Go Back   Hardware Canucks > HARDWARE CANUCKS COMMUNITY > HardwareCanucks F@H Team

    
Reply
 
LinkBack Thread Tools Display Modes
  #1 (permalink)  
Old February 14, 2012, 10:40 PM
LCB001's Avatar
Folding Captain
 
Join Date: Feb 2008
Location: Aylmer QC.
Posts: 1,774

My System Specs

Default LTMD: Key New Technology For Accelerating Folding And Misfolding Simulations In FAH

Prof. Pande posted an update on his blog on some of the new stuff their working on, the bit about producing a GPU core that could turn into the first hybrid GPU-CPU core sounds especially interesting...

Quote:

Here's an update one one of our key projects looking into protein folding, performed in collaboration with Prof. Jesus Izaguirre's lab at Notre Dame. Below is an update from Prof. Izaguirre on the progress of this project.

The Izaguirre Lab at the University of Notre Dame (Your Page Title) has been collaborating with the Pande Lab at Notre Dame to produce a new GPU core that leverages the amazing speed of OpenMM implicit-solvent force calculations (the heart of the GPU core in Folding@home) with new Long Timestep Molecular Dynamics (LTMD). This combination currently allows nearly a 10-fold speedup over OpenMM for systems as small as the WW domain (35 residues, 544 atoms) up to the Lambda repressor (80 residues, 2000 atoms). This translates into about 10 microseconds per day of simulation, which brings single trajectory millisecond simulations closer to FAH.

In collaboration with Cauldron Development (lead by Joseph Coffland, primary developer of the Folding@home client and also some cores), we hope to produce a GPU core that might be the first hybrid CPU-GPU core. There are technical questions on how to best do this, and we will engage our enthusiastic beta-tester GPU donors to discuss how to best approach this core when we are closer to production mode.

Going forward, we will continue to improve the LTMD GPU technology to obtain larger speedups for ever larger and biomedically relevant systems. A particularly excitement development will be the extension of LTMD GPU technology to explicit solvent simulations.

As far as scientific simulations, we are simulating the folding of about 80 mutants of the Pin1 WW domain, a protein implicated in some cancers and Alzheimer's disease. Understanding the role of mutations on misfolding can have important biomedical consequences, since many diseases have at least some component of misfolding of proteins. Another exciting project we are about to start is to simulate the dimerization during folding of proinsulin and proinsulin mutants, which results in some types of Type IA young and adult onset diabetes.

Thanks to the FAH donors, testers, and to the Pande Lab for their generosity and leadership which has allowed our technological developments and simulations to come this far.

__________________
Folding For Team 54196

Reply With Quote
  #2 (permalink)  
Old February 15, 2012, 06:52 AM
stoanee's Avatar
Hall Of Fame
F@H
 
Join Date: Jun 2007
Location: Lacombe Alberta
Posts: 3,252

My System Specs

Default

Interesting stuff, I like it when they tell us what they are doing in terms that I can more or less understand. It looks like my gpu folder will have some interesting beta projects to fold.

__________________
heatware
Reply With Quote
  #3 (permalink)  
Old February 15, 2012, 08:00 AM
Top Prospect
F@H
 
Join Date: Jan 2012
Posts: 104

My System Specs

Default

Wow, this looks really interesting!
__________________
Reply With Quote
  #4 (permalink)  
Old February 15, 2012, 08:05 AM
krazyups's Avatar
MVP
F@H
 
Join Date: Mar 2008
Location: McGregor, Ontario
Posts: 277

My System Specs

Default

I also like when they provide the potential outcomes from folding these particular proteins. Alzheimer's has hit my family pretty hard, and everyone knows a few people who had/have cancer.
__________________
Reply With Quote
Reply


Tags
core , folding performance , folding update , folding@home , pande , stanford

Thread Tools
Display Modes

Similar Threads
Thread Thread Starter Forum Replies Last Post
Folding client V7 - SLI - Cannot use system during folding..fix? Jake_HT HardwareCanucks F@H Team 8 January 18, 2012 10:17 AM
6 GPU folding computer/need help with dedicated folding machine Silent_Avenger New Builds 11 December 25, 2011 01:17 PM
Country Folk Technology enaberif Off Topic 1 February 3, 2009 11:40 AM
All you need to know about SSD technology Cranky Storage 4 January 18, 2009 07:09 AM
Price and Technology Breakthrough!!! Shadowmeph Press Releases & Tech News 1 December 22, 2007 12:17 PM