Chris Dwyer Assistant Professor Dept. of Electrical and Computer Engineering Dept. of Computer Science Duke University Computer-Aided Design for DNA Self-Assembly: Process and Applications ICCAD 2005 Motivation log Cost ($/gate) log Length (m) log Switching time (s) [Annotated with CNT technology, original source: George Bourianoff and ITRS, ca. 2003.] 1
Outline • DNA Basics • Self-assembled Nanostructures – DNA Scaffolds – DNA Guided Self-assembly • CAD Tool Support • Self-assembled Systems – New Constraints – Alternative Architectures • Conclusions DNA Basics • A DNA strand: – A linear array of bases (A, T, G, and C) – Directional (one end is distinct from the other) – In nature, the source of genetic information • DNA will form a double helix: – When the bases on each strand (aligned “head-to- toe”) are complementary: A with T, and G with C – But only under certain “natural” environmental conditions (low) temperatures (T m : sequence dependent) and in an ionic solution. 2
DNA Basics • DNA hybridization is the process that forms the double helix • Sequence and temperature control the hybridization event ∆ T DNA Basics • A common form of the double helix (B-form) has some well-known geometric properties: – 3.4 Å per base pitch along the helix – One complete turn between every 10 th and 11 th base • Flexibility: the bonds along the sugar- phosphodiester backbone of each strand can rotate – double stranded DNA has a ~50nm persistence length (fairly rigid) – single stranded DNA has a strongly-sequence dependent persistence length (but, it’s flexible) 3
Outline � DNA Basics • Self-assembled Nanostructures – DNA Scaffolds – DNA Guided Self-assembly • CAD Tool Support • Self-assembled Systems – New Constraints – Alternative Architectures • Conclusions Self-assembled Nanostructures • Self-assembly is ubiquitous in nature • Generally defined as spontaneously generated order • Thermodynamics drive the self-assembly process – we can guide the process by the choice of materials and environmental conditions B < 20 nm feature sizes ∆ T A A·B 4
DNA Scaffolds - Geometry • The geometric properties of double strands can form specific, controlled self-assembled nanostructures: ∆ T 3.4 Å DNA Self-assembled Tiles 9 strands Cost ($) is proportional to the total number of unique strands (& quantity) 5
DNA Scaffolds – Hierarchical Assembly • Self-assembly can occur in hierarchies (reduces cost): – tiles (from single strands to tiles) – grids (from tiles to grids) – lattice (from grids or tiles to larger lattice) 30 nm DNA Scaffolds - Functionalization • Tiles can be functionalized (decorated) with nanoscale components (thus, the DNA serves as a scaffold) • Tiles can be functionalized before OR after grid/lattice assembly • Example chemical functionalities include: – biotin / streptavidin – DNA / nanoparticle (rods, spheres, etc.) 6
DNA Scaffolds - Functionalization • Biotin / streptavidin (protein + active chemicals) • The DNA provides a scaffold for the protein The manufacturing scale is incredible: ~10 16 grids per mL! BELOW : AFM images of some grids functionalized with streptavidin “Letters”: ~60nm on a side (1 experiment made ~10 14 of each) Trivia: The collection of books and manuscripts in the Library of AFM images of a 1.4 Tb/in 2 ROM (barcode) Congress contains ~10 14 letters. A Brief Interlude About Yield • The term “yield” is well-defined in multiple fields – Chemistry/Physics/Materials Science: extrinsically (mass) – Engineering: pass/fail (devices, circuits, systems) • Yield in DNA self-assembly is ambiguous – Reason 1 : Surface deposition is the major technique used to assay experimental results. Substrate-to-substrate variations change the deposition rate! – Reason 2 : Partial products are common but there is no functional test (unlike with current silicon processes) – It comes down to undefined specifications 7
DNA Scaffolds - Functionalization • Perhaps in the future.... + Crossed carbon nanotube DNA Self-assembly “FET” / SBT • Nanotechnology , vol. 13, pp. 601-604, 2002. Outline � DNA Basics � Self-assembled Nanostructures � DNA Scaffolds • DNA Guided Self-assembly • CAD Tool Support • Self-assembled Systems – New Constraints – Alternative Architectures • Conclusions 8
DNA Guided Self-assembly • Nanoparticles (rods, spheres, etc.) can be functionalized with DNA • DNA hybridization stabilizes interactions between particles if the strands are complementary • Sequence design and particle choice yields controlled nanostructure formation DNA Guided Self-assembly • Example: A two particle tether ∆ T 9
DNA Guided Self-assembly • An active component: – ring-gate FETs (RG-FETs) (or surrounding-gate FETs) DNA Guided Self-assembly • Active components for circuitry: Au – CdSe – Au (metal, semiconductor, metal or MSM) rods 500 nm wide 10
DNA Guided Self-assembly • Perhaps in the future... – The fabrication of integrated electronic systems • IEEE Trans. on VLSI , vol. 12, pp. 1214-1220, 2004. • IEEE Trans. on Nano. , 2 (2): pp. 69-74, 2003. • Nanotechnology , vol. 13, pp. 601-604, 2002. Self-assembled Nanostructures • Recap: Two Fabrication Methods – Scaffolds – DNA Guided Assemblies Nanorod assemblies Scaffolds 30 nm 11
Outline � DNA Basics � Self-assembled Nanostructures � DNA Scaffolds � DNA Guided Self-assembly • CAD Tool Support • Self-assembled Systems – New Constraints – Alternative Architectures • Conclusions CAD Tool Support • New technology fabric : New tool support – Goal : apply conventional circuit design approaches to these new technologies • First, identify a design context: – Tool flow – Layout tools – DNA sequence design • The big picture: Moving towards full system design... 12
Tool Flow Power & Timing Estimate System Architectural Description Simulator (custom) Behavioral Verification Layout Tools Device-level (custom) Layout Description Synthesis Tools Functional Verification SPICE Tool Flow Self-assembled Assembler Assembly Order & Fabrication (custom) DNA Sequences Orders Layout Back-annotated Circuit Timing & Power Verification Extractor SPICE (custom) (custom) 13
CAD Tool Support – Circuit Layout • Bootstrap the automated / cell layout systems with manual layout tools and standard cell designs DNA scaffold layout tool DNA-rod layout tool CAD Tool Support – Optimized Fabrication • The new aspects for the process tools: – DNA sequence design – Assembly orders (unique per design) Self-assembled Assembler Assembly Order & Fabrication (custom) DNA Sequences Orders Layout 14
CAD Tool Support: Wrap-up • Current tool status: � Cluster-based sequence optimization � Layout tools � Carbon-nanotube & MSM device models for a custom SPICE kernel (semi-empirical) � Assembly orders / “artwork” gen. (for large circuits) • Tool wish list: 1. yield-aware design optimizations, 2. refined (high ω ) device models, 3. better automated full custom support. Outline � DNA Basics � Self-assembled Nanostructures � DNA Scaffolds � DNA Guided Self-assembly � CAD Tool Support • Self-assembled Systems – New Constraints – Alternative Architectures • Conclusions 15
Self-assembled Systems • There are a variety of self-assembled systems – crossbars, micron-scale assemblies, biological systems... • The Systems Focus: self-assembled computer architectures New Constraints • Self-assembly imposes: – chaos / randomness at some length scale (>1-10 µ m) • DNA hybridization imposes: – order at some length scale (< 1-5 µ m) • The two can work together but some fundamental assumptions must change: – Wire / bus interconnect • No large-scale interconnect networks / limited local – Severe area / cost tradeoff • Large (> 1-10 µ m on a side) circuit footprints are impractical – Reliability • The substrate can be defective • The devices can be defective 16
Alternative Architectures • The task: Given a device technology, design a system – The new constraints prevent wholesale adoption of conventional architectures / system designs • Two common solutions given a defect-prone technology: – reconfigurable resources – redundant components (e.g. TMR, n-MR, multiplexing, etc.) Alternative Architectures • (Self-) Reconfigurability is key, however.... • The large number of simple processing nodes in a system (as many as we can assemble, ~10 14 +) precludes the use of an explicit defect map • The goal : To stitch a sufficient number of computational resources together to execute application code 17
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