Efficient algorithms for computing with protein-based volumetric memory processors

Sanguthevar Rajasekaran, Vamsi Kundeti, Robert Birge, Vipin Kumar, Sartaj Sahni

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


With an ever increasing volume of digital data there is a huge increase in the demand for much faster, smaller, and denser storage technologies. Conventional 2-D (surface) storage/memory technologies may soon be replaced with much faster and denser 3-D volumetric (holographic) storage technologies. Photo sensitive protein bacteriorhodopsin has been proven to have great chemical, thermal, and holographic properties and is a good choice for both associative and volumetric memories. Associative memory systems have a wide range of practical applications. However, there is a lack of a formal computational model that can be used to analyze the performance of different algorithms on architectures that support associative memory. We first address this issue by defining a new computational model on protein-based associative memory processors. We also present and analyze algorithms for several fundamental problems on this new model. Secondly, we employ balanced modulated codes in volumetric memories to reduce the bit error rate and improve fidelity. Conventional coding schemes such as 6:8 coding, limit the size of the page to 8 bits and achieve a code rate (utility) of only 75%. As the technology matures we need efficient algorithms to produce these codes with better utility. In this paper,1 we address this problem and give algorithms that can generate these codes with superior utility.

Original languageEnglish (US)
Article number5608504
Pages (from-to)881-890
Number of pages10
JournalIEEE Transactions on Nanotechnology
Issue number4
StatePublished - Jul 2011

Bibliographical note

Funding Information:
Manuscript received January 23, 2010; accepted September 12, 2010. Date of publication October 25, 2010; date of current version July 8, 2011. This work was supported in part by the National Science of Foundation under Grant 0326155 and Grant 0829916 and in part by the National Institutes of Health under Grant 1R01GM079689-01A1. The review of this paper was arranged by Associate Editor G. Timp.


  • Associative memory
  • associative memory processors
  • bacteriorhodopsin
  • coding theory
  • parallel computing
  • protein-based memory
  • volumetric memory


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