No wonder you activities are, reading will be always needed. It is not only to fulfil the duties that you need to finish in deadline time. Reading will encourage your mind and thoughts. Of course, reading will greatly develop your experiences about everything. Reading molecular biology of the gene is also a way as one of the collective books that gives many advantages. The advantages are not only for you, but for the other peoples with those meaningful benefits.

Molecular Biology of the Gene.

A device, system and method for molecular computing which not only includes a suitable, renewable power source, but actually is able to receive power through the performance of the computations themselves. The molecular computing machine of the present invention actually employs the free-energy difference between its input and output to accomplish a computation, preferably by using its input DNA molecule as a partial source of energy, or alternatively by using the input DNA molecule as the sole source of energy. This molecular finite automaton preferably transforms an input DNA molecule into an output DNA molecule by digesting the input as it computes.

Programmable and autonomous computing machine made of biomolecules

Summary form only given. Nucleic acids have proven to be remarkably versatile as an engineering material for chemical tasks including the storage of information, catalyzing reactions creating and breaking bonds, mechanical manipulation using molecular motors, and constructing supramolecular structures. This talk will focus particularly on molecular self-assembly, giving examples of engineered DNA "tiles" that crystallize into two-dimensional sheets, one-dimensional tubes and ribbons, and information-guided patterns such as a Sierpinski triangle and a binary counter. A theme is how cooperative binding can be used to control nucleation and direct selective tile attachment. Such "algorithmic" self-assembly may provide a bottom-up fabrication method for creating complex, well-defined supramolecular structures that can be used as scaffolds or templates for applications such as arranging molecular electronic components into active circuits

/pdf/algorithmic-self-assembly-of-dna-2wgck1v5s8.pdf

Algorithmic Self-Assembly of DNA

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605–608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynam...

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Recent research has considered DNA as a medium for ultra-scale computation and for ultra-compact information storage. One potential key application is DNA-based, molecular cryptography systems. We present some procedures for DNA-based cryptography based on one-time-pads that are in principle unbreakable. Practical applications of cryptographic systems based on one-time-pads are limited in conventional electronic media by the size of the one-time-pad; however DNA provides a much more compact storage medium, and an extremely small amount of DNA suffices even for huge one-time-pads. We detail procedures for two DNA one-time-pad encryption schemes: (i) a substitution method using libraries of distinct pads, each of which defines a specific, randomly generated, pair-wise mapping; and (ii) an XOR scheme utilizing molecular computation and indexed, random key strings. These methods can be applied either for the encryption of natural DNA or for artificial DNA encoding binary data. In the latter case, we also present a novel use of chip-based DNA micro-array technology for 2D data input and output. Finally, we examine a class of DNA steganography systems, which secretly tag the input DNA and then hide it within collections of other DNA. We consider potential limitations of these steganographic techniques, proving that in theory the message hidden with such a method can be recovered by an adversary. We also discuss various modified DNA steganography methods which appear to have improved security.

/pdf/dna-based-cryptography-yk3xbmo1pr.pdf

DNA-based Cryptography

Adleman has solved the Hamiltonian path problem by encoding the vertices and edges of the Hamiltonian graph in oligonucleotides of DNA, hybridizing the oligonucleotides to produce potential answers, and extracting the DNA which corresponds to the Hamiltonian path. Depending on the conditions under which the DNA reactions occur, the possibility of false positives, or wrong solutions to the Hamiltonian path problem which appear correct, are possible. This possibility was veri ed by experiment. The primary mechanism for the production of false positives is hybridization stringency that depends on the reaction conditions, of which the most important is temperature. Depending on the temperature, two oligonucleotides can hybridize without exact matching between their base pairs. For DNA-based solutions to combinatorial problems to become a viable and practical technology, the possibility of false positives must be eliminated. This can be accomplished by encoding the vertices and edges of the Hamiltonian graph in DNA oligonucleotides, or codewords, that are a minimum distance, which depends on temperature, from each other. This reliable encoding eliminated the risk of a false positive, which was supported by an experimental trial. The encoding was produced by a genetic algorithm search of the space of possible codewords. The Hamming bound was shown to be an upper bound on the number of vertices that could be encoded in DNA without introducing the possibility of false Hamiltonian paths.

Good encodings for DNA-based solutions to combinatorial problems.

DNA-based computing uses the tendency of nucleotide bases to bind (hybridize) in preferred combinations to do computation. Depending on reaction conditions, oligonucleotides can bind despite noncomplementary base pairs. These mismatched hybridizations are a source of false positives and negatives, which limit the efficiency and scalability of DNA-based computing. The ability of specific base sequences to support error-tolerant Adleman-style computation is analyzed, and criteria are proposed to increase reliability and efficiency. A method is given to calculate reaction conditions from estimates of DNA melting.

Reliability and Efficiency of a DNA-Based Computation

Computation based on manipulation of DNA molecules has the potential to solve problems with massive parallelism. DNA computation, however, is implemented with chemical reactions between the nucleotide bases, and therefore, the results can be error-prone. Application of DNA based computation to traditional computing paradigms requires error-free computation, which the DNA chemistry is unable to support. Careful encoding of the nucleotide sequences can alleviate the production of errors, but these good encodings are difficult to find. In this paper, an algorithm for evolutionary computation with DNA is sketched. Evolutionary computation does not require error-free DNA chemistry, and in fact, takes advantage of errors to produce change and variation in the population. An application of the DNA based evolution program to a search for good DNA encodings is sketched.

A DNA based implementation of an evolutionary search for good encodings for DNA computation

Artificial immune systems attempt to distinguish self from nonself through string matching operations. A detector set of strings is selected by eliminating random strings that match the self strings. DNA based computers have been proposed to solve complex problems that defy solution on conventional computers. They are based on (hydrogen bonding based) matchings (called hybridizations) between Watson-Crick complementary pairs, Adenine-Thymine or Cytosine-Guanine. Therefore, a single strand (an oligonucleotide) will bind with other oligonucleotides that match most closely its sequence under the operation of Watson-Crick complementation. In this paper, an algorithm for implementing an artificial immune system for self-nonself discrimination based on DNA is described. This procedure takes advantage of the inherent pattern matching capability of DNA hybridization reactions and the notion of similarity naturally found in DNA hybridization.

A DNA based artificial immune system for self-nonself discrimination

DNA computing holds out the promise of important and significant connections between computers and living systems, as well as promising massively parallel computations. Before these promises are fulfilled, however, important challenges related to errors and practicality have to be addressed. On the other hand, new directions toward a synthesis of molecular evolution and DNA computing might circumvent the problems that have hindered development, so far.

S.E. Stevens

Papers

Good encodings for DNA-based solutions to combinatorial problems.

Reliability and Efficiency of a DNA-Based Computation

A DNA based implementation of an evolutionary search for good encodings for DNA computation

A DNA based artificial immune system for self-nonself discrimination

DNA Computing: A Review