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Although DNA computers haven't overtaken silicon-based microprocessors, researchers have made some progress in using genetic code for computation. In 2003, Israeli scientists demonstrated a limited, but functioning, DNA computer. What is a DNA Computer? DNA computers will be the next-generation computers made of genes' building blocks. Because of their speed, miniaturization and data storage potential, DNA computers are being considered as a replacement for silicon-based computers. Current DNA computer research has already proven that DNA computers are capable of solving complex mathematical equations and storing enormous amounts of data. Limitation of Silicon Chips Silicon-based computer chips have been around for more than 40 years and manufacturers have been successful in making silicon-based chips smaller, more complex and faster than their predecessors. According to Moore's Law, microprocessor size is halved every eighteen months. However, there is a limitation to 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 siliconbased 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 byproducts. Last but not the least, DNA computers will be much smaller than siliconbased computers as one pound of DNA chips can hold all the information stored in all the computers in the world. 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 parallel calculations, 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 by DNA 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. History of DNA Computers The first person who thought of and experimented with DNA as an alternative to silicon chips was Leonard Adleman, a computer scientist working in the University of Southern California. The 1994 experiment using DNA as a way of solving complex mathematical problems was a product of a book's influence (Molecular Biology of the Gene written by James Watson).
DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals. In the current technology of logic gates, binary codes from the silicon transistors are converted into 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 logic gates. DNA computers are, however, still in its infancy and though it may be very fast in providing possible answers, narrowing these answers down still takes days. Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. 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 genetic information are called genes, but other DNA sequences have structural purposes, or are 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. These two 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 the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription. Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside 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 the chromosomes, 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 to make the next microprocessor that will topple speed records. Sooner or later, though, this competition is bound to hit a wall. Microprocessors made of silicon will eventually reach their limits of speed and miniaturization. Chip makers need a new material to produce faster computing speeds. You won't believe where scientists have found the new material they need to build the next generation of microprocessors. Millions of natural supercomputers exist inside living organisms, including your body. DNA (deoxyribonucleic acid) molecules, the material our genes are made of, have the potential to perform calculations many times faster than the world's most powerful human-built computers. DNA might one
day be integrated into a computer chip to create a so-called biochip that will push computers even faster. DNA molecules have already been harnessed to perform complex mathematical problems. Hamilton Path problem Adleman is often called the inventor of DNA computers. His article in a 1994 issue of the journal Science outlined how to use DNA to solve a well-known mathematical problem, called the directed Hamilton Path problem, also known as the "traveling salesman" problem. The goal of the problem is to find the shortest route between a number of cities, going through each city only once. As you add more cities to the problem, the problem becomes more difficult. Adleman chose to find the shortest route between seven cities. You could probably draw this problem out on paper and come to a solution faster than Adleman did using his DNA test-tube computer. Here are the steps taken in the Adleman DNA computer experiment: 1. Strands of DNA represent the seven cities. In genes, genetic coding is represented by the letters A, T, C and G. Some sequence of these four letters represented each city and possible flight path. 2. These molecules are then mixed in a test tube, with some of these DNA strands sticking together. A chain of these strands represents a possible answer. 3. Within a few seconds, all of the possible combinations of DNA strands, which represent answers, are created in the test tube. 4. Adleman eliminates the wrong molecules through chemical reactions, which leaves 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 far from challenging silicon-based computers in terms of speed. The Adleman DNA computer created a group of possible answers very quickly, but it took days for Adleman to narrow down the possibilities. Another drawback of his DNA computer is that it requires human assistance. The goal of the DNA computing field is to create a device that can work independent of human involvement. Three years after Adleman's experiment, researchers at the University of Rochester developed logic gates made of DNA. Logic gates are a vital part of how your computer carries out functions that you command it to do. These gates convert binary code moving through the computer into a series of signals that the computer uses to perform operations. Currently, logic gates interpret input signals from silicon transistors, and convert those signals into an output signal that allows the computer to perform complex functions. The Rochester team's DNA logic gates are the first step toward creating a computer that has a structure similar to that of an electronic PC. Instead of using electrical signals to perform logical operations, these DNA logic gates rely on DNA code. They detect fragments of genetic material as input, splice together these fragments and form a single output. For instance, a genetic gate called the "And gate" links
two DNA inputs by chemically binding them so they're locked in an end-to-end structure, similar to the way two Legos might be fastened by a third Lego between them. The researchers believe that these logic gates might be combined with DNA microchips 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 conventional computers. In the next section, we'll look at how DNA computers could surpass their silicon-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 than 40 years. In that time, manufacturers have crammed more and more electronic devices onto their microprocessors. In accordance with Moore's Law, the number of electronic devices put on a microprocessor has doubled every 18 months. Moore's Law is named after Intel founder Gordon Moore, who predicted in 1965 that microprocessors would double in complexity every two years. Many have predicted that Moore's Law will soon reach its end, because of the physical speed and miniaturization limitations of silicon microprocessors. DNA computers have the potential to take computing to new levels, picking up where Moore's Law leaves off. There are several advantages to using DNA instead of silicon: • 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 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. Unlike conventional computers, DNA computers perform calculations parallel to other calculations. Conventional computers operate linearly, taking on tasks one at a time. It is parallel computing that allows DNA to solve complex mathematical problems in hours, whereas it might take electrical computers hundreds of years to complete them. The first DNA computers are unlikely to feature word processing, e-mailing and solitaire programs. Instead, their powerful computing power will be used by national governments for cracking secret codes, or by airlines wanting to map more efficient
routes. Studying DNA computers may also lead us to a better understanding of a more complex computer -- the human brain. APPLICATIONS 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”. George Klington Fernandez. A DMI - St. Eugene University, Zambia