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Nanowires Course outline 1 Introduction 2 Theoretical background Biochemistry/molecular biology 3 Theoretical background computer science 4 History of the field 5 Splicing systems 6 P systems 7 Hairpins 8 Detection techniques 9 Micro technology introduction 10 Microchips and fluidics 11 Self assembly 12 Regulatory networks 13 Molecular motors 14 DNA nanowires 15 Protein computers 16 DNA computing - summery 17 Presentation of essay and discussion Introduction Molecular electronics www.scientificamerican.com Molecular electronics Biological Systems Molecular Electronics Devices Use molecular electronics to study biological systems. Molecular electronics Incentives Molecules are nano-scale Self assembly is achievable Very low-power operation Highly uniform devices Quantum Effect Devices Building quantum wells using molecules Electromechanical Devices Using mechanical switching of atoms or molecules Electrochemical Devices Chemical interactions to change shape or orientation Photoactive Devices Light frequency changes shape and orientation. Molecular electronics Definition is a field emerging around the premise that it is possible to build individual molecules that can perform functions identical to those of the key components of today’s microcircuits. Why molecular electronics? Chip-fabrication specialists will find it economically infeasible to continue scaling down microelectronics. stray signals on the chip the need to dissipate the heat from so many closely packed devices the difficulty of creating the devices in the first place Molecular electronics, any better? Modern technologies can only go so far. Solution (new development) DNA - It is promising to achieve super-high density memory and high sensitive detection technology. Cell Computing Silicon transistors at 120 nm in length will still be 60,000 times larger in area than molecular electronic devices. Recent research Recent studies have shown that individual molecules can conduct and switch electric current and store information. July of 1999 – HP and the University of California at Los Angeles build an electronic switch consisting of a layer of several million organic substance molecules of an called rotaxane. Linking a number of switches version of an AND gate is produced. a Recent research June 2002 - Fuji Xerox biotechnology made a prototype transistor of DNA from salmon sperm. Researchers successfully passed an electric current through the DNAtransistor. This demonstrates that behaves in a similar semiconductor. Super smaller chip in 10 years. the chain fashion to Recent research Atomic force microscope image of semi-conductive DNA compound http://www.fujixerox.co.jp/research/eng/category/inbt/m_electronics/index.html Self assembly Molecular self-assembly the autonomous organization of components into patterns or structures without human intervention (Whitesides 2002) Current Problem: Forming electrical interconnects between molecules Self assembly www.scientificamerican.com Molecular electronics Thiol Acetylene linkage Benzene ring Molecular electronics Mechanical synthesis Molecules aligned using a scanning tunneling microscope (STM) Fabrication done molecule by molecule using STM Chemical synthesis Molecules aligned in interactions Self assembly Parallel fabrication place by chemical an atomic relay A very short Electronics course Transistors A device composed of semiconductor material that amplifies a signal or opens or closes a circuit. Invented in 1947 at Bell Labs, transistors have become the key ingredient of all digital circuits, including computers. Today's microprocessors contains tens of millions of microscopic transistors. Transistors Transistors consist of three terminals; the source, the gate, and the drain. Transistors In the n-type transistor, both the source and the drain are negatively-charged and sit on a positively-charged well of psilicon. Transistors When positive voltage is applied to the gate, electrons in the p-silicon are attracted to the area under the gate forming an electron channel between the source and the drain. Transistors When positive voltage is applied to the drain, the electrons are pulled from the source to the drain. In this state the transistor is on. Transistors If the voltage at the gate is removed, electrons aren't attracted to the area between the source and drain. The pathway is broken and the transistor is turned off. DNA wires DNA Well known from biology Forms predictable structure Controllable self assembly through base pair sequences May be selectively processed using restriction enzymes http://www.chemicalgraphics.com/ DNA in microelectronics As the major component in a Single Electron Tunneling (SET) Transistor As tags to connect up nano-circuitry including wires and nanoparticles (taking advantage of DNA selectivity) As basis for computation) a Qubit (for quantum DNA SET transistor DNA Single electron transistor Main strand Gate strand Equivalent Electrical Circuit E. Ben-Jacob , Phys. Lett. A 263, 199 (1999). Main strand Assumptions Chemical bonds(in DNA) can act as tunnel junctions in the coulomb blockade regime, could emit electricity, given a proper coating. Has the ability to coat a DNA strand with metal in nanometer scale. Operation Schematic image with 2 grains in DNA connected by P-bond. Dark circle->carbon atoms, white circles>oxygen atoms. DNA pairs P-bond -> tunneling junction. H-bonds -> capacitor. The grain itself -> inductive properties. DNA pairs P bond: Has 2 bonds, 1 bond. The electron can be shared with 2 oxygen, resembles an electron in well, put it on the lowest level. When electron enters, it meet the barrier set by energy gap. But the gap is narrow and electron can walk trough. small so the DNA pairs H-bonds: Can be the capacitor. The proton in the h-bond can screen a net charge density on either side, by movement. Thus the net charge could be in the side of the h-bond. The grains: Can be the inductive properties. Due to the hopping of additional electrons. But can be ignored (L & Lo is small, consistent to the usual SET) DNA pairs Consist of 2 strands (1 main, 1 gate) Connect the end base of the gate strand with a complimentary strand. Both strands should be metal-coated, except (a) the grain in the main strand, which connect to the gate strand, the connective h-bond. 2 adjacent P-bonds, (b) Connect the main strand with voltage source (V) the DNA pairs The end of the gate strand with another voltage source (Vg) that acts as gate source. Functionalisation of nanoparticles DNA may be attached to surface area of nanoparticles to construct desired assemblies. May provide insight to possible solution to connecting transistors Functionalisation of nanoparticles Mirkin et al.: Nature, 1996, 382, 607 Functionalisation of nanoparticles Mirkin et al.: Nature, 1996, 382, 607 Functionalisation of nanoparticles 8 nm gold particles attached to a 31 nm gold particle with DNA http://www.chem.nwu.edu/~mkngrp/dnasubgr.html DNA conductance Double helix – a backbone and base pairs Building blocks A, T, C & G Example: 10 base pairs per turn, distance of 3.4 Angstroms between base pairs. Arbitrary sequences possible A challenge for nanotechnology is controlled / are the base pairs: reproducible growth. DNA is an example with some success. However, there are many copies in a solution! 2D and 3D structures with DNA base pairs as a building block have been demonstrated Lithography? Not yet. DNA base-pairs DNA conductance Conductivity in DNA has been controversial Electron transfer experiments (biochemistry) / possible link to cancer Transport experiments (physics) DNA conductance Metallic, No gap Current Current ~ 1nA ~ 10nA Semiconducting / Insulating Voltage (V) Porath et. al, Nature (2000) Voltage 20mV Fink et. al, Science (1999) Counter-ions Is conduction through the base pair or backbone? - Basepair When DNA is dried, where are the counter ions? Crystalline / non crystalline? Counter ions significantly modify the energy levels of the base pairs Counter-ion important Resistance species increases is also with length of the DNA (exponential within the of simple models) the sample context Counter-ions DNA-based metalised nanowires 10 nm wires: AuPd on DNA Needed Smaller wires and constructs Difficult to make conventional means Find if DNA is wires a good this scale substrate metalisation (and for which metals) Conducting and superconducting wires by for Which DNA? λ-DNA: double-stranded, 2 nm width, 16 micron length Poly-C, Poly-A, etc.: Single-stranded, all same base, 1 nm width Designed, complementary strands: Self assembly presents possibility for complex structures λ-DNA, uncoated: ~5 nm wires Metalised DNA 1) 2) Earlier construction of DNA-templated nanowires Braun Richter Nanotubes, other substrates 1: 100 nm thick wires, Ag on DNA 2: 50 nm thick wires, Pd on DNA E. Braun, Y.Eichen, U. Sivan, and G. Ben-Yoseph, Nature (London) 391, 775 (1998). J. Richter et al. Appl. Phys. Lett. 78, 536 (2001) Methods Suspend DNA across undercut 100 nm trench -or Suspend across cuts in thin (60 nm) membrane –variable width carved by focused ion beam Metalize by sputtering or evaporation Image with scanning electron microscope Make electrical measurements Methods Schematic of undercut trench Set-up Schematic of electrode overlaying wire Methods Hitachi 4700 Scanning Electron Microscope More metalised DNA-wires AuPd sputtered on λ DNA Osmium plasma coated on λ DNA Wires made repeatedly, variety of coatings (or none) Width range from <5 nm bare DNA wires to >30 nm heavily coated in AuPd. The thinnest contiguous wires are ~10 nm thick Metalised DNA-wires Variable width cuts in membrane, made by focused ion beam. DNA bridges the cuts. Longest wire to date: 960 nm (~30 nm thick) Appearance of multi-strand “Ropes” Metalised DNA-wires Multi-strand “rope,” 3 nm AuPd coating, total thickness: 3040 nm Length: 960 nm Two wires connected by “rope” visible on surface of membrane, length: 550 nm on right, 670 nm on left Is it functional? Measurement contacts produced photolithography techniques by Potentially superconducting or 3He system First Mo0.79Ge0.21 coated samples: superconductivity standard samples in 4He test for Not yet .... First MoGe sample weakly conductive, superconductivity- too thin! Room temperature: 2.3 MΩ, Lowest point: 750 kΩ, sharp upturn near usual critical temperature (near 4 K) Possible film Next samples: Si coat discontinuities or oxidation no of 7 nm MoGe with protective Variations More conductivity measurements Different DNA structures Normal and Device possibilities? As thin as possible (preferably functional) superconducting wires Variations Poly-C wire with 2 nm AuPd, total width: 5 nm. DNA template DNA templated electronics The DNA acts as a scaffold for positioning a single-walled carbon nanotube at the heart of a field-effect transistor, as well as a template for the metallic wires connecting the device. K Keren et al. 2003 Science 302 1380 DNA templated electronics DNA templated electronics What do we need to realise this assemble a DNA network localise moleculra scale electronic components transform DNA into conducting wires DNA templated wires silver wires formed on aldehyde derivitesed DNA continuous gold wires DNA templated gold wires wire width ~50nm DNA width ~2nm R~26 Ω Sequence specific molecular lithography Sequence specific molecular lithography RecA polymerised on DNA (cryo-TEM) 3-armed junction formation building blocks synapsis final product branch migration AFM image of 3-armed junction Sequence specific molecular lithography patterning of DNA metallization Sequence specific molecular lithography Sequence specific molecular lithography RecA nuleoprotein filament localised on aldehydederivatized DNA sample after silver deposition AFM sample after gold deposition SEM Sequence specific molecular lithography optical lithography molecular lithography Others Carbon nanotubes Carbon nanotubes The device - which consists of a single-walled carbon nanotube sandwiched between two gold electrodes operates at extremely fast microwave frequencies. The result is an important step in the effort to develop nanoelectronic components that could be used to replace silicon in a range of electronic applications (S Li et al. 2004 Nano Lett. 4 753). http://physicsweb.org/article/news/8/4/15 Superconductivity in nanotubes Left red data show insulating like behavior with resistance upturns at the lowest temperatures, blue data show superconducting behavior Right V-I data for a strongly superconducting sample at various temperatures. Courtesy, A. Bollinger Buckyball www.osti.gov/accomplishments/ smalley.html Cellular computing Cellular computing Goals To use a cell as the smallest DNA-based molecular computer More specifically, to mimic some or all of a cells mechanisms in order to produce a quasi molecular (QMC), or a true molecular (TMC) computer computer Quasi cellular computing Most of the input and output operations are driven by an external force Input and programming provided, QMC provides output All molecular computers are of this type, with the exception of the cell Goal for QMC’s: to develop QMC’s that are more efficient, and less dependent on outside interaction True cellular computing “All computational operations (input, output, state transitions) are driven by self organizing chemical reactions” (Ji 1999) All processes are internally driven, no outside help is needed Only known example is a cell Goal for TMC’s: to fabricate an artificial TMC with the properties of a living cell Cells versus computers Qualities of cells that are similar to those in computers Have inputs, state transitions, and outputs as indicated by their programming Have a language to communicate between cells Have information and energy storage mechanisms: IDS’s http://www.rkm.com.au/CELL/ Cells versus computers Cells Computers Current carried by: Chemicals Wires Reactions or Enzymes processes turned on or off by: Transistors Information stored in: Capacitors Biopolymers, IDS’s Computational DNA programs stored in: Software Cells versus computers Cells Computers Programmability No- not yet Yes SelfYes Reproducibility No- not yet Ji, Sungchul. The Cell as the Smallest DNA Based Molecular Computer. BioSystems (1999):52 123-133.
