DNA COMPUTERS
ABSTRACT
In this presentation, I have tried to give an overview of DNA computers, the possible advantages of DNA computers over the conventional computers, and the potential applications that might emerge from, or serve to motivate, the creation of a working Bio molecular Computer. The emerging paradigms of DNA based (or bio molecular) computation has yet to find a practical use, despite many possible advantages over existing computational methods. Possible applications are discussed for different models of DNA computations of DNA computers have also been discussed. Results show that DNA computers are highly promising and are superior to silicon based computers in many ways.
Chapter-1
INTRODUCTION
The most significant technology in the future of engineering is DNA Computers. DNA stands for Deoxyribose Nucleic Acid. DNA is what makes up your genes and stores all the information about you inside your cells. It is the instructions for what you look like and how you function. Each microscopic cell in your body contains the entire DNA needed to build you, which is a lot of information. DNA is made up of sugar (Deoxyribose), phosphate and nitrogenous bases like Adenine (A), Guanine (G), Thymine (T), Cytosine(C). This natural supercomputer is very useful to us since it has huge data storage potential and it can solve complicated calculations and mathematical problems.
Right now humans are very dependent on computers and relying on computer technology to keep increasing at the rate it is. Soon the silicon based microprocessors aren’t going to be able to be made any more powerful. Microprocessors will become obsolete and replacement will be needed. DNA computers are the replacement. Millions of natural supercomputers (DNA) exist inside the living organisms, including your body. The Guinness World Reports has recognized the DNA computer as the “the smallest biological computing device.”
DNA computers are a very new concept. The idea was conceived just eleven ago. But in just eleven years, scientists have already been able to use DNA to solve difficult math problems. DNA computers are still decades away from being able to compete with silicon based computers, but will eventually be much more powerful than silicon based computers. The first DNA computers will not be like a home PC. They will be used to solve huge, complicated mathematical problems such as breaking codes etc.
Our society is becoming increasingly reliant on computers and will need faster and faster computers. DNA computers have the potential to provide that and more. The creation of practical DNA computers will start a whole new computer revolution.
INVENTION
Dr Leonard Adleman is often called the inventor of DNA computers. He invented the DNA computer in the year 1994.His article in the journal “SCIENCE” outlined how to use DNA to solve a well- known mathematical problem, called the directed Hamilton Path problem , also known as “travelling salesman” problem .The goal of the problem is to find the shortest route between number of cities, going through each city once. As you add more cities to the problem ,the problem becomes more difficult. Adleman chose to find the shortest route between seven cities.
Adleman came to the solution by using his DNA test-tube computer. Here are the steps taken in the Adleman DNA test-tube experiment:
- Strands of DNA represent the seven cities. In genes, genetic code is represented by the letters A , T, C and G . Some sequence of these four letters represented each city and possible flight path.
- These molecules are then mixed in a test-tube, with some of these DNA strands sticking together chain of these strands represent a possible answer, and are created in the test-tube.
- Within a few seconds, all of the possible combinations of DNA strands which represent answers are created in the test-tube.
- Adleman eliminated the wrong molecules through chemical reactions which leave behind only the flight paths that connect all seven cities.
That is, Adleman developed a method of manipulating DNA which, in effect, conducts trillions of computations in parallel. Essentially he coded each city and each possible flight as a sequence of 4 components. For example he coded one city as GCAG and another as TCGG.
The incredible thing is that once the DNA sequences had been created he simply "just added water" to initiate the "computation":. The DNA strands then began their highly efficient process of creating new sequences based on the input sequences.
If an "answer" to the problem for a given set of inputs existed then it should amongst these trillions of sequences. The next (difficult) step was to isolate the "answer" sequences. To do this Adleman used a range of DNA tools. For example, one technique can test for the correct start and end sequences, indicating that the strand has a solution for the start and end cities. Another step involved selecting only those strands which have the correct length, based on the total number of cities in the problem (remembering that each city is visited once).
Finally another technique was used to determine if the sequence for each city was included in the strand. If any strands were left after these processes then: a solution to the problem existed, and the answer(s) would be in the sequence(s) on the remaining strands.
His attempt at solving a seven-city, 14 flight map took seven days of lab work. This particular problem can be manually solved in a few minutes but the key point about Adleman's work is that it will work on a much larger scale, when manual or conventional computing techniques become overwhelmed. "The DNA computer provides enormous parallelism... in one fiftieth of a teaspoon of solution approximately 10 to the power 14 DNA 'flight numbers' were simultaneously concatenated in about one second".
Adleman’s primary intention was to prove the feasibility of bio-molecular computation but his work also gave an indication that the emergence of this new computational paradigm could provide an advantage over conventional electronic computing techniques . Specifically, DNA was shown to have massively parallel processing capabilities that might allow a DNA based computer to solve hard computational problems in a reasonable amount of time.
Computers today use binary codes - 1’s and 0’s or on’s and off’s . These codes are the basis for all possible calculation a computer is able to perform . Because the DNA molecule is also a code , Adleman saw the possibility of employing DNA as a molecular computer . However, rather than relying in the position of electronic switches in a microchip , Adleman relied on the much faster reactions of DNA nucleotides binding with their compliments , a brute force method that would indeed work .
Chapter-3
WORKING
OF A DNA COMPUTER
Computing with DNA generated a tremendous amount of excitement by offering a brand new paradigm for performing and viewing computations. The main idea is the encoding of data in DNA strands and the use of tools from molecular biology to execute computational operations. DNA computers work by encoding the problem to be solved in the language of DNA.-Adenine (A), Thymine (T), Guanine (G), and Cytosine(C). Using these base four number system, the solution to any conceivable problem can be encoded. Inside the cell you will find an incredible number of molecules. Some of them act as motors, some of them store information like DNA, some transmit energy and many, many other things –there are literally ten thousands of different molecules and these make up the tool box for the third millennium engineer. Other active tools developments have given engineers at the molecular level perform operations like those of a motor, or a scissors, or a splicer, or a duplicator many much finer and more precise operations for specialized purposes. By learning to direct the activities of these molecular tools that already exist, engineers will be able to create product seeds that grow into the desired product when given proper nourishment.
Think of DNA as software, and enzymes as hardware. Put them together in a test –tube. The way in which these molecules undergo chemical reactions with each other allows simple operations to be performed as a by-product of the reactions. Every possible sequence can be chemically created in a test tube on trillions of different DNA strands, and the correct sequences can be filtered out using genetic engineering tools. This massive process of elimination method of finding the solutions to problems, a kind of Darwinian survival of fittest at the molecular level has evolved to become the universal method of storing and processing information in living things. The scientists tell the devices what to do by controlling the composition of DNA software molecules. It’s a completely different approach to pushing electrons around a dry circuit in a conventional computer.
To a naked eye, the DNA computer looks like clear water solution in a test-tube. There is no mechanical device. A trillion bio-molecular devices could fit into a single drop of water.. Instead of showing up on a computer screen, results are analysed using a technique that allows scientists to see the length of the DNA output molecule.
Once the input, software and hardware molecules are mixed in a solution it operates to completion without intervention. To present the output to the naked eye, human manipulation is needed.
ADVANTAGES OF DNA
COMPUTERS
The Advantages of DNA Computers are as follows:
v DNA Computers are more compact. They are thousand times smaller than silicon based computers.
v They can hold more data. One pound of DNA has the ability to store more data than every electronic device made to date. A water droplet sized DNA Computer has more computing power than today’s most powerful supercomputers. A cubic centimetre of DNA can hold tetra bytes of data than a trillion music CD’s. Therefore it can handle massive amounts of working memory.
v Another advantage of DNA Computing over silicon based computers is the ability to do parallel calculations. Silicon based microprocessors can only do one calculation at a time while DNA computer will be able to do many simultaneous. It can handle millions of operations in parallel and can conduct large parallel searches.
v In terms of speed, DNA Computers surpass conventional computers. While desktop PC is designed to perform one calculation very fast, DNA strands produce billions of potential answers simultaneously. This makes the DNA Computer suitable for solving “fuzzy logic” problems that have many possible solutions rather than the either/or logic of binary computers. In the future, some speculate, there may be hybrid machines that use traditional silicon for normal processing tasks but have DNA co-processors that can take over specific tasks they would be more suitable for.
v It can compute with extremely high energy-efficiency. Its energy efficiency is more than a million times that of a PC. It also has more computing power.
v It can generate a complete set of potential solutions to hard computational problems.
v Unlike the toxic materials used to make traditional microprocessors, biochips can be made cleanly. Thus it is ecofriendly.
v As long as there are cellular organisms there will always be sufficient supply of DNA.
v The large supply of DNA makes it a cheap resource.
v DNA is self-complementary, allowing single strands to seek and find their own opposite sequences, and can be easily copied.
DISADVANTAGES OF DNA
COMPUTERS
The disadvantages of DNA computers are as follows:
Ø One of the drawbacks of DNA computers is that it requires human assistance or mechanical intervention. The goal of the DNA computing field is to make DNA computers that can work independent of human involvement.
Ø Each stage of parallel operations requires time measured in hours or
days, with extensive human or mechanical intervention between steps. Hence it
is time consuming.
Ø Generating solution sets, even for some relatively simple problems, may require impractically large amounts of memory.
Ø Many empirical uncertainties, including those involving: actual error rates, the generation of optimal encoding techniques, and the ability to perform necessary bio-operations conveniently in vitro or in vivo.
Ø The DNA computers do not feature word processing, e-mail and solitaire programs.
Ø The error rate in DNA computing is high.
APPLICATIONS OF DNA
COMPUTERS
v DNA Computers can be used to solve complex problems. For example, Adleman (inventor of DNA computer) solved a problem requiring the evaluation of more than a million possible solutions which is too complex for anyone to solve without the aid of the computer. It required a set of 20 values that satisfy a complex tangle of relationship. The problem is as follows:
Adleman’s chief scientist, Nicolas Chelyapov , offered this illustration : Imagine that a fussy customer walks on to a million- car auto square and gives the dealer a complicated list of criteria for the car he wants: “First “, he says,” I want it be either a Cadillac, or a convertible or red .” Second, “If it is a Cadillac, then it has to have four seats or a locking gas.” Third, “If it is a convertible, it should not be a Cadillac, or it should have two seats.” The customer rattles off a list of 24 such conditions, and the salesman has to find one car in stock that meets all the requirements. (Adleman and his team chose a problem they knew had exactly one solution.) The salesman will have to run through the customer’s entire list for each of the million cars in turn – a hopeless task unless he can move and think at superhuman speed. This serial method is the way a digital electronic computer solves such a problem.
In contrast, a DNA computer operates in parallel – with countless molecules shimmying around together at once. This is equivalent to each car having a valet inside who will listen to the customer, read his list over a PA system and will drive off the lot the moment his car fails one of the conditions. By the time the consumer finishes his list, his dream car will be waiting alone on the lot.
v DNA computers can also be used in detection of diseases like cancer. The bio-computer senses messenger RNA, the DNA-like molecule that helps create proteins from the information in genes. In particular, it can detect the abnormal messenger RNAs produced by genes involved in certain types of lung and prostate cancer.
When the computer senses one of these RNAs it releases an anti-cancer drug also made of DNA, which damps expression of the tumour-related gene. Billions of these computers can be packed into a single drop of water, so they could easily fit inside a human cell. This helps in diagnosing the disease from within cells and dispenses drugs as necessary.
v The powerful computing power of the DNA computers will be useful to governments for cracking secret codes, or by airlines wanting to map routes. Studying DNA computers may also lead us to a better understanding of a complex computer—the human brain.
v Through the use of its massive parallelism and potentially non-deterministic mechanisms, DNA based models of computation might be useful for simulating or modelling other emerging computational paradigms, like quantum computing, which may not be feasible until much later.
v The bio-molecular computing can be applied in the emerging science of nanotechnology, specifically nano-fabrication, making use of both the small scale computational abilities of DNA and the manufacturing abilities of RNA...
v DNA computers can also be used to detect other chemical and bio-chemical substances.
‘DNA
computer’ cracks code
A ‘DNA computer’ has been used for the first time to find the only
correct answer from over a million possible solutions to a computational
problem. Leonard Adleman of the
Scientists have previously used DNA computers to crack computational problems with up to nine variables, which involve selecting the correct answer from 512 possible solutions. But now Adleman’s team has shown that a similar technique can solve a problem with 20 variables, which has 220 - or 1 048 576 – possible solutions.
Adleman and colleagues chose an ‘exponential time’ problem, in which each extra variable doubles the amount of computation needed. This is known as an NP-complete problem, and is notoriously difficult to solve for a large number of variables. Other NP-complete problems include the ‘travelling salesman’ problem – in which a salesman has to find the shortest route between a number of cities – and the calculation of interactions between many atoms or molecules.
Adleman and co-workers expressed their problem as a string of 24 ‘clauses’, each of which specified a certain combination of ‘true’ and ‘false’ for three of the 20 variables. The team then assigned two short strands of specially encoded DNA to all 20 variables, representing ‘true’ and ‘false’ for each one.
In the experiment, each of the 24 clauses is represented by a gel-filled glass cell. The strands of DNA corresponding to the variables – and their ‘true’ or ‘false’ state – in each clause were then placed in the cells.
Each of the possible 1 048 576 solutions were then represented by much longer strands of specially encoded DNA, which Adleman’s team added to the first cell. If a long strand had a ‘subsequence’ that complemented all three short strands, it bound to them. But otherwise it passed through the cell.
To move on to the second clause of the formula, a fresh set of long strands was sent into the second cell, which trapped any long strand with a ‘subsequence’ complementary to all three of its short strands. This process was repeated until a complete set of long strands had been added to all 24 cells, corresponding to the 24 clauses. The long strands captured in the cells were collected at the end of the experiment, and these represented the solution to the problem.
According to Adleman and co-workers, their demonstration represents a watershed in DNA computation comparable with the first time that electronic computers solved a complex problem in the 1960s. They are optimistic that such ‘molecular computing’ could ultimately allow scientists to control biological and chemical systems in the way that electronic computers control mechanical and electrical systems now.
v The potential applications of re-coding natural DNA into a computable form are many and include DNA sequencing, DNA fingerprinting, DNA mutation detection or population screening and other fundamental operations on DNA. In case of DNA mutation detection, the strand being operated on would already be partially known and therefore fewer steps would need to be taken to re-code the DNA into a redundant form applicable for computational form.
CHAPTER-7
CURRENT RESEARCH
Currently, at the
The research on DNA computers is
ongoing still. All over the world,
research teams like the one at the
CHAPTER-8
CONCLUSION
With so many different methods and models emerging from the current research, DNA computing can be more accurately described as a collection of new computing paradigms rather than a single focus. Each of these different paradigms within bio-molecular computing can be associated with different potential applications that may prove to place them at an advantage over conventional methods. Many of these models share certain features that lend them to categorization by these potential advantages. However, there exist enough similarities and congruencies that hybrid models will be possible and will be mutually beneficial for practical applications. Advancements in DNA computing may also serve to enhance understanding of both the natural and computer sciences. For these reasons, and due to the many areas dependent on each of computer science, mathematics, natural science, engineering, continued interdisciplinary collaboration is very important to any future progress in all areas of this new field.
DNA computers are compact. They can do parallel calculations and can solve huge complicated problems. With so many possible advantages over conventional techniques, DNA computing has great potential for practical use. Future work in this field should begin to incorporate cost-benefit analysis so that comparisons can be more appropriately made with existing techniques and so that increased funding can be obtained for this research that has the potential to benefit many circles of Science and Industry. Thus DNA computers are highly promising and will create a revolution in the world of computers.
As of now, the DNA computer can only perform rudimentary functions, and it has no practical applications. "Our computer is programmable, but it's not universal," said Shapiro. "There are computing tasks it inherently can't do."
The device can check whether a list of zeros and ones has an even number of ones. The computer cannot count how many ones are in a list, since it has a finite memory and the number of ones might exceed its memory size. Also, it can only answer yes or no to a question. It can't, for example, correct a misspelled word.
REFERENCES
Reference to internet sources
1. http://www.computer
.howstuffworks.com/dna-computer.htm
2. http://www.news.nationalgeographic.com/news/DNAcomputer.html
Comments
Post a Comment