challenges for biomolecular computing alvin r. lebeck department of computer science duke university...
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Challenges for Biomolecular Computing
Alvin R. Lebeck
Department of Computer Science
Duke University
+ =
Duke Computer Architecture
2© 2008 A. R. LebeckDuke 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© 2008 A. R. LebeckDuke 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– ~1014 letters/mL! (~1014 letters in all books in Library of Congress)
– Mole-core Computer--Avagadro (6.02x1023)
• Defects
• Abstractions– Do we maintain current or create new?
4© 2008 A. R. LebeckDuke 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© 2008 A. R. LebeckDuke 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]
A
3.6
1.01.1
1.2
1.31.4 1.5
1.7
1.6 1.T
2.H
2.0 2.1
2.2
2.32.4
2.5
2.T
2.72.6
3.H
3.0
3.4
3.5
3.73.1
3.2
3.3
3.T
1.H
VIA
SOSA - Data Parallel Architecture [NANOARCH 2006,
ASPLOS 2006, JETC 2007]
NANA - General Purpose Architecture [JETC 2006]
MA
EA