基于链置换神经网络的印刷体汉字数字识别

链置换技术是一种体外恒温无酶的分子计算技术,近年来已成为DNA计算领域的常用技术,而人工神经网络是一种模仿生物神经网络结构和功能的计算模型。基于链置换技术可以用生物分子构建神经网络,并作为分类器用于执行各种模式识别任务。文章以链置换逻辑门为基础,构建了一个赢家通吃的分子神经网络计算系统,完成了印刷体汉字数字的模式识别任务。首先将代表数字模式的图片转化成用DNA序列编码的分子数据,再将人工合成的DNA数据链输入到分子神经网络计算系统中,该网络能够利用DNA链置换技术执行生物分子计算,从而实现对输入DNA数据模式的分类,最终的分类结果将会通过荧光分子修饰单链DNA输出,并通过光电信号转换自动识别。仿真实验和生物实验证明了基于链置换的分子神经网络可以出色地完成印刷体汉字数字识别的任务。     

异或门的DNA计算模型

利用DNA链置换反应分别求解二输入和三输入异或门逻辑电路.对于二输入异或门电路,将不同输入值编译成不同数量输入链,将特定数量的输入链加入反应器中,与反应器中的反应链发生链置换反应,充分反应后,通过判断检验器中绿色荧光分子明灭从而得到异或门电路的解;二输入异或门逻辑电路可以推广到三输入异或门逻辑电路.该方法具有操作简单,实验成本低,可行性高等优点.     

高灵敏度的精确DNA链置换逻辑门研究

随着生物化学技术的不断发展,以DNA分子作为存储数据和运算媒介的新型计算模型引起了研究者的广泛关注.采用编码DNA序列构建分子逻辑门是实现DNA可编程计算的基础,虽然传统的跷跷板门(seesaw gate)作为一种DNA逻辑门能够实现阶跃函数的效果,但是它在阈值附近的变化相对平缓,而且当输入超过阈值后,输出随输入增加难以稳定于期望数值,为此文章提出了基于DNA链置换的阶跃函数门.该逻辑门以四域信号链作为统一的DNA编码形式,通过湮灭反应设定阈值信号,通过支点互补程度控制反应顺序,使逻辑门的输出信号不但在阈值附近具有较高的突变灵敏度和准确度,而且当输入超过阈值后能稳定于期望值.随后基于阶跃函数门提出了能够区分"无信号输入信号"和"输入信号为低位"的与、或、非和异或门,解决了非门难以直接表示、需要通过双轨逻辑间接表示的问题.     

基于分子信标的逻辑门的计算模型

基于DNA计算的布尔电路的模拟是DNA计算研究中的一个非常具有应用前景的潜在的研究方向。利用分子信标和三链核酸分子的高度特异性及稳定性,提出了一个逻辑与、逻辑或门的DNA计算模型。基于分子信标的二种状态,将逻辑门的信息处理过程分为计算和输出二个子过程,从而使得这种基于DNA分子的逻辑门具有重复可用性,为构建基于DNA分子的大规模集成电路奠定了基础。     

基于DNA链置换的分子逻辑门计算模型

DNA计算是近年来的研究热点,分子逻辑门是DNA计算机体系结构和运算实现的重要基础。将DNA自组装与链置换技术和荧光标记相结合,在现有的链置换逻辑计算模型的基础上,构造了非门,与门,与非门,或门和或非门。可在室温下进行,减少了因复杂的生物操作步骤带来的误差。使用荧光检测来判断逻辑结果,操作简单,容易检测,且灵敏度高。     

自组装DNA计算研究难点与展望

随着DNA计算领域研究的深入,自装组DNA计算的研究成为了并行计算领域的研究热点,在本文中,作者主要分析讲述当前自组装DNA计算的几种结构形式：一维的、二维的以及三维的自组装DNA分子结构特点和发展现状,并且提出现在自组装DNA计算发展的难点以及今后的发展展望。随着多学科交叉融合力度的加大,自组装DNA计算将会成为生物信息学、应用数学、计算机仿真学、智能计算、纳米材料科学等多领域专家的重要研究方向。     

基于DNA链置换的可满足性问题的计算模型

可满足性问题是经典的NP完全问题之一。本文建立了一个基于DNA链置换的可满足性问题的计算模型,可满足性问题的约束条件被映射成计算模型上的荧光个数,将可满足性问题中变量的两种取值(0和1)分别设计成不同的DNA链,通过DNA链置换反应,最后观察反应后的计算模型上荧光个数找出可满足性问题的可行解。该模型具有操作简单,结果便于观察和检测的优点。     

DNA折纸术——全编程的信息工具

DNA作为信息分子在构建2D及3D几何形状的纳米级结构上有多种优点.二维和三维结构的组装可以通过DNA链的组合、DNA块的拼接实现.而随着DNA折纸术的出现,更是实现任意平面结构设计的可能.DNA二维平面的设计已被证实是图灵等价的.本文主要介绍基于DNA折纸的计算模型及DNA折纸术在信息领域方面的应用.     

基于聚合酶链置换反应的2D-LASM混沌文本加密算法

针对现有的基于DNA序列进行信息加密算法中没有涉及到DNA计算中化学反应这一问题,提出了基于聚合酶链置换反应的2D-LASM混沌映射文本加密算法.该算法将混沌映射产生的伪随机序列和明文信息进行异或操作,然后转换成DNA序列;随后再将DNA序列进行聚合酶链置换反应得到新的DNA序列.对新的DNA序列进行解码,得到密文.最...     

通过DNA聚合剪切放大体系提高RNA的检测灵敏度

基于循环的DNA剪切循环放大分子机器构建了一个RNA传感器。该分子机器以RNA为输入,产生大量的DNA片段,并替换报告探针上的荧光DNA从而产生荧光信号,实现对靶RNA浓度的放大检测。本分子机器分为两部分,反应部分和报告部分。在反应部分,以靶RNA为输入条件,以一个特殊设计的探针为反应模板引发一个自发连续的DNA聚合-剪切反应网络,重复产生大量信号DNA链;这些信号DNA链进入报告部分,通过杂交替换反应从一个报告探针上替换下带有荧光DNA序列,释放到溶液中。这样通过剪切产生的大量DNA适体序列被释放到溶液中,并替换报告探针上的荧光DNA,实现信号的放大。     

A molecular cryptography model based on structures of DNA self-assembly

With the progress of DNA computing, DNA- based cryptography becomes an emerging interdisciplinary research field. In this paper, we present a novel DNA cryptography that takes advantage of DNA self assembled structure. Making use of the toehold strands recognition and strand displacement, the bit-wise exclusive-or （XOR） operation is carried out to fulfill the information encryption and decryption in the form of a one-time-pad. The security of this system mainly comes from the physical isolation and specificity of DNA molecules. The system is con- structed by using complex DNA self-assembly, in which technique of fluorescent detection is utilized to implement the signal processing. In the proposed DNA cryptography, the XOR operation at each bit is carried out individually, thus the encryption and decryption process could be con- ducted in a massive, parallel way. This work may dem- onstrate that DNA cryptography has the great potential applications in the field of inRwmation security.     

Molecular logic computing model based on self-assembly of DNA nanoparticles

In this paper, a logic computing model was constructed using a DNA nanoparticle, combined with color change technology of DNA/Au nanoparticle conjugates, and DNA computing. Several important technologies are utilized in this molecular computing model: DNA self-assembly, DNA/Au nanoparticle conjugation, and the color change resulting from Au nanoparticle aggregation. The simple logic computing model was realized by a color change, resulting from changing of DNA self-assembly. Based on this computing model, a set of operations computing model was also established, by which a simple logic problem was solved. To enlarge the applications of this logic nanocomputing system, a molecular detection method was developed for H1N1 virus gene detection.     

Molecular logic computing model based on DNA self-assembly strand branch migration

In this study,the DNA logic computing model is established based on the methods of DNA self-assembly and strand branch migration.By adding the signal strands,the preprogrammed signals are released with the disintegrating of initial assembly structures.Then,the computing results are able to be detected by gel electrophoresis.The whole process is controlled automatically and parallely,even triggered by the mixture of input signals.In addition,the conception of single polar and bipolar is introduced into system designing,which leads to synchronization and modularization.Recognizing the specific signal DNA strands,the computing model gives all correct results by gel experiment.     

DNA计算机

脱氧核糖核酸（简称DNA）是生物体内的一种具有双螺旋结构的遗传物质,用DNA可以进行运算,即构成的DNA计算机能很快地求解复杂的问题;以DNA编码为信息的载体,DNA计算机中的输入和输出设备都是DNA的,链用一系列二进制的数代表所求问题中的变量,用DNA中特有的寡核苷酸序列表示这些二进制的数,再将DNA利用分子生物和化学组装技术组装到芯片上,利用DNA杂交化学方法,排除各种代表不正确解的寡核苷酸序列,最后通过聚合酶链式反应（PCR）和各种检测技术读出保留在芯片上的DNA序列,读出的DNA序列所代表的二进制数即为所求问题的解,本文将从DNA运算过程入手,介绍DNA计算机的原理和DNA计算机的若干最新研究进展。     

三维DNA自组装在多维背包问题中的应用研究

利用DNA自组装执行计算的思想已从实验上被证明了其可行性．已有多种理论模型被提出用以解决各种NP问题．基于DNA Tile自组装模型理论在二维下的扩展,本文设计了可以实现这一算法的三维DNA Tile组装系统,提出了一种用于解决多维背包问题的三维DNA自组装模型．该模型可以非确定性的输出可行性解决方案．分析表明系统可以在线性组装步骤内完成计算,所需的Tile种类数与问题维数无关．为探索三维DNA自组装的计算能力进行了一次有意义的尝试．     

DNA modular subtraction algorithm based on linear self-assembly

This paper presents a DNA algorithm based on linear self-assembly which gives the result of the modular subtraction operation of two nonnegative integers. For two n-bit nonnegative integers A and B, the algorithm gives the result of A-B mod 2 ⁿ . An extended borrow tag which indicates the relation of the minuend and the subtrahend is included in the resulting strand so that the pre-classification based on A>B or B>A is not required before the experiment. From the resulting strand, we can draw the information of operation result, operands, borrow, and the tag of the relation between the minuend and the subtrahend. The algorithm takes advantage of the parallelism characteristic of DNA computing: while given two sets of operands (one the minuend set and the other subtrahend set), the modular subtraction operation of these two sets can be achieved by a parallel processing procedure. The feasibility of the algorithm is based on a known experiment. The algorithm is of spontaneous characteristic which prevents the scale of the experimental procedures from growing with the length of the operands. As for the length of the operands n, there are O(n) kinds of strands required in the experiment, and the biochemical experimental procedures can be accomplished in constant number of steps.     

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.     

Complex shapes self-assembled from single-stranded DNA tiles

Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a 'single-stranded tile' (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly. Although ribbons and tubes with controlled circumferences have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands--folded into a 3 nm-by-7 nm tile and attached to four neighbouring tiles--acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.