Emerging Technologies

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Emerging Technologies
State university of New York at New
Paltz Electrical and Computer Engineering
Department
Dr. Yaser M. Agami Khalifa
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Outlines

• Nanotech Goes to Work DNA Computing
• Digitally Programmed Cells
• Evolvable Hardware

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Definition

• Molecular nanotechnology Thorough, inexpensive
  control of the structure of matter based on
  molecule-by-molecule control of products and
  byproducts the products and processes of
  molecular manufacturing, including molecular
  machinery.

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Programmable Molecules

• The tweezers exploit the complementary nature of
  the two strands that make up the famous double
  helix that is DNA.
• A stretch of single-stranded DNA will stick
  firmly to another single strand only if their
  sequences of bases match up correctly.

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How it Works

• The tweezers comprise three single strands of
  synthetic DNA. Two strands act as the arms one
  strand straddles the others and acts as a kind of
  backbone and hinge holding the whole V-shaped
  structure together.

• The tweezers comprise three single strands of
  synthetic DNA. Two strands act as the arms one
  strand straddles the others and acts as a kind of
  backbone and hinge holding the whole V-shaped
  structure together.
• The arms extend far enough to leave a number of
  unpaired bases dangling free beyond the backbone.
  
• When a fourth DNA strand is added to the test
  tube, it grabs the unpaired bases and zips the
  tweezers shut. Again, just a few bases are
  allowed to hang unpaired, which permits a fifth
  strand to rip away the first fuel unit and open
  the tweezers.

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Where is it going

• Dr Yurke said of his team's DNA tweezers "This
  may lead to a test-tube based nanofabrication
  technology that assembles complex structures,
  such as circuits, through the orderly addition of
  molecules."
• The Bell Laboratories are already working to
  attach DNA to electrically conducting molecules
  to assemble rudimentary molecular-scale
  electronic circuits.

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How will nanotechnology improve our lives?

• One of the first obvious benefits is the
  improvement in manufacturing techniques. We are
  taking familiar manufacturing systems and
  expanding them to develop precision on the atomic
  scale.

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• Some of the most dramatic changes are expected in
  the realms of medicine. Scientists envision
  creating machines that will be able to travel
  through the circulatory system, cleaning the
  arteries as they go sending out troops to track
  down and destroy cancer cells and tumors or
  repairing injured tissue at the site of the
  wound, even to the point of replacing missing
  limbs or damaged organs.

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• Nanotechnology is expected to touch almost every
  aspect of our lives, right down to the water we
  drink and the air we breathe. Once we have the
  ability to capture, position, and change the
  configuration of a molecule, we should be able to
  create filtration systems that will scrub the
  toxins from the air or remove hazardous organisms
  from the water we drink. We should be able to
  begin the long process of cleaning up our
  environment.

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What progress is being made today in
nanotechnology?

• Scientists are working not just on the materials
  of the future, but also the tools that will allow
  us to use these ingredients to create products.
  Experimental work has already resulted in the
  production of moleculat tweezers, a carbon
  nanotube transistor, and logic gates.

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• Theoretical work is progressing as well. James M.
  Tour of Rice University is working on the
  construction of molecular computer. Researchers
  at Zyvex have proposed an Exponential Assembly
  Process that might improve the creation of
  assemblers and products, before they are even
  simulated in the lab. We have even seen
  researchers create an artificial muscle using
  nanotubes, which may have medical applications in
  the nearer term.

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RecentChemicals Map Nanowire Arrays (Feb. 04)

• One promising possibility for replacing today's
  chipmaking technologies when they can no longer
  shrink circuit size is arrays of nanowires whose
  junctions form tiny, densely packed transistors.
• Harvard University and California Institute of
  Technology researchers have devised a scheme to
  chemically modify selected nanowire junctions to
  make them react differently to electrical current
  than the junctions around them.

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• The chemical modification makes cross points more
  sensitive to switching voltage than unmodified
  cross points, making it possible to selectively
  address nanowire outputs using far fewer control
  wires.
• This makes connecting nano components to
  ordinary-size circuits possible and is also a
  step toward making the integrated memory and
  logic needed to make a functional nanocomputer.

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• Prototype memory and processors could be built
  within two to five years, and commercial devices
  within five to ten years, according to the
  researchers. The research appeared in the
  November 21, 2003 issue of Science.

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Recent Updates (Friday 2/6/04)

• Researchers from the University of California at
  Berkeley and Stanford University have fabricated
  a circuit that combines carbon nanotube
  transistors and traditional silicon transistors
  on one computer chip. Connecting minuscule
  nanotube transistors to traditional silicon
  transistors enables the atomic-scale electronics
  to communicate with existing electronic
  equipment.

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Digitally Programmed Cells
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Motivation

• Goal program biological cells
• Characteristics
• small (E.coli 1x2?m , 109/ml)
• self replicating
• energy efficient
• Potential applications
• smart drugs / medicine
• agriculture
• embedded systems

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Approach
logic circuit
high-level program
genome
microbial circuit compiler

• in vivo chemical activity of genomeimplementscom
  putation specified by logic circuit

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Key Biological Inverters

• Propose to build inverters in individual cells
• each cell has a (complex) digital circuit built
  from inverters
• In digital circuit
• signal protein synthesis rate
• computation protein production decay

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Digital Circuits

• With these inverters, any (finite) digital
  circuit can be built!

C

A
C
D
D
gene
B
C
B
gene
gene

• proteins are the wires, genes are the gates
• NAND gate wire-OR of two genes

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Components of Inversion

• Use existing in vivo biochemical mechanisms
• stage I cooperative binding
• found in many genetic regulatory networks
• stage II transcription
• stage III translation
• decay of proteins (stage I) mRNA (stage III)

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• The majority of genes are expressed as the
  proteins they encode. The process occurs in two
  steps
• Transcription DNA ? RNA
• Translation RNA ? protein
• Taken together, they make up the "central dogma"
  of biology DNA ? RNA ? protein.

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Stage I Cooperative Binding
C
C

• fA input protein synthesis rate
• rA repression activity (concentration
  of bound operator)
• steady-state relation C is sigmoidal

rA
fA
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Stage II Transcription
T
rA
yZ
transcription
repression
mRNA synthesis
T

• rA repression activity
• yZ mRNA synthesis rate
• steady-state relation T is inverse

yZ
rA
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Stage III Translation
L
fZ
yZ
translation
output protein
mRNA synthesis
mRNA
L

• fZ output signal of gate
• steady-state relation L is mostly linear

fZ
yZ
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Putting it together
signal
L
T
C
rA
fA
fZ
yZ
cooperative binding
transcription
translation
repression
input protein
output protein
mRNA synthesis
input protein
mRNA

• inversion relation I
• ideal transfer curve
• gain (flat,steep,flat)
• adequate noise margins

I
fZ I (fA) L T C (fA)
gain
fZ
0
1
fA
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Inverters Dynamic Behavior

• Dynamic behavior shows switching times

A

active gene
Z
time (x100 sec)
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Connect Ring Oscillator

• Connected gates show oscillation, phase shift

A
B
C
time (x100 sec)
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Memory RS Latch
_ R

A
_ S
B
time (x100 sec)
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Limits to Circuit Complexity

• amount of extracellular DNA that can be inserted
  into cells
• reduction in cell viability due to extra
  metabolic requirements
• selective pressures against cells performing
  computation

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Challenges

• Engineer component interfaces
• Develop instrumentation and modeling tools
• Create computational organizing principles
• Invent languages to describe phenomena
• Builds models for organizing cooperative behavior
• Create a new discipline crossing existing
  boundaries
• Educate a new set of engineering/biochemistry
  oriented students

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Evolvable Hardware
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The EHW Controlled Prosthetic Artificial Hand
Project

• Conventional EMG(Electromyograph)-contorolled
  prosthetic hands take almost one month until
  users master the control of hand movements.
• The EHW controller, however, succeeded in
  reducing such rehabilitation time drastically
  (about ten minutes!).
• The EHW for the hand adaptively synthesizes a
  pattern recognition circuit which is tailored to
  each user, because EMG has strong individual
  differences. A gate-level EHW LSI is developed
  for this EMG hand.

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