A DNA computer is a molecular computer that works biochemically.

It "computes" using enzymes Concept first thought by Leonard Aldeman, in 1994

Source : http://www.wiggler.gr/wp-content/maya_ii/

To the naked eye, the DNA computer looks like clear water solution in a test tube. Instead of showing up on a computer screen, results are analyzed using a technique that allows scientists to see the length of the DNA output molecule.

DNA computing was proposed as a means of solving a class of intractable computational problems ,in which the computing time can grow exponentially with the problem size.
(Liu et al. Nature, 403, 175-179 (13 January 2000)

Use of DNA based computers provides almost 2000 times more data storage capacity . DNA computations may use a billion times less energy than an electronic computer while storing data in a trillion times less space. Computing with DNA is highly parallel

Integrative knowledge is gaining momentum day by day. The challenge to integrate biological systems with the information systems is a huge one. Molecular biology is a science more closely based on concepts linked to arithmetic and computation.

The central dogma of life i.e. typically, replication, transcription and translation have the same form: begin core action check point repeat end


There are two reasons for using molecular biology to solve computational problems.

1) The information density of DNA is much greater than that of silicon : 1 bit can be stored in approximately 1 nm3. Others storage media, such as videotapes, can store 1 bit in 1012 nm3. 2) Operations on DNA are massively parallel: a test tube of DNA can contain trillions of strands. Each operation on a test tube of DNA is carried out on all strands in the tube in parallel.

Turing machine the simplest form of a computer. It was the first computer invented on paper (theoretically) (Turing, 1937).
Source : http://en.wikipedia.org/wiki/Turing_machine

It is a simple machine reading and modifying a tape carrying a linear sequence of symbols. Its most important feature is the requirement for a physical separation between a string of symbols, the data/program and a machine possessing specific properties that enable it to manipulate (read and write on) the string of symbols.

The genetic program had to be something that had to continuously passed and in an exact manner

The discovery of the processes  that organize the regulation of gene expression  genetic code Led to the idea that life could be represented as the result of the expression of a program, viewed as a linear string of symbols, the chain of nucleotides in DNA. Described as a recipe.

Proofs :

1) The basis of genetic engineering is the manipulation of DNA molecules and expression in foreign cells 2) Natural transformation, which identified DNA as the carrier of the genetic program. 3) Horizontal gene transfer.

Thus, a large number of genes coming from the outside can be expressed and understood by a of bacterium.

Concept first thought by Leonard Aldeman, in 1994 DNA is a double stranded helix where the two strands are linked by base pairs A to T and G to C. These nucleotides would essentially take the place of the binary code of 1's and 0's used in the computers today. A single strand of DNA is similar to a string consisting of a combination of four different symbols A G C T.

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Instead of using electrical impulses to represent bits of information, the DNA computer uses the biochemical properties of these molecules by examining the patterns of combination or growth of the molecules or strings. In a DNA computer, computation takes place in test tubes or on a glass slide coated in 24K gold. DNA computers will work through the use of DNAbased logic gates. These would use DNA codes in place of electrical signals as inputs to the DNA logic gates.

(Aldeman Science 266, 1021 (1994)

A program on a DNA computer is executed as a series of biochemical operations, which have the effect of Synthesizing Extracting Ligating Cutting Modifying Separating Amplifying Annealing Cloning

The Hamiltonian Path Problem is to start at node 1, end at node 5, and visit each node exactly once while following the available edges. A DNA based computer Program was designed, by engineering Baumgardner et al. 2009 the DNA of Escherichia coli with Salmonella typhimurium Hin/hixC recombinase system, to find the unique Hamiltonian path. (1 4 7 2 3 6 5)
(Baumgardner et al. Journal of Biological Engineering 2009)

ALGORITHM  Input :A directed graph G with n vertices, and designated vertices 1 and 5.
Generate paths in G randomly in large quantities Reject all paths that do not begin with 1 and do not end in 5. Reject all paths that do not involve exactly n vertices. Reject all paths that do not involve designated edges

Output : YES, if any path remains; NO, otherwise.

For step 1, each node of the graph was encoded as a random 20-base strand of DNA. Then, for each edge of the graph, a different 20-base oligonucleotide was generated that contains the second half of the source code plus the first half of the target node. For step 2, the product of step 1 was amplified by PCR using oligonucleotide primers representing 1 and 5. This amplified and thus retained only those molecules encoding paths that begin with 1 and end with 5 ~1014 computations are carried out in a single second.

For step 3, agarose gel electrophoresis was done which allowed separation and recovery of DNA strands of the correct length. The desired path, if it exists, would pass through all seven nodes, each of which was assigned a length of 20 bases. Thus PCR products encoding the desired path would have to be 140 bp. For step 4, The solution strand was filtered using affinity chromatography

DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The burnt pancake problem involves a stack of pancakes of different sizes, each of which has a golden and a burnt side. The aim is to sort the stack so the largest pancake is on the bottom and all pancakes are golden side up in the fewest number of flips

(Haynes et al. Journal of Biological Engineering 2 2008 )

Flips of the DNA fragment pancakes are driven by the S. typhimurium Hin /hix DNA recombinase system in E. coli DNA segments are sorted by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; E. coli cells become antibiotic resistant when the segments are properly sorted.

(Haynes et al. Journal of Biological Engineering 2 2008 )

The type of bacteria known as magnetotactic bacteria, contain structures called magnetosomes, In the presence of a magnetic field, these induce a torque on the bacteria, making them swim according to the direction of the field. An electronic microcircuit that contains both the bacteria and an array of conductors that produce magnetic fields has been developed . By carefully controlling which conductors are active, the microcircuit can make the bacteria move in specific directions. A computer and an optical microscope provide a feedback loop, tracking the motion of the bacteria and adjusting the conductors to achieve the desired behaviour

(Martel et al. The international journal of robotics research 2009)

E. coli has been programmed to emit red or green florescent light in response to varying concentrations of a signal chemical emitted by another of E. coli The cells glowed green when they sensed a higher concentration of the signal chemical and red when They sensed a lower concentration. The bulls eye pattern formulation could help in detection of anthrax

Source : http://www.livescience.com/ technology/050428_bacteria_computer.html

Advantages

Disadvantages

Generating solution sets for Can perform millions of operations relatively simple problems, may simultaneously. require impractically large amounts of memory. For every correct answer there are millions of incorrect paths generated that are worthless Still at a conceptual stage The first DNA computers are unlikely to feature word processing, e-mailing and solitaire programs

Amount of working memory Conduct large parallel searches.

Lesser energy dissipation Could be used by national governments for cracking secret codes, or by airlines wanting to map more efficient routes etc..

Though still at a conceptual stage, the future of bacteria as computers and making computers seems very bright owing to the extensive fastpaced research in this direction as the in-silico technology has almost reached a plateau stage. The DNA based computers will surely be the next generation computers, which would also be used for other allied purposes such as detection of diseases and also in intelligence systems for the country