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1.
许进  张雷 《计算机学报》2003,26(1):1-11
基于生化反应机理的DNA计算机模型受到科学领导内许多不同科学者们的关注与兴趣。DNA计算已经形成国际科学前沿领域内研究的一个新的热点。DNA计算机的研制需要诸如生物工程、计算机科学、数学、物理、化学、信息科学、微电子技术、激光技术以及控制科学等许多学科的共同协作攻关。该系列文章拟对DNA计算机的基本原理、研究进展DNA计算的模型以及当前研究中的难点给予研讨。该文属首篇,重点讨论了DNA计算机的基本原理,引入了生物计算系统的概念,并较系统地讨论了DNA计算模型在图与组合优化中的研究进展。  相似文献   
2.
DNA计算模型在圆柱度误差评定中的应用   总被引:5,自引:0,他引:5  
李郝林 《计量学报》2004,25(2):107-110
提出了DNA计算模型应用于圆柱度误差评定的方法,除了常规遗传算法搜索效率高、全局优化性能好的特点外,该方法的一个突出特点是可以根据待求设计参数的取值范围,设计相应的参数遗传密码表,从而将所有的误差评定算法统一在一个算法之中。  相似文献   
3.
Libraries of DNA oligonucleotides manufactured by an in vitro selection protocol were characterized for their non-crosshybridizing properties. Cloning and sequencing after several iterations of the protocol showed that the sequences, in general, became more non-crosshybridizing. Gel electrophoresis of protocol product, also, indicated non-crosshybridization, and showed evolution in the population of molecules under the non-crosshybridization selection pressure. Melting curves of protocol product also indicated non-crosshybridization when compared to control samples. Thus, it appears that the protocol does select populations of non-crosshybridizing sequences.  相似文献   
4.
In many implementations of DNA computing, reliable detection of hybridization is of prime importance. We have applied several well-established DNA mutation scanning methods to this problem. Since they have been developed for speed and accuracy, these technologies are very promising for DNA computing. We have benchmarked a heteroduplex migration assay and enzymatic detection of mismatches on a 4 variable instance of 3SAT, using a previously described blocking algorithm. The first method is promising, but yielded ambiguous results. On the other hand, we were able to distinguish all perfect from imperfect duplexes by means of a CEL I mismatch endonuclease assay.  相似文献   
5.
This paper describes a tissue P system for solving the Shortest Common Superstring Problem in linear time. This tissue P system is well suited for parallel and distributed implementation using a microfluidic device working with DNA strands. The approach is not based on the usual brute force generate/test technique applied in DNA computing, but it builds the space solution gradually. The possible solutions/superstrings are build step by step through the parallel distributed combination of strings using the overlapping concatenation operation. Moreover, the DNA microfluidic device solves the problem autonomously, without the need of external control or manipulation.An erratum to this article can be found at  相似文献   
6.
Bilinearity, complementarity and antiparallelism of the double stranded DNA structure are proved, in a general and abstract setting, as requirements of an efficient duplication algorithm for ‘mobile strings’.  相似文献   
7.
Problems in game theory can be used for benchmark DNA computations. Large numbers of game strategies and chance events can be assembledinto finite state machines. These many machines perform, in parallel,distinct plays of a game. Strategies can be exposed to selection and breeding.The computational capabilities of DNA are matched with aspects of game theory, but the most interesting problems are yet to be treated.  相似文献   
8.
Computation by Self-assembly of DNA Graphs   总被引:2,自引:0,他引:2  
Using three dimensional graph structure and DNA self-assembly we show that theoretically 3-SAT and 3-colorability can be solved in a constant number of laboratory steps. In this assembly, junction molecules and duplex DNA molecules are the basic building blocks. The graphs involved are not necessarily regular, so experimental results of self-assembling non regular graphs using junction molecules as vertices and duplex DNA molecules as edge connections are presented.  相似文献   
9.
Software Tools for DNA Sequence Design   总被引:3,自引:0,他引:3  
The design of DNA sequences is a key problem for implementing molecular self-assembly with nucleic acid molecules. These molecules must meet several physical, chemical and logical requirements, mainly to avoid mishybridization. Since manual selection of proper sequences is too time-consuming for more than a handful of molecules, the aid of computer programs is advisable. In this paper two software tools for designing DNA sequences are presented, the DNASequenceGenerator and the DNASequenceCompiler. Both employ an approach of sequence dissimilarity based on the uniqueness of overlapping subsequences and a graph based algorithm for sequence generation. Other sequence properties like melting temperature or forbidden subsequences are also regarded, but not secondary structure errors or equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology. In the second part of this paper, sequences generated with the DNASequenceGenerator are compared to those from several publications of other groups, an example application for the DNASequenceCompiler is presented, and the advantages and disadvantages of the presented approach are discussed.  相似文献   
10.
Simulations of DNA Computing with In Vitro Selection   总被引:1,自引:0,他引:1  
An attractive feature of DNA-based computers is the large number of possible sequences (4 n ) of a given length n with which to represent information. The problem, however, is that any given sequence is not necessarily independent of the other sequences, and thus, reactions among them can interfere with the reliability and efficiency of the computation. Independent sequences might be manufactured in the test tube using evolutionary methods. To this end, an in vitro selection has been developed that selects maximally mismatched DNA sequences. In order to understand the behavior of the protocol, a computer simulation of the protocol was done, results of which showed that Watson-Crick pairs of independent oligonucleotides were preferentially selected. In addition, to explore the computational capability of the selection protocol, a design is presented that generates the Fibonacci sequence of numbers.  相似文献   
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