PPT

advertisement
Course outline
1
Introduction
2
Theoretical background
Biochemistry/molecular biology
3
Theoretical background computer science
4
History of the field
5
Splicing systems
6
P systems
7
Hairpins
8
Detection techniques
9
Micro technology introduction
10
Microchips and fluidics
11
Self assembly
12
Regulatory networks
13
Molecular motors
14
DNA nanowires
15
Protein computers
16
DNA computing - summery
17
Presentation of essay and discussion
Introduction
Sizes
Organ  Tissue  Cell  Molecule  Atoms

A cell is
molecules

Proper
an
organization
communication
between
of
millions
these
of
molecules
is essential to the normal functioning of the
cell

Structure provides an
molecules communicate
understanding
of
how
Nanotechnology

The creation of functional materials, devices
and systems through control of matter at the
scale of 1 to 100 nm, and the exploitation of
novel properties and phenomena at the same
scale.

Self-assembling
highly
functional
molecular
machines aimed at performing specific tasks.
Often highly ordered repeated patterns of a
single functional unit.

1 nm = 0.0000000001 m or 0.0000001 mm
Molecular machines
ribosomes
 make proteins in cells
protein
DNA
mRNA
Molecular machines
protein motors
 move material in cells

ATP synthase rotor size: 10nm
Nature, 386, 299 (1997)
Protein motors
Bacterial chemotaxis
Bacterial chemotaxis

Bacteria move using flagellar motors

Protein network directs movement based on external
conditions and random motion: attractants/repellents

Simulate chemotaxis network (7 proteins)
Bacterial chemotaxis

Bacteria
move
towards
chemical
attractants and away from repellents

Process:
 attractants/repellents
bind
to
chemorecptors
 chemoreceptors transmit information
to a central processing system
 central
processing integrates many
inputs and sends a signal to
control flagellar motors

Interesting
sensitivity
[ Pfeffer ]
feature:
adaptation
of
Movement of flagellar rotation

Bacteria swim by rotating flagella

Motor located at
junction
flagellum and cell envelope
of

Motor can rotate
counterclockwise
or
CW
clockwise
CCW
CW
Bacterial motor
Bacterial motor and drive train.
Above: Rotationally averaged reconstruction of electron micrographs of purified
hook-basal bodies. The rings seen in the image and labeled in the schematic
diagram (right) are the L ring, P ring, MS ring, and C ring. (Digital print
courtesy of David DeRosier, Brandeis University.)
Biased random walk
Bacteria
 swim smoothly for 1sec (30 m)
 tumble, change direction by an average of 60
deg
Tumbling frequency

Movement with respect to attractants:
 increasing concentrations  less tumbling
 decreasing concentrations  more tumbling

Temporal or spatial regulation? [Koshland/Macnab]
 mix a bacterial suspension without attractant
with solution containing attractant
 tumbling suppressed within a second
 bacteria swam for long distances in a straight
line
 solution has
regulation!

no
spatial
gradient

temporal
Specifically, compares past second versus previous
three seconds
Information flow in chemotaxis
Structure of the chemoreceptors
ligand binding domain
Chemotaxis protein network
The flagella
The flagella
Microtublar motors
Microtubule motor proteins
Two main families of microtubule motor proteins carry out
ATP-dependent movement along microtubules:
1. Kinesin: Most members of the kinesin family of motor
proteins walk along microtubules toward the plus end,
away from the centrosome (MTOC).
2. Dynein: The dyneins walk along microtubules toward the
minus end (toward the centrosome).
In each case there is postulated to be a reaction cycle
similar (but not identical) to that of myosin.
The motor domain undergoes conformational changes as ATP
is bound and hydrolyzed, and products are released.
Kinesins

Kinesins are a large family of proteins with
diverse structures. Mammalian cells have at
least 40 different kinesin genes.

The
best
studied
is
referred
to
as
conventional kinesin, kinesin I, or simply
kinesin.

Some
are
referred
proteins (KRPs).

Kinesin I has a structure analogous
distinct from that of myosin.

There are 2 copies each of a heavy chain and a
light chain.
to
as
kinesin-related
to
but
Kinesin I
C-terminal
tail domains
light chains
stalk
domain
N-terminal heavy
chain motor
domains (heads)
hinge
Kinesin I

Each heavy chain of kinesin I includes a globular ATP-binding motor
domain at the N-terminus.

Stalk domains of heavy chains interact in an a-helical coiled coil
that extends from heavy chain neck to tail.

The coiled coil is interrupted by a few hinge regions that give
flexibility to the otherwise stiff stalk domain.
Kinesin I
C-terminal
tail domains
light chains
stalk
domain
N-terminal heavy
chain motor
domains (heads)
hinge
Kinesin I

N-termini of the 2 light chains associate with the 2 heavy chains
near the tail. The diagram above is over simplified.

Light chains at the N-terminus include a series of hydrophobic
heptad repeats predicted to interact with similar repeats in the
heavy chains near the tail region, in
a 4-helix coiled coil.
Kinesin I
C-terminal
tail domains
stalk
domain
light chains
N-terminal heavy
chain motor
domains (heads)
hinge
Kinesin I
C-terminal tail domains of kinesin light chains include several
"tetratrico peptide repeats" (TPRs). The 34 amino acid TPRs mediate
protein-protein interactions.
Kinesin light chain TPRs are involved in binding of kinesins to
cargo.
C terminal domains of heavy chains may also participate in binding
some kinesins to cargo.
Cargo proteins
bound by
kinesins are
diverse.
microtubule
Cargo
scaffolding
protein
cargo
vesicle
kinesin
receptor

Some organelle membranes contain transmembrane receptor proteins
that
bind
kinesins.
Kinectin
is
an
ER
membrane
receptor
for
kinesin-I.

Scaffolding
proteins,
first
identified
as
being
involved
in
assembling signal protein complexes, mediate binding of kinesin
light chains to some cargo proteins or receptors.

Some membrane-associated Rab GTPases, that provide specificity for
vesicle transport & fusion, are known to bind particular kinesins.
Cargo
scaffolding
protein

In absence
kinesin
of cargo, the
kinesin heavy
folds at hinge
regions,
bringing
heavy chain
tail domains
receptor
microtubule
chain stalk
cargo
vesicle
inactive kinesin
into contact with the motor domains.

In
this
folded
over
state
kinesin
exhibits
decreased
ATPase
activity and diminished binding to microtubules.

This may prevent wasteful hydrolysis of ATP by kinesin when it is
not transporting cargo.
Cargo
scaffolding
protein
kinesin
receptor
microtubule
Unfolding
cargo
vesicle
inactive kinesin
of
kinesin
into
its
more
extended
active
conformation is promoted by:

phosphorylation of kinesin light chains, catalyzed by a
specific kinase, or

binding of cargo.
Kinesin transport
Kinesin transporting a vesicle
along a microtubule
(+)
microtubule
(-)
Observations of conventional kinesin transporting elongated
particles have demonstrated that cargo particles do not roll
along
the
microtubule.
Instead
kinesin
walks
maintaining the orientation of a cargo particle.
along,
Kinesin transport
Kinesin transporting a vesicle
along a microtubule
(+)

microtubule
(-)
Movement of the 2-headed kinesin is processive, meaning that it
takes many steps without dissociating from a microtubule. A hand
over hand reaction cycle involving the 2 heads has been proposed.

Myosin V, which transports vesicles along actin filaments, also
exhibits processive movement.
Kinesin transport
View an animation emphasizing the cycle of
ATP
binding,
hydrolysis
&
product
dissociation during processive movement of
kinesin along a microtubule.
Flagella
Cilium

plasma
membrane
Cilia & flagella are bounded by the
plasma membrane.

A
basal
body,
which
is
a
single
axoneme
centriole cylinder, is at the base
of each cilium or flagellum.

Cilia
&
flagella
have
a
core
axoneme, a complex of microtubules
and
associated
proteins.
Some
distinctions:
 Flagella
rotary
basal body
(centriole)
cytosol
are usually 1 or 2 per cell. They tend to have a
or
sinusoidal
movement.
They
may
have
additional
structures outside the core axoneme
 Cilia are usually many per cell. They tend to have a whip-like
movement.
Flagella
plasma
membrane
B
AA
B
radial
spoke

An axoneme includes:

Nine
doublet
nexin
link
microtubules
around the periphery. The
dynein
arm
A tubule of each doublet
has attached dynein arms.

Two
singlet
microtubules,
by a sheath.

central
surrounded
Cilium
cross section
central sheath
Nexin links & radial spokes. These provide elastic connections between
microtubule doublets and between the A tubule of each doublet and the
central sheath.
Flagella

Few mammalian cell types have motile cilia
or flagella, including some respiratory
epithelial cells and sperm cells.

Many mammalian cells have a single short
non-motile primary cilium.

The
photoreceptor
structure
of
each
retinal rod & cone cell develops from a
non-motile cilium.
DNA machines
DNA secondary structures

Secondary structures are made of base pairs.
They are
energy.

stable
with
respect
to
free
Nearest neighbor model (Zimm et al., 1964).
Summing up stacking energies of adjacent
base pairs and mismatched pairs

Folding
problem
(Zuker
et
al.,
1981)
DNA secondary structures
Base sequence (linear structure)
5’
3’
Secondary structure
folding
5’
TTC…GCA
inverse folding
3’
Thermo-dynamical model

Inverse folding problem (Hofacker et al., 1994).
Optimization with the fold function for evaluation

Search for sub-optimal structures (Wuchty et al., 1999).
Enumeration of (sub-optimal) structures whose energy
is under mfe+d

Computation of the partition function (McCaskill, 1990).
Computation of the frequency of a structure

Estimation of the energy barier between structures (Flamm
et al., 2000).
DNA nanomachines

Various DNA nanomachine
 DNA motor by B-Z transiton
(Seeman et al., 1999)
 molecular tweezers (Yurke et
al., 2000)
 three-state
machine
(Simmel
et al., 2002)
 PX-JX2 (Yan et al., 2002)
 Hybridization
inhibition by
bulge loop (Tuberfield et al.,
2003)

Designing
DNA
sequence
with
bistable structures (Flamm et
al., 2001)
B-Z DNA nano-mechanical device
Seeman, 1999
Yurke’s DNA tweezers
Yurke’s DNA tweezers
Yurke’s DNA tweezers
Yurke’s DNA tweezers
Yurke’s DNA tweezers
Yurke’s DNA tweezers
http://news.bbc.co.uk/1/hi/sci/tech/873097.stm
Yurke’s DNA tweezers
Simmel’s 3-state machine
Yurke’s DNA tweezers
 Because
and
the thermodynamic paths for opening
closing
the
molecular
tweezers
are
different it is a thermodynamic engine.
 It
is a clocked molecular motor.
 Biological
molecular
motors
are
catalysts
that convert fuel to waist product.
 Hence,
DNA systems in which interactions are
catalytically controlled are of interest in
devising free running DNA motors.
Bulge loops
Hybridization inhibition by bulge loops (Tuberfield et al., 2003)
PX-JX2 by Yan
Self-guided self-assembly
DNA template for molecular motors
A DNA lattice
More complex patterns of motors on lattices can allow for
sophisticated molecular robotics tasks.
DNA template for molecular motors
Motor
Ab
DNA tile
A bifunctional antibody (Ab) is shown bound to a
DNA aptamer on a tile and to a motor protein, thus
immobilizing the motor onto the tile.
DNA nano-mechanical device

Walking triangles By binding the short red
strand (top figure) versus the long red
strand (bottom figure) the orientation of and
distance between the triangular tiles is
altered.
These changes are observable by
AFM.

Applications Programmable state control for
nano-mechanical devices.

Also as a visual output method.
DNA nano-mechanical device
8 turns
180ْ ْ
10.5 turns
DNA motor devices

Designs
for
the
first
autonomous
DNA
nanomechanical devices that execute cycles of
motion without external environmental changes.

Rolling DNA device uses hybridization energy

Walking DNA device uses ATP consumption

These DNA devices translate across a circular
strand of ssDNA and rotate simultaneously.

Generate
random
bidirectional
movements
that
acquire after n steps an expected translational
deviation of O(n1/2).
Reif, 2002
DNA motor devices
Walking DNA device
Rolling DNA device
Rolling DNA
Device
Walking DNA
Devi
ce
dsDNA
Walk
er
dsDNA
: walker
ssDNA
ssDNA road
Road:
ssDNA
ssDNA
ssDNA road
dsDNA
Roller:roller
Road:
Bidi
rectionalTr
ansl
at
ional
Bidirectional
translation and
& Ro
tati
ona
l
Move
me
ntmovement
rotation
Bidirectional Random
Translational& Rotational
Movement
Carbon nanotubes
Molecular machines
carbon nanotubes and buckyballs
 strong, light, flexible, electronic devices
 easy to make

hard to arrange
Carbon nanotubes
Single sheet of graphite
Strongest known fibers.
10-100 times more stronger
than steel per unit weight
Carbon nanotubes
Can behave as a semiconductor or metal
Nanomachines
Nanomachines
Molecular machines

complex molecules for robot parts

currently
 only theory
 hard to make
 hard to assemble

potential: cheap, fast, strong parts
example designs: E. Drexler, R. Merkle, A. Globus
example medical applications: R. Freitas, Jr., Nanomedicine, 1999
Molecular mechanics

Internuclear distance for bonds

Angle (as in H2O)

Torsion (rotation about a bond, C2H6

Inter-nuclear distance for van der Waals

Spring constants for all of the above

More terms used in many models

Quite accurate in domain of parameterization
Molecular mechanics
Limitations

Limited ability to deal with excited states

Tunneling (actually a consequence of the pointmass assumption)

Rapid nuclear movements reduce accuracy

Large changes in electronic structure caused by
small
changes
in
nuclear
position
reduce
accuracy
Hydrocarbon bearing
Hydrocarbon universal joint
Rotary to linear
NASA Ames
Bucky gears
NASA Ames
Bearing
Neon pump
Applications
Nanomedicine

Disease and ill health are caused
largely by damage at the molecular
and cellular level

Today’s surgical tools are huge and
imprecise in comparison
Nanomedicine

In the future, we will have fleets of
surgical tools that are molecular both in
size and precision.

We will also have computers much smaller
than a single cell to guide those tools.
Nanomedicine
Size of a robotic arm
~100 nanometers
8-bit computer
Mitochondrion
~1-2 by 0.1-0.5 microns
Nanomedicine
Mitochondrion
Size of a robotic arm
~100 nanometers
“Typical” cell:
~20 microns
Typical cell
Mitochondrion
Molecular computer
+ peripherals
Remove infections
Clear obstructions
Respirocytes
http://www.foresight.org/Nanomedicine/Respirocytes.html
Release and absorb

ATP, other metabolites

Na+, K+, Cl-, Ca++, other ions

Neurotransmitters, hormones, signaling molecules

Antibodies, immune system modulators

Medications

etc.
Correcting DNA
Nanomedicine

Nanosensors, nanoscale scanning

Power (fuel cells, other methods)

Communication

Navigation (location within the body)

Manipulation and locomotion

Computation

http://www.foresight.org/Nanomedicine
Nanomachines in biology

Nanoscale machines already exist in biology,i.e.
functional molecular components of cells.

They exist in enormous variety and sophistication
 Biochemical motors
 Ribosomes make proteins in an assembly-line
like (sequential) process
 Topoisomerase unwinds double-stranded DNA when
it becomes too tightly bound
Nanomachines in biology

Self-replicating molecular nanomachines have
already invaded just about every corner of
the earth – they are called biological
cells.

They used atoms, molecules and energy forms
to
construct
complex
objects
from
the
primeval soup
Nanowires
Introduction
Molecular electronics
www.scientificamerican.com
Molecular electronics
Biological Systems
Molecular Electronics Devices
Use molecular electronics to study biological systems.
Molecular electronics
Incentives

 Molecules are nano-scale
 Self assembly is achievable
 Very low-power operation
 Highly uniform devices
Quantum Effect Devices

 Building quantum wells using molecules
Electromechanical Devices

 Using mechanical switching of atoms or molecules
Electrochemical Devices

 Chemical interactions to change shape or orientation
Photoactive Devices

 Light frequency changes shape and orientation.
Molecular electronics
Definition
is a field emerging around the premise that it
is possible to build individual molecules that
can perform functions identical to those of
the key components of today’s microcircuits.
Why molecular electronics?
Chip-fabrication
specialists
will
find
it
economically infeasible to continue scaling
down microelectronics.
 stray signals on the chip
 the need to dissipate the heat from so many

closely packed devices
the difficulty of creating the devices in
the first place
Molecular electronics, any better?

Modern technologies can only go so far.

Solution (new development)
 DNA - It is promising to achieve
super-high density memory and high
sensitive detection technology.
 Cell Computing

Silicon transistors at 120 nm in length
will still be 60,000 times larger in area
than molecular electronic devices.
Recent research

Recent studies have shown that individual
molecules can conduct and switch electric
current and store information.

July of 1999 – HP and the University of
California
at
Los
Angeles
build
an
electronic switch consisting of a layer
of
several
million
organic
substance
molecules
of
an
called
rotaxane.
Linking a number of switches version of an AND gate is produced.
a
Recent research
June 2002 - Fuji Xerox biotechnology made
a prototype transistor of DNA from salmon
sperm.

Researchers
successfully
passed
an
electric
current
through
the
DNAtransistor.

This
demonstrates
that
behaves
in
a
similar
semiconductor.

Super smaller chip in 10 years.
the
chain
fashion
to
Recent research
Atomic force microscope image of semi-conductive DNA compound
http://www.fujixerox.co.jp/research/eng/category/inbt/m_electronics/index.html
Self assembly
Molecular self-assembly

the
autonomous
organization
of
components into patterns or structures
without human intervention (Whitesides
2002)

Current Problem: Forming electrical
interconnects between molecules
Self assembly
www.scientificamerican.com
Molecular electronics
Thiol
Acetylene linkage
Benzene ring
Molecular electronics

Mechanical synthesis
 Molecules aligned using a scanning tunneling
microscope (STM)
 Fabrication done molecule by molecule using
STM

Chemical synthesis
 Molecules
aligned
in
interactions
 Self assembly
 Parallel fabrication
place
by
chemical
an atomic relay
A very short
Electronics course
Transistors
A device composed of semiconductor
material that amplifies a signal or
opens or closes a circuit. Invented in
1947 at Bell Labs, transistors have
become
the
key
ingredient
of
all
digital circuits, including computers.
Today's microprocessors contains tens
of millions of microscopic transistors.
Transistors
Transistors consist of three terminals; the source, the gate,
and the drain.
Transistors
In the n-type transistor, both the source and the drain are
negatively-charged and sit on a positively-charged well of psilicon.
Transistors
When positive voltage is applied to the gate, electrons in the
p-silicon are attracted to the area under the gate forming an
electron channel between the source and the drain.
Transistors
When positive voltage is applied to the drain, the electrons
are pulled from the source to the drain. In this state the
transistor is on.
Transistors
If the voltage at the gate is removed, electrons aren't
attracted to the area between the source and drain. The
pathway is broken and the transistor is turned off.
DNA wires
DNA

Well known from biology

Forms predictable structure

Controllable
self
assembly
through base pair sequences

May be selectively processed
using restriction enzymes
http://www.chemicalgraphics.com/
DNA in microelectronics

As
the
major
component
in
a
Single
Electron Tunneling (SET) Transistor

As tags to connect up nano-circuitry
including wires and nanoparticles (taking
advantage of DNA selectivity)

As
basis
for
computation)
a
Qubit
(for
quantum
DNA SET transistor
DNA
Single electron transistor
Main strand
Gate strand
Equivalent Electrical Circuit
E. Ben-Jacob , Phys. Lett. A 263, 199 (1999).
Main strand
Assumptions

Chemical bonds(in DNA) can act as
tunnel
junctions
in
the
coulomb
blockade
regime,
could
emit
electricity, given a proper coating.

Has the ability to coat a DNA strand
with metal in nanometer scale.
Operation
Schematic image with 2 grains in DNA connected by
P-bond. Dark circle->carbon atoms, white circles>oxygen atoms.
DNA pairs

P-bond
-> tunneling junction.

H-bonds
-> capacitor.

The grain itself -> inductive properties.
DNA pairs



P bond: Has 2  bonds, 1  bond.
The  electron can be shared with 2 oxygen,
resembles an electron in well, put it on the
lowest level.
When electron enters, it meet the barrier set
by energy gap.

But the gap is narrow and
electron can walk trough.
small
so
the
DNA pairs

H-bonds: Can be the capacitor.

The proton in the h-bond can screen a net charge
density on either side, by movement.

Thus the net charge could be in the side of the h-bond.

The grains: Can be the inductive properties.

Due to the hopping of additional electrons.

But can be ignored (L & Lo is small, consistent to the
usual SET)
DNA pairs

Consist of 2 strands (1 main, 1 gate)

Connect the end base of the gate strand with a
complimentary strand.

Both strands should be metal-coated, except (a)
the grain in the main strand, which connect to the
gate strand, the
connective h-bond.

2
adjacent
P-bonds,
(b)
Connect the main strand with voltage source (V)
the
DNA pairs
The end of the gate strand with another voltage source (Vg)
that acts as gate source.
Functionalisation of nanoparticles

DNA may be attached to surface area
of
nanoparticles
to
construct
desired assemblies.

May provide insight to possible
solution to connecting transistors
Functionalisation of nanoparticles
Mirkin et al.: Nature, 1996, 382, 607
Functionalisation of nanoparticles
Mirkin et al.: Nature, 1996, 382, 607
Functionalisation of nanoparticles
8 nm gold particles attached to a 31 nm gold particle with DNA
http://www.chem.nwu.edu/~mkngrp/dnasubgr.html
DNA conductance

Double helix – a backbone and base pairs

Building
blocks
A, T, C & G

Example: 10 base pairs per turn, distance of
3.4 Angstroms between base pairs.

Arbitrary sequences possible

A challenge for nanotechnology is controlled /
are
the
base
pairs:
reproducible growth. DNA is an example with
some success. However, there are many copies in
a solution!

2D and 3D structures with DNA base pairs as a
building block have been demonstrated

Lithography? Not yet.
DNA base-pairs
DNA conductance

Conductivity in DNA has
been controversial

Electron transfer experiments (biochemistry) /
possible link to cancer

Transport experiments (physics)
DNA conductance
Metallic, No gap
Current
Current
~ 1nA
~ 10nA
Semiconducting / Insulating
Voltage (V)
Porath et. al, Nature (2000)
Voltage 20mV
Fink et. al, Science (1999)
Counter-ions

Is conduction through the base
pair or backbone? - Basepair

When DNA is dried, where are the
counter ions?

Crystalline / non crystalline?

Counter ions significantly modify
the energy levels of the base
pairs

Counter-ion
important

Resistance
species
increases
is
also
with
length
of
the
DNA
(exponential within the
of simple models)
the
sample
context
Counter-ions
DNA-based metalised nanowires
10 nm wires:
AuPd on DNA
Needed

Smaller wires and constructs

Difficult to make
conventional means

Find
if
DNA
is
wires
a
good
this
scale
substrate
metalisation (and for which metals)

Conducting and superconducting wires
by
for
Which DNA?

λ-DNA:
double-stranded,
2 nm width, 16 micron
length

Poly-C,
Poly-A,
etc.:
Single-stranded, all same
base, 1 nm width

Designed,
complementary
strands:
Self assembly
presents possibility for
complex structures
λ-DNA, uncoated:
~5 nm wires
Metalised DNA
1)
2)

Earlier construction of DNA-templated nanowires

Braun

Richter

Nanotubes, other substrates
1:
100 nm thick wires, Ag on DNA
2:
50 nm thick wires, Pd on DNA
E. Braun, Y.Eichen, U. Sivan, and G. Ben-Yoseph, Nature (London) 391, 775 (1998).
J. Richter et al. Appl. Phys. Lett. 78, 536 (2001)
Methods
Suspend DNA across undercut 100 nm trench
-or

Suspend
across
cuts in
thin (60 nm)
membrane –variable width carved by focused
ion beam

Metalize by sputtering or evaporation

Image with scanning electron microscope

Make electrical measurements
Methods
Schematic of undercut trench
Set-up
Schematic of electrode overlaying wire
Methods
Hitachi 4700 Scanning Electron Microscope
More metalised DNA-wires
AuPd sputtered on λ DNA
Osmium plasma coated on λ DNA

Wires made repeatedly, variety of coatings (or none)

Width range from <5 nm bare DNA wires to >30 nm heavily
coated in AuPd. The thinnest contiguous wires are ~10 nm
thick
Metalised DNA-wires
Variable width cuts in membrane, made by focused ion beam. DNA
bridges the cuts.


Longest wire to date: 960 nm (~30 nm thick)
Appearance of multi-strand “Ropes”
Metalised DNA-wires
Multi-strand “rope,” 3 nm AuPd
coating,
total thickness: 3040 nm Length: 960 nm
Two wires connected by “rope”
visible on surface of membrane,
length: 550 nm on right, 670 nm
on left
Is it functional?

Measurement contacts produced
photolithography techniques
by

Potentially superconducting
or 3He system

First Mo0.79Ge0.21 coated samples:
superconductivity
standard
samples
in
4He
test for
Not yet ....

First MoGe sample weakly conductive,
superconductivity- too thin!

Room temperature:
2.3 MΩ, Lowest point:
750 kΩ, sharp upturn near usual critical
temperature (near 4 K)

Possible
film

Next samples:
Si coat
discontinuities
or
oxidation
no
of
7 nm MoGe with protective
Variations

More conductivity measurements

Different DNA structures

Normal and

Device possibilities?

As thin as possible (preferably
functional)
superconducting wires
Variations
Poly-C wire with 2 nm AuPd, total width: 5 nm.
DNA template
DNA templated electronics
The DNA acts as a scaffold for positioning a
single-walled carbon nanotube at the heart of
a field-effect transistor, as well as a
template for the metallic wires connecting
the device.
K Keren et al. 2003 Science 302 1380
DNA templated electronics
DNA templated electronics
What do we need to realise this

assemble a DNA network

localise moleculra scale electronic components

transform DNA into conducting wires
DNA templated wires
silver wires
formed on aldehyde derivitesed DNA
continuous gold wires
DNA templated gold wires
wire width ~50nm
DNA width ~2nm
R~26 Ω
Sequence specific molecular lithography
Sequence specific molecular lithography
RecA polymerised on DNA (cryo-TEM)
3-armed junction formation
building blocks
synapsis
final product
branch migration
AFM image of 3-armed junction
Sequence specific molecular lithography
patterning of DNA metallization
Sequence specific molecular lithography
Sequence specific molecular lithography
RecA nuleoprotein filament
localised on aldehydederivatized DNA
sample after silver deposition
AFM
sample after gold deposition
SEM
Sequence specific molecular lithography
optical lithography
molecular lithography
Others
Carbon nanotubes
Carbon nanotubes
The device - which consists of
a single-walled carbon nanotube
sandwiched
between
two
gold
electrodes
operates
at
extremely
fast
microwave
frequencies.
The
result
is
an
important step in the effort to
develop
nanoelectronic
components that could be used
to replace silicon in a range
of electronic applications (S
Li et al. 2004 Nano Lett. 4
753).
http://physicsweb.org/article/news/8/4/15
Superconductivity in nanotubes

Left red data show insulating like behavior with
resistance upturns at the lowest temperatures, blue data
show superconducting behavior

Right V-I data for a strongly superconducting sample at
various temperatures.
Courtesy, A. Bollinger
Buckyball
www.osti.gov/accomplishments/ smalley.html
Cellular computing
Cellular computing
Goals

To use a cell as the smallest DNA-based
molecular computer

More specifically, to mimic some or all
of a cells mechanisms in order to
produce a quasi molecular computer (QMC),
or a true molecular computer (TMC)
Quasi cellular computing

Most of the input and output operations are
driven by an external force
 Input
and programming provided, QMC
provides output
 All molecular computers are of this type,
with the exception of the cell

Goal for QMC’s: to develop QMC’s that are
more efficient, and less dependent on
outside interaction
True cellular computing

“All
computational
operations
(input,
output, state transitions) are driven by
self organizing chemical reactions” (Ji
1999)
 All processes are internally driven, no
outside help is needed
 Only known example is a cell

Goal for TMC’s: to fabricate an artificial
TMC with the properties of a living cell
Cells versus computers
Qualities of cells that are
similar
to
those
in
computers

Have
inputs,
state
transitions, and outputs
as indicated by their
programming

Have
a
language
to
communicate between cells

Have
information
and
energy storage mechanisms:
IDS’s
http://www.rkm.com.au/CELL/
Cells versus computers
Cells
Computers
Current carried by: Chemicals
Wires
Reactions or
Enzymes
processes turned on
or off by:
Transistors
Information stored
in:
Capacitors
Biopolymers,
IDS’s
Computational
DNA
programs stored in:
Software
Cells versus computers
Cells
Computers
Programmability No- not yet
Yes
SelfYes
Reproducibility
No- not yet
Ji, Sungchul. The Cell as the Smallest DNA Based Molecular Computer. BioSystems (1999):52 123-133.
Download