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SELF ASSEMBLY IN
NANOTECHNOLOGY
Self Assembly
• Self Assembly is defined as the
spontaneous association of numerous
individual units of material into well
organized, well defined structures without
external instruction.
The Proposition of Bottom Up
Manufacturing
• In 1959 Richard Feynman in an address of
the American Physical Society proposed
that there was plenty of room at the bottom.
It was possible to use very small objects to
create large objects.
• This was the beginning of the idea for
nanotechnology and self assembly.
Size of Nanotechnology
• Nanotechnology involves very
small objects.
– Objects less than one-billionth of a meter.
• The size of a marble compared to the
earth.
– Building materials for nanotechnology are at the
molecular level.
www.
nisenet.org/publicbeta/articles/think_small/index.ht
Self Assembly is the Key to
Inexpensive Nano-Fabrication
• Molecular self assembly has advantages
• It is low in cost.
– Reduced fuel costs.
• Depend on chemical and physical forces to combine
materials not petroleum.
• Can have high reproducibility.
– In nature, materials self assemble with little
variation.
• Is able to use a variety of materials for
creation.
– All the building blocks of biology and chemistry.
Building at the Nanoscale
• Involves a knowledge of many disciplines
–
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Chemistry
Biology
Physics
Electronics
Mathematics
Fundamental Knowledge May
Need to be Modified
• Understanding how the properties of atoms
and molecules will vary at such a small
scale.
– Randomization may play a big role.
– Atomic properties may vary at such a small scale.
Biology Uses Nanoscale
Molecules
• Self assembly takes place every day inside
your body
– Molecules self organize to form structurally
defined and stable arrangements.
• Cell membranes
• Proteins
– Enzymes
• Cell organelles
– To view self assembly in a cell go to:
http://multimedia.mcb.harvard.edu/media.html
and view the Inner Life video
Chemical bonds define physical
structure
• The angle of the bonds formed between the
atoms will define the structure of the
substance formed.
– Tetrahedral structure of water
– Cube structure of salt
– Hexagonal structure of carbon-carbon
interactions
Tetrahedral Structure of Water
www.progressivegardens.com/growers_guide/waterstructure.jpg
Chemical Forces Organize Self
Assembly
• Strong Interactions at the chemical level will
define some assembly these include
– Covalent Bonds
• The sharing of electrons between atoms as in water.
– Ionic bonds
• The formation of charged particles as in salt.
Bond Structure
www.accessexcellence.org/RC/VL/GG/ecb/covalent_ionic_bonds.html
Weak Chemical Interactions
• Modify structure within molecules
• Organize structure between molecules
• Examples include:
– Hydrogen bonds
– Van der Waals forces
– Hydrophobic hydrophilic interactions
Hydrogen Bonds
• Form when an electron negative atom
usually one with more protons than another
atom pulls the electrons away from the
smaller atom.
• Leading to a charge separation with the
atom with the most protons having a
negative charge and the atom with the least
protons having a positive charge.
– Most common when hydrogen is bonded to a
oxygen, nitrogen or fluorine atom.
Hydrogen Bond
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/image12.gif
Vander Waals Forces
• Are weak bonds between molecules caused
by the random fluctuations in electrons.
– The atoms within the molecules exist as
transient dipoles.
• One part has a weak negative charge another part a
weak positive charge.
– Example: water
Vander Waals Forces
http://www.straightdope.com/mailbag/WaterPolarity.jpg
Hydrophilic –Hydrophobic
Interactions
• Molecules can exist as polar and nonpolar
molecules.
– Polar molecules have charges and interact with
other charged molecules.
• NaCl readily dissolves in water another charged
molecule.
– Nonpolar molecules do not have charges.
• Olive oil is an example.
• Nonpolar molecules readily dissolve in other nonpolar
molecules.
– Butter and olive oil will mix.
• But do not readily dissolve in polar molecules.
– Oil and water do not mix.
Hydrophilic –Hydrophobic
Interactions
http://www.biologycorner.com/resources/lipidbilayer.gif
Forces of Chemical Reactions
• Two forces control whether or not reactions
will occur spontaneously.
– Entropy - the amount of order in a system.
– Enthalpy – the energy found in the bonds in the
chemical reaction.
– Chemical reactions occur spontaneously if the
disorder in the system is increased (entropy) and
the molecules) formed have less energy then the
original molecules (enthalpy).
Entropy
www-lmmb.ncifcrf.gov/~toms/icons/s.harris-dep...
A Non Biological Forces Can
Lead to Self Assembly
• Magnetism – the power of attraction that
exists in materials such as iron.
• Ferromagnetism is defined as the state
when the relevant electron spins within a
material all point in the same direction.
– Attraction of a metal to a magnet can lead to a
stable structure.
– nanotechnologya\V_ H_ Crespi Magnetism @
Penn State Physics.htm
Magnetism
http://www.teachnet-lab.org/ps101/bglasgold/magnetism/magnetism2.jpg
Biological Materials used in Self
Assembly
• Nanotechnologists are using a variety of
biological materials to create
nanostructures.
• These include:
– Carbon based materials such as carbon
nanotubes and buckyballs
– Proteins – enzymes and antibodies
– Lipids
– DNA
Carbon based Nanostructures
• Graphite nanotubes were first discovered in
1991 by Sumio Iijima in Japan.
• The carbon atoms in the tubes are arranged
in hexagons.
• Nanotubes can act as transistors, and pairs
of nanotubes can act as logic structures.
• They have been added to golf balls, tennis
rackets and other materials to increase their
strength .
Graphite (Carbon Nanotube)
• Note the hexagonal structures,
each point in the structure is a
carbon atom.
http://www.nanotech-now.com/images/junction-large.jpg
Paper Battery of Nanotubes
• In August 2007 at RPI a paper was created
using carbon nanotubes.
– This paper can extract energy from human blood
and sweat.
– The battery can be formed into many different
shapes and it power increased by adding more
sheets of paper
– Morgan, R. Amazing Battery made of Paper
Discover January 2007 p.51
Carbon Nanotube Paper Battery
http://www.eurekalert.org/multimedia/pub/4801.php?from=99678
Buckyballs
• Buckministerfulleren C60 or buckyballs can
be created by vaporizing carbon.
– It consists of 60 atoms of carbon.
• Evidence of this carbon form was first
published in 1985 in Nature by Kroto et al.
• Their uses include:
– reinforcement, adding strength to substances.
– Some are being used for drug release in
buckysomes.
Buckministerfulleren C60 or a
Buckyball
Buckysome
The therapeutic agent attached to the
buckysome.
http://www.wipo.int/ipdl/IPDL-IMAGES/PCTIMAGES/21082003/US0304416_21082003_gz_en.x4-b.jpg
Nanowire
• A nanowire is an extremely thin wire with a
diameter on the order of a few nanometers.
– Germanium and silicon nanowires can be made.
– Function in lithographic printing and silicon
chips.
Uses of Nanowires
• In 2007, orderly arrays of
nanowires were grown on
crystals in a technique that
could lead to high density
memory chips and transparent
LEDS.
News 172:334 http://www.newstarget.com/012956.html
•Science
Another
use is a detector of
Biological Compounds of
NanoScience
• Proposed Biological Compounds include:
– Proteins
• Complex structure lets them have specific
characteristics and shape.
– Lipids
• Hydrophilic and hydrophobic interactions permit them
to assume specific shapes and to interact with the
bodies of cells.
– Nucleic Acids
• Their specific bonding permits the creation of specific
shape and the ability to change that shape under
different conditions.
Proteins Structure
• Proteins are created from amino acids
– The 20 amino acids found in nature have unique
properties.
• Some are acidic some are basic and some are neutral.
• Long strings of amino acids form the basic (primary)
structure of a protein.
General Amino Acid Structure
• Variation in the R group leads to acidic and
basic and neutral amino acids.
Marieb, E. and Hoehn, Human Anatomy and Physiology 7th ed., 2007. Pearson
Education, Inc. p. 49
Bonds form Chains of Amino
Acids
• Two amino acids join together in a peptide
bond.
Marieb, E. and Hoehn, Human Anatomy and Physiology 7th ed., 2007. Pearson
Education, Inc. p. 49
Protein folding Creates Three
Dimensional Structure
• Hydrogen bonds between the amino and
carboxyl groups creates two main forms of
secondary protein structure.
– An alpha helix and a beta pleated sheet.
Two main primary structures of
polypeptide chains.
• Two main secondary structures of proteins.
Marieb, E. and Hoehn, Human Anatomy and Physiology 7th ed., 2007.
Pearson Education, Inc. p. 51
Proteins can create Unique
Structures
• Enzymes and antibodies are unique proteins
that because of their specific structure can
only attach to other unique structures.
– This ability makes them important to
nanotechnology because they can be used to
bind and cause self assembly by joining together
two or more substances.
Structure of an Antibody
• Three dimensional antibody structure
• The antigen binding site is where other
substances bind.
Marieb, E. and Hoehn, Human Anatomy and Physiology 7th ed., 2007.
Pearson Education, Inc. p. 807
Functions of Antibodies in
Nanoscience
• Sensors for biological molecules, bacteria
and viruses.
The Y shaped structures are the antibodies.
http://chemistry.nrl.navy.mil/6170/6177/researchareas.php
Molecular Motors
• Protein molecules have been investigated
as molecular motors.
• Three of the proteins that have been studied
include:
– F1-F0 ATPase an enzyme
– Kinesin and dynein
– Myosin
F1-F0 ATPase
• Found in membranes of mitochondria, and
chloroplasts in all living organisms.
• The enzyme consists of 3 major units the F0
unit, the central stalk that connects the F0
motor to the F1 motor and the F1 motor .
• The motor rotates one way during ATP
production and the opposite way during
ATP hydrolysis or break down.
• To view a video on the function and
structure of the ATPAse go to:
http://multimedia.mcb.harvard.edu/media.ht
ml
Converting the ATPase to a
NanoMotor
• Monetemagno’ s
group modified the
form of the ATPase.
– They attached it to a
metal surface by
modifying its protein
structure.
– They added a metal
rotor so they could
observe the rotation.
ATPase Motor
Animation of ATPase Motor
• Molecular Model T Scientific American
• http://www.sciam.com/article.cfm?articleID=
000988D5-647B-1C75-9B81809EC588EF21
Facts About the ATPase Motor
• Efficiency of 80 -100%.
• Can be turned on and off by adding a zinc
binding site and removing zinc from the
system.
• Relatively short life span.
• Could be used to generate electrical current.
• Chip based drug delivery pumps.
• Step in the right direction but probably not
the motor of the future.
Kinesin Linear Motor
• Moves in discreet steps along microtubules
in a specific direction depending on the
polarity of the microtubules.
• Can be used as a delivery device for the
separation, sorting and assembly of
materials.
• Need to be able to guide the transportation
along specific pathways.
– Currently using enclosed fluidic channels.
Animation of the Motion of
Kinesin
animation website http://www.flileibniz.de/~kboehm/Kinesin.html
Directed Movement of Kinesin
• Using an electrical field researches were
able to direct the movement of kinesin
proteins to a given location.
Source: Dominiczak, P. Nanotoday 1 (3)
Microtubules Steered in the Right
Direction 2006 p 10
Dynein
• Walks with a step size about thrice the size
of kinesin.
• Dynein can shorten its stepsize.
• When a heavier load is added, however, a
dynein motor changes gears This gives
dynein more power to pull the heavier cargo.
• The dynein dynactin motor to move in both
directions along the microtubule.
Animation and Structure of the
Protein Dynein
http://www.fbs.leeds.ac.uk/research/contractility/dynein/model-
page.htm
Uses of Dynein in
Nanotechnology
• Can be used to ferry cargo of different
weights.
• Can move cargo in 2 directions unlike
kinesin.
Myosin V Motor
• Protein that walks over actin filaments.
Myosin Motor
• Myosin V moves along actin
chains in a linear fashion.
• In a hand over hand stepping
mechanism one head domain
dissociates from an actin
filament only when the other
head domain binds to the next
subunit .
• Can be used to ferry materials
in the cell.
Motor Proteins
• Motor proteins have a variety of motions
from linear to rotary.
• Different movements can be used to
manufacture machines with different
characteristics.
Lipids
• Neutral fats or triglycerides are structures
that can be used to create nanoscale
particles.
• Structure of a lipid
– Made up of fatty acids.
• Long chains of hydrocarbons with one end terminated
by a carboxyl group (COOH).
– Three fatty acids can be combined with a
glycerol molecule to make a triglyceride.
Properties of Lipids
• The long chains of fatty acids make the lipid
hydrophobic, it does not readily dissolve in
water .
• If one of the fatty acids is replaced by a
phosphate group the resulting molecule a
phospholipid has a hydrophobic region
(fatty acid) and a hydrophilic region
(phosphate group).
• This orients the molecule in water.
Phospholipid
Cellare
Membrane
Phosphate
groups In
(balls
oriented toward the
water parts inside and outside the cell).
www.biologycorner.com/resources
/lipidbilayer.gif
Uses of Lipids in Nanoscience
• Liposomes – balls of phospholipids act as
vehicles for the controlled delivery of
substances, such as drugs, genes,
pesticides, cosmetics, and foodstuffs.
– Fat soluble materials can be sequestered in the
bilayer .
– Water soluble materials can be sequestered in
the interior.
– Antibodies embedded in the phospholipid
membrane direct the site of fusion of the
liposome to the correct cells.
Liposomes
http://www.uic.edu/classes/bios/bios100/lectf03am/liposome.jpg
Liposome Gel
• All of the active principles of the gel are
extracted from Ginkgo Biloba. It is able to
penetrate into the deeper layers of the skin
and helps to delay the visible signs of aging.
http://www.make-upusa.com/skincare/liposomegel.htm
Nucleic acids in Nanoscience
• The precise structure of the nucleic acid
DNA makes it a good prospect for self
assembly in nanotechnology.
– The ability to precisely order the molecules in the
DNA molecule makes it possible to create
specific structures.
– The machines to precisely create DNA and
manipulate it already exist in the biotechnology
field.
– The ability of the DNA molecule to change its
gross structure under chemical conditions
makes it applicable for switches.
Structure of DNA
• The building blocks of the nucleic acids are
nucleotides consisting of a pentose sugar
linked to a phosphate group and organic
base (thymine, guanine, cytosine, and
adenine in DNA or guanine, cytosine,
adenine and uracil in RNA).
• The phosphate groups link the sugars of the
nucleotides together forming long stands of
DNA or RNA.
Nucleotide Structure
Variations in the base create the 5
types of nucleotides.
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/nucleotide.gif
http://www.apsu.edu/robertsonr/chem1020/Image12.gif
Structure of DNA
• Two strands of DNA can bond together
using hydrogen bonds between base pairs.
– In DNA thymine always pairs with adenine and
cytosine always base pairs with guanine via
hydrogen bonds.
– The most common form of DNA is the double
helix.
– It is called the B or right handed DNA structure.
Structure of a Triglyceride
• Glycerol with three fatty acid molecules.
Marieb, E. and Hoehn, Human Anatomy and Physiology 7th ed., 2007. Pearson
Education, Inc. p. 47
Base Pairs of Nucleotides and
Double Helix of DNA
http://info.cancerresearchuk.org/images/gpimages/ys_DNA_4and5
Other forms of DNA
• DNA can consist of left handed forms.
– Combinations of left and right handed forms.
• Branched forms.
• Arrays of branched forms.
Structural Forms of DNA
• Right (B) and left (Z) handed forms of DNA.
Normal
DNA
A DNA Switch
• Combining the B and Z forms can create a
molecular switch
– Under the correct chemical conditions the DNA
can switch its form and orientation acting like a
chemical switch.
Structural Forms of DNA
Example of a 4 stranded form of DNA.
Seeman, N. 1999 Tibtech 17, 437-442.
http://www.halcyon.com/nanojbl/NanoConProc/nanocon5.
html#anchor344973
Branched DNA Molecules Uses
• According to Seeman the branched DNA
molecules can be used to:
– Create cages to orient other molecules (bricks
plus mortar).
• If combined with metal atoms it can act as a molecular
wire.
– To orient the components of molecular
electronics with precision (smart glue).
LaBean T. H. and Li, H. 2007 Nanotoday (2 (2), 26-35
Seeman, N. 1999 Tibtech 17, 437-442.
Expected Used For DNA
Structures
• DNA computing
• Patterning of nanomaterials, for sensors and
bionanomachines.
– Can be used to orient carbon nanotubes which is
currently difficult.
• The nano sorter: DuPont uses DNA to sort carbon
nanotubes by conductivity. (Nanotech).
– Can also be attached to buckyballs.
– Can be attached to proteins a such as antibodies
and enzymes
– It is being used to create chips to probe for RNA.
Talbot, D. 2003 Technology Review
http://www.smh.com.au/news/technology/researchers-make-nanoscale-dnaresearch-tool/2008/01/11/1199988556980.html
Quantum Dots
• A quantum dot is a crystal a few nanometers
in diameter.
– They can be made from a variety of metals
including gold.
– They will shine a different color depending on
their concentration and size.
– Dots can be bound to a variety of materials and
incorporated in films.
Quantum Dot Function
• Quantum dots function by moving electrons
from their valance band to the conduction
band.
– When the electrons travel back to their valance
band they emit a characteristic wavelength of
light.
– Decreasing the size of the quantum dot shifts the
size of the bandwidth between the valance band
and the conduction band.
• This shifts the light emitted further into the blue or
higher frequency range.
• Animation of how quantum dots work:
Uses Quantum Dots
• Next generation LEDs.
• Night vision pigments and inks.
– Fluorescent inks can be added to documents to
prevent counterfeiting.
http://www.evidenttech.com/applications
Uses Quantum Dots
• Bioreagents to take the place of stains and
dyes can be used to locate specific proteins,
antibodies and DNA and RNA.
• As components of solar cells.
Advantages of Self Assembled
Nanotechnology
• Ability to work at a much smaller scale than
ever before:
– In medicine
– In electronics
– In research
• Ability to work with new materials from
biological organisms.
• Energy and materials savings.
Cantilevered Biosensor
• Adding biological agents from antibodies to
DNA and RNA makes it possible to detect
very small amount of materials.
http://www.nccr-nano.org/nccr/research/modules/module_01
Mobile Carbon Structures
• A molecular wheel the
turning can be seen in
the rotation of the blue
dots in the top two
frames
• The molecule is made
from multiples of a
hydrocarbon called
triptycence.
http://www.nano.org.uk/Wheel.htm
Challenges for Self Assembled
Nanotechnology
• Mass production with a high degree of
fidelity
• Finding a constant and consistent energy
source at the nanoscale.
• Understanding how the biological world will
treat materials its has only before seen
created by biological means.