New Paper published on the Playstation 3 Folding@Home client

Vijay Pande's blog yet again brings good news with yet another Paper being published, this time about the Playstation 3 Folding@Home client - Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3.

A collaborated effort between the Folding@Home and Sony Development teams, this is the first paper resulting from the Playstation 3's involvement in the Project. The paper is more of a 'how does it work' with details about how the PS3 accelerates simulations through use of it's powerful streaming processor, the CELL Broadband Engine.

The abstract reads:

"Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors."

Papers of this type not only help the Folding@Home team at Stanford, but can potentially help many others outside of the Project. Whether it helps out others involved in the field of Molecular Dynamics, or people that intend to use and program for the CELL processor, knowledge gained can be knowledge shared!

Another new Paper! Ribosome Gate

Only on Tuesday Vijay Pande announced on his blog that the Project published New Alzheimer's Disease Work. Now another paper, Folding@Home's 59th to be exact, has been published - 'Side-chain recognition and gating in the ribosome exit tunnel'.

The Ribosome plays a very important role in Protein research says Vijay:

"The ribosome is a fascinating molecular machine, responsible for the synthesis of proteins. For this reason it is of fundamental importance to protein folding (as the last step in the central dogma of biology) as well as to human health (since the ribosome is the target of a very large fraction of antibiotics)."

Vijay mentions that this paper has been made possible by the contributions of folders running 'bigWU' enabled classic clients stating:

"the ribosome is so huge that it would not run on regular classic clients."

It's certainly good to see a couple more important research papers come out lately, and only a day after another! I can't wait to see what other papers get released and how they can help us move forward in the Protein research field.

New Alzheimer's Disease Work published

The latest news from Vijay Pande's blog is about the publication of a key paper relating to Alzheimer's Disease - 'Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach'.

Vijay comments saying:

"I am very happy to announce that a first key work from the Folding@home project on Alzheimer's Disease (AD) was just published"

"In many ways, this paper is the "tip of the iceberg" for the Folding@home activities in AD, with a lot more interesting results to come, especially in terms of experimental tests of our predictions and interesting new possibilities for new drugs and AD therapeutics. So, while we're excited that this result is now past peer review, we're even more excited for what's coming down the pipeline, waiting peer review. We'll keep you posted as more results become public, hopefully with some even bigger announcements in 2009."

Hopefully this will mean Folding@Home as a Project will start to see some real fruit for all it's labour!

UPDATE:

"It was asked which clients participated. This work started several years ago and took some time to analyze and then publish. So, it ran exclusively on classic clients. For the follow up simulations, we are using a mixture of GPU, SMP, and classic clients. Due to the large number of classic clients, they allow us to calculations not possible on the other platforms. However, the raw speed (but smaller number) of the GPU and SMP clients allow us to get a good rough idea quickly, refining later with classic clients."