1. Challenges for Biomolecular Computing Alvin R. Lebeck Department of Computer Science Duke University + = Duke Computer Architecture

2. 2 © 2008 A. R. Lebeck Duke Computer Architecture Challenges Circuit design Defect tolerance Circuit layout Device characteristics Automating layout My Research Goals To design computing systems for future technologies –High performance –New application domains Computer Architecture Physics, Chemistry (CNT, DNA self assembly) Devices, circuit design and layout Challenges DNA Self-assembly Emerging devices Interconnect Challenges Defect tolerance Execution model Instruction set Memory

3. 3 © 2008 A. R. Lebeck Duke Computer Architecture Challenges 1 Infant field –No clear winner for device or fabrication method –Self-assembly will likely be part of it –Likely many devices in different places (Randomness) Scale –~10 14 letters/mL! (~10 14 letters in all books in Library of Congress) –Mole-core Computer--Avagadro (6.02x10 23 ) Defects Abstractions –Do we maintain current or create new?

4. 4 © 2008 A. R. Lebeck Duke Computer Architecture Hardware & Software Designing for defects –No external defect map –BIST –Self-organization/self-healing Build a big system from small nodes (e.g., LUTs) Asynchronous Circuits (w/ transient faults?) Programming Systems with Lots of Nodes in Arbitrary Topology Program Robustness w/ Unknown and Changing Hardware

5. 5 © 2008 A. R. Lebeck Duke Computer Architecture Duke Nanosystems Overview DNA-based Self- Assembly Nanoelectronic Devices Large Scale Interconnection [NANONETS 2006] Circuit Architecture [FNANO 2004] Logical Structure & Defect Isolation [NANOARCH 2005] SOSA - Data Parallel Architecture [NANOARCH 2006, ASPLOS 2006, JETC 2007] NANA - General Purpose Architecture [JETC 2006]