publication of new paper on FAH (bigadv) results

[kasson]

We are excited to announce the publication today of a new FAH paper based on many of our bigadv projects (primarily the 268x series). This is the kind of analysis that is extremely difficult to perform without the help of our donors.

http://www.stanford.edu/group/pandegrou ... pers#ntoc1
http://pubs.acs.org/doi/abs/10.1021/ja200310d

Peter M. Kasson, Erik Lindahl, and Vijay S. Pande. Journal of the American Chemical Society (2011) Epub 25 Feb.

SUMMARY. Building on our previous simulations of membrane fusion, we have used the power of Folding@Home to systematically analyze the fusion reaction between two vesicles and the molecular nature of water in this reaction. For purposes of computational tractability, many approaches neglect the detailed structure of water for large membrane simulations. In this case, we show that this detailed structure affects both the thermodynamics and the dynamics of the fusion reaction. These results have important implications for how we should perform vesicle fusion simulations; they also give a new example of structured water between two flexible hydrophilic interfaces. This water structure may be important in a number of cell-cell interactions.

ABSTRACT. Membrane interfaces are critical to many cellular functions, yet the vast array of molecular components involved make the fundamental physics of interaction difficult to define. Water has been shown to play an important role in the dynamics of small biological systems, for example when trapped in hydrophobic regions, but the molecular details of water have generally been thought dispensable when considering large membrane interfaces. Nevertheless, spectroscopic data indicate that water has distinct, ordered behavior near membrane surfaces. While coarse-grained simulations have achieved success recently in aiding understanding the dynamics of membrane assemblies, it is natural to ask, does the missing chemical nature of water play an important role? We have therefore performed atomic-resolution simulations of vesicle fusion to understand the role of chemical detail, particularly the molecular structure of water, in membrane fusion and at membrane interfaces more generally. These membrane interfaces present a form of hydrophilic confinement, yielding surprising, non-bulk-like water behavior.

[rjbelans]

Thank you for posting it. It's always good to see the results of the work we do.

[GreyWhiskers]

I'm also glad to see the results published from this work.

I am curious about the science aspects of a couple of things:

1. I realize that the results go into the big peer reviewed journals, and the only way these journals survive financially is to have rather pricey subscription services, and "pay per view", but are there any of the Pande Group papers that are available to the folders in more than the summary and abstract? All the links on the science results pages are to the abstract on the various papers' web sites, with ways one can pay to get the whole article.

2. I'm sure there must be some papers accessible to the donors I haven't found relating how the WUs we fold are broken out into the whole project - the smaller uniprocessor WUs, the core 11/15/16 GPU WUs, and the various SMP WUs, culminating in the million-atom bigadv WUs. Are big molecules broken into many smaller segments that are issued as WUs? What are the "runs" "clones" "generations" exactly? How does one set of runs set up a subsequent set?

Thanks.

[kasson]

Many of the journals make the full text available for free after a period of time. But another good place to go is the NCBI search engine. For instance, if you look for my publications:
http://www.ncbi.nlm.nih.gov/pubmed?term=kasson%20pm
you will see that all except 3 of the FAH-related ones (the two most recent and one old one) have a "free full text" link.

I'm not sure if any of the papers explicitly break down how we translate the scientific work into FAH terms. We're in the midst of working on a new backend architecture. The paper for that (currently under review so not yet available) does talk a bit more about how we do such things. So stay tuned...

[PantherX]

... Are big molecules broken into many smaller segments that are issued as WUs? What are the "runs" "clones" "generations" exactly? How does one set of runs set up a subsequent set?...

This is an explanation of PRCGs that is easy to understand (http://fahwiki.net/index.php/Runs%2C_Clones_and_Gens).

[GreyWhiskers]

PantherX - thanks for the link. Dan Ensign's paper was great. It seems to be an endangered species these days. I had done some searches the other day and came to references to files posted on Folding-community.org - but that whole site seems to be down. Every one of the links in Ensign's paper is dead.

Maybe I missed it, but Ensign's paper is worthy of a part in the FAH FAQ, IMHO.

[PantherX]

folding-community.org was the predecessor of foldingforum.org and will not be "revived". (Not sure but I read somewhere that you can still access it as an archive).

[Jonazz]

Are there new papers being planned on influenza/viruses? It's been almost a year and there are tons of SMP/bigadv projects out there regarding the flu.

[bruce]

Are there new papers being planned on influenza/viruses? It's been almost a year and there are tons of SMP/bigadv projects out there regarding the flu.

Papers are written when there are scientific conclusions to be reported.

"almost a year" and "tons of SMP/bigadv projects" doesn't mean much. There are easier projects and there are harder projects. Some projects can be solved in a year ... some cannot. I don't know the magnitude of the computational work required for this particular study but look at what was said in another topic regarding a GPU project: viewtopic.php?f=17&t=20444&p=203559#p203559

[Jesse_V]

Exactly Bruce. On the SMP FAQ, it says "... Right now, we achieve this by running for many months to years (indeed, our first Alzheimer's Disease simulations ran for almost two years straight). That's where the SMP and GPU (and PS3) clients come in. They give us considerably longer trajectories in the same wall clock time, allowing us to turn what used to take years to simulate even on FAH, to a few weeks to months." So even they finish the simulation in a matter of "months" (doesn't exclude the possibility of a year) it may take considerable time to get to a publication, as stated on the Results page: "We stress that it can take quite a while to go from a result to a published peer review article (often as much as a year)". And do we know that each simulation is directly followed by a paper, or that there aren't any follow-up simulations?