doi: 10.7873/DATE.2015.0370

NoC-Enabled Multicore Architectures for Stochastic Analysis of Biomolecular Reactions

Turbo Majumder1, Xian Li2,a, Paul Bogdan3 and Partha Pande2,b

1Department of Electrical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.

2School of EECS, Washington State University, Pullman, WA 99164-2752, USA.

3Department of Electrical Engineering, University of Southern California, 3740 McClintock Avenue, Los Angeles, CA 90089-2560, USA.


Recent medical challenges such as cancer, drug-resistant microbes or diabetes crucially affect human health. To tackle these, modern medicine must analyze molecular interactions and rely on powerful computational platforms for the design and performance evaluation of medical therapies. Towards this end, we propose a Network-on-Chip (NoC)-based multicore platform enabling the efficient analysis of stochastic molecular interactions among biological entities. Our in-depth analysis of the stochastic interactions among biological components and the characterization of their computational and communication requirements allows us to design a high-performance NoC architecture sustaining a throughput of over 1.36E5 events/ms, while consuming only 15 mJ per 1E5 stochastic events. Our proposed NoC-based multicore can offer a throughput improvement of 23% over a regular mesh-based NoC, while consuming 20% less energy.

Keywords: Network-on-Chip, Multicore, Cyber-physical system, Personalized medicine, Gene therapy, Stochastic simulation.

Full Text (PDF)