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Caltech collaboration for DNA-organized Nanoelectronics
The Caltech DNA-nanoelectronics team
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.
Goal: To use DNA self-assembly to overcome the challenges
of optical and e-beam lithography in creating nanoscale circuits.
State of the art, DNA self-assembly 1, DNA origami
100 nanometer shapes with 200 pixel patterns, 6 nanometer resolution,100 billion per drop, 90% yield (Rothemund)uses many distinct DNA strands, relatively expensive for higher complexity
100 nanometers200 nanometers
Arbitrary shapes Arbitrary patterns on top of shapes 100 nm100 nm
State of the art DNA self-assembly 2, DNA tiles, tubes
and crystalsATGGA GACCA
CTGGT TACCT
42 nucleotides, 14.3 nm
ATGGA GACCA
CTGGT TACCT
ATGGA GACCA
CTGGT TACCTATGGA GACCA
CTGGT TACCTATGGA GACCA
CTGGT TACCT
6 tile wideDNA ribbon:
State of the art DNA self-assembly 3, algorithmic +
combination
Challenges for DNA organizednanoelectronics 1A
Si/ SiO2
Pd
+
+
Challenge 1: "Functionalization" electronically or optically active materialsmust 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 CNTsand allows them to disperse inbuffer solution.
An origami is made with 'red' and'blue' DNA hooks, having differentDNA sequences on top and bottom.Two batches of CNTs are madewith complementary red or bluestrands.
Red and blue CNT assembleinto crossbar FET on theorigami.
A device measurement is made
Challenges for DNA organizednanoelectronics 1B
To make nanostructures more rigid and to avoid aggregationorigami-ribbon hybrids are used.
crossbar
red tube blue tubes
50 nm
MOSFET geometry
ChannelGate
red and blue hooks
Challenges for DNA organizednanoelectronics 1C
Over 30% of tubes are within 10 degrees of the desired orientation
Characterization of DNA self-assembled CNT FET
------ Vg= 0.5V-- -- Vg= -0.5V
-- - -- Vg= 0.5V
VSD [V]
I SD
[nA
]
Vg [V]
I SD [n
A]
-0.5 0.0 0.5 1.00
100
200
300
400
-0.5 0.0 0.5
0
100
200
VSD = 0.85VISD
VSD
Vg
ab
ISD
Orientation of SWNT
0
5
10
15
20
25
30
35
40
0-20 20-40 40-60 60-80 80-100 100-120120-140140-160160-180
22%2%
76%
Red side (-1)Unknown (0)Blue side (1)Fr
eque
ncy
Angle
Challenges for DNA organizednanoelectronics 2
Challenges for DNA organizednanoelectronics 3,4
Challenge 3, "Wiring-up" and "Bridging length scales": DNA nanostructureshave a fundamental size mismatch with electronics at a larger spatial scale.
Still hard to build, we would liketo self-assemble connections.
E-beam cannot achieve wiring tocomplex objects at the nanoscale.
Challenge 4, "Scaling-up": 200 pixels for DNA origami is a start, butwe expect to want billions of devices. Similarly, a single FET isnice butwe desire circuits.
E-beam patterningcan only wire-upsimple nanodevices.
single origamimax 200 devices
VLSI chip
Challenges for DNA organizednanoelectronics 4,5
Rothemund’s AimsRothemund's Aims:
To create DNA structures with features that bridge the nano andmicroscales so that a complete device can be fabricated...
To continue work with IBM, to replicate positioning andorienting work at Caltech, so that CNT devices can be moreeasily characterized and integrated.
To combine multiple origami to create large origami breadboards.
A
B
C
D
A B C D
jigsaw puzzle stacking bonds enable 800 pixels
origami shapespatterned DLC on Si placed shapes CNT organization
Bridging nano and micro
Bridging the nano and micro scales
N
P
tiles
metallize strands with nanogoldmineralize strands bearing peptides
cross-shaped origami
100 nm
50 x 2microns
furthertileadditions
Divergent wiresPatterning of nanotubes (wires) so that theydiverge and can be wired up at the microscale
+ =
CNT FET
+ =
(or colored tracks may be metallized)
Winfree’s Aims
n
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 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.
From counters todemultiplexers and squares
AND gate
AND gate, lower input negated
NOT gate
0
0
0
1
0
0
0
0
0
0 1 1 0
Self-assembly can compute:a simple example is counting.
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.
Counting to a fixed length from an origamienables programmed growth of NxN squares
1n
1
n
10n
0
n
0
1c
1
n
00c
0
c
1Rc
L0
S
Counting tile set.
The pattern left behind isa template for a demultiplexer
Self-assembled memorycircuit
0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
1
1
0
1 0 0 1
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.
Bockrath's Aims:
To self-assemble and characterize circuits of more than onecarbon-nanotube based device to create elementary logic gatesand memory elements.
To use short length-sorted carbon nanotubes to increase the yieldof existing devices. (Many problems arise from very long tubesacting as bridges between multiple origami).
To self-assemble novel devices to explore transport physics innanostructures.
Bockrath’s Aims
Rationally Engineered Logic gates and MemoryElements Utilizing Multiple Nanotubes
Vs
Vin
Vout
Vs
Vout
Vs
Vs
Vin1
Vout
Vin2
Inverter
SRAM
NOR
Nanotube assembly Schematic circuit diagram
B
VI
Novel Devices Probing Transport Physics in Nanostructures: PhaseCoherence in Strongly-Interacting Electron Systems
Nanotubes act as a “which path?” interferometer enabling the study of phasecoherent transport in Nanotube-based Luttinger liquids via a transport experiment.The setup is analogous to a double slit experiment in optics. The magnetic field Btunes the phase by the Ahoronov-Bohm effect. Tubes must be closer together thanthe phase coherence length in the electrodes, which is readily obtainable usingDNA based self-assembly.
Tunable separation with desired values ~5-20nm
DNA origami template forparallel nanotubes
Interferometer device
source drain
Many possibilities exist for making novel devices. Novel Devices ProbingTransport physics
Goddard’s AimsGoddard'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 casesDNA may be removed from devices post-assembly, in other casesmay remain. Thus it is important to simulate electron transport incarbon nanotube devices, with and without intervening DNA, startingwith atomistic simulation (Next slide).
Simulations of the placement process:The interactions which bind DNA structures to technologicalsurfaces like silicon or diamond-like carbon are poorly understood.The best choice of experimental conditions, as well as the bestchoice of DNA shapes to bind can be explored by atomistic andmesoscale simulation. Free energies of correct and mismatchedbinding, and possible kinetic traps can be explored.
patterned DLC on Sipossible kinetic traps
and mismatches
• Size of molecules << scattering lengths (e.g. mean free path, de Brogliewavelength, etc.) -> quantum descriptions necessary.
• 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 andnanotubes 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.
HOMOLUMO
FE
V
2µ
1µ
ICNT
DNA
Organic molecule
CNT
V
DNA-origami CNT-based TransistorJunctions
Theory and Modeling to Describe…
Multiscale Methodology:1st-principles I-V validated by
rotaxane modelingDensity-functional theory (Hohenberg-Kohn-Sham)
Ballistic transport theory (Landauer, Buttiker)
T(E,V)
contact widening
self-energy
Green’s ftn. Formalism (Fisher-Lee)
transmission
electro-chemical potential
conductance
current
HneV !=" , 11µµ
I =2e
hT (E,V ) f
1(E ! µ
2) ! f
2(E ! µ
1)[ ]dE
!"
"
#
G =dI
dV!2e
2
hT
Gm= (E
mS
m! H
m! "
1! "
2)!1
#1,2= i "
1,2! "
1,2
+( )
T (E,V ) = Tr !1G!
2G
+( )
F = md
2R
dt2
Molecular MechanicsDynamics
geometry
OSS
SS OO O
OO
O
O
O
N N
N N
OSO
S +
+ +
+
4PF6–
O O OO
O
S S
O O OS
S
S
SO O O
O
O
SS
N
N
N
N
+
++
+
4 P F6–
5
4
3
2
1
0
0 .1 00 .0 50 .0 0-0 .0 5-0 .1 0
-3
-2
-1
0
1
2
3
6 04 02 00-2 0-4 0-6 0
Mono-disulfide [2]Rotaxane Bis -disulfide [2]Rotaxane
- 3- 2- 101
x10-9
4 00- 4 0x 1 0
- 3
@ gate voltage 2.55V
2 0 01 0 0
0- 1 0 0
- 2 0 0
x10-9
1 0 05 00- 5 0- 1 0 0x1 0
- 3
@ gate voltage 2.4V
Lower current, asymmetric I-V Higher current, symmetric I-V
dI/dV vs. junction bias and gate bias
source to drain voltage (mV )
gate
vol
tage
(V)
nA nA
source to drain voltage (mV )
gate
vol
tage
(V)
symmetric dI/dV plot vs junction bias
OSS
SS OO O
OO
O
O
O
N N
N N
OSO
S +
+ +
+
4PF6–
OSS
SS OO O
OO
O
O
O
N N
N N
OSO
S +
+ +
+
4PF6–4PF6–
O O OO
O
S S
O O OS
S
S
SO O O
O
O
SS
N
N
N
N
+
++
+
4 P F6–
5
4
3
2
1
0
0 .1 00 .0 50 .0 0-0 .0 5-0 .1 0
-3
-2
-1
0
1
2
3
6 04 02 00-2 0-4 0-6 0
Mono-disulfide [2]Rotaxane Bis -disulfide [2]Rotaxane
- 3- 2- 101
x10-9
4 00- 4 0x 1 0
- 3
@ gate voltage 2.55V
2 0 01 0 0
0- 1 0 0
- 2 0 0
x10-9
1 0 05 00- 5 0- 1 0 0x1 0
- 3
@ gate voltage 2.4V
Lower current, asymmetric I-V Higher current, symmetric I-V
dI/dV vs. junction bias and gate bias
source to drain voltage (mV )
gate
vol
tage
(V)
nA nA
source to drain voltage (mV )
gate
vol
tage
(V)
symmetric dI/dV plot vs junction bias
dI/dVe.g. Rotaxane switch
Γ1 Γ2
1m
2
Further validation: bi-phenyl-dithiol modeling
Au (111)
! "=2
1
))(,(2
)( 21
µ
µdEffVET
h
eVI
T(E)
I(V)molecule
contact
contact
Relevance to ONR
Relevance to the Office of Naval Research
DNA self-assembly uses non-hazardous "green" chemistries,decreasing the Navy's environmental footprint.
Fundamental advances in microelectronics underlie all ofour country's defense systems, from networked warfare toavionic systems. Eventually, self-assembly based methods maybe the only path forward to more powerful nanoelectronic systems.
DNA self-assembly techniques may yield lower costelectronics "grown" from cheap components withoutcapital investment in conventional chip fabs.
Budget
Budget for 4 years, $2.6 million including:
PI: Paul Rothemund: $200K/yr for Senior Research Associate salary and materials
Co-PI: Mark Bockrath $100K/yr for 1 graduate student and materials
Co-PI: Bill Goddard $100K/yr for 1 graduate student and materials
Co-PI: Erik Winfree $100K/yr for 1 graduate student and materials
Equipment $150K/yr including plasma etcher/cleaner ($20K), wafer-scale Atomic Force Microscope ($200K) temperature-controlled dynamic light scattering ($50K).