Dna Computer Report

8/7/2019 Dna Computer Report

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1.INTRODUCTION

What is a DNA Computer?

DNA computers can be defined as the use of biological molecules,

primarily DNA (or RNA), to solve computational problems that are adapted

to this new biological format.

Basics of DNA Computing

1. DNA computing is utilizing the property of DNA for massively parallel

computation.

2. With an appropriate setup and enough DNA, one can potentially solve huge

problems by parallel search.

3. Utilizing DNA for this type of computation can be much faster than utilizing a

conventional computer.

4. Leonard Adleman proposed that the makeup of DNA and its multitude of

possible combining nucleotides could have application in computational research

techniques.

Dept. of CSE, The Oxford College of Engineering -1-


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2.UNIQUENESS OF DNA

1. Can store information at the nanoscale

1 gram can store as much information as would

fit on 1 trillion CD's.

This image shows 1 gram of DNA on a CD. The

CD can hold 800 MB of data.

The 1 gram of DNA can hold about 1x1014 MB of

data.

The number of CDs required to hold this amount

of information, lined up edge to edge, would circle

the Earth 375 times, and would take 163,000 centuries

to listen to.

2. Can be synthesized quickly and cheaply.

1017 copies of a short sequence costs less than

CAN$50.

3. Can be copied, or sorted by length.

4. Enormous parallelism.

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.

5. Extraordinary energy efficiency.

Adleman figured his computer was running

2 x 1019 operations per joule.



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3.ADLEMANs SOLUTION OF THE HAMILTONIAN

DIRECTED PATH PROBLEM (HDPP).

I believe things like DNA computing will eventuallyI believe things like DNA computing will eventually

lead the way to a molecular revolution, whichlead the way to a molecular revolution, which

ultimately will have a very dramatic effect on the world. L. Adlemanultimately will have a very dramatic effect on the world. L. Adleman

Traveling Salesman Problem:

Find a path from city 1 to city 7 going through all the cities only once.



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The following algorithm solves the Hamiltonian Path

problem.

1. Generate random paths through the graph.

2. Keep only those paths that begin with the start city (1) and conclude with the end city

(7).

3. If the graph has n cities, keep only those paths with n cities. (n=7).

4. Keep only those paths that enter all cities at least once.

5. Any remaining paths are solutions.



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Encode Graph into DNA sequences

Step 1 : Represent each city by a single DNA strand 20

nucleotides long randomly chosen.

The molecules can be made by a machine calledDNA Synthesizer.



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Represent the route between any two cities by a single DNA

strand 20 nucleotides long.



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Step 2:Select paths that start and end with the correct cities.

1.Millions of strands of DNA representing every city and every possible route between

any two cities are placed in a test tube where the strands combine.

2. We select only strings that have City 1 at one end and City 7 at the other by using

Polymerase Chain Reaction (PCR).

The polymerase chain reaction (PCR) i s a biochemistry and molecular biology

technique forexponentially amplifying DNA, via enzymaticreplication, without using a

living organism (such as E. coli or yeast). As PCR is an in vitro technique, it can be

performed without restrictions on the form of DNA, and it can be extensively modified to

perform a wide array ofgenetic manipulations.

PCR is commonly used in medical and biological research labs for a variety of tasks,

such as the detection ofhereditary diseases, the identification ofgenetic fingerprints, the

diagnosis of infectious diseases, the cloning of genes, paternity testing, and DNA

computing.

PCR was invented by Kary Mullis. At the time he thought up PCR in 1983, Mullis was

working in Emeryville, California forCetus Corporation, one of the first biotechnology

companies.

3.

What we end up with after PCR is a test tube full of double stranded DNA of various

lengths.

http://en.wikipedia.org/wiki/Biochemistryhttp://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/Exponential_growthhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/DNA_replicationhttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/E._colihttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/In_vitrohttp://en.wikipedia.org/wiki/In_vitrohttp://en.wikipedia.org/wiki/Genetic_engineeringhttp://en.wikipedia.org/wiki/Hereditary_diseasehttp://en.wikipedia.org/wiki/Genetic_fingerprinthttp://en.wikipedia.org/wiki/Diagnosishttp://en.wikipedia.org/wiki/Infectious_diseasehttp://en.wikipedia.org/wiki/Cloninghttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Paternity_testinghttp://en.wikipedia.org/wiki/DNA_computinghttp://en.wikipedia.org/wiki/DNA_computinghttp://en.wikipedia.org/wiki/Kary_Mullishttp://en.wikipedia.org/wiki/Emeryvillehttp://en.wikipedia.org/wiki/Cetus_Corporationhttp://en.wikipedia.org/wiki/Biotechnologyhttp://en.wikipedia.org/wiki/Biochemistryhttp://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/Exponential_growthhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/DNA_replicationhttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/E._colihttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/In_vitrohttp://en.wikipedia.org/wiki/Genetic_engineeringhttp://en.wikipedia.org/wiki/Hereditary_diseasehttp://en.wikipedia.org/wiki/Genetic_fingerprinthttp://en.wikipedia.org/wiki/Diagnosishttp://en.wikipedia.org/wiki/Infectious_diseasehttp://en.wikipedia.org/wiki/Cloninghttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Paternity_testinghttp://en.wikipedia.org/wiki/DNA_computinghttp://en.wikipedia.org/wiki/DNA_computinghttp://en.wikipedia.org/wiki/Kary_Mullishttp://en.wikipedia.org/wiki/Emeryvillehttp://en.wikipedia.org/wiki/Cetus_Corporationhttp://en.wikipedia.org/wiki/Biotechnology


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Step 3: Select paths that contain the correct number of cities.

We now want to select those paths that are seven cities long.

To accomplish this we can use a technique called Gel Electrophoresis.

Gel Electrophoresis

Gel electrophoresis is a group of techniques used to separate molecules based on

physical characteristics such as size, shape, orisoelectric point. Gel electrophoresis is

usually performed for analytical purposes, but may be used as a preparative technique to

partially purify molecules prior to use of other methods such as mass spectrometry, PCR,

cloning, DNA sequencing, orimmuno-blotting for further characterization.

http://en.wikipedia.org/wiki/Isoelectric_pointhttp://en.wikipedia.org/wiki/Mass_spectrometryhttp://en.wikipedia.org/wiki/Polymerase_chain_reactionhttp://en.wikipedia.org/wiki/Cloninghttp://en.wikipedia.org/wiki/DNA_sequencinghttp://en.wikipedia.org/wiki/Western_Blothttp://en.wikipedia.org/wiki/Isoelectric_pointhttp://en.wikipedia.org/wiki/Mass_spectrometryhttp://en.wikipedia.org/wiki/Polymerase_chain_reactionhttp://en.wikipedia.org/wiki/Cloninghttp://en.wikipedia.org/wiki/DNA_sequencinghttp://en.wikipedia.org/wiki/Western_Blot


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DNA electrophoresis apparatus.An agarose gel is placed in this buffer-filled box

and electrical current is applied via the power supply to the rear. The negative terminal is

at the far end (black wire), so DNA migrates towards the camera.

Separation of large (macro) molecules depends upon two forces: charge and mass. When

a biological sample, such as proteins or DNA, is mixed in abuffersolution and applied to

a gel, these two forces act together. The electrical current from one electrode repels the

molecules while the other electrode simultaneously attracts the molecules. The frictional

force of the gel material acts as a "molecular sieve," separating the molecules by size.

During electrophoresis, macromolecules are forced to move through the pores when the

electrical current is applied. Their rate of migration through the electric field depends on

the strength of the field, size and shape of the molecules, relative hydrophobicity of the

samples, and on the ionic strength and temperature of the buffer in which the molecules

aremoving. After staining, the separated macromolecules in each lane can be seen in a

series of bands spread from one end of the gel to the other.

http://www.bergen.org/AAST/projects/Gel/buffer.htmhttp://www.bergen.org/AAST/projects/Gel/buffer.htm


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Step 4: select paths that have a complete set of cities.

Now we filter the DNA molecules by city, one city at a time. Since the DNA

we start with contains seven cities, we will be left with strands that encode

each city once.

DNA containing a specific sequence can be purified from a sample of mixed

DNA by a technique calledAffinity Purification.

An iron bead is attached to a fragment complementary to a substring.

A magnetic field is the used to pull out all of the DNA fragments containing such a

sequence.

Reading out the answer

To find the answer we can sequence the DNA strands or use a method called

Graduated PCR.



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4.INFORMATION STORAGE IN DNA

With bases spaced at 0.35 nm along DNA, data density is over a million Gbits/inch

compared to 7 Gbits/inch in typical high performance HDD.

Nucleic Acids are used because of density, efficiency and speed. DNA molecules can

store far more information than any existing computer memory chip.

A single bacterium cell measures just a micron square - about the same size as a single

silicon transistor - but holds more than a megabyte of DNA memory and has all the

computational structures to sense and respond to its environment.



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5.EFFICIENCY OF DNA COMPUTERS

While traditional computers represent information as a sequence of 0s and 1s, DNA

computers encode the information directly in their chemical sequence. The density of

information that can be stored on DNA is 1 bit per cubic nanometer which is a trillionth

of the space required of conventional computers with a density of 1 bit per 1012 cubic

nanometers. Also, DNA computers are efficient according to Adleman. 1 joule is

sufficient for 2 * 1019 operations where an operation is defined to be the ligation of two

DNA molecules. Computers have an efficiency of about 109 operations per joule.



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However, as others have pointed out , Adleman did not include the cost of extracting the

information, the PCR that was needed to amplify the initial DNA, and so forth. One way

that DNA may be used is to store information. Searching for information would only

require the synthesis of a small probe complementary to the region of interest, and then to

locate where the probe bound to the DNA. DNA in a test tube could hold a million times

more information than is thought to be stored in the human brain.

Because the biochemical operations involved are subject to errors , rigorous tests of the

accuracy is needed.

Every a set of strands is tailored to a specific problem, so we need a new set each new

problem.

While a DNA computer takes much longer than a normal computer to perform each

individual calculation, it performs an enourmous number of operations at a time and

requires less energy and space than normal computers.

6.ADVANTAGES OF DNA COMPUTERS

Parallel Computing- DNA computers are massively parallel.

Incredibly light weight- With only 1 LB of DNA you have more computing power

than all the computers ever made.

Low power- The only power needed is to keep DNA from denaturing.

Solves Complex Problems quickly- A DNA computer can solve hardest of

problems in a matter of weeks.



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DNA computers show promise because they do not have the limitations of silicon-based

chips. For one, DNA based chip manufacturers will always have an ample supply of raw

materials as DNA exists in all living things; this means generally lower overhead costs.

Secondly, the DNA chip manufacture does not produce toxic by-products. Last but not

the least, DNA computers will be much smaller than silicon-based computers as one

pound of DNA chips can hold all the information stored in all the computers in theworld.

With the use of DNA logic gates, a DNA computer the size of a teardrop will be more

powerful than today's most powerful supercomputer. A DNA chip less than the size of a

dime will have the capacity to perform 10 trillion

parallel calculations at one time as well as hold ten terabytes of data. The capacity to

perform parallel calculations, much more trillions of parallelcalculations, is something

silicon-based computers are not able to do. As such, a complex mathematical problem

that could take silicon-based computers thousands of years to solve can be done byDNA

Computers in hours. For this reason, the first use of DNA computers will most probably

be cracking of codes, route planning and complex simulations for the government.

7.DISADVANTAGES OF DNA COMPUTERS

High cost istime.

Occasionally slower-Simple problems are solved much faster on electronic

computers. It can take longer to sort out the answer to a problem than it took to solve the

problem.

n-Reliability- There is sometime errors in the pairing of DNA strands .

Although Adleman's first application of the computer took only milliseconds to produce a

solution, it took about a week to fish the solution molecules out from the rest of the



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possible path molecules that had formed. To make these computers more realistically

viable, the DNA splicing and selection equipment needs to be refined for this purpose

and better methods for fishing developed. There is also no guarantee that the solution

produced willnecessarily be the absolute best solution, though it will certainly be a very

good one, arrived at in a much shorter time than with a conventional computer. DNA

computers could not (at this point) replace traditional computers. They are not

programmable and the average dunce can not sit down at a familiar keyboard and get to

work. Some think that in the future, computers will be a combination of the current

models and DNA,using the most attractive features of both to create a vastly improved

total product. However, research is ongoing in doing Boolean logic with DNA and

designing universal (programmable) DNA computers.

And of course we are talking about DNA here, the genetic code of life itself. It certainly

has been the molecule of this century and most likely the next one. Considering all the

attention that DNA has garnered, it isnt too hard to imagine that one day we might have

the tools and talent to produce a small integrated desktop machine that uses DNA, or a

DNA-like biopolymer, as a computing substrate along with set of designer enzymes.

Perhaps it wont be used to play Quake IV or surf the web -- things that traditional

computers are good at -- but it certainly might be used in the study of logic, encryption,

genetic programming and algorithms, automata, language systems, and lots of other

interesting things that haven't even been invented yet.



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8.FUTURE OF DNA COMPUTERS

The most logical applications will be in:

Biology, Chemistry, Medicine

1.Enabling a computing system to read and decode natural DNA directly.Such a computer also might be able to perform DNA fingerprinting matching a sample

of DNA, such as that in blood found at a crime scene, with the person from whom it

came.



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2.Another promising direction is the molecular self-assembly of DNA to build complex

molecular structures, which could have an impact on other fields, such as

Nanotechnology.

Military

Researchers from Stanford and Princeton Universities, have outlined a way for a DNA

computer to crack messages coded with the U.S. government's own Data Encryption

Standard, which is used to protect a wide range of data, including telephone

conversations on classified topics and data transmissions between banks and the Federal

Reserve.

Some centers of research in this area are at the University of Southern California at Los

Angeles, with Dr. Adleman, Princeton, with Dr. Richard Lipton and his graduate students

Dan Boneh and Eric Baum, and the NEC Research Institute in Princeton, NJ. With

others elsewhere, they are developing new branches in this young field. Advancements

are being made in cryptography. Researchers are working on decreasing error in and

damage to the DNA during the computations/reactions. The Princeton contingent has

published papers on models for universal DNA computers, while others have described

methods for doing addition and matrix multiplication with these computers.

Currently, molecular computing is a field with a great deal of potential, but few results of

practical value. In the wake of Adleman's solution of the Hamiltonian path problem, there

came a host of other articles on computation with DNA; however, most of them were

purely theoretical. Currently, a functional DNA "computer" of the type most people are

familiar with lies many years in the future. But work continues: in his article Speeding

Up Computation via Molecular Biology Lipton shows how DNA can be used to construct

a Turing machine, a universal computer capable of performing any calculation. While it

currently exists only in theory, it's possible that in the years to come computers based on

the work of Adleman, Lipton, and others will come to replace traditional silicon-based

machines.

http://www.neci.nj.nec.com/ftp://ftp.cs.princeton.edu/pub/people/rjl/bio.psftp://ftp.cs.princeton.edu/pub/people/rjl/bio.pshttp://www.neci.nj.nec.com/ftp://ftp.cs.princeton.edu/pub/people/rjl/bio.psftp://ftp.cs.princeton.edu/pub/people/rjl/bio.ps


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The field of DNA computing is truly exciting for the revolution it implies will occur

within the next few years. It also demonstrates the current trend of merging and lack of

distinction between the sciences, where a computer scientist can mess around with

biology equipment and come up with something new and valuable.

9.CONCLUSION

The beauty of DNA research trends is found in the possibility of mankinds utilization of

its very life building blocks to solve its most difficult problems.

The field of DNA computing is still in its infancy and the applications for this technology

are still not fully understood.

Is DNA computing viable perhaps, but the obstacles that face the field such as the

extrapolation and practical computational environments required are daunting.

However DNA computers wont flourish soon in our daily environment due to the

technologic issues. NA computing has lead to a very important theoretical research.

The paradigm of DNA computing has lead to a very important theoretical research.



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10. BIBLIOGRAPHY

http://www.ieee.org

http://en.wikipedia.org/wiki/dnacomputers

Mind Sports Worldwide (Feb/2000)http://www.msoworld.com/mindzine/news/chess/web_round/web_round12.html

Scientific Guide to DNA Computers:http://dna2z.com/dnacpu/dna2.html

Arstechnica Review(4/2000):

http://www.ieee.org/http://en.wikipedia.org/wiki/dnacomputershttp://www.ieee.org/http://en.wikipedia.org/wiki/dnacomputers


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http://arstechnica.com/reviews/2q00/dna/dna-2.html

Leonard Adlemans Home Page:http://www-scf.usc.edu/~pwkr/adleman-home.html



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