Posted on 12/08/2008 12:10:04 PM PST by texas booster
... We present a novel computational approach for describing the formation of oligomeric assemblies at experimental concentrations and timescales. We propose an extension to the Markovian state model approach, where one includes low concentration oligomeric states analytically. This allows simulation on long timescales (seconds timescale) and at arbitrarily low concentrations (e.g., the micromolar concentrations found in experiments), while still using an all-atom model for protein and solvent.
As a proof of concept, we apply this methodology to the oligomerization of an Abeta peptide fragment (Abeta 21–43). Abeta oligomers are now widely recognized as the primary neurotoxic structures leading to Alzheimer's disease. Our computational methods predict that Abeta trimers form at micromolar concentrations in 10 ms, while tetramers form 1000 times more slowly. Moreover, the simulation results predict specific intermonomer contacts present in the oligomer ensemble as well as putative structures for small molecular weight oligomers. Based on our simulations and statistical models, we propose a novel mutation to stabilize the trimeric form of Abeta in an experimentally verifiable manner.
Congratulations to Texas Booster, who will pass Three Million points today!
Thanks, for all that you do!
I hit #1 for the team...(for the past 24 hours...) at one point today. I’ve closed to just over 8,000,000 from the lead, and ~2,800,000 behind you. Watch out...here I come.
Folding systems at 20 paces?
I haven't been the #1 producer but a few times since the group started growing a few tears ago.
Passing me won't mean much, but if you pass lrenh or Klutz then you will have really accomplished something!
fyi...
Egon (just) and Pseudocode (recently) broke a million!
It looks like SazanEyes is folding with us and making a prodigious daily contribution! (2nd highest on the list today... Nice!)
http://folding.extremeoverclocking.com/team_summary.php?s=&t=36120
Anyone know SazanEyes’ FR name?
Hi guys, I fold as SazanEyes. I don’t post to FR much, but I wanted to give a boost to the team of Reagan. :-)
Actually, I’m also folding for another team right now, but I’ll probably switch all my hardware over to the FReeper team at the end of the month. This is what’s coming:
http://folding.extremeoverclocking.com/user_summary.php?s=&u=384443
Wow David, that’s pretty impressive!
Care to tell us a bit about the hardware you’re using?
And THANKS for folding, and thanks again for folding with us!
Right now I have two NVidia 8800 GS cards (overclocked) folding for FR. For the other team I’m using four 9800 GX2s, one 8800 GTS, and a PlayStation 3. It’s actually a pretty small setup. Most of the points come from the quad 9800 GX2 box, which was built specifically for F@H.
If anyone has a relatively modern graphics card (NVidia 8000 series or better, or recent ATI card), definitely install the GPU F@H client for it. It can do a ton of work.
I am amazed that you produce so much work from just a few systems. I keep about 40 systems running, but half of my points come from one NVidia 9600 card.
Could we call on you to assist others in getting GPUs working smoothly some weekend?
Yea, I would be interested. How do I check what graphics card I have?
Also, I just saw that I made the top 20 producers list. That's a first for me, I think.
Ever been invited to this?
http://www.majorgeeks.com/Belarc_Advisor_d1385.html
If you have an NVidia or an ATI graphics card we can proceed.
Yes. I had it on my older computer for a while. Had enough computer problems I gave up on reinstalling it.
Not sure if I’ll install it on this one, or not. Just got it back from overhaul and am a bit picky about clogging the works up with much of anything unnecessary.
I think it’s a great project.
Of course I doubt the oligarchy really WANTS Alzheimer’s patients healed etc.
Part of me thinks they’d take the findings and make it worse and more of a problem.
Thanks.
Congrats on your achievement.
Bump for later
How do I find out?
If you don’t want to install Belarc and are using Windows (2000/XP/Vista/7), try this:
1. Open the Start menu and right-click on the My Computer (or just Computer) item in the right column of the menu. (If you have a My Computer on your desktop, you can also right-click on that.)
2. In the pop-up menu, click on Manage.
3. When the Computer Management program opens, click on Device Manager.
4. You should see a tree view of all the parts in your computer. Look for the Display Adapters entry and expand it.
5. Let us know what it says your display adapter is called. For example, my desktop has “NVIDIA GeForce 8800 GTS” listed.
If it says NVIDIA 8xxx or 9xxx or GTX 2xx, or ATI 2xxx or 3xxx or 4xxx, then you can probably use your GPU to fold.
If you want to just try installing the software to see if it works, it’s available here:
http://folding.stanford.edu/English/DownloadWinOther
The GPU2 program has a standard Windows installer. You just download the install program, run it, click OK a few times, and everything is set up for you (just like the CPU version). If you want a detailed walkthrough to the install/setup process, look here:
http://www.hardforum.com/showthread.php?t=1339662
That page also explains how to run Folding@home on multiple graphics cards if you happen have more than one in your computer.
Right now I only have two PCs (with 10 GPUs) folding for the team. I stopped using one PC and the PS3 to try to save a little money on electricity, but my points per day have actually gone up thanks to the new work units.
I’d be glad to help others start GPU folding and offer some tips. For example, if you want to run F@H on your graphics card 24/7, then you probably want to adjust your card’s fan speed to make sure it stays cool. The most popular program to do this is RivaTuner:
http://majorgeeks.com/download737.html
BTW, I finally reached #20 on the team today in total points. I might be able to make #10 by the end of the month.
Keep in mind that I have been folding since 2001 or 2002 with CPUs, between 30 and 50 systems most of that time. Klutz has has over 400 CPUs running at once.
Here you come with 10 GPUs and a Playstation (!!) and will pass my points total in 3 months. Arrrgh.
I also saw that Stanford has looked at the whole FLOPS issues and decided to adjust FLOPs (but not points).
F@H is now running at 8.8 petaFLOPS. Insane.
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