Implementing models for DNA computing: concerns from the lab

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http://computer.howstuffworks.com/dna-computer3.htm

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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.

While still in their infancy, DNA computers will be capable of storing billions of times more data than your personal computer. In this article, you’ll learn how scientists are using genetic material to create nano-computers that might take the place of silicon-based computers in the next decade.

A Fledgling Technology

DNA computers can’t be found at your local electronics store yet. The technology is still in development, and didn’t even exist as a concept a decade ago. In 1994, Leonard Adleman introduced the idea of using DNA to solve complex mathematical problems. Adleman, a computer scientist at the University of Southern California, came to the conclusion that DNA had computational potential after reading the book “Molecular Biology of the Gene,” written by James Watson, who co-discovered the structure of DNA in 1953. In fact, DNA is very similar to a computer hard drive in how it stores permanent information about your genes.

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.

A Successor to Silicon

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.

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DNA computing is a form of computing which uses DNA and molecular biology, instead of the
traditional silicon-based computer technologies. A single gram of DNA about the size of half inch cube can hold as much information as a trillion compact disks.

This field was initially developed by Leonard Adleman of the University of Southern California. In 1994, Adleman demonstrated a proof-of-concept use of DNA as form of computation which was used to solve the traveling salesman problem. In addition, Bernhard Yurke (Bell Labs) has developed DNA motors. Since the initial Adleman experiments advances have been made, and various Turing machines has been proved to be constructable.

There are works over one dimensional lengths, bidimensional tiles, and even three dimensional DNA graphs processing.

On April 28, 2004, Ehud Shapiro and researchers at the Weizmann Institute announced in the journal Nature that they had constructed a DNA computer from biomatter extracted from human feces. This was coupled with an input and output module and is capable of diagnosing cancerous activity within a cell, and then releasing an anti-cancer drug upon diagnosis.

DNA computing is fundamentally similar to parallel computing — we take advantage of the many different molecules of DNA to try many different possibilities at once. The number of possible solutions to a problem grows very quickly with the size of the problem, exhibiting exponential growth. For very large problems, the amount of DNA required will be too large to be practical. Thus, DNA computing does not provide any new capabilities from the standpoint of computational complexity theory, the study of which computational problems are difficult.

DUE  April 8, 2005

Overview of DNA computing applications (’98).
Implementing models for DNA computing: concerns from the lab
Implementing addition with DNA computation
A mathematical interpretation of DNA operations
A comparison between DNA computing and quantum computing.
DNA computing by splicing.
DNA computing by self-assembly.
Cryptography using DNA
Complexity measures of DNA computing.
The sticker model for DNA computation.
Computing Boolean formulas with molecules.
Design a DNA algorithm for a computational problem of your
choice.
Aqueous Computing
Watson Crick Automata

Instructions for Final Exam Report:

Your final essay should be of 1500 words. It should be of essay type(not just  title headings). No pictures necessary. The exam should be written in your own words . You should not use sentences taken from published papers or online resources. Failure to do so , it  is considered to be plaigirism and the penalty for that is a failing grade in the course and a possible expulsion from the university. You should also include the list of references(published articles) you used for the report. No online references are allowed.

Submission :
Please print your paper and put it in my mail box by Friday April  8 before Noon. NO online submission. Any submission after noon will not be accepted or graded.  Best to give it to me during class hours on Thursday if you have it ready.

I satirized myself in that last post. It sounds like a nightmare scenario but there is a lot of it that I find desirable.

5:00am on Tuesday morning. Frustrated with an overdue assignment that I thought would be simple. It is like a little pebble I am tripping over after climbing mountains. There are a bunch of complex, half-formed ideas and sentiments in my head that want to be expressed and purged but I’m too fried to explore them. I wouldn’t say my life is out of control right now but it’s moving at supersonic speed. When I came home today after my last presentation I loved the way my apartment looked. The vibrant, chaotic beauty of it. I wanted to savour and remember that image because I know I’ll miss it. I love the person I am now. I have truly surprised myself, back in January I really thought I was dead meat. I’ve achieved so much more than I thought I could.

Earlier I was taking a break in my dark apartment. It was raining outside and I felt drained and phased from all the work I’ve been doing lately. A kind of crash down from operating at such a high level for such a long time. I was just lying in my bowl chair in the dark and listening to good music that was accentuating my mellow mood. A large shadow shifted behind me and I knew something had just entered my apartment. I didn’t feel like moving to look though. And I know it was something very unusual. Maybe it sensed I wasn’t in the mood to pay attention to it.

My April calendar monkey is a vervet. He has a big furry white chest and a little black face. This one looks much different than the March Japanese Macaque who had a solemn, rundown look. Unlike the macaque, the vervet isn’t looking into the camera with sad eyes, he’s gazing off into the distance with an alert, focused expression. There is newly gained wisdom in his eyes and a determined set to his jaw. You can tell this monkey has been through a lot of shit and there is still more on the horizon. He can handle it though. He has a quiet confidence and passionate core that give him strength to persevere.

http://24.103.166.19:8888/Protein-Secondary-Structure-Display.ppt

Protein-Secondary-Structure-Display.ppt

I hate when the weather starts to get better. It makes working night shifts incredibly unbearable. I feel like a dark little troll. I used to revel in the sun. I used to be out in it all day long, everyday. l;kfjgkldgjoieguwoiugb

Since I know everyone wants to hear about it, I’m going to write about my haircut. I’ve been looking a little too much like Megaman lately. Sporting a large unkept mass of thick black locks that blows majestically in the wind. Like just about everything else, Megaman can pull it off (and with incredibly sexy results too). I needed something a little cleaner for my upcoming presentations though.

I went to the Gentleman’s Barber. The woman who did it is my least favorite on staff but she did a passable job. I like the Italian guys (if there’s one thing Italian guys know, it’s hair). My favorite woman wasn’t there. Too bad. I go there because it’s obvious that they take pride in what they do, only doing men’s cuts and really taking their time to do a fine job. They warm up the shaving cream and shave your neck and around the ears with a metal razor too. That’s the best. So much better than the place on campus where they shave you down in about five minutes and hustle you out the door.

Blah.. I can’t believe I actually broadcasted that I was listening to Chesney Hawkes on my last post. I like the hook but the soft synth interludes are cheesey beyond belief. I think it’s on my best of 1992 list. Some people have comfort food, I have comfort music that I retreat into during times of high stress. I’ll listen to club tracks with wicked hooks and the best tracks of 1980-1997, as previously and painstakingly chosen by me. I’ve decided that 1998 was the year that pop music got really crummy. 1999 was the worst year ever.

I think my posts are probably going to be pretty lame for a while. Burn out city. I coded most of the day. Still, I’m feeling fairly decent. I took the bike out for the first time of 2005, worked out and despite having some amusing quirks, my protein structure prediction program has actually started to work.

Happy Easter. No bunny trail this year unfortunately. No Easter chocolate either. My apartment is looking a lot like I am. Disheveled. Messy. Toasted. Sunday afternoon detox. Wicked headache. Likely due to stress and copious amounts of sugar and caffeine. Maybe it’s just dehydration. I was flying last night though. I’ll be ok, there be a brimming giant coffee right hurr.

I worked a crazy shift last night. I got some odd requests from the residents.  My favorite was received from a drunk first floor buisnessman calling from a bar. It was a panicked request to enter his unit and move all the beer from freezer to fridge to prevent explosion. He’s a nice guy, I didn’t mind helping him out. It was Sleeman’s Clear if you’re curious, wouldn’t have been my choice. Anyway, the supervisor is away and I’m being an even worse employee than usual. I wasn’t even pretending to do my job. I locked myself in (and everyone else out of) the exercise room and watched boxing. I flagrantly listened to Luna at the front desk. I neglected to do other more boring stuff (this has the potential to land me in a lot more trouble). Some school work got accomplished though.

Upon awakening yesterday, I was angry at myself for deleting Ms. Pacman. It’s good that I seized that moment of clarity and personal conviction because I wanted to play bad. What else. I hurt my vocal chords yesterday singing Just a Friend by Biz Markie in the shower. I’m enjoying my near eastern mythology lectures. The cannonites aren’t all that bad. They’ve got some funky gods and goddesses. Fallible sexual pagan gods are where it’s at. Hepcat.

My Thursday presentation weighs heavy on my mind cause the program I’m presenting still isn’t working. It’s reflective of its creator, there are some nice extra features but it still doesn’t do what its supposed to.

My discipline is breaking down. A truth I’ve learned through many painful lessons is that I am utterly incapable of working at home. Home is home and the place of food, sleep, sex, video games and movies. Hmmm, that’s an interesting chronology that just flowed out of my impaired consciousness. I wonder if it means anything. I don’t think so, I rarely watch movies or play video games anymore. Deadline panic is providing the impairment. I am having difficulty preventing my perspective from widening out from the tunnel vision that I so desperately need to maintain right now.

My life is full of ghosts. Some of them interact in a seemingly indirect way and some of them are openly aggressive. However, they all want me to fail. Sue is the cunning one. She won’t confront me openly and but she gets into my head. Constantly forming and revising her long term strategy to confound my efforts at every turn. Devious, diabolical Sue. Too good for straight up chasing, the constant thorn in my side.

I die by Inky’s nasty hands often too. He’s got those wild eyes. Crazy bastard. You never know what Inky’s gonna do. That mental instability makes him unpredictable and dangerous. Inky’s always sinking those grimy green teeth into my supple yellow flesh.

The angry red ghost, Blinky is an idiot. In his mindless rage he is utterly predictable and easy to confuse. My elegant dancing is no match for simple Blinky.

Pinky’s a determined chaser too, but likewise can’t handle my smooth moves. She’s the delicate lady of the bunch, not a thug like Blinky or Inky. She will chase but doesn’t have the stomach for the kill, she just wants to get ahead of you and get in your way. It’s always Sue though, cerebral Sue. Always in my next section, always one step ahead, blocking that next energizer while Blinky and Pinky pressure from behind.

I’m deleting Ms. Pacman right now. What a mistake installing that was this morning. I had a nap this evening and all I dreamed about was grids, ghosts and kinky pacman sex. Nothing got done. I’ll chalk today up to post thesis decompression and start work early, early tomorrow. And I will delete my pixelated temptress after a few more games.

Your Homicidal Rampage! by crash_and_burn
Your name:
Weapon of Choice:	Cigarette lighter
Your Favorite Target:	Hospital workers
Your Kill Count:	1,067,985,234
Your Battle Cry:	“Moo!”
Years You Spend in Jail:	44
How Much Money In Damages You Cause:	$284,056,710,428,038
Your Homocidal Insanity Level:: 83%
Quiz created with MemeGen!

I envision more of a GGUUUURRRRRRRRAAAAAAAAAAAAAAAARARRGGGGGGHHHHHHHHHH!!!!!!!!!!!!!!!!!!!!!!!

Wow. I got some great comments on my last post. I thought a post on hockey would bore everyone to death. Thank you.

Question: What was the Billboard number one song of 1966?
Answer: Sgt Barry Sadler – Ballad Of The Green Beret

So today in an effort to calm myself while I frantically tried to weave a connecting thread through the disjoint sections of my thesis, I listened to the top 100 hits of 1966. I was surprised to find a really cheesy, patriotic, lame song at the top of this great musical year. What was in the number two spot?  Diana Ross – You Cant Hurry Love. A supremely superior song. I can’t help but wonder if racism was in play to keep a black woman out of number one. I envision an old prejudiced grump with some power to wield ordering someone at Billboard, “Bump her out of the top spot! Here, put this patriotic ballad in as number one, do it for your country son. What are you? A pinko?” (I have no clue if anyone actually talked like this in 1966)

Have a look at what else Sgt Barry beat out:
#8, The Beatles – We Can Work It Out.
#18, The Rolling Stones – Paint It Black.
#25, Nancy Sinatra – These Boots are Made for Walking.
#34, Percy Sledge – When A Man Loves a Woman.
#37, The Beach Boys – Good Vibrations.
#43,  Stevie Wonder – Uptight Everything’s Alright.

The injustice continues all the way down. That lousy Green Beret song is incredibly horrible and it was number one. Number one! I don’t even know why I am pretending to be shocked. Musical crap always seems to float to the top.

Fighting soldiers from the sky,
Fearless men who jump and die.
Men who mean just what they say,
The brave men of the Green Beret

Ok, nevermind. With brilliant ryhmes like, “from the sky”, “jump and die”, I’m surprised it wasn’t number one in 1967 too. All right, I need to move on, nobody likes sarcasm. I’ve probably deeply offended someone. I apologize. Go U.S.A.

Worked on the thesis all day for the last time, it’s not great but good enough I suppose. I’m handing it in tomorrow on time. This calls for a single banana.

Not more because now I’m entering a tough stretch of presentations and assignments. However, I’ve felled the giant and the end is near.

My undergraduate thesis is due in two days.

I played hockey growing up. In the small city I’m from hockey is huge. One block west of my childhood home exists two outdoor rinks. One and a half blocks to the east are another two rinks. In Thunder Bay, outdoor (and indoor) hockey rinks are everywhere, and they are always in use. Before coming to London and exploring a few other cities a little, it was my misconception that this was the norm for Canada. At the NHL level Thunder Bay is probably over represented. Currently, Steve Rucchin, Anaheim’s captain is probably the most recognizable player. There are quite a few other less renown players too.

With the exception of one year, I didn’t play at the elite level, I played tier-two. Still, I was pretty good. I was one of only a handful of kids who attended hockey camp during the summers and as a result I probably developed more skill. I was always one of the best skaters on my team. I enjoyed playing the most during my first few years as a center, lots of fun and freedom. It got less fun when a coach converted me into a defenseman. Defenseman rarely score. Playing defense slowly and surely soured my love for league play. I didn’t complain much though. My reward was three consecutive “Most Sportsman Like Player” awards. At the NHL level that trophy is named the Lady Bing. You can’t really brag about perennially winning the Lady Bing.

I was undersized. (My dad was a short kid who grew a huge amount during late high school to a respectable 5’11. I followed a similar pattern, only making it to 5’10 though. I blame it on my horrible high school eating patterns.) Anyway, small is not good for defensemen. Height isn’t critical in hockey like in basketball but it helps with leverage. The few times I attempted to stand someone up at the blue line, I would usually just get run over.

In grade eight my defense partner was a huge overdeveloped gorilla man-child. A huge kid. He must have been close to six feet and 250 pounds. A total monster. He was slow as molasses too, the worst skater in existence. I remember how hilarious it was when he moved to hit someone, his target would cower in fear as this giant mass of humanity approached, but he took so long to actually get there and had so little momentum the hit was always so weak and pathetic. The coach’s logic of pairing me with him was that I could skate and would be able to get back quickly to cover for his fat lumbering ass. His not so secret weapon was an absolutely booming shot. So whenever I took a point shot (admittedly not my strong point) everyone would get pissed and chastise me because they wanted the monster taking all the shots. That was it, I wasn’t having fun any more. I quit in grade nine.

So I didn’t play for a year. I still played outdoor pickup games for fun though. In grade eleven I was somehow coerced into becoming an organizer for unofficial, unauthorized games. I would collect ten to fifteen dollars from 10 to 20 kids and then would rent ice for an hour at one of the city arenas. Any profit was gladly given to me for this task and dealing with the rink rats. Those informal high school games were a lot of fun. I haven’t played at all since coming to university, just a few sporadic recreational skates. Maybe if I find myself in a somewhat stable position this fall, I’ll look into finding a beer league to join. And I’m not playing defense.