DNA Computing - Thinking beyond Silicon

Hi all,
This article was written by me during my college days. I was just goind through the folders in my system when I stumbled upon this article and thought can share this piece of information with ya. Hope you have a good read

KP - The DevilzAdvocate

“Have you ever wondered as to how genetic information is transferred from one generation to another? Have you ever pondered over how the mutations and evolutions take place? And will you believe if it is said that all these activities are done by millions of supercomputers present inside living organisms? If not, welcome to the world of DNA Computers.”



DNA Computer- A stumper that intrigues us
A DNA computer is a molecular computer that works biochemically. DNA is modified bio-chemically by a variety of enzymes, which are tiny protein machines that read and process DNA according to nature's design. There is a wide variety and number of these "operational" proteins, which manipulate DNA on the molecular level. Many copies of the enzyme can work on many DNA molecules simultaneously. Thus we can say that a DNA computer works in a massively parallel fashion.

Computer with a Chemistry Lab Mien?

The basic notion of a computer, having various Input and output devices and software running them does not fit here. A DNA computer is nothing but a mixture of solution containing the DNA strands and the enzymes taken in a test tube coaxed to crunch algorithms and spit out data.


DNA VS SILICON
"The inside of a computer is as dumb as hell, but it goes like mad!" was a statement made by Richard Feynman with regards to the systems based on the Von Neumann architecture. DNA computers on the other hand are non von Neumann machines which are capable of massive parallel processing and hence the process of computation is approached from a different perspective. Typically, increasing performance of silicon computing means faster clock cycles, where the emphasis is on the speed of the CPU(increasing it will cost you more money :) ) and not on the size of the memory. For DNA computing, the power comes from the memory capacity and parallel processing.

PATRIARCH OF DNA COMPUTING:
In 1994, Leonard Adleman solved directed Hamiltonian path (HP) problem popularly known as the Travelling Salesman Problem (TSP) in seven days. It was a problem that an average desktop machine could solve in the blink of an eye. But what’s special about his work that we are talking about? It was a landmark demonstration of computing at molecular level. His work brought into limelight the power of DNA in computing. Adleman considered seven nodes each representing a city to solve the problem.
Steps involved in Adleman’s experiment:

• Generate all possible routes.
• Select itineraries that start with the proper city and end with the final city.
• Select itineraries with the correct number of cities.
• Select itineraries that contain each city only once.

All of the above steps were accomplished with standard molecular biology techniques.

APPLICATIONS – An Overview:
CRYPTOGRAPHY:
A field in which DNA computing appears to be particularly interesting is the cryptography. The DES is the Data Encryption Standard that is the IBM's widely used encryption procedure. It uses a 56 bit key to encrypt 64 bit messages. The encryption procedure is known, and the security is based only on the secret encryption key. In [Bon95a], a molecular program that breaks DES is proposed. That is, one (plain-text, cipher-text) pair is given, and the key that maps the plain-text into the cipher-text is found. Conventional (silicon based) computers - using brute force - would take 104 years to solve the same problem (finding the key that maps a particular pair).
SOLVING NP PROBLEMS:
NP problems are a class of problems which have an exponential increase in time complexity as the number of instances increase. DNA Computers can be used to solve NP class of problems in relatively lesser time because of the parallel processing ability. This is best illustrated by Adleman’s 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 into blood maintain equilibrium. Autonomous bio-molecular computers may work as doctors in a cell.

WILL DNA SUPPLANT SILICON??
DNA's key advantage is that it will make computers smaller than any computer that has come before them, while at the same time holding more data. One pound of DNA has the capacity to store more information than all the electronic computers ever built; and the computing power of a teardrop-sized DNA computer, using the DNA 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 larger than 1 cubic centimeter (0.06 cubic inches). With this small amount of DNA, a computer would be able to hold 10 terabytes of data, and perform 10 trillion calculations 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 doesn’t behave as expected makes things difficult to obtain accurate results. Human intervention is required in each step of 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”.