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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 – – – – – 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.