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Juggling Molecules with Linux
An anonymous reader writes "This article at LinuxDevices.com describes an interesting project at the University of Vermont in which researchers use real-time Linux to build a laser trap that manipulates individual molecules by means of a computer-controlled laser beam. The project makes use of RTLinux, a real-time enhanced version of Linux that allows the system to process interrupts every 50 microsecond, sample new data, and timeshare the laser beam position. 'If the computer failed to respond, for even a millisecond, then we would drop the balls,' explained one of the researchers. Gives a whole new meaning to BSOD, eh?"
I do not see why.
...is doing something useful. Just kidding! Don't kill me. Mod Flaimbait, please
When it's juggling a molecule, a bowling ball, and a chainsaw, then I'll be impressed;-)
If brevity is the soul of wit, then how does one explain Twitter?
move the fleet away from the death star!
Holding the balls. The perfect job for Lunix. It's the Lunix Gay Conspiracy all over again!
How am I supposed to fit a pithy, relevant quote into 120 characters?
I think it gives a whole new meaning to the phrase: "don't drop the ball!"
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Dr. Torvalds: You know, I have one simple request... and that is to have penguins with frickin' laser beams attached to their heads. Now evidently, my megaloptic Naval colleage informs me that IT'S A TRAP!
I know several researchers who have been using realtime Linux on the desktop while performing studies regarding the user experience of systems with minimal latency. Their preliminary findings are that users much prefer the instantaneous response that a realtime system offers, even if the system does not perform as well when it comes to raw data crunching. For future desktop systems, heavily multithreaded, realtime apps are the way to go.
Cyric Zndovzny at your service.
Linux based sharks with frickin' laser beams on their heads....
So I guess the laser juggler program would be a "chocolate" Linux application. Mmmm
Why not just use DOS or mac OS 8. Seriously. For instrument control you want your program running and screw everything else. Modern OS are the bane of instrument control, even so-called RT systems. They just seem to go out to lunch every now and then.
Some drink at the fountain of knowledge. Others just gargle.
Victor Yodaiken (who wrote TFA) is the clown who patented his technique for implementing RTLinux. I much prefer RTAI for real-time linux, both because it is IMO a superior implementation, a better license, and it doesn't give support or credibility to Yodaiken.
huh, another contender ... I'll have to check it out. I used to work at QNX who also make a real-time posix-compliant OS, but it's geared more for embedded systems than desktop use (although it *can* be used on a desktop)
my geeklog
I was under the impression that the whole idea of a laser trap is that you CAN'T drop the ball. Small particles get trapped in the beam due to photon pressure, if the particle shifts away from the center of the beam, it automatically is recentered. Then you can move the beam to manipulate the particle which is attached to a molecule. They use these to fold and unfold proteins, lipid layers, DNA, etc.
I mean, it's great that they're using a realtime kernel, but they really shouldn't NEED it.
-- sometimes AND gates turn me on.
+100 Insightful
See my journal for slashdot ID's by year. Mine created in 2005. http://slashdot.org/journal/289875/slashdot-ids-by-year
I've made some use of RTLinux myself - one aspect that we got to wonder about is to which extent you can move the controller outside of the computer and into its own embedded device. In this case, it seems that it's the diversity of experiments that is the deciding factor for using the computer.
It is a little odd that they talk about 1 millisecond, when the time between interrupts is 50 microseconds. To miss for "even" 1 millisecond would mean missing 20 interrupts! That's just some hype, IMHO. What I find more interesting (but can't find in TFA) is the tolerance for delay per interrupt: if the interrupts are 50 microseconds apart on average, but sometimes 20 apart and sometimes 70, what is the result for the experiment? I think that that's where you're going to see the real test for RT Linux.
see a Text Widget
Imagine a Beowulf cluster of these things! Anyone up for some 80's style disco dancing with laser beams?
Sooo... basically they're using an operating system to do what they should have an FPGA perform?
... is beyond me.
I mean, rah-rah-go-linux... but sounds like a dramatic over-use of power. Why one would use a modern OS to perform tasks that should be handled by dedicated hardware
[note to mods: If you don't get the joke you should read the other headlines on today's index]
;-)
Should read:
"World's fastest Linux-based laser trap"
...but does it have enough horsepower to generate a mime trapped in a box? I doubt it.
Fedore Core 3 comes with an application for juggling molecules. It's called "katomic". It actually allows one to assemble molecules from its constituent atoms. The miracles of modern science never cease to amaze me.
You want a BSOD, eh? How about this: You build a gun that has an actuator attached to the serial port of a computer running Windows NT. The computer sends, via the serial port, a watchdog-style "keep alive" signal, say, every 100 microseconds. The actuator is designed such that once powered on, if the watchdog timer skips a single beat or delivers it too late, the gun is fired.
At this time, a volunteer (say, Gill Bates) would be tied to a chair and placed in front of this gun, while the Windows NT system runs Exchange and IIS, and while a user browses pr0n sites via Internet Explorer. This is, actually, quite a safe experiment, as we all know that Windows NT never crashes.
The lunix is on the grass
The lunix is on the grass
Remembering games and daisy chains and laughs
Got to keep the lunix on the path
-- Fink Ployd.
Oh well, what the hell...
For a 200MHz Pentium (this is an old review), the testers tried sending one billion interrupts with a latency check. When they required 8 microsecond latency, they missed one interrupt in a billion. When they only needed 10ms latency, they didn't lose any.
Comparable figures are available for various real-time Linux systems. Note that these figures are for a 650MHz CPU. The times are slightly better than for QNX, but the CPU is 3x faster.
Bear in mind that "RTLinux" programs aren't running under Linux. They're running below Linux. They can't make most system calls, for example. QNX programs are ordinary programs, and can make system calls.
The Linux 2.6 kernel isn't bad, though. Running real-time with millisecond response as high-priority Linux threads can actually work in 2.6. In 2.4, no way. You have to be very careful not to load any high-latency drivers, though.
"Hey Bob.. over at the University of Vermont we were able to juggle molecules with lasers! Isn't that GREAT?" "Wow, that's awesome Jim.. all my team is working on is that boring old CURE FOR CANCER. Have fun with the laser-linux circus."
I juggle molecules all the time - In fact, I never juggle anything EXCEPT molecules.
Of course, I usually juggle lots of them at once.
I don't dispute your friends' findings, but I'm wondering why a RT based OS would really improve the user experience?
Here's why I ask: A RT system is typically real time for some dedicated purpose. Not all pieces of the system have to be RT; just the important bits. Now, an average user PC is NOT a specialized device at all. It can be running a number of applications and, except for cases where a given process has a higher priority, all the processes typically get an opportunity for equal time from the CPU. A desktop system with a RT OS would also fit this description too, right?
Now, given that: where's the RT aspect in all of this? What's actually RT in this situation? The pre-emptive multitasking loop? The UI event/response loop? The IO loop (assuming you could describe it that way)? The video update loop? What about this would give the user a better experience?
Please mod this post only if you think others should/n't read this. I have enough ego^H^H^Hkarma. Thanks!
Is Slashdot nothing but a Rah Rah site for Linux then? They could have just as easily used QNX, Windows CE or even Embedded XP.
3 9286.html
:(
Yes, CE has very good real-time response.
Read, if you dare:
http://www.windowsfordevices.com/articles/AT67610
And QNX kicks RTLinux ass in almost every respect for this type of work. In short, the people that chose to use RTLinux were probbly just idiots that didn't know any better
...and the article is written by Victor YODAiken. Coincidence? I think not...
Visit http://ringbreak.dnd.utwente.nl/~mrjb/growingbettersoftware to download your free copy of the book
The Amiga had CPU clock-cycle-precise interrupts. IE, the very slowest 1985 Amigas (A1000) could throw interrupts every 1/7.16MHz seconds, or about 140 nanoseconds. 2005 Linux has an interrupt precision of 50 microseconds.
Way to go, RTLinux! You are now only 2800 times slower than a 20 year old box. Not that any other system is better...
I choose to remain celibate, like my father and his father before him.
Bah! Come back to me when you can do it with sharks with frickin' lasers on their heads!
I just want to take over the world...Why does that automatically make me EVIL?
I think he was trying to say to the Slashdot audience, 'Stop saying Microsoft is x times better than Linux and therefore Linux should die. Look here! Here's something that we need Linux for, we could not have done this with Microsoft.'
In other words, it is good that Linux exists for specialist projects and any attempt to ban Linux (eg. by patenting algorithms used in the Linux kernel and making it illegal to distribute) would have harmful effects on society, making these sort of experiments much more difficult/impossible.
Allow alternatives to Microsoft exist. Oppose efforts to make Linux illegal (via software patents for example). Do this even if you think personally Linux sucks. Other people will thank you.
I'll probably be modded down for this...
A friend of mine implemented tetris using a laser to trap 1 mirometre glass beads. Short story + picture + video here. More explanation here.
The A1000 came before the A500. They both had the 7.something MHz clock.
How interesting. I just saw a lecture by one of the men that won a nobel prize for this very thing, Steven Chu. What is being done here is essentially what is called Optical Tweezers.
The way this works is that the laser is fired, in timed pulses at a molecule. When the laser hits it from an opposing direction, it starts to cancel out the kinetic energy that the molecule has, and therefore cooling it. (I think it was something to the order of 2.0 × 10^-06 degrees above absolute zero).
In a nutshell, this is what is going on:
-SteveAlmost Absolute Zero == Essentially No Movement == Essentially "Frozen" Object
Are you sure you're on the right site, buddy?
It is the way of the Slashdot.
Is it really true in your reality that Slashdotters say that "Microsoft is x times better than Linux"? Or is x less than 1?
If the computer failed to respond, for even a millisecond, then we would drop the balls...
:)
Not a very patient porn-surfer, are we?
Those who sacrifice security to condemn liberty deserve to repeat history or something. - Benjamin Santayana
I'm the chemist turned admin turned programmer turned biophysicist that started the 'alpha' project in the Warshaw lab.
If hankering for more details see:
http://www.uvm.edu/~dgaffney/bmes99/
This trap is now more than 6 years old. We're still doing cool stuff though (oooh, aaah, pretty quantum dots), so if you're interested in how your body converts chemical energy into mechanical work, see the department home page:
http://physioweb.med.uvm.edu/
Join us as a technician, graduate student or post-doc. Burlington is a great town, and the department is the best muscle research center on the planet.
Regards,
Don (dpg2)
P.S. - please do have a look at the first site above; MGA, our fanastic CIT sysadmin would love a "slashdot-effect" story to share with his friends.