computing as a discpline”and “Computing Curricula 1991” are briefly introduccd,and their main contributions to the methodology of computer science and technology are porinted out.Then based on the general methodology of science and technology,the definition of computer science and technology is given,and its three paradigms (abstraction,theory,design),fundamental problem,core concept,mathematical methods and system approaches are presented.Finally,we conclude that the methodology of computer science and technology is a new theory in the computing cognition field.     

Study on Parallel Computing

In this paper, we present a general survey on parallel computing. The main contents include parallel computer system which is the hardware platform of parallel computing, parallel algorithm which is the theoretical base of parallel computing, parallel programming which is the software support of parallel computing. After that, we also introduce some parallel applications and enabling technologies. We argue that parallel computing research should form an integrated methodology of ＂architecture algorithm programming application＂. Only in this way, parallel computing research becomes continuous development and more realistic.     

Progress and Challenges in High Performance Computer Technology

High performance computers provide strategic computing power in the construction of national economy and defense, and become one of symbols of the country＇s overall strength. Over 30 years, with the supports of governments, the technology of high performance computers is in the process of rapid development, during which the computing performance increases nearly 3 million times and the processors number expands over 10 hundred thousands times. To solve the critical issues related with parallel efficiency and scalability, scientific researchers pursued extensive theoretical studies and technical innovations. The paper briefly looks back the course of building high performance computer systems both at home and abroad, and summarizes the significant breakthroughs of international high performance computer technology. We also overview the technology progress of China in the area of parallel computer architecture, parallel operating system and resource management, parallel compiler and performance optimization, environment for parallel programming and network computing. Finally, we examine the challenging issues, ＂memory wall＂, system scalability and ＂power wall＂, and discuss the issues of high productivity computers, which is the trend in building next generation high performance computers.     

Aqueous Computing: A Survey with an Invitation to Participate

The concept of aqueous computing is presented here,first infull generality,and afterward,using an implementation in a specific enzymatic technology.Aqueous computing arose in the context of biomoloecular (DNA) computing,but the concept is independent of the specifics of its biochemical origin.Alternate technologies for realizing aqueous computing are being considered for future implementation.A solution of an instance of the Boolean satisfiability problem,(SAT),is reported here that provides a new example of an aqueous computation that has been carried out successfully.This small instance of the SAT problem is sufficiently complex to allow our current enzymatic technology to be illustrated in detail.The reader is invited to participate in the rich interdisciplinary activity required by wet lab computing.A project is suggested to the reader for determining the three-colorings of a graph.The basic operations required for this project are exhibited in the solution of the SAT example reported here.     

Trends in Computing with DNA

As an emerging new research area, DNA computation, or more generally biomolecular computation, extends into other fields such as nanotechnology and material design, and is developing into a new sub-discipline of science and engineering. This paper provides a brief survey of some concepts and developments in this area. In particular several approaches are described for biomolecular solutions of the satisfiability problem (using bit strands, DNA tiles and graph self-assembly). Theoretical models such as the primer splicing systems as well as the recent model of forbidding and enforcing are also described. of DNA nanostructures and nanomechanical devices as wellWe review some experimental results of self-assemblyas the design of an autonomous finite state machine.     

DNA计算中的数据与计算模型

对DNA计算的通用性及单链、双链、粘性末端、发夹、质粒、k-臂DNA分子等各种数据作了简单介绍,并对基于DNA分子结构特性和基于DNA计算机研制过程两个方面的DNA计算模型进行了分析对比。针对各种不同的DNA数据及特性,提出了混合DNA计算模型的研究思路,并从不同角度论述了混合DNA计算模型的可行性。     

DNA计算的研究进展及展望

DNA计算是在计算科学和分子生物学的基础上发展起来的一个新颖而极具发展潜力的学科。由于它具有信息处理的巨并行性、低耗能以及高存储密度等特点,DNA计算已被广泛应用于解决各种复杂性计算问题以及模拟电子计算机进行四则运算。DNA计算机的研制也正在向着实用化阶段迈进。综述了当前DNA计算的运行机理与计算模型,重点讨论了当前研究的热点与难点问题,并对未来的发展进行了展望。     

DNA计算原理及系统分析

DNA计算是一种模拟生物分子DNA的结构并借助于分子生物技术进行计算的新方法,它开创了以化学反应作为计算工具的先例,具有广阔的应用前景。DNA计算的两个主要特点是计算的高度并行性和巨大的信息存储容量。该文简要介绍了DNA计算的原理及其数学计算的基本思想;对DNA计算的特点及其系统进行了分析。比较了DNA计算机与图灵机的异同;最后对DNA计算的发展前景进行展望。     

用于DNA数值计算的一种信息传递模式(英文)

数值计算是DNA计算的一个重要的研究方向,它直接导致了世界上第一台DNA计算机的诞生．而设计一个可以在较大范围内使用的计算机的一个前提条件是它执行数值计算的能力．这里引入一种通用的信息传递模式,利用这种模式的生化反应对DNA单链和不完全双链执行剪接操作,设计了一种N进制各位同时运算的并行计算的加法和减法的通用模型,可以实现数值计算的DNA自装配,使用DNA计算机进行数值计算比使用传统电子计算机进行数值计算的优势在于算法的巨大并行性．     

微流控DNA计算的研究进展及展望

DNA计算机具有超强的并行运算能力和巨大的数据存储能力,被认为有望解决电子计算机所面临的瓶颈问题。微流控技术提供了一个可实现自动化操作、通用型DNA计算机的支持平台。借助于微流控技术,将DNA计算相关的生化反应有机地集成在芯片平台上加以实现,进一步提高了DNA计算的可靠性、减少了实验过程的手工操作和反应时间。在介绍DNA计算机的基本概念和微流控技术基础上,围绕微流控DNA计算机的原理、模型和应用等关键问题,分析了微流控DNA计算机的体系结构及设计方法,讨论了微流控DNA计算机未来可能的发展方向。     

基于DNA序列的计算技术

DNA计算是由生物学和计算机科学相互结合形成的交叉学科,该文将对此学科的发展进行介绍。首先介绍如何借助于处理DNA序列的方法来解决卖货郎问题,并以此表明DNA计算的可行性;再对DNA的切片重组系统和图灵机系统进行比较,以此说明用切片重组系统来实现图灵机功能的可行性,最后简单介绍待解决的问题.     

DNA计算机原理、进展及难点(Ⅳ):论DNA计算机模型

在DNA计算机研究中,所建模型的好坏直接影响着DNA计算中诸多问题,如编码的难易程度、整个生物操作或生化反应的设计、解空间的大小、计算时间多少、应用范围以及通用性的程度等.如何建立快速的、功能强的、具有一定通用性的DNA计算机模型,是从事DNA计算机研究者一直关注与感兴趣的难题.为此,该文将主要围绕着DNA计算机的模型建立展开讨论,重点讨论10年来所建立起来的一些主要模型.共分为三种类型:第一种是利用DNA分子结构与特性所建立起来的几种主要模型;第二种是利用生物操作方式所建立的三种模型:试管型、表面型与芯片型;第三种是所谓的DNA计算机模型.文中讨论了这些模型的基本原理、功能、优缺点以及应用的研究进展等.最后,对DNA计算机模型研究中的难点进行了分析,并给出了相应的解决思路.     

利用脱氧核酶调控基因表达的DNA计算模型研究(英文)

用于逻辑调控基因表达分子自动机的研究是DNA计算的重要研究领域．文中将脱氧核酶技术应用于DNA计算研究当中,利用脱氧核酶的特性,特别是可以作为反义药物的特点,作为构建分子自动机的主要材料,设计了调控基因H—ras表达的DNA计算模型,而且模型也可适用于其它过表达基因的调控．结合DNA计算具备的高度并行性和智能性的优点,该模型为DNA计算在基因表达调控方面的应用做了进一步探索．     

Towards a re-programmable DNA computer

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.