Emerging Technologies

State university of New York at New PaltzElectrical and Computer Engineering Department

Dr. Yaser M. Agami Khalifa

Outlines

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

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.

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.

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.

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.

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.

• 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.

• 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.

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.

• 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.

Recent:Chemicals 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.

• 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.

• 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.

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.

Digitally Programmed Cells

• Goal: program biological cells• Characteristics

small (E.coli: 1x2m , 109/ml)self replicatingenergy efficient

• Potential applications“smart” drugs / medicineagricultureembedded systems

Motivation

Approach

logiccircuit

microbialcircuit

compiler

genomehigh-levelprogram

in vivo chemical activity of genomeimplements

computation specified by logic circuit

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

Digital Circuits

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

A

B

C D

C

CA

B

D= gene

gene

gene

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

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)

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.

input protein synthesis raterepression activity

(concentration of bound operator)

• steady-state relation C is sigmoidal

Stage I: Cooperative Binding

inputprotein

repression

cooperativebinding

inputprotein

“clean” digital signal

C

C

0 1

Stage II: Transcription

repression activity

mRNA synthesis rate

• steady-state relation T is inverse

invert signal

repression mRNAsynthesis

transcription

T

T

Stage III: Translation

output signal of gate

• steady-state relation L is mostly linear

scale output

outputprotein

mRNAsynthesis

mRNA

translation

L

L

inversion relation I :

“ideal” transfer curve: gain (flat,steep,flat) adequate noise margins

Putting it together

IL ∘ T ∘ C ()

inputprotein

outputprotein

repression

cooperativebinding

mRNAsynthesis

transcription

inputprotein mRNA

translation

signal

LTC

I

“gain”

0 1

activegene

Inverter’s Dynamic Behavior

• Dynamic behavior shows switching times

[A]

[Z]

[ ]

time (x100 sec)

Connect: Ring Oscillator

• Connected gates show oscillation, phase shift

time (x100 sec)

[A]

[C]

[B]

B_S

_R

Memory: RS Latch

time (x100 sec)

_[R]

[B]

_[S]

[A]

=A

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

Challenges

• Engineer component interfaces

• Develop instrumentation and modeling tools

• Create computational organizing principles Invent languages to describe phenomenaBuilds models for organizing cooperative behavior

• Create a new discipline crossing existing boundariesEducate a new set of engineering/biochemistry

oriented students

Evolvable Hardware

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.