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Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
Viii. molecular electronics and nanoscience
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Viii. molecular electronics and nanoscience

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  • 1. VIII. Molecular Electronics and Nanoscience
  • 2. Molecular Electronics and Nanoscience Why Molecular Electronics Moore’s Law Devices: Top-down and Bottom-Up Fabrication Single Molecule Systems and Materials Many-Molecule Systems and Thin Films DNA Computing
  • 3. •Role of contacts
  • 4. •Molecular device ContactContact Molecule  what type of behaviour we can expect for a •complete system?
  • 5. •Ballistic conductor •Contacts of finite transparency •P1 •P2  The model: •– Electrons tunnel with some probability (contact •transparency) into the channel •– Transport is coherent •– Contacts are ”reflectionless”  The question:  What is the resistance of the channel? Where the heat is •dissipated?
  • 6. •Ballistic conductor model  Electrons moving from left to right have •potential µ1, from right to left µ2.
  • 7. Why Molecular Electronics
  • 8. Moore’s Law
  • 9. Silicon and Moore’s Law • Heat dissipation. – At present, a state-of-the-art 500 MHz microprocessor with 10 million transistors emits almost 100 watts--more heat than a stove- top cooking surface. • Leakage from one device to another. – The band structure in silicon provides a wide range of allowable electron energies. Some electrons can gain sufficient energy to hop from one device to another, especially when they are closely packed. • Capacitive coupling between components. • Fabrication methods (Photolithography). – Device size is limited by diffraction to about one half the wavelength of the light used in the lithographic process. • ‘Silicon Wall.’ – At 50 nm and smaller it is not possible to dope silicon uniformly. (This is the end of the line for bulk behavior.)
  • 10. Silicon and Moore’s Law • Moore’s second law. – Continued exponential decrease in silicon device size is achieved by exponential increase in financial investment. $200 billion for a fabrication facility by 2015. • Transistor densities achievable under the present and foreseeable silicon format are not sufficient to allow microprocessors to do the things imagined for them.
  • 11. Moore’s “Second Law" Plant cost Mask cost generation X1000$
  • 12. Why Molecular Electronics? • If current trend continues, it will reach molecular scale in two decades. • There are many molecules with interesting electronic properties. Semiconductor devices shrink to the nano-scale Year 1950 1960 1970 1980 1990 2000 2010 1 cm 1 m 100 nm 1-5nm TransistorSize
  • 13. Devices: Top-down and Bottom-up Fabrication
  • 14. Electronics Development Strategies • Top-Down. – Continued reduction in size of bulk semiconductor devices. • Bottom-up (Molecular Scale Electronics). – Design of molecules with specific electronic function. – Design of molecules for self assembly into supramolecular structures with specific electronic function. – Connecting molecules to the macroscopic world.
  • 15. Bottom-Up (Why Molecules?) • Molecules are small. – With transistor size at 180 nm on a side, molecules are some 30,000 times smaller. • Electrons are confined in molecules. – Whereas electrons moving in silicon have many possible energies that will facilitate jumping from device to device, electron energies in molecules and atoms are quantized - there is a discrete number of allowable energies. • Molecules have extended pi systems. – Provides thermodynamically favorable electron conduit - molecules act as wires. • Molecules are flexible. – pi conjugation and therefore conduction can be switched on and off by changing molecular conformation providing potential control over electron flow. • Molecules are identical. – Can be fabricated defect-free in enormous numbers. • Some molecules can self-assemble. – Can create large arrays of identical devices.
  • 16. • Top-down Synthesis 1. Lithography
  • 17. Developing Positive Negative Etching and Stripping Polymer Resist Thin Film Substrate Resist Resist Exposing Radiation Figure 1.1. Schematic of positive and negative resists.
  • 18. Figure 1.6. Schematic of a focused ion beam system.
  • 19. 1m 400nm 300nm 200nm 160 nm 120nm 100nm 80nm 60nm 100 nm Carbon Nanotubes/Nanocones with Various Catalyst Patterning Dimensions by E-beam Lithography
  • 20. Molecular Self-Assembly • Self-Assembly on Metals – (e.g., organo-sulfur compounds on gold) • Assembly Langmuir-Blodgett Films – Requires amphiphilic groups for assembly • Carbon Nanotubes – Controlling structure
  • 21. Figure 2.1. The process of forming a self-assembled monolayer. A substrate is immersed into a dilute solution of a surface-active material that adsorbs onto the surface and organizes via a self- assembly process. The result is a highly ordered and well-packed molecular monolayer. (Adapted from Ref. 9 by permission of American Chemical Society.)
  • 22. Cyclic Peptide Nanotubes as Scaffolds for Conducting Devices Hydrogen-bonding interactions promote stacking of cyclic peptides Pi-systems stack face-to-face to allow conduction along the length of the tube Cooper and McGimpsey - to be submitted CYCLIC BIOSYSTEMS
  • 23. Spontaneous self-directed chemical growth allowing parallel fabrication of identical complex functional structures.
  • 24. Self-assembly
  • 25. .Characterization and Handling of Ultra-small particles or Assemblies –a. Optical Tweezers –b. Electromagnetic tweezers –c. In nanotemplates –d. Structural Analysis by TEM, SEM, X-ray, etc.
  • 26. Ballistic Nanotube MOS Transistors (Chen,Hastings) W d D L SWNTSWNT SiO2 Source Al-Gate Ti HfO2 Drain L L~20L~20 nmnm Placement of Nanotubes by E-Field (The first-demo) Nanotube Field-Effect Transistor(FET) E-Beam Lithography
  • 27. • Measurements
  • 28. Figure 3.1. Schematic showing all major components of an STM. In this example, feedback is used to move the sensor vertically to maintain a constant signal. Vertical displacement of the sensor is taken as topographical data Coarse approach mechanism S c a n n e r Sensor Sample Reference - Signal feedback data Figure 3.1. Schematic showing all major components of an SPM. In this example, feedback is used to move the sensor vertically to maintain a constant signal. Vertical displacement of the sensor is taken as topographical data.
  • 29. •1980’s Single Molecule Detection. How to image at the molecular level. How to manipulate at the molecular level. • Scanning Probe Microsopy. STM (IBM Switzerland, 1984) AFM Molecules as Electronic Devices: Historical Perspective
  • 30. Major equipment • Focused Ion Beam System (FIB) (scheduled for installation in mid 2007) • Atomic Layer Deposition System (ALD) • Rapid Thermal Processing System (RTP) • Plasma Enhanced Chemical Vapor Deposition System (PECVD) • Standard Resolution Electron Beam Lithography (EBL) • Atomic Force Microscope for Nanopatterning, and Manipulation (AFM) • Atomic Force Microscope for Atomic Resolution Imaging (AFM) • Quartz Crystal Microbalance (QCM) • 4-furnace bank of 3-zone oxidation, dopant diffusion, and annealing furnaces • Class 100 Clean Room • Spin-Coating Station • Photolithography System • Surface Profiler • Chemical Treatment Station (cleaning, etching, and functionalization) • Ion Milling System • Plasma Cleaning/Oxidation System • Gas Cabinet Bank • Experimental Materials Thermal Evaporator • Standard Materials Thermal Evaporator • Electron-Beam Evaporator • Multi-target Sputtering System • Probe Station and Device Characterization System • Four-Point Resistance Measurement System • Ellipsometer • Optical Microscopes • Dicing Saw • Equipment Cooling Systems (3) • Inductive Coupled Plasma (ICP) Etching System (scheduled for installation in Feb. 2006) • Experimental materials sputtering system (scheduled for installation in mid 2006) • Ultra-High Resolution EBL and SEM System Clean Room Photolithography Rapid Thermal Processing Quartz MicroBalance Plasma Enhanced Chemical Vapor Deposition Reactive Ion Etching Atomic Layer Deposition
  • 31. IV. Nanotemplates • G. Inorganic • H. Organic
  • 32. Fig.2 (a) Nanostructure of anodically formed Al2O3 template. (b) its cross-section, (c) catalyst deposited at the bottom of the pores, (e) vertically aligned nanotubes, and (f) TEM image of a nanotube.
  • 33. (Chen, Singh, DeLong, Saito, Yang, Bhattacharyya, and Sumanasekeras) Nano-scale Material Research (a) (b) (c) Catalyst 200nm 200 nm Vertically aligned MWNTs embedded in AAO insulator (d) Si substrate SiO2 SiO2 Carbon nanotubes AlSiO2 Hexagonal Cells Nano-template Horizontally aligned The first vertically aligned nanotubes on silicon substrates using templates
  • 34. • Fig. 3 Schematic representing the helix-coil transitions within the pore of a Poly-L-Glutamic Acid functionalized membrane (a) random-coil formation at PH > 5.5 , (b) helix formation at low pH ( <4 ).
  • 35. Single Molecule Devices
  • 36. Using a Single Molecule
  • 37. Cornell group
  • 38. What Might Single Molecule Devices Do?
  • 39. Single-Electron Memory Cell Fe+3 Fe+2 Heme group e- e- Au
  • 40. Molecular Abacus The “bead” can be reversibly switched between two positions by pH. Ashton et al. JACS, 120, 11932(1998)
  • 41. Some Fancy Molecules Rotaxane Catenane Pretzelane Handcuffcatenane
  • 42. Synthesis of a Rotaxane Molecule Amabilino and Stoddart, Chemical Reviews 95, 2725 (1995).
  • 43. Angew. Chem., Int. Ed. 2000, 39, 3284-3287. Molecular Motor Molecular Oscillator
  • 44. Molecular Sensor K+ K+ Molecular Recognition: A capability that Si lacks K + Ag + K+ K+ K + Ag + Crown ether • A small difference in the diameters of the K+ and Ag+ can cause a huge difference in the binding capacity
  • 45. Heath and Ratner, Physics Today, May 2003, p. 43 Many Ideas for Single Molecule Devices
  • 46. Nano-switch
  • 47. Single Molecule Systems and Materials
  • 48. Molecular conduction molecule
  • 49. Molecules as Electronic Devices: Historical Perspective •1970’s: Single Molecule Devices? • In the 1970’s organic synthetic techniques start to grow up prompting the idea that device function can be combined into a single molecule. • Aviram and Ratner suggest a molecular scale rectifier. (Chem. Phys. Lett. 1974) • But, no consideration as to how this molecule would be incorporated into a circuit or device.
  • 50. Molecular Rectifiers Arieh Aviram and Mark A. Ratner IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA Department of Chemistry, New York New York University, New York 10003, USA Received 10 June 1974 Abstract The construction of a very simple electronic device, a rectifier, based on the use of a single organic molecule is discussed. The molecular rectifier consists of a donor pi system and an acceptor pi system, separated by a sigma- bonded (methylene) tunnelling bridge. The response of such a molecule to an applied field is calculated, and rectifier properties indeed appear.
  • 51. Acceptor Donor
  • 52. Single Molecule Systems and Materials
  • 53. Elastic Inelastic V h/e V h/e V h/e V IdI/dVd 2 I/dV 2 h/e Finding a true molecular signature: Inelastic Electron Tunnelling Spectroscopy (IETS)
  • 54. Towards Single Molecule Electronics Can a single molecule behave like a diode, transistor (switch), memory ? If that’s possible, how long will the molecule last ? First, let’s look at many molecules acting in parallel. Nitzan and Ratner, Science 300, 1384 (2003); Heath and Ratner, Physics Today, May 2003, p. 43
  • 55. Single-Molecule Conductivity L ELECTRODE R ELECTRODEMOLECULE
  • 56. L ELECTRODE R ELECTRODEMOLECULE Fermi energy Molecular Orbitals
  • 57. eV V L ELECTRODE R ELECTRODEMOLECULE I Molecular Orbitals
  • 58. Molecular Electronics: Measuring single molecule conduction Kushmerick et al. PRL 89 (2002) 086802 Cross-wire Wang et al. PRB 68 (2003) 035416 Nanopore STM Break Junction B. Xu & N. J. Tao Science (2003) 301, 1221 Electromigration H. S. J. van der Zant et al. Faraday Discuss. (2006) 131, 347 Nanocluster Dadosh et al. Nature 436 (2005) 677 Scanning Probe Cui et al. Science 294 (2001) 571 Reichert et al. PRL 88 176804 Mechanical Break Junction
  • 59. Mechanically-Controlled Break Junction Resistance is a few megohms. (Schottky Barrier) Molecular Junction
  • 60. A schematic representation of Reed and Tour’s molecular junction containing a benzene-1,4-dithiolate SAM that bridges two proximal gold electrodes. Break Junctions At the beginning of single molecule electronics, break junctions were very popular: Just crack a thin Au wire open in a vice and adjust the width of the crack with piezos (as in STM). Then pour a solution of molecules over it. Alternatively, one can burn out the thinnest spot of a thin Au wire by running a high current density through it (using the effect of electromigration). These days, many try to achieve a well-defined geometry using a STM or AFM, with a well-defined atom at the end of the tip and another well- defined atom at the surface as con- tacts to a single molecule.
  • 61. Nanotube conductivity is quantized. Nanotubes found to conduct current ballistically and do not dissipate heat. Nanotubes are typically 15 nanometers wide and 4 micrometers long. Carbon Nanotubes Gentle contact needed
  • 62. Using a Few Molecules Observe tunneling through 1, 2, 3, 4, 5 alkanethiol molecules Cui et al., Science 294, 571 (2001)
  • 63. “The resistance of a single octanedithiol molecule was 900 50 megaohms, based on measurements on more than 1000 single molecules. In contrast, nonbonded contacts to octanethiol monolayers were at least four orders of magnitude more resistive, less reproducible, and had a different voltage dependence, demonstrating that the measurement of intrinsic molecular properties requires chemically bonded contacts”. Cui et al (Lindsay), Science 294, 571 (2001) 
  • 64. Dynamics of current voltage switching response of single bipyridyl-dinitro oligophenylene ethynylene dithiol (BPDN-DT) molecules between gold contacts. In A and B the voltage is changed relatively slowly and bistability give rise to telegraphic switching noise. When voltage changes more rapidly (C) bistability is manifested by hysteretic behavior Lortscher et al (Riel), Small, 2, 973 (2006)
  • 65. Chem. Commun., 2006, 3597 - 3599, DOI: 10.1039/b609119a Uni- and bi-directional light-induced switching of diarylethenes on gold nanoparticles Tibor Kudernac, Sense Jan van der Molen, Bart J. van Wees and Ben L. Feringa “In conclusion, photochromic behavior of diarylethenes directly linked to gold nanoparticles via an aromatic spacer has been investigated. Depending on the spacer, uni- (3) or bidirectionality (1,2) has been observed.” Switching with light
  • 66. Current–voltage data (open circles) for (a) open molecules 1o and (b) closed molecules 1c Nanotechnology 16 (2005) 695–702 Switching of a photochromic molecule on gold electrodes: single-molecule measurements J. He, F. Chen, P. Liddell, J. Andr´easson, S D Straight, D. Gust, T. A. Moore, A. L. Moore, J. Li, O. F Sankey and S. M. Lindsay
  • 67. Conductance through a C60 Molecule Distance dependence tells whether it is tunneling (exponential decay) or quantum conductance through a single or multiple orbitals (G0). Kröger et al., J. Phys. Condend. Matter 20, 223001 (2008)
  • 68. (a) Structures of the long and short linked cobalt coordinated terpyridine thiols used as gate molecules. (b) A topographic AFM image of the gold electrodes with a gap. (c) A schematic representation of the assembled single atom transistor. A Molecular Transistor
  • 69. Many-molecule Systems and Thin Films
  • 70. mNDR = molecular Negative Differential Resistance Measured using a conducting AFM tip Negative Differential Resistance One electron reduction provides a charge carrier. A second reduction blocks conduction. Therefore, conduction occurs only between the two reduction potentials.
  • 71. Voltage-Driven Conductivity Switch Applied perpendicular field favors zwitterionic structure which is planar Better pi overlap, better conductivity.
  • 72. Dynamic Random Access Memory Voltage pulse yields high conductivity State - data bit stored Bit is read as high in low voltage region
  • 73. Device is fabricated by sandwiching a layer of catenane between an polycrystalline layer of n-doped silicon electrode and a metal electrode. The switch is opened at +2 V, closed at -2 V and read at 0.1 V. Voltage-Driven Conductivity Switch
  • 74. High/Low Conductivity Switching Devices Respond to I/V Changes Voltage-Driven Conductivity Switch
  • 75. n-type Voltage-Driven Conductivity Switch
  • 76. Other Molecular Switches Chen et al., Science 286, 1550 (1999) Large On-Off Ratios
  • 77. Data Storage via the Oxidation State of a Molecule Electrochemistry
  • 78. 40 nm line width, 40 Gbit/inch2 HP Molecular Memory
  • 79. Output: Stored Data Input: Address Molecular Memory MRAM (Magnetic Random Access Memory) Crossbar Memory Architecture DRAM 1 0
  • 80. HP Molecular Memory The blue ring can shuttle back and forth along the axis of the rotaxane molecule, between the green and red groups. Rotaxane molecules switch between high and low resis- tance by receiving a voltage pulse.
  • 81. Collier et al., Science 289, 1172 (2000). (Many Molecules) HP Molecular Memory Change the resistance between low and high by voltage pulses. Is the resistance change really due to the rotaxane ring shuttling back and forth? Other molecules exhibit the same kind of switching. One possible model is the creation and dissolution of metal filaments which create a short between the top and bottom electrodes. (Some- thing like that happens in batteries).
  • 82. Robert F. Service, Science 302, 556 (2003).
  • 83. Quantum Dot Molecular Switch Self-Organizing Memory + Data Processor Heath et al., Science 280, 1716 (1998) People have been thinking about how to combine memory with logic (= a microprocessor) in a molecular device. Self-assembly is the preferred method. It generates errors, though. They need to be absorbed by a fault-tolerant architecture (e.g. in the HP Teramac)
  • 84. DNA Computing
  • 85. DNA Computing I believe things like DNA computing will eventually lead the way to a “molecular revolution,” which ultimately will have a very dramatic effect on the world. L. Adleman
  • 86. What is DNA? • All organisms on this planet are made of the same type of genetic blueprint. • Within the cells of any organism is a substance called DNA which is a double-stranded helix of nucleotides. • DNA carries the genetic information of a cell. • This information is the code used within cells to form proteins and is the building block upon which life is formed. • Strands of DNA are long polymers of millions of linked nucleotides.
  • 87. Graphical Representation of inherent bonding properties of DNA
  • 88. Double Helix shape of DNA The two strands of a DNA molecule are anti parallel where each strand runs in an opposite direction. GC base pair and AT base pair
  • 89. Adleman’s Experiment • Hamilton Path Problem (also known as the travelling salesperson problem) Perth Darwin Brisbane Sydney Melbourne Alice Spring Is there any Hamiltonian path from Darwin to Alice Spring?
  • 90. Adleman’s Experiment (Cont’d) • Solution by inspection is: Darwin  Brisbane  Sydney  Melbourne  Perth  Alice Spring • BUT, there is no deterministic solution to this problem, i.e. we must check all possible combinations. Perth Darwin Brisbane Sydney Melbourne Alice Spring
  • 91. Adleman’s Experiment (Cont’d) 1. Encode each city with complementary base - vertex molecules Sydney - TTAAGG Perth - AAAGGG Melbourne - GATACT Brisbane - CGGTGC Alice Spring – CGTCCA Darwin - CCGATG
  • 92. Adleman’s Experiment (Cont’d) 2. Encode all possible paths using the complementary base – edge molecules Sydney  Melbourne – AGGGAT Melbourne  Sydney – ACTTTA Melbourne  Perth – ACTGGG etc…
  • 93. Adleman’s Experiment (Cont’d) 3. Merge vertex molecules and edge molecules. All complementary base will adhere to each other to form a long chains of DNA molecules Solution with vertex DNA molecules Solution with edge DNA molecules Merge & Anneal Long chains of DNA molecules (All possible paths exist in the graph)
  • 94. Adleman’s Experiment (Cont’d) • The solution is a double helix molecule: CCGATG – CGGTGC – TTAAGG – GATACT – AAAGGG – CGTCCA TACGCC – ACGAAT – TCCCTA – TGATTT – CCCGCA Darwin Brisbane Sydney Melbourne Perth Alice Spring Darwin Brisbane Brisbane Sydney Sydney Melbourne Melbourne Perth Perth Alice Spring
  • 95. Basics And Origin of DNA Computing • DNA computing is utilizing the property of DNA for massively parallel computation. • With an appropriate setup and enough DNA, one can potentially solve huge problems by parallel search. • Utilizing DNA for this type of computation can be much faster than utilizing a conventional computer • Leonard Adleman proposed that the makeup of DNA and its multitude of possible combining nucleotides could have application in computational research techniques.
  • 96. Problems with Adleman’s Experiment • The researchers performed Adleman’s Experiment and the results obtained were inconclusive. • The researchers state that “At this time we have carried out every step of Adleman’s Experiment but have not gotten an unambiguous final result.” • The problem is because of the underlying assumption that the biological operations are error-free.
  • 97. Problem Instance • There are 2 problems with extraction: – The removal of strands containing the sequence in not 100% efficient. – May at times inadvertently remove strands that do not contain the specified sequence. • Adleman’s did not encounter problems with extraction because only a few operations were required. • However, for a large problem instance , the number of extractions required may run into hundreds or even thousands.
  • 98. • Time- Adleman talked of a week of work in lab, but tuning such an experiment could take one month work • Contradictory results- We do not know a lot of experiments like Adleman’s, nor Adleman’s trials of repeating the experiment. Problems Contd.
  • 99. Advantages of a DNA Computer • Parallel Computing- DNA computers are massively parallel. • Incredibly light weight- With only 1 LB of DNA you have more computing power than all the computers ever made. • Low power- The only power needed is to keep DNA from denaturing. • Solves Complex Problems quickly- A DNA computer can solve hardest of problems in a matter of weeks
  • 100. Disadvantages of DNA Computer • High cost is time. • Occasionally slower-Simple problems are solved much faster on electronic computers. • It can take longer to sort out the answer to a problem than it took to solve the problem. • Reliability- There is sometime errors in the pairing of DNA strands
  • 101. DNA Chip Source: Stanford Medicine Magazine, Vol 19, 3 Nov 2002 http://mednews.stanford.edu/stanmed/2002fall/translational-dna.html
  • 102. Chemical IC Source: Tokyo Techno Forum 21, 21 June 2001 http://www.techno-forum21.jp/study/st010627.htm
  • 103. The Smallest Computer • The smallest programmable DNA computer was developed at Weizmann Institute in Israel by Prof. Ehud Shapiro last year • It uses enzymes as a program that processes on on the input data (DNA molecules). • http://www.weizmann.ac.il/mathusers/lbn/new_pag es/Research_Biological.html
  • 104. References • “Molecular Computation of Solutions to Combinatorial Problems”, L.M. Adleman, Science Vol.266 pp1021-1024, 11 Nov 1994 • “Computing With Cells and Atoms – an introduction to quantum, DNA and membrane computing”, C.S. Calude and G. Paun, Taylor & Francis, 2001 • “The Cutting Edge Biomedical Technologies in the 21st Century”, Newton, 1999 • “Human Physiology: From Cells to Systems 4th Ed.”, L. Sherwood, Brooks/Cole, 2001

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