Folding@home: Lessons from eight years of volunteer distributed computing

@article{Beberg2009FoldinghomeLF,
  title={Folding@home: Lessons from eight years of volunteer distributed computing},
  author={Adam L. Beberg and Daniel L. Ensign and Guha Jayachandran and Siraj Khaliq and Vijay S. Pande},
  journal={2009 IEEE International Symposium on Parallel \& Distributed Processing},
  year={2009},
  pages={1-8}
}
  • A. L. Beberg, D. Ensign, V. Pande
  • Published 23 May 2009
  • Computer Science
  • 2009 IEEE International Symposium on Parallel & Distributed Processing
Accurate simulation of biophysical processes requires vast computing resources. Folding@home is a distributed computing system first released in 2000 to provide such resources needed to simulate protein folding and other biomolecular phenomena. Now operating in the range of 5 PetaFLOPS sustained, it provides more computing power than can typically be gathered and operated locally due to cost, physical space, and electrical/cooling load. This paper describes the architecture and operation of… 

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References

SHOWING 1-10 OF 24 REFERENCES
Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problem
TLDR
Novel methods to fundamentally speed previously intractable problems using a new computational paradigm: distributed computing are reviewed.
Accelerating molecular dynamic simulation on the cell processor and Playstation 3
TLDR
Algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3, are detailed, with a comparison of improved performance on the PS3's Cell processor over more traditional processors.
Transition networks for modeling the kinetics of conformational change in macromolecules.
BOINC: a system for public-resource computing and storage
  • D. Anderson
  • Computer Science
    Fifth IEEE/ACM International Workshop on Grid Computing
  • 2004
TLDR
The goals of BOINC are described, the design issues that were confronted, and the solutions to these problems are described.
Detection-dependent kinetics as a probe of folding landscape microstructure.
TLDR
A lower limit for the roughness of the free energy surface is estimated based on the range of rates observed in the folding/unfolding kinetics of the engineered trpzip2 peptide at different tryptophan fluorescence wavelengths, each yielding a different rate.
Diffusion–collision model for protein folding
The basic equations for the elementary step in the diffusion–collision–coalescence model of protein folding are derived for the case of two radially diffusing spherical microdomains. Refinements and
Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics.
TLDR
The uncertainty analysis is extended to derive similar closed-form solutions for the distributions of the eigenvalues and eigenvectors of the transition matrix, quantities that have numerous applications when using the model.
Condor-a hunter of idle workstations
TLDR
The design, implementation, and performance of the Condor scheduling system, which operates in a workstation environment, are presented and a performance profile of the system is presented that is based on data accumulated from 23 stations during one month.
The architecture of a distributed computer system
TLDR
Ogham is designed to allow local-area-interconnected microcomputers to be used as a computing facility for the investigation of distributed operating systems and related topics.
Screen Savers of the World Unite!
TLDR
Unused CPU time on desktop computers could be put to good use, if distributed computing succeeds in capturing people's imagination and raising biological and other scientific computation to fundamentally new predictive levels.
...
...