IS DNA SURPASSING SILICON?

8/9/2019 IS DNA SURPASSING SILICON?

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IS DNA SURPASSING SILICON?

Although DNA computers haven't overtaken silicon-based microprocessors,researchers have made some progress in using genetic code forcomputation. In 2003, Israeli scientists demonstrated a limited, butfunctioning, DNA computer.

What is a DNA Computer?

DNA computers will be the next-generation computers made of genes' buildingblocks. Because of their speed, miniaturization and data storage potential, DNAcomputers are being considered as a replacement for silicon-based computers.Current DNA computer research has already proven that DNA computers arecapable of solving complex mathematical equations and storing enormous amountsof data.

Limitation of Silicon Chips

Silicon-based computer chips have been around for more than 40 years andmanufacturers have been successful in making silicon-based chips smaller, morecomplex and faster than their predecessors. According to Moore's Law,microprocessor size is halved every eighteen months. However, there is a limitationto how small, fast and compact silicon computer chips can be.

Advantages of DNA Computers

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 amplesupply of raw materials as DNA exists in all living things; this means generally loweroverhead 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 inall the computers in the world.

With the use of DNA logic gates, a DNA computer the size of a teardrop will be morepowerful than today's most powerful supercomputer. A DNA chip less than the sizeof a dime will have the capacity to perform 10 trillion parallel calculations at onetime as well as hold ten terabytes of data. The capacity to perform parallelcalculations, much more trillions of parallel calculations, is something silicon-basedcomputers are not able to do. As such, a complex mathematical problem that couldtake silicon-based computers thousands of years to solve can be done by DNAcomputers in hours. For this reason, the first use of DNA computers will mostprobably be cracking of codes, route planning and complex simulations for the

government.

History of DNA Computers

The first person who thought of and experimented with DNA as an alternative tosilicon chips was Leonard Adleman, a computer scientist working in the University ofSouthern California. The 1994 experiment using DNA as a way of solving complexmathematical problems was a product of a book's influence (Molecular Biology ofthe Gene written by James Watson).
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DNA computers will work through the use of DNA-based logic gates. These logicgates are very much similar to what is used in our computers today with the onlydifference being the composition of the input and output signals. In the currenttechnology of logic gates, binary codes from the silicon transistors are convertedinto instructions that can be carried out by the computer. DNA computers, on the

other hand, use DNA codes in place of electrical signals as inputs to the DNA logicgates. DNA computers are, however, still in its infancy and though it may be veryfast in providing possible answers, narrowing these answers down still takes days.

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the geneticinstructions used in the development and functioning of all known living organismsand some viruses. The main role of DNA molecules is the long-term storage ofinformation. DNA is often compared to a set of blueprints or a recipe, or a code,since it contains the instructions needed to construct other components of cells,such as proteins and RNA molecules. The DNA segments that carry this geneticinformation are called genes, but other DNA sequences have structural purposes, orare involved in regulating the use of this genetic information.

Chemically, DNA consists of two long polymers of simple units called nucleotides,with backbones made of sugars and phosphate groups joined by ester bonds. Thesetwo strands run in opposite directions to each other and are therefore anti-parallel.Attached to each sugar is one of four types of molecules called bases. It is thesequence of these four bases along the backbone that encodes information. Thisinformation is read using the genetic code, which specifies the sequence of theamino acids within proteins. The code is read by copying stretches of DNA into therelated nucleic acid RNA, in a process called transcription.

Within cells, DNA is organized into structures called chromosomes. Thesechromosomes are duplicated before cells divide, in a process called DNA replication.

Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNAinside the cell nucleus and some of their DNA in the mitochondria. Prokaryotes(bacteria and archaea) however, store their DNA in the cell's cytoplasm. Within thechromosomes, chromatin proteins such as histones compact and organize DNA.These compact structures guide the interactions between DNA and other proteins,helping control which parts of the DNA are transcribed.

Introduction to How DNA Computers Will Work

Even as you read this article, computer chip manufacturers are furiously racing tomake the next microprocessor that will topple speed records. Sooner or later,

though, this competition is bound to hit a wall. Microprocessors made of silicon willeventually reach their limits of speed and miniaturization. Chip makers need a newmaterial to produce faster computing speeds.

You won't believe where scientists have found the new material they need to buildthe next generation of microprocessors. Millions of natural supercomputers existinside living organisms, including your body. DNA (deoxyribonucleic acid) molecules,the material our genes are made of, have the potential to perform calculations manytimes faster than the world's most powerful human-built computers. DNA might one
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day be integrated into a computer chip to create a so-called biochip that will pushcomputers even faster. DNA molecules have already been harnessed to performcomplex mathematical problems.

Hamilton Path problem

Adleman is often called the inventor of DNA computers. His article in a 1994 issue ofthe journal Science outlined how to use DNA to solve a well-known mathematicalproblem, called the directed Hamilton Path problem, also known as the"traveling salesman" problem. The goal of the problem is to find the shortest routebetween a number of cities, going through each city only once. As you add morecities to the problem, the problem becomes more difficult. Adleman chose to findthe shortest route between seven cities.

You could probably draw this problem out on paper and come to a solution fasterthan Adleman did using his DNA test-tube computer. Here are the steps taken in theAdleman DNA computer experiment:

1. Strands of DNA represent the seven cities. In genes, genetic coding isrepresented by the letters A, T, C and G. Some sequence of these four lettersrepresented each city and possible flight path.

2. These molecules are then mixed in a test tube, with some of these DNAstrands sticking together. A chain of these strands represents a possibleanswer.

3. Within a few seconds, all of the possible combinations of DNA strands, whichrepresent answers, are created in the test tube.

4. Adleman eliminates the wrong molecules through chemical reactions, whichleaves behind only the flight paths that connect all seven cities.

The success of the Adleman DNA computer proves that DNA can be used to

calculate complex mathematical problems. However, this early DNA computer is farfrom challenging silicon-based computers in terms of speed. The Adleman DNAcomputer created a group of possible answers very quickly, but it took days forAdleman to narrow down the possibilities. Another drawback of his DNA computer isthat it requires human assistance. The goal of the DNA computing field is to createa device that can work independent of human involvement.

Three years after Adleman's experiment, researchers at the University of Rochesterdeveloped logic gates made of DNA. Logic gates are a vital part of how yourcomputer carries out functions that you command it to do. These gates convertbinary code moving through the computer into a series of signals that the computeruses to perform operations. Currently, logic gates interpret input signals from silicontransistors, and convert those signals into an output signal that allows the computerto perform complex functions.

The Rochester team's DNA logic gates are the first step toward creating a computerthat has a structure similar to that of an electronic PC. Instead of using electricalsignals to perform logical operations, these DNA logic gates rely on DNA code. Theydetect fragments of genetic material as input, splice together these fragmentsand form a single output. For instance, a genetic gate called the "And gate" links
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two DNA inputs by chemically binding them so they're locked in an end-to-endstructure, similar to the way two Legos might be fastened by a third Lego betweenthem. The researchers believe that these logic gates might be combined with DNAmicrochips to create a breakthrough in DNA computing.

DNA computer components -- logic gates and biochips -- will take years to

develop into a practical, workable DNA computer. If such a computer is ever built,scientists say that it will be more compact, accurate and efficient than conventionalcomputers. In the next section, we'll look at how DNA computers could surpass theirsilicon-based predecessors, and what tasks these computers would perform.

Silicon vs. DNA Microprocessors

Silicon microprocessors have been the heart of the computing world for more than40 years. In that time, manufacturers have crammed more and more electronicdevices onto their microprocessors. In accordance with Moore's Law, the numberof electronic devices put on a microprocessor has doubled every 18 months. Moore'sLaw is named after Intel founder Gordon Moore, who predicted in 1965 that

microprocessors would double in complexity every two years. Many have predictedthat Moore's Law will soon reach its end, because of the physical speed andminiaturization limitations of silicon microprocessors.

DNA computers have the potential to take computing to new levels, picking upwhere Moore's Law leaves off. There are several advantages to using DNA instead ofsilicon:

As long as there are cellular organisms, there will always be a supply of DNA. The large supply of DNA makes it a cheap resource. Unlike the toxic materials used to make traditional microprocessors, DNA

biochips can be made cleanly. DNA computers are many times smaller than today's computers.

DNA's key advantage is that it will make computers smaller than any computer thathas come before them, while at the same time holding more data. One pound ofDNA has the capacity to store more information than all the electronic computersever built; and the computing power of a teardrop-sized DNA computer, using theDNA logic gates, will be more powerful than the world's most powerfulsupercomputer. More than 10 trillion DNA molecules can fit into an area no largerthan 1 cubic centimeter (0.06 cubic inches). With this small amount of DNA, acomputer would be able to hold 10 terabytes of data, and perform 10 trillioncalculations at a time. By adding more DNA, more calculations could be performed.

Unlike conventional computers, DNA computers perform calculations parallel to

other calculations. Conventional computers operate linearly, taking on tasks one ata time. It is parallel computing that allows DNA to solve complex mathematicalproblems in hours, whereas it might take electrical computers hundreds of years tocomplete them.

The first DNA computers are unlikely to feature word processing, e-mailing andsolitaire programs. Instead, their powerful computing power will be used by nationalgovernments for cracking secret codes, or by airlines wanting to map more efficient
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routes. Studying DNA computers may also lead us to a better understanding of amore complex computer -- the human brain.

APPLICATIONS

CRYPTOGRAPHYA field in which DNA computing appears to be particularly interesting is thecryptography. The DES is the Data Encryption Standard that is the IBM's widely usedencryption procedure. It uses a 56 bit key to encrypt 64 bit messages. Theencryption procedure is known, and the security is based only on the secretencryption key. In [Bon95a], a molecular program that breaks DES is proposed. Thatis, one (plain-text, cipher-text) pair is given, and the key that maps the plain-textinto the cipher-text is found. Conventional (silicon based) computers - using bruteforce - would take 104 years to solve the same problem (finding the key that maps aparticular pair).

SOLVING NP PROBLEMS:

NP problems are a class of problems which have an exponential increase in timecomplexity as the number of instances increase. DNA Computers can be used tosolve NP class of problems in relatively lesser time because of the parallelprocessing ability. This is best illustrated by Adlemans experiment.

BIOMEDICAL AND PHARMACEUTICAL FIELDS

DNA Computers can monitor blood in vitro levels. If there are any chemical

imbalances, the DNA would synthesize the needed replacement and release it intoblood maintain equilibrium. Autonomous bio-molecular computers may work asdoctors in a cell.

WILL DNA SUPPLANT SILICON??

DNA's key advantage is that it will make computers smaller than any computer thathas come before them, while at the same time holding more data. One pound ofDNA has the capacity to store more information than all the electronic computersever built; and the computing power of a teardrop-sized DNA computer, using theDNA logic gates, will be more powerful than the world's most powerful

supercomputer. More than 10 trillion DNA molecules can fit into an area no largerthan 1 cubic centimeter (0.06 cubic inches). With this small amount of DNA, acomputer would be able to hold 10 terabytes of data, and perform 10 trillioncalculations at a time. By adding more DNA, more calculations could be performed.

However, setting up and extracting results from a DNA computer can take days and

sometimes week. The fact that DNA doesnt behave as expected makes things

difficult to obtain accurate results. Human intervention is required in each step of
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result synthesis which brings in the drawbacks of human errors. Ehud Shapiro,

whose team has the Guinness record for the smallest biological computing device

says, I think they will live together happily and be used for different applications.

George Klington Fernandez. A

DMI - St. Eugene University, Zambia

IS DNA SURPASSING SILICON?

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