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

Course outline

Introduction

A cell is an organization of millions of

molecules

Proper communication between these molecules is

essential to the normal functioning of the cell

Structure provides an understanding of how

molecules communicate

Organ Tissue Cell Molecule Atoms

Sizes

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

Nanotechnology

ribosomes make proteins in cells

DNA mRNA

protein

Molecular machines

protein motors move material in cells ATP synthase rotor size: 10nm

Nature, 386, 299 (1997)

Molecular machines

Protein motors

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)


[ Pfeffer ]

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 feature: adaptation of

sensitivity


Bacteria swim by rotating flagella

Motor located at junction of

flagellum and cell envelope

Motor can rotate clockwise or

counterclockwise

CW CCW CW

Movement of flagellar rotation

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.)

Bacterial motor

Biased random walk

Bacteria swim smoothly for 1sec (30 m) tumble, change direction by an average of 60 deg

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 no spatial gradient temporal

regulation!

Specifically, compares past second versus previous

three seconds

Tumbling frequency

Information flow in chemotaxis

ligand binding domain

Structure of the chemoreceptors

Chemotaxis protein network

The flagella

The flagella

Microtublar motors

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.

Microtubule motor proteins

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 to as kinesin-related

proteins (KRPs).

Kinesin I has a structure analogous to but

distinct from that of myosin.

There are 2 copies each of a heavy chain and a

light chain.

Kinesins

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

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 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.

Kinesin I

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 proteins

bound by

kinesins are

diverse.

Cargo

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.

In absence

of cargo, the

kinesin heavy

chain stalk

folds at hinge

regions,

bringing

heavy chain

tail domains

Cargo

Unfolding 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.

Cargo

Observations of conventional kinesin transporting elongated

particles have demonstrated that cargo particles do not roll

along the microtubule. Instead kinesin walks along,

maintaining the orientation of a cargo particle.

Kinesin transport

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.

Kinesin transport

http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/movies/kinesin.dcr

Flagella are usually 1 or 2 per cell. They tend to have a

rotary 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.

Cilia & flagella are bounded by the

plasma membrane.

A basal body, which is a single

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

Nexin links & radial spokes. These provide elastic connections between

microtubule doublets and between the A tubule of each doublet and the

central sheath.

An axoneme includes:

Nine doublet microtubules

around the periphery. The

A tubule of each doublet

has attached dynein arms.

Two singlet central

microtubules, surrounded

by a 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.

Flagella

DNA machines

Secondary structures are made of base pairs.

They are stable with respect to free

energy.

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

5’ 3’

TTC…GCA

3’

5’

Base sequence (linear structure) Secondary structure

folding

inverse folding

DNA secondary structures

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).

Thermo-dynamical model

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)

DNA nanomachines

B-Z Z-B

D A

D

A

B-Z DNA nano-mechanical device

Seeman, 1999

Yurke’s DNA tweezers





http://news.bbc.co.uk/1/hi/sci/tech/873097.stm



Simmel’s 3-state machine

Because the thermodynamic paths for opening

and 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.


Hybridization inhibition by bulge loops (Tuberfield et al., 2003)

Bulge loops

PX-JX2 by Yan

Self-guided self-assembly

A DNA lattice

More complex patterns of motors on lattices can allow for

sophisticated molecular robotics tasks.

DNA template for molecular motors

Motor

DNA tile

Ab

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 template for molecular motors

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

10.5 turns

180 ْ ْ

DNA nano-mechanical device

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

Bidirectional RandomTranslational& RotationalMovement

ssDNARoller:ssDNA

Road:

Rolling DNADevice

Bidirectional Translational& Rotational Movement

dsDNAWalker:

ssDNARoad:

Walking DNADevice

Walking DNA device Rolling DNA device

ssDNA road ssDNA road

dsDNA walkerdsDNA roller

Bidirectional translation and rotation movement

DNA motor devices

Carbon nanotubes

Molecular machines

carbon nanotubes and buckyballs strong, light, flexible, electronic devices easy to make hard to arrange

Strongest known fibers.10-100 times more strongerthan steel per unit weight

Single sheet of graphite

Carbon nanotubes

Can behave as a semiconductor or metal

Carbon nanotubes

Nanomachines

Nanomachines

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

Molecular machines

example medical applications: R. Freitas, Jr., Nanomedicine, 1999

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

Limited ability to deal with excited states

Tunneling (actually a consequence of the point-

mass assumption)

Rapid nuclear movements reduce accuracy

Large changes in electronic structure caused by

small changes in nuclear position reduce

accuracy

Limitations

Molecular mechanics

Hydrocarbon bearing

Hydrocarbon universal joint

NASA Ames

Rotary to linear

Bucky gears

NASA Ames

Bearing

Neon pump

Applications

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

Mitochondrion~1-2 by 0.1-0.5 microns

Size of a robotic arm~100 nanometers

8-bit computer

Nanomedicine

“Typical” cell: ~20 microns

MitochondrionSize of a robotic arm ~100 nanometers

Nanomedicine

Mitochondrion

Molecular computer + peripherals

Typical cell

Remove infections

Clear obstructions

http://www.foresight.org/Nanomedicine/Respirocytes.html

Respirocytes

ATP, other metabolites

Na+, K+, Cl-, Ca++, other ions

Neurotransmitters, hormones, signaling molecules

Antibodies, immune system modulators

Medications

etc.

Release and absorb

Correcting DNA

Nanosensors, nanoscale scanning

Power (fuel cells, other methods)

Communication

Navigation (location within the body)

Manipulation and locomotion

Computation

http://www.foresight.org/Nanomedicine

Nanomedicine

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

Nanomachines in biology

Nanowires

Introduction

www.scientificamerican.com

Molecular electronics

Biological Systems Molecular Electronics Devices

Use molecular electronics to study biological systems.


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.


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.


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

Why molecular electronics?

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.

Molecular electronics, any better?

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 molecules of an organic

substance called rotaxane. Linking a

number of switches - a version of an

AND gate is produced.

Recent research

June 2002 - Fuji Xerox biotechnology made

a prototype transistor of DNA from salmon

sperm.

Researchers successfully passed an

electric current through the DNA-

transistor.

This demonstrates that the chain behaves

in a similar fashion to semiconductor.

Super smaller chip in 10 years.

Recent research

Recent research

http://www.fujixerox.co.jp/research/eng/category/inbt/m_electronics/index.html

Atomic force microscope image of semi-conductive DNA compound

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

Self assembly

Benzene ring

Acetylene linkageThiol


Mechanical synthesis Molecules aligned using a scanning tunneling

microscope (STM) Fabrication done molecule by molecule using

STM

Chemical synthesis Molecules aligned in place by chemical

interactions Self assembly Parallel fabrication


an atomic relay

Electronics course A very short

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

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 p-silicon.

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

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

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 a Qubit (for quantum

computation)

DNA in microelectronics

DNA Single electron transistor

E. Ben-Jacob , Phys. Lett. A 263, 199 (1999).

Gate strand

Main strandMain strand

DNA SET transistor

Equivalent Electrical Circuit

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.

Assumptions

Schematic image with 2 grains in DNA connected by

P-bond. Dark circle->carbon atoms, white circles-

>oxygen atoms.

Operation

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 small so the

electron can walk trough.

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 2 adjacent P-bonds, (b) the

connective h-bond.

Connect the main strand with voltage source (V)

DNA pairs

The end of the gate strand with another voltage source

(Vg) that acts as gate source.

DNA pairs

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


Mirkin et al.: Nature, 1996, 382, 607


http://www.chem.nwu.edu/~mkngrp/dnasubgr.html

8 nm gold particles attached to a 31 nm gold particle with DNA


Double helix – a backbone and base pairs

Building blocks are the base pairs:

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 /

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 conductance

DNA base-pairs

Conductivity in DNA has been controversial

Electron transfer experiments (biochemistry) /

possible link to cancer

Transport experiments (physics)

DNA conductance

Voltage (V)

Current

~ 1nA

Semiconducting / Insulating

Porath et. al, Nature (2000)

Current

~ 10nA

Voltage

Metallic, No gap

20mV

Fink et. al, Science (1999)

DNA conductance

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 species is also

important

Resistance increases with the

length of the DNA sample

(exponential within the context of

simple models)

Counter-ions

Counter-ions

10 nm wires: AuPd on DNA

DNA-based metalised nanowires

Smaller wires and constructs

Difficult to make wires this scale by

conventional means

Find if DNA is a good substrate for

metalisation (and for which metals)

Conducting and superconducting wires

Needed

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

Which DNA?

Earlier construction of DNA-templated nanowires

Braun 1: 100 nm thick wires, Ag on DNA

Richter 2: 50 nm thick wires, Pd on DNA

Nanotubes, other substrates

Metalised DNA

1) E. Braun, Y.Eichen, U. Sivan, and G. Ben-Yoseph, Nature (London) 391, 775 (1998).2) J. Richter et al. Appl. Phys. Lett. 78, 536 (2001)

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

Methods

Schematic of electrode overlaying wire

Set-up

Hitachi 4700 Scanning Electron Microscope

Methods

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

More metalised DNA-wires

Longest wire to date: 960 nm (~30 nm thick) Appearance of multi-strand “Ropes”

Variable width cuts in membrane, made by focused ion beam. DNA bridges the cuts.

Metalised DNA-wires

Multi-strand “rope,” 3 nm AuPd coating, total thickness: 30-40 nm Length: 960 nm

Two wires connected by “rope” visible on surface of membrane, length: 550 nm on right, 670 nm on left

Metalised DNA-wires

Measurement contacts produced by standard

photolithography techniques

Potentially superconducting samples in 4He or 3He system

First Mo0.79Ge0.21 coated samples: test for

superconductivity

Is it functional?

First MoGe sample weakly conductive, no

superconductivity- too thin!

Room temperature: 2.3 MΩ, Lowest point:

750 kΩ, sharp upturn near usual critical

temperature (near 4 K)

Possible discontinuities or oxidation of

film

Next samples: 7 nm MoGe with protective Si

coat

Not yet ....

More conductivity measurements

Different DNA structures

Normal and superconducting wires

Device possibilities?

As thin as possible (preferably

functional)

Variations

Poly-C wire with 2 nm AuPd, total width: 5 nm.

Variations

DNA template

K Keren et al. 2003 Science 302 1380

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.

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

continuous gold wires

silver wiresformed on aldehyde derivitesed DNA

DNA templated gold wires

wire width ~50nm

DNA width ~2nm

R~26 Ω

Sequence specific molecular lithography

Sequence specific molecular lithographyRecA polymerised on DNA (cryo-TEM)

3-armed junction formation

building blocks synapsis

branch migrationfinal product

AFM image of 3-armed junction


patterning of DNA metallization


Sequence specific molecular lithographyRecA nuleoprotein filament localised on aldehyde- derivatized DNA

sample after silver deposition

sample after gold deposition

AFM

SEM

Sequence specific molecular lithographyoptical lithography molecular lithography

Others

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

Carbon 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

Superconductivity in nanotubes

www.osti.gov/accomplishments/ smalley.html

Buckyball

Cellular computing

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)

Cellular computing

Goals

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

Quasi 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

True cellular computing

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 processes turned on or off by:

Enzymes Transistors

Information stored in:

Biopolymers, IDS’s

Capacitors

Computational programs stored in:

DNA Software


Cells Computers

Programmability No- not yet Yes

Self-Reproducibility

Yes No- not yet

Ji, Sungchul. The Cell as the Smallest DNA Based Molecular Computer. BioSystems (1999):52 123-133.


Documents

Course outline