Distributed caching strategy

Keum J. Kim, Eunice E. Santos, Eugene Santos

Research output: Chapter in Book/Report/Conference proceedingConference contribution


When compared to biological experiments, using computational protein models can save time and effort in identifying native conformations of proteins. Nonetheless, given the sheer size of the conformation space, identifying the native conformation remains a computationally hard problem - even in simplified models such as hydrophobic-hydrophilic (HP) models. Distributed systems have become the focus of protein folding, providing high performance computing power to accommodate the conformation space. To use a distributed system efficiently (with limited resources), an appropriate strategy should be designed accordingly. Communication incurs overhead but can provide useful information in distributed systems through careful consideration. Our study focuses on understanding the behavior of distributed systems and developing an efficient communication strategy to save computational effort in order to obtain good solutions. In this paper, we propose a distributed caching strategy, which reuses partial results of computations and transmits the cached and reusable information among neighboring inter-connected processors. In order to validate this idea in a practical setting, we present algorithms to retrieve and restore the cached information and apply them to 2D triangular HP lattice models through coarse-grained parallel genetic algorithms (CPGAs). Our experimental results demonstrate the time savings as well as the limits in caching improvements for our distributed caching strategy.

Original languageEnglish (US)
Title of host publicationIntelligent Computing
Subtitle of host publicationTheory and Applications VI
StatePublished - Jun 3 2008
Externally publishedYes
EventIntelligent Computing: Theory and Applications VI - Orlando, FL, United States
Duration: Mar 17 2008Mar 18 2008

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
ISSN (Print)0277-786X


ConferenceIntelligent Computing: Theory and Applications VI
Country/TerritoryUnited States
CityOrlando, FL


  • Caching
  • Coarse-grained parallel genetic algorithms
  • Distributed caching
  • Distributed systems
  • HP model
  • Migration
  • Parallel evolutionary algorithms
  • Protein folding
  • Stochastic methods
  • Triangular lattice

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering


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