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Yet another question for lancer

PuffTrek

GROUP: Members

POSTS: 369

Report this Aug. 19 2005, 8:40 pm

Quote (lanceromega @ Aug. 19 2005, 6:17 am)

Work on DNA computers have show the massive computing power that DNA can apply to a problem.

Recent work in this has shown that a single teaspoon of DNA can solve a mean path problem that would require a Cray supercomputer a 100 years, in mere minutes..

A single teaspoon of DNA can also store more data than all the hard drives and disk arrays on the planet.. This is the designing hand behind evolution, a chemical computer that could only be suppass by a quantum computer.


I think I have an idea about what you mean by this statement, but would you mind explaining it into further detail, or just give a link to someone elses website who has explained it. It seems really interesting...could lead to bio-computing.

If I understand it properly, we'd need to make every single dna "pair" (Forgive my lack of terminology, its been about 4 years since I last took a biology class) as the information is being writen, sort of like how a sector of a hdd is writen as information is being stored onto it.

How far do you estimate we are from utilising this technology.

lanceromega

GROUP: Members

POSTS: 3859

Report this Aug. 19 2005, 10:16 pm

Quote (PuffTrek @ Aug. 18 2005, 6:40 pm)
Quote (lanceromega @ Aug. 19 2005, 6:17 am)

Work on DNA computers have show the massive computing power that DNA can apply to a problem.

Recent work in this has shown that a single teaspoon of DNA can solve a mean path problem that would require a Cray supercomputer a 100 years, in mere minutes..

A single teaspoon of DNA can also store more data than all the hard drives and disk arrays on the planet.. This is the designing hand behind evolution, a chemical computer that could only be suppass by a quantum computer.


I think I have an idea about what you mean by this statement, but would you mind explaining it into further detail, or just give a link to someone elses website who has explained it. It seems really interesting...could lead to bio-computing.

If I understand it properly, we'd need to make every single dna "pair" (Forgive my lack of terminology, its been about 4 years since I last took a biology class) as the information is being writen, sort of like how a sector of a hdd is writen as information is being stored onto it.

How far do you estimate we are from utilising this technology.

This technology is usable now , In 1994, University of Southern California computer scientist Leonard Adelman suggested that DNA could be used to solve complex mathematical problems. Adelman found a way to harness the power of DNA to solve the Hamiltonian path problem (the traveling salesman problem), whose solution required finding a path from start to end going through all the points (cities) only once.

Each city was encoded as its own DNA sequence (DNA sequence consists of a series of nucleotides represented by the letters A, T, G, C).

The DNA sequences were set to replicate and create trillions of new sequences based on the initial input sequences in a matter of seconds (called DNA hybridization). The theory holds that the solution to the problem was one of the new sequence strands. By process of elimination, the correct solution would be obtained.

Adelman's experiment is regarded as the first example of true nanotechnology.

The main benefit of using DNA computers to solve complex problems is that different possible solutions are created all at once. This is known as parallel processing. Humans and most electronic computers must attempt to solve the problem one process at a time (linear processing). DNA itself provides the added benefits of being a cheap, energy-efficient resource.

In a different perspective, more than 10 trillion DNA molecules can fit into an area no larger than 1 cubic centimeter. With this, a DNA computer could hold 10 terabytes of data and perform 10 trillion calculations at a time. A single gram of DNA about the size of an half-inch cube can hold as much information as a trillion compact discs.

See :

http://www.cis.udel.edu/~dna3/DNA/dnacomp.html

PuffTrek

GROUP: Members

POSTS: 369

Report this Aug. 19 2005, 11:22 pm

Ok, I'm pretty sure I undersand how they would be used to work as a processor, well more accuratly trillions of processors, but how would that technology be utilized to act as a hard drive in the manner you described? If you just created one strand and got it to reproduce, then that would be the processor function you described, but it wouldn't serve as a hard drive...

Wouldn't you need to encode each dna base pair (I believe thats the correct termenology) the atgc on demand? Sort of like creating the dna strand from scratch? Or could the reproduction of the dna be changed in some way to allow it for data storage?

lanceromega

GROUP: Members

POSTS: 3859

Report this Aug. 20 2005, 8:50 pm

Quote (PuffTrek @ Aug. 18 2005, 9:22 pm)
Ok, I'm pretty sure I undersand how they would be used to work as a processor, well more accuratly trillions of processors, but how would that technology be utilized to act as a hard drive in the manner you described? If you just created one strand and got it to reproduce, then that would be the processor function you described, but it wouldn't serve as a hard drive...

Wouldn't you need to encode each dna base pair (I believe thats the correct termenology) the atgc on demand? Sort of like creating the dna strand from scratch? Or could the reproduction of the dna be changed in some way to allow it for data storage?

Well You would use the dna is several different manner.

DNA used as a storage medium would basically have the information incoded into it base pair, as a form of medium storage single string of DNA would be to store as much data as entire libraries.

DNA used as processor would be design to reproduce them self in a manner that would allow it perform it computation and then store the answer..

Creating the DNA strand you need would be difficult but major research has also been done on DNA machines that would once made be used to create other DNA pattern on demands

A DNA walker, a DNA machine that moves molecules have already been created:


DNA machines take a walk

By Eric Smalley and Kimberly Patch, Technology Research News

Researchers working to form nanoscale machines and materials are increasingly tapping nature's building blocks. Two particularly helpful molecules are DNA, which encodes instructions for making the proteins that carry out life's processes, and the motor protein kinesin, which is part of the a cell's transportation system.

DNA molecules contain strings of four types of bases -- adenine, cytosine, guanine and thymine -- attached to a sugar-phosphate backbone. Single strands self-assemble into structures like life's familiar double helix when their bases match up. Researchers can manipulate artificial strands of DNA by controlling these connections.

Kinesin molecules have a pair of short extensions, or legs, at one end and a tail at the other end. The legs attach to a microtubule protein, and step to move the kinesin bipedal molecule forward along the microtubule molecule. The tail grabs cell structures like vesicles and mitochondria to transport the structures over a cell's extensive network of microtubules.

Several research teams have built DNA walkers, inspired in part by kinesin, that move along DNA tracks.

Researchers from Duke University and the University of Oxford in England have devised a a series of DNA stations that pass a DNA fragment from one to the next. The walker works autonomously, using enzymes present in the environment to initiate each step of the process.

Researchers at the California Institute of Technology have built a bipedal DNA walker that improves the gate of a walker originally designed by researchers at New York University from shuffling, with one leg always in back of the other, to leg-over-leg walking.

Both types of walkers could eventually be used to construct nanoscale devices, synthesize and deliver drugs, and carry out DNA computation. "Eventually, it may be possible to program synthetic motors that can haul diverse molecules along intricate paths for use in nanoscale factories or molecular medicine," said Niles Pierce, an assistant professor of applied and computational mathematics and bioengineering at Caltech.

The Caltech prototype is designed to mimic kinesin, and consists of a DNA track with four anchorage sites and a bipedal DNA walker. The anchorage sites are single strands of DNA set five nanometers apart along the double helix track, and the walker is a double helix structure with strands separated at one end.

The walker's loose strands form a pair of 23-base legs, and the four anchorage sites contain different sequences of 20 bases.

To set up the process, the researchers add an attachment strand that joins at one end with the first anchorage strand and at the other end with one leg. A short segment in the middle of the attachment strand that does not match up with the leg or anchorage strands provides flexibility.

To make the device take a step, the researchers add a second attachment strand that moves the second leg by fixing it the second anchorage strand. To make it take another step, the researchers free the first leg with a detachment strand that removes the first attachment strand, then swing the leg forward and bind it to the third anchorage with a third attachment strand. In this way, the walker progresses one leg in front of the other along the track.

The prototype falls short of kinesin in several regards, according to Pierce. Kinesin runs autonomously whereas the researchers' DNA walker requires DNA fuel strands -- the attachment and detachment strands -- to be administered at each step, he said. Kinesin also moves at about 100 steps per second while the researchers' device takes around two steps per hour, he said.

The Duke University walker consists of a double-stranded DNA track with three DNA anchorage site segments attached to the track by single-strand hinge segments of DNA. The anchorage DNA is double-stranded, but one strand shorter, leaving a three-base extension at the free end. The walker is a six-base single strand.

The walker begins attached to the first anchorage. The three bases at the free end of the walker attach to the end of the second anchorage, causing the first and second anchorages to swing on their hinges toward each other. An enzyme frees the walker from the first anchorage and alters the anchorage to keep the walker from stepping backwards. The free end of the walker then attaches to the third anchorage. A second enzyme cuts the walker free from the second anchorage to complete the move to the third anchorage site.

Unlike the bipedal DNA walkers, which require DNA strands to be added at each step of the process, the Duke device operates continuously because none of its components interfere with each other and so can all be present in the environment. "Our walker operates in an autonomous fashion while previous constructions by other groups require... the adding and removal of fuel DNA strands to drive the walker," said Hao Yan, a Duke University researcher who is now an assistant professor of chemistry and biochemistry at Arizona State University.

The DNA walker could eventually be used to carry out computations and to precisely transport nanoparticles of material, according to Yan. The walker can be programmed in several ways. "For example, we can encode information in [the] walker fragments as well as in the track so that while performing motion, the walker simultaneously carries out computation," said Yan.

The walker could also be programmed to transport tiny bits of material, said Yan. "If integrated with a well-defined large-scale nanostructure such as two-dimensional DNA nano-grids, the walker might be able to precisely transport a nanoparticle from one location to another location on the nanostructure... in a programmable and autonomous fashion," he said.

The DNA walkers advance DNA nanotechnology by anchoring controlled, progressive motion to a structure. This is a key step toward harnessing the work of DNA machines. "Ultimately, our objective in pursuing rational DNA design is to develop a molecular compiler that takes as input a conceptual design for a device and produces as output a list of DNA sequences that can be expected to assemble into the desired system," said Caltech's Pierce. "

The Goal is creation of the molecule machines that would automate the process, manufacturing DNA sequences on demand in the matter of minutes..

But due to delicate nature of DNA, most of these DNA machine will most likely be used in medical and biological research, already DNA machines have been look at as a method to attack Tumors and virus by having them alter the basic DNA of these cells and virus and shut them down. The DNA machine will be desire to recognize and leave the host body cells allone and self destruct after their mission have been completed.

Nanobot made of DNA would be less toxic to human body than those made of carbon as recent research as shown toxic effect of nano structure constructed from carbon on fish brains.



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