Goal: To use DNA self-assembly to overcome the challenges of optical and e-beam lithography in creating nanoscale circuits.

Transcription

1 Goal: To use DNA self-assembly to overcome the challenges of optical and e-beam lithography in creating nanoscale circuits. PI Paul Rothemund, computer scientist, Senior Research Associate (research faculty) Expert in creating complex shapes and patterns using DNA self-assembly. Interested in scaling up DNA self-assembly, bridging nano, micro and macro scales. PI Erik Winfree, computer scientist, Associate Professor Expert in creating complex shapes and patterns using DNA self-assembly. Interested in creating large, complex patterns using algorithmic self-assembly. PI Marc Bockrath, applied physicist, Assistant Professor Expert in nanoscale device fabrication, physics and properties of single molecules. Interested in carbon nanotube (CNT) circuit fabrication and characterization. Hareem Maune, graduate student synthesizing and testing CNT devices PI William Goddard, theoretical chemist, Full Professor Expert in atomistic simulation of chemical systems. Interested in simulation of DNA-CNT device and circuit systems. Andres Jaramillo-Botero, Director Caltech Center for Multi-scale Modelling Siping Han, graduate student, synthesizing and modelling CNT devices metallization of DNA nanostructures.

2 1 nanometer shapes with 2 pixel patterns, 6 nanometer resolution, 1 billion per drop, 9% yield (Rothemund) uses many distinct DNA strands, relatively expensive for higher complexity 1 nm Arbitrary shapes Arbitrary patterns on top of shapes 1 nm 2 nanometers 1 nanometers

3 ATGGA GACCA ATGGA GACCA ATGGA CTGGT GACCA TACCT ATGGA GACCA CTGGT 42 nucleotides, 14.3 nm TACCT CTGGT TACCT ATGGA CTGGT GACCA TACCT CTGGT TACCT 6 tile wide DNA ribbon:

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5 Challenge 1: "Functionalization" electronically or optically active materials must be coupled to DNA nanostructures in high yield at specificed locations. We focus on carbon nanotubes (CNTs) but also work on metallization. DNA noncovalently wraps CNTs and allows them to disperse in buffer solution. An origami is made with 'red' and 'blue' DNA hooks, having different DNA sequences on top and bottom. Two batches of CNTs are made with complementary red or blue strands. Red and blue CNT assemble into crossbar FET on the origami. + + A device measurement is made Si/ SiO 2 Pd

6 To make nanostructures more rigid and to avoid aggregation origami-ribbon hybrids are used. red and blue hooks red tube blue tubes MOSFET geometry 5 nm crossbar Gate Channel

7 Over 3% of tubes are within 1 degrees of the desired orientation Frequency Orientation of SWNT 22% 2% 76% Red side (-1) Unknown () Blue side (1) Angle Characterization of DNA self-assembled CNT FET b V SD I SD a I SD [na] I SD [na] V g =.5V V g = -.5V V g =.5V V SD [V] 1 V g I SD V SD =.85V V g [V]

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9 Challenge 3, "Wiring-up" and "Bridging length scales": DNA nanostructures have a fundamental size mismatch with electronics at a larger spatial scale. E-beam patterning can only wire-up simple nanodevices. Still hard to build, we would like to self-assemble connections. E-beam cannot achieve wiring to complex objects at the nanoscale. Challenge 4, "Scaling-up": 2 pixels for DNA origami is a start, but we expect to want billions of devices. Similarly, a single FET is nice but we desire circuits. single origami max 2 devices VLSI chip

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11 Rothemund's Aims: To continue work with IBM, to replicate positioning and orienting work at Caltech, so that CNT devices can be more easily characterized and integrated. origami shapes patterned DLC on Si placed shapes CNT organization To combine multiple origami to create large origami breadboards. A B C D jigsaw puzzle stacking bonds enable 8 pixels A B C D To create DNA structures with features that bridge the nano and microscales so that a complete device can be fabricated...

12 Bridging the nano and micro scales cross-shaped origami tiles further tile additions 5 x 2 microns 1 nm metallize strands with nanogold mineralize strands bearing peptides P N

13 Patterning of nanotubes (wires) so that they diverge and can be wired up at the microscale + = CNT FET + = (or colored tracks may be metallized)

14 Winfree's Aims: To use combined existing DNA self-assembly techniques (DNA origami, ribbons, algorithmic self-assembly, and periodic DNA crystals) to create squares of programmable size. These squares will have a pattern that is appropriate for a memory with demultiplexers, an architecture perfectly suited for useful circuits. To explore the addition of actual nanoelectronic components to the memory pattern, for example a crossbar lattice of carbon nanotubes. an origami seed n encoding the number n is added to a soup of tiles The 'computed' output is a square of size n tiles x n tiles with the origami embedded in one corner.

15 n n Self-assembly can compute: a simple example is counting. Counting tile set. 1 n n n 1 1 c c c c R 1 L S The pattern left behind is a template for a demultiplexer AND gate AND gate, lower input negated NOT gate Counting to a fixed length from an origami enables programmed growth of NxN squares A counter grown from origami Full N x N squares remain an important challenge. Error rates must be reduced. A termination scheme for counters must be demonstrated.

16 Input lines encode binary values for 6 (vertical) and 9 (horizontal) which are demultiplexed to access the red memory element. The light gray pattern underneath which determines the circuit would be created by the self-assembly of this 21 x 21 square.

17 Bockrath's Aims: To use short length-sorted carbon nanotubes to increase the yield of existing devices. (Many problems arise from very long tubes acting as bridges between multiple origami). To self-assemble and characterize circuits of more than one carbon-nanotube based device to create elementary logic gates and memory elements. To self-assemble novel devices to explore transport physics in nanostructures.

18 Rationally Engineered Logic gates and Memory Elements Utilizing Multiple Nanotubes Nanotube assembly Schematic circuit diagram Inverter V s V out V in SRAM V s V out NOR V s V s V out V in1 V in2

19 Novel Devices Probing Transport Physics in Nanostructures: Phase Coherence in Strongly-Interacting Electron Systems Many possibilities exist for making novel devices. DNA origami template for parallel nanotubes Tunable separation with desired values ~5-2 nm Interferometer device B V source drain I Nanotubes act as a which path? interferometer enabling the study of phase coherent transport in Nanotube-based Luttinger liquids via a transport experiment. The setup is analogous to a double slit experiment in optics. The magnetic field B tunes the phase by the Ahoronov-Bohm effect. Tubes must be closer together than the phase coherence length in the electrodes, which is readily obtainable using DNA based self-assembly.

20 Goddard's Aims: Electron transport in DNA-carbon nanotube hybrids: The effect of an insulating DNA layer between carbon nanotubes, silicon nanowires, and quantum dots is unknown. In some cases DNA may be removed from devices post-assembly, in other cases may remain. Thus it is important to simulate electron transport in carbon nanotube devices, with and without intervening DNA, starting with atomistic simulation (Next slide). Simulations of the placement process: The interactions which bind DNA structures to technological surfaces like silicon or diamond-like carbon are poorly understood. The best choice of experimental conditions, as well as the best choice of DNA shapes to bind can be explored by atomistic and mesoscale simulation. Free energies of correct and mismatched binding, and possible kinetic traps can be explored. patterned DLC on Si possible kinetic traps and mismatches

21 DNA-origami CNT-based Transistor V Junctions V I CNT DNA CNT µ 1 LUMO HOMO µ 2 E F Organic molecule Size of molecules << scattering lengths (e.g. mean free path, de Broglie wavelength, etc.) -> quantum descriptions necessary. Theory and Modeling to Describe Quantum chemistry of molecule(s) + nanotube -> charge flow & bonding -> geometry & energy spectrum of the entire system. Organo-metallic interface mechanics and transport. Need to treat molecule as finite and nanotubes as semi-infinite electrodes. Escape currents (through organic insulator layer). Conformation effects on electronic transport. Effect of finite bias. IV characteristic of self-assembled CNT-based transistor junctions.

22 Multiscale Methodology: 1st-principles I-V validated by rotaxane modeling Density-functional theory (Hohenberg-Kohn-Sham) ( #1,2 = i "1,2! " ( + 1,2 ) T (E,V ) = Tr!1G! 2G + self-energy contact widening ) -4 4 Lower current,x 1asymmetric -3 I-V 1 transmission Ballistic transport theory (Landauer, Buttiker) 2e T (E,V )[ f1 (E! µ2 )! f2 (E! µ1 )] de current #!" h T(E,V) 2 di 2e G=! T conductance dv h " e.g. Rotaxane switch 6 di/dv di/dv vs. junction bias and gate bias S S O O +N O O O N+ S S S S O O O +N O O O N+ -9 source to drai n volta ge (mv ) x1 I= gate volta ge 2.55V na -9 Gm = (Em Sm! H m! "1! " 2 )!1 2 Γ1 x1 Green s ftn. Formalism (Fisher-Lee) m 1 gate voltage (V) µ1 " µ1 = ev, n! H electro-chemical potential na Molecular Mechanics Dynamics d2r geometry F=m 2 dt

23 Further validation: bi-phenyl-dithiol modeling T(E) contact 2e µ 2 I V ) =! T ( E, V )( f1 " f h µ 1 ( 2 ) de molecule I(V) contact Au (111)

24 Relevance to the Office of Naval Research Fundamental advances in microelectronics underlie all of our country's defense systems, from networked warfare to avionic systems. Eventually, self-assembly based methods may be the only path forward to more powerful nanoelectronic systems. DNA self-assembly uses non-hazardous "green" chemistries, decreasing the Navy's environmental footprint. DNA self-assembly techniques may yield lower cost electronics "grown" from cheap components without capital investment in conventional chip fabs.

25 Budget for 4 years, $2.6 million including: PI: Paul Rothemund: $2K/yr for Senior Research Associate salary and materials Co-PI: Mark Bockrath $1K/yr for 1 graduate student and materials Co-PI: Bill Goddard $1K/yr for 1 graduate student and materials Co-PI: Erik Winfree $1K/yr for 1 graduate student and materials Equipment $15K/yr including plasma etcher/cleaner ($2K), wafer-scale Atomic Force Microscope ($2K) temperature-controlled dynamic light scattering ($5K).