DNA Computer : Computing next generation
DNA is what makes up your genes and stores all the information about you inside your cells. What else DNA can do? Probably it is a basis of next generation computers.
Abstract
"Human cells and computers process and store information in much the same way. Computer stores data in strings made up of the numbers 0 and 1. Living things store information with molecules represented the letters A,T,C and G." – Adleman
Introduction
Reading James Watson’s textbook " Modecular Biology of the Gene" (1953), Adleman , Univiersity of Southern California computer scientist found a way towards DNA computing.
Dr. Adleman an "Inventor of DNA computers" published details of DNA computing in issue of Journal Science in 1994 first time and made world wondering on living computer.
Here is a look on the invention of new generation of computers.
What is basis?
DNA: Deoxyribonucleic acid
DNA is what makes up your genes and stores all the information about you inside your cells.
" DNA is the molecule that encodes and carries genetic information. It is a structural plan for proteins. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases adenine (A), guanine (G), cytosine (C), and thymine (T). One oxygen atom is missing in the sugar content of the nucleotide - thus the prefix "deoxy". In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner."
DNA has a unique data structure. Above definition clearly explains strand of DNA. Nucleotides (bases) are spaced every 0.35 nanometers along the DNA molecule, giving data density of 18 Mbits per inch.
Performance of DNA computing
In bacteria, DNA can be replicated at a rate of about 500 base pairs a second. It is nearly 10 times faster tan human cells with low error rates. That comes to 1000 bits per second. The feature of replication enzymes can start on the second replicated strand of DNA even before they are finished copying the first one. So rate is nearly of 2000 bits per second. With each additional strand data rate increases by 1000 bits per second.
Iteration speeds up data rate. After 10 iterations DNA is being replicated at a rate of about 1 Mbit per second. After 30 iterations it increases to 1000 Gbits per second.
More than 10 trillion DNA molecules can fit into an area no larger than 1 cubic centimeter (0.06 cubic inches). DNA computer is capable enough to hold 10 terabytes of data with performance of 10 trillion calculations at a time.
In simple words, DNA computers can perform an amazing number of calculations simultaneously; specifically, on the order of 10^9 calculations per mL of DNA per second! That’s how its effective density is roughly 100,000 times greater than modern hard disks.
"A single strand of DNA does not yield much power. But DNA can be replicated, so that you can have as much DNA as you need to perform incredibly difficult tasks. And the strange property of a DNA computer is that it can test all the solutions simultaneously - a truly parallel task." - Tormod Guldvog (Hypography Sci-Tech)
Any transistor base computers generally handle operations in a sequential manner. A von Neumann machine (Modern CPUs) repeats "fetch and execute" cycle over and over again. Where as DNA computers are non-von Neuman. In DNA computer power comes from memory capacity and parallel processing.
However, DNA computing is still very much a dream for scientists. They hope to harness the enormous data-storing capacity of DNA, biological molecules that are also able to perform operations similar to silicon computers.
Hamiltonian Path problem
Hamiltonian path problems is a classic mathematical problem of " traveling salesman" where one needs to find how a salesman can visit number of cities without passing through any city twice. It is very simple if numbers of cities are less. But it becomes difficult for any silicon computers to find out when numbers of cities increases.
Adleman used standard molecular biology techniques to solve by exploiting the predictability of how DNA interacts. He first generated all the possible itineraries and then selected the correct itinerary. This is the advantage of DNA. It’s small and there are combinatorial techniques that can quickly generate many different data strings.
A recent experiment says, "DNA computer can solve the problem for up to 15 cities."
Inventing future computer
Weizmann System
Until now, DNA processors have needed intensive tending and have been limited to specific problems. Israeli scientists Ehud Shapiro and colleagues have designed Weizmann System that uses DNA to carry out any calculation and require little human intervention. The system emulates a Turing machine, which is one of the fundamental concepts in computing. Such a machine examines data step by step, making decisions on what to do next based on that data. In theory, any Turing machine can do any computing problem. In nature, DNA molecules work in a very similar way, unzipping and recombining according to information coded into sequences of chemicals. – Journal of Nature
Team of Israeli scientists used DNA to create a programmable computer that's smaller than a drop of water.
"The long-term goal is to eventually create autonomous, programmable molecular computing devices that can operate in vivo, eventually inside the human body, and function as 'doctors in a cell" - Ehud Shapiro, a computer scientist (Weizmann Institute of Science).
DNA Computer for Gene Analysis
Olympus Optical Co. Ltd. has developed what the company says is the first commercially practical DNA computer that specializes in gene analysis. The computer was developed in conjunction with Akira Toyama, an assistant professor at Tokyo University
The new computer is divided into two sections: a molecular calculation component and an electronic calculation component. The former calculates DNA combinations of molecules, implements chemical reactions, searches, and pulls out the right DNA results. The latter executes processing programs and analyzes these results. The company will start gene analysis using the DNA computer on a trial basis for a year, and hopes to offer the service on a commercial basis for researchers in 2003.
Cracking codes.
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 University of Southern California in the US and colleagues used different strands of DNA to represent the 20 variables in their problem, which could be the most complex task ever solved without a conventional computer. The researchers believe that the complexity of the structure of biological molecules could allow DNA computers to outperform their electronic counterparts in future.
Maya: Playing tic-tac-toe
Scientists have built a DNA computer to play tic-tac-toe. MAYA, the DNA computer, is the brainchild of Milan Stojanovic, from Columbia University, and Darko Stefanovic of the University of New Mexico
It is just a beginning
"DNA would ultimately replace silicon chips. A single gram of dried DNA, about the size of a half-inch sugar cube, can hold as much information as a trillion compact discs. I'm just not sure how!" - Adelman
Reference and Further Readings
- Adleman, L.M., Molecular computation of solutions to combinatorial problems, Science, 226 (1994), 1021-1024
- Journal reference: " Nature Biotechnology"
- "New Scientist"- Magazine
- DNA computer plays tic-tac-toe By Michael Stroh, The Baltimore Sun, August 18, 2003; Robert S. Boyd, Knight Ridder Newspapers, August 18, 2003
DNA Computing A Primer By Will Ryu
Olympus develops DNA computer By Kuriko Miyake, IDG News Service
DNA computer’ cracks code By Katie Pennicott,PhysicsWeb.
How DNA Computers Will Work by Kevin Bonsor
"Human cells and computers process and store information in much the same way. Computer stores data in strings made up of the numbers 0 and 1. Living things store information with molecules represented the letters A,T,C and G." – Adleman
Introduction
Reading James Watson’s textbook " Modecular Biology of the Gene" (1953), Adleman , Univiersity of Southern California computer scientist found a way towards DNA computing.
Dr. Adleman an "Inventor of DNA computers" published details of DNA computing in issue of Journal Science in 1994 first time and made world wondering on living computer.
Here is a look on the invention of new generation of computers.
What is basis?
DNA: Deoxyribonucleic acid
DNA is what makes up your genes and stores all the information about you inside your cells.
" DNA is the molecule that encodes and carries genetic information. It is a structural plan for proteins. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases adenine (A), guanine (G), cytosine (C), and thymine (T). One oxygen atom is missing in the sugar content of the nucleotide - thus the prefix "deoxy". In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner."
DNA has a unique data structure. Above definition clearly explains strand of DNA. Nucleotides (bases) are spaced every 0.35 nanometers along the DNA molecule, giving data density of 18 Mbits per inch.
Performance of DNA computing
In bacteria, DNA can be replicated at a rate of about 500 base pairs a second. It is nearly 10 times faster tan human cells with low error rates. That comes to 1000 bits per second. The feature of replication enzymes can start on the second replicated strand of DNA even before they are finished copying the first one. So rate is nearly of 2000 bits per second. With each additional strand data rate increases by 1000 bits per second.
Iteration speeds up data rate. After 10 iterations DNA is being replicated at a rate of about 1 Mbit per second. After 30 iterations it increases to 1000 Gbits per second.
More than 10 trillion DNA molecules can fit into an area no larger than 1 cubic centimeter (0.06 cubic inches). DNA computer is capable enough to hold 10 terabytes of data with performance of 10 trillion calculations at a time.
In simple words, DNA computers can perform an amazing number of calculations simultaneously; specifically, on the order of 10^9 calculations per mL of DNA per second! That’s how its effective density is roughly 100,000 times greater than modern hard disks.
"A single strand of DNA does not yield much power. But DNA can be replicated, so that you can have as much DNA as you need to perform incredibly difficult tasks. And the strange property of a DNA computer is that it can test all the solutions simultaneously - a truly parallel task." - Tormod Guldvog (Hypography Sci-Tech)
Any transistor base computers generally handle operations in a sequential manner. A von Neumann machine (Modern CPUs) repeats "fetch and execute" cycle over and over again. Where as DNA computers are non-von Neuman. In DNA computer power comes from memory capacity and parallel processing.
However, DNA computing is still very much a dream for scientists. They hope to harness the enormous data-storing capacity of DNA, biological molecules that are also able to perform operations similar to silicon computers.
Hamiltonian Path problem
Hamiltonian path problems is a classic mathematical problem of " traveling salesman" where one needs to find how a salesman can visit number of cities without passing through any city twice. It is very simple if numbers of cities are less. But it becomes difficult for any silicon computers to find out when numbers of cities increases.
Adleman used standard molecular biology techniques to solve by exploiting the predictability of how DNA interacts. He first generated all the possible itineraries and then selected the correct itinerary. This is the advantage of DNA. It’s small and there are combinatorial techniques that can quickly generate many different data strings.
A recent experiment says, "DNA computer can solve the problem for up to 15 cities."
Inventing future computer
Weizmann System
Until now, DNA processors have needed intensive tending and have been limited to specific problems. Israeli scientists Ehud Shapiro and colleagues have designed Weizmann System that uses DNA to carry out any calculation and require little human intervention. The system emulates a Turing machine, which is one of the fundamental concepts in computing. Such a machine examines data step by step, making decisions on what to do next based on that data. In theory, any Turing machine can do any computing problem. In nature, DNA molecules work in a very similar way, unzipping and recombining according to information coded into sequences of chemicals. – Journal of Nature
Team of Israeli scientists used DNA to create a programmable computer that's smaller than a drop of water.
"The long-term goal is to eventually create autonomous, programmable molecular computing devices that can operate in vivo, eventually inside the human body, and function as 'doctors in a cell" - Ehud Shapiro, a computer scientist (Weizmann Institute of Science).
DNA Computer for Gene Analysis
Olympus Optical Co. Ltd. has developed what the company says is the first commercially practical DNA computer that specializes in gene analysis. The computer was developed in conjunction with Akira Toyama, an assistant professor at Tokyo University
The new computer is divided into two sections: a molecular calculation component and an electronic calculation component. The former calculates DNA combinations of molecules, implements chemical reactions, searches, and pulls out the right DNA results. The latter executes processing programs and analyzes these results. The company will start gene analysis using the DNA computer on a trial basis for a year, and hopes to offer the service on a commercial basis for researchers in 2003.
Cracking codes.
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 University of Southern California in the US and colleagues used different strands of DNA to represent the 20 variables in their problem, which could be the most complex task ever solved without a conventional computer. The researchers believe that the complexity of the structure of biological molecules could allow DNA computers to outperform their electronic counterparts in future.
Maya: Playing tic-tac-toe
Scientists have built a DNA computer to play tic-tac-toe. MAYA, the DNA computer, is the brainchild of Milan Stojanovic, from Columbia University, and Darko Stefanovic of the University of New Mexico
It is just a beginning
"DNA would ultimately replace silicon chips. A single gram of dried DNA, about the size of a half-inch sugar cube, can hold as much information as a trillion compact discs. I'm just not sure how!" - Adelman
Reference and Further Readings
- Adleman, L.M., Molecular computation of solutions to combinatorial problems, Science, 226 (1994), 1021-1024
- Journal reference: " Nature Biotechnology"
- "New Scientist"- Magazine
- DNA computer plays tic-tac-toe By Michael Stroh, The Baltimore Sun, August 18, 2003; Robert S. Boyd, Knight Ridder Newspapers, August 18, 2003
DNA Computing A Primer By Will Ryu
Olympus develops DNA computer By Kuriko Miyake, IDG News Service
DNA computer’ cracks code By Katie Pennicott,PhysicsWeb.
How DNA Computers Will Work by Kevin Bonsor
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