DOW-UAP-D150, AAWSAP DIRD, Quantum Computing and Utilizing Organic Molecules in Automation Technology, December 2010

This document is a Defense Intelligence Reference Document (DIRD), a technical reference format used by the Defense Intelligence Agency (DIA) to capture baseline knowledge on a specific topic for later analytic use. DIRDs are best understood as reference and synthesis products rather than as original research. It is one of 38 DIRDs produced under the Advanced Aerospace Weapon System Applications Program (AAWSAP) between 2009 and 2011. Because AAWSAP’s scope permitted a broad range of supporting topics, not every DIRD in the series directly concerns aerospace systems or future threat assessment. The following summary reflects the DIRD’s scope and framing at the time of writing and should not be read as implying current validation of the concepts discussed. This DIRD surveys advanced computing concepts for future space and automation applications, focusing on quantum and molecular (DNA-based) computing as potential alternatives to conventional silicon electronics. The report introduces quantum computing principles alongside DNA-based logic gates, self-assembly, and nanoscale repair mechanisms, arguing that these unconventional architectures might eventually offer advantages in radiation tolerance, physical robustness, and specialized onboard processing for space-based platforms. It notes that near-term practical barriers remain substantial. Quantum systems continue to depend on complex cryogenics, shielding, and unsolved reliability challenges, while DNA-based computing remains a far-future concept rather than a viable alternative to general-purpose processors. Overall, the document presents both frameworks as long-term possibilities to complement, rather than immediately replace proven space-qualified electronics. It concludes that the stronger, nearer-term cases for such architectures are in highly specialized or hybrid roles rather than in fully mature general-purpose onboard computing applications.

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Defense
Intelligence
Reference
Document
Defense Futures
10 December 2010
!COD: 10 December 2010
DIA-08-1102-005
Quantum Computing and
Utilizing Organic Molecules in
Automation Technology
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Quantum Computing and Utilizing Organic Molecules in
Automation Technology
The Defense Intelligence Reference Document provides non-substantive but
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Prepared by:
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Contents
Summary........................................................................................................................ 5
Introduction ................................................................................................................... 7
Ultrafast Computing Power in Aerospace Applications ................................................... 7
Making Digital Circuits Faster..................................................................................... 8
Applications of Quantum Computers ........................................................................ 10
The Closed Box and Fault Tolerance ......................................................................... 11
Scalability ................................................................................................................ 12
Universal Logic......................................................................................................... 12
Initialization and Measurement................................................................................ 13
The Quantum Dot Approach ................................................................................. 13
Electrostatic Quantum Dots in Graphene.............................................................. 14
Quantum Dots in Graphene Nanoribbons ............................................................. 15
Graphene Disc in Single-Layer Graphene ............................................................. 16
Graphene Disc in Bilayer Graphene ...................................................................... 17
Manipulation of Spin Qubits in Graphene Quantum Dots Relative to GaAs ........... 18
Spin Relaxation and De-phasing in Graphene Quantum Dots ............................... 19
Spin Relaxation Due to Spin-orbit Interaction ...................................................... 20
Research with Graphene Quantum Dots ............................................................... 21
Summary of Additional Inorganic Technologies ....................................................... 21
Photon Technologies ............................................................................................ 21
Ion and Atomic Trap Technologies ....................................................................... 22
Nuclear Magnetic Resonance (NMR) Technologies ............................................... 22
Superconducting Technologies ............................................................................. 22
DNA-based Designs for Molecular Computers........................................................... 23
DNA Background .................................................................................................. 23
Error Suppression Mechanisms in DNA Self-Assembly.......................................... 28
Self-assembly with DNA-based Microfluidic Devices ............................................ 31
DNA Origami ........................................................................................................ 32
Engineering DNA-Based Logic Gates .................................................................... 35
Logic Operation by Deoxyribozymes .................................................................... 35
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Deoxyribozyme-based Boolean Automata ............................................................ 39
Robotic Bases (The DNA Robot) ........................................................................... 40
DNA Nanomotors.................................................................................................. 41
The Nano Walker; a Spider-like Approach ............................................................ 43
Discussion ................................................................................................................ 45
Conclusion................................................................................................................ 46
References ................................................................................................................ 48
Figures
Figure 1. Hexagonal structure of graphene..................................................................... 14
Figure 2. Quantum dot in graphene nanoribbon..............................................................15
Figure 3. Left; Energy diagram for quantum dot in single-layer graphene. Right; Bound
state levels as function of dot radius............................................................. 16
Figure 4. (a) Color scale plot of the transconductance. (b) One of the vertices of the
honeycomb structure at Vsd = 800 µV: Charge stability diagrams for series-
coupled quantum dots...................................................................................... 16
Figure 5. Quantum dot in bilayer graphene..................................................................... 17
Figure 6. Bilayer graphene tunneling device structure................................................. 18
Figure 7. Qubit piano........................................................................................................19
Figure 8. Long distance coupling of three graphene qubits............................................ 19
Figure 9. A DNA nanomachine driven by repeated sequential addition of DNA control
strands..............................................................................................................23
Figure 10. Recombinant DNA molecule with restriction enzyme cleavage and sticky end
ligation....................................................................................................... 25
Figure 11. Two symmetric DNA nanomotifs and the crystals grown using them.......... 26
Figure 12. (top a-e) The XOR Cellular Automaton and Its Implementation by Tile-Based
Self-Assembly............................................................................................. 27
Figure 12 (continued). (bottom a-e) AFM Images of Algorithmic Self-assembly of
Sierpinski Triangle Crystals........................................................................... 28
Figure 13. Error Suppression with the PTM Method........................................................ 30
Figure 14. Simulation results of growth in (A} the OTM, (B) the PTM, and (C} the LTM.30
Figure 15. Three Types of Error in DNA Tile Self-assembly (a) Growth error (b) Facet
error (c) Nucleation error. Red lines indicate the mismatched sides.......... 31
Figure 16. Micro-fluidic device for DNA tile self-assembly............................................ 32
Figure 17. (A) Schematic diagram of a 16-column microfluidic DNA synthesizer
(B) Close up schematic of the column array............................................... 33
Figure 18. Design of DNA origami................................................................................ 34
Figure 19. Several DNA origami folding paths.............................................................. 34
Figure 20. Functional design of a DNA based logic gate............................................... 37
Figure 21. Simplistic rendering of a DNA logic gate...................................................... 38
Figure 22. Basic gate structures, derived from allosterically regulated deoxyribozyme
E6, for playing tic-tac-toe against a human opponent................................ 39
Figure 23. First Generation (MAYA I) DNA-based Logic Circuit that plays tic-tac-toe... 40
Figure 24. A single molecule DNA-based nanomotor driven by photons....................... 42
Figure 25. AFM Scan of walkers as they follow a track pattern places on the surface.. 43
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Figure 26. The Nano walker made at Columbia University is a protein molecule
decorated with three legs--single-stranded DNAzymes, synthetic DNA
molecules that act as enzymes and catalyze a reaction............................. 44
Figure 27. Deoxyribozyme-based molecular walker and origami prescriptive landscape.
..................................................................................................................................... 45
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Quantum Computing and Utilizing Organic Molecules in
Automation Technology
Summary
Powerful onboard computing hardware is a desired option for future space travel. Without
large data processing capability, the copious amounts of data acquired during flight from
astronomical sensors as well as crew and vehicle sensors will need to be sent back to
earthbound machines for processing, introducing delays measured in hours for routine
calculations. Current commercial computer hardware trajectories in silicon substrate
semiconductors are not likely to produce a radiation-hard or small and portable
supercomputer without significant mission-specific alteration. Alternatives to traditional
computing technology include computers based on entangled quantum states and molecular
computing hardware based on DNA molecules.
Included in this review is significant introduction to the necessary elements of quantum
computing and a summary of the state-of-the-art technologies. Following is background on
DNA and production of engineered DNA chains. Finally, DNA logic gates are presented along
with a treatment of nanomachines that will repair DNA circuitry. Forecasts of technology
development in the 10-20 and 40-year horizons are included along the way, as well as
summary discussion and a conclusion.
The first operating quantum computers capable of solving real-world problems will
commence within 10 years and be based on ion trap technology. This is entirely based on the
amount of research resources dedicated to the problem and the fact that there appear to
only be engineering challenges remaining. Atomic and ion traps require very substantial
cryogenic and EM shielding systems and are not practical for space travel.
Pure photonic technologies available today have difficulty with both miniaturization and
scalability. However, the amount of active work in the field makes a disruptive advance likely
in the 10-year timeframe. Optical computers will likely be realized in the 20-year horizon;
however, the very powerful promise of quantum computing will still have issues with photon
loss in any solid state device. The 40-year horizon will see photon technologies play an
essential but supporting role in distributed quantum computing. Realized all-optical non­
quantum systems will have radiation tolerance advantages over current semiconductor
technology and are likely to augment or even replace general-purpose computing devices for
space travel.
Hybrid designs utilizing arrays of quantum dots and photon communication channels will be
an option for space travel supercomputing on the 40-year timescale. These systems operate
at attainable temperatures without cryonics, and require no more shielding than humans. It
is likely that spintronics will be an essential ingredient.
Simple organic computing based on DNA tiles will be realized in the next 20 years. On the
40-year time horizon, useful DNA-based devices will be essential space exploration tools.
These could take the form of orbital-delivered wireless sensors searching planetary/asteroid
features or for essential compounds such as high concentrations of water. DNA computers
will also be realized on the 40-year timeline. Their advantage over solid state devices will be
the ability to repair nanoscale elements damaged in normal use or by cosmic radiation.
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These will not be the fastest systems in the astro-arsenal, but self-repair may make them
the most robust.
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INTRODUCTION
Computers today are not what they used to be. In the 17th century, a computer was merely a
person who performs computations. In this sense, the first computers were universally
programmable and were ultimately utilizing organic (DNA) hardware architecture. The
modern sense of a computer as a machine that manipulates input to produce deterministic
output emerged from the work of Turing in the 1930s. A Turing machine consists of four
parts: tape containing cells of symbols, read head, action table, and state register. In
operation, the state register is initialized, the first cell of the tape is read by the head, the
table translates the symbol into an action in the state register, and the tape is advanced to
read the next symbol. The read, action, advance tape loop is repeated until the program
ends.(1) Any calculation a modern digital computer can perform can be accomplished using a
Turing machine.a
Modern digital processing hardware, first used in the ENIAC in the 1950s, is based on logic
gates. All functions of a computer consist of the basic logic elements AND, OR, NOT, etc.
These are accomplished electronically by producing logic gates, combinations of transistors
that perform the logic function on input data. A common exercise in didactic digital logic
pedagogy is to design all of the basic logic gates using only NANO or NOR gates; thus, any
hardware element that can execute the NAND function can build a complete computer.b
Optimum designs are regularly more elegant than combining a single two-input gate, but it is
sufficient as proof of principle for any architecture to be able to produce an inverter and a
simple logic gate (AND/OR).
The quest for faster computing can be accomplished by making current hardware
architecture