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Tuesday, February 19, 2008, 11:40amAuditorium - French Family Science Center, Room 2231
Speaker: Oleg Prezhdo (University of Washington)
Title: "DYNAMICS ON THE NANOSCALE: Time-domainab initio studies of carbon nanotubes, quantum dots, andmolecule-semiconductor interfaces"Host: David Beratan
BioNano Methods & Materials
Methods Biology, Molecular biology Nano-scale Analysis & Manipulation
TEM, SEM, STM, AFM, SPM, QCM, SPR, SERS,NSOM, EDS, XPS
Materials (properties and synthesis) CNT, MWNT, SWNT, FWNT, C60
Nanoparticles Nanowires
Bio & Nano Methods
Biology, Molecular biology Enzymatic procedures Cell biology Chemistry & Biochemistry
Nano-scale Analysis & Manipulation Electron microscopy (TEM, SEM) Local probe methods (STM, AFM, SPM) QCM, SPR, SERS, NSOM
Biological Methods
Enzymes. Biochem. ELISA. IRMA. DNA/Protein manipulations.
PCR, random and site-specific mutagenesis. Alanine-scanning mutagenesis. Circular permutation.
Cell/tissue culture methods. PAGE, FACS, FRET. Microscopy.
DNA modifying enzymes
Ligase Phosphatase, Kinase Polymerase (DNA, RNA, RT) Nuclease (Endo, Exo) Restriction Endonucleases, Methylase Topoisomerase, gyrase DNA binding and repair enzymes
Ligase
Repairs nicks in phosphodiesterbackbone.
Overlapped or blunt-end. 5’ phosphate required.
5’ 3’ 5’ 3’
3’ 5’
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
5’ 3’
3’ 5’
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Ligation
5’ 3’ 5’ 3’
3’ 5’ 3’ 5’
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
5’ 3’
3’ 5’
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Ligation
Phosphatase, Kinase Phosphatase removes 5’ phosphate. AlkPhos.
CAP. Kinase adds 5’ phosphate. Also catalyses
phosphate exchange reaction useful forradiolabeling. PNK.
DNA Polymerases Replication PCR
5’ to 3’ DNA synthesis (template and primer required). Proofreading:
3’ to 5’ exonuclease activity 5’ to 3’ exonuclease activity
Example sources:T7, T4, thermophiles
Also:reverse transcriptase
Restriction endonucleases
Discovered by “restriction” ofmating types in bacteria.
“Internal cuts” of DNAphosphodiester backbone.
Usually palindromic recognitionsequences.
Paired with methylase enzymesto protect DNA from cleavage.
Proteins that act on DNA (cont.)
Topoisomerase (topo I) Remove DNA supercoils by mechanism involving single-
strand break. Tyr-phosphate transesterase.
Gyrase (e. coli topo II) Introduce supercoiling by 2-strand break mechanism
Holliday Junction -binding protein SS-binding protein Rec A DNA repair enzymes
PAGE
FACS
Nano & Surface Methods
Microscopies Optical, EM, SPM, NSOM
Nanofabrication Electron beam, dip-pen Imprint stamping Direct write (2D, 3D)
Other QCM, SPR
Optical Microscope; EM
Fluorescence Microscopy
Confocal Microscopy
Size scale
(i) imaging (atomic scale resolution)(ii) element analysis
TEM(Transmission Electron Microscope)
(i) imaging,(ii) element analysis(iii) e-beam lithography
SEM(Scanning Electron Microscope)
(i) imaging,(ii) direct electrical measurement(iii) dip-pen nanolithography
AFM(Atomic Force Microscope)
(i) imaging (atomic scale resolution)(ii) direct electrical measurement
STM(Scanning Tunneling Microscope)
Sung Ha Park
Four major tools for nanotech
http://www.microscopy.ethz.ch/methods.htm
STM
Local probe. Brought togetherknown materials and techniques.
Tunneling junction gives atomicresolution.
Electronic-mechanical hybrid.
Schematic diagram of AFM Schematic diagram of AFM
• Atomic force betweenAFM tip and specimen
Sung Ha Park
Atomic force microscopy(AFM)
AKA: SPMAlso note: force spectroscopy, dip-pen nanolithography
DPN (dip-pen nanolithography)
Electron beam lithographyElectron beam lithography
Sung Ha Park
Scanning electron microscopy(SEM)
TEM
TEM, sample
TEM, shadow
Energy dispersive X-ray microanalysis(EDX, EDXS, EDS)
The collected datacube contains 2.5 million X-rays andwas acquired for 30 minutes. Data from the SmartMap filehas been used to reconstruct X-ray maps for the majorelements in the sample: including titanium (orange), andaluminium (green) (Figure 8a). Representative spectradescribing the different phases clearly identify thealuminum oxide (Figure 8b) and titanium carbide (Figure8c).
EDX, example
Spectra have been reconstructed from 20nmsquare areas across a TiC grain to study thechemistry at grain boundaries in this ceramicmaterial (Figure 9). Using the quantitativelinescan software in INCAEnergyTEM, thechemistry variations across these grainboundaries can be determined (Figure 10).
Electron energy loss spectroscopy
EELS
EDX vs EELS
Auger Electron Spectroscopy 1. Ionization: A hole in an inner
shell (here: K shell) is generatedby an incident high-energyelectron that loses thecorresponding energy Etransferred to the ejected electron.
2. Auger-electron emission: Thehole in the K shell is filled by anelectron from an outer shell (here:L1). The superfluous energy istransferred to another electron(here: L3) which is subsequentlyejected as Auger electron.
Since Auger electrons have anenergy in the range of some 100eV to a few KeV, they are stronglyabsorbed by the specimen.Consequently, only Auger electronfrom the surface can be measured,making Auger spectroscopy asurface method.
XPS X-ray Photoelectron Spectroscopy (XPS) is able to
analyze the chemical composition of various materialsurfaces up to 1 nm depth.
X-ray bombardment of surface leads to electronejection. Detectors analyze the characteristic energyof the electrons and determine the type of atom (andits chemical state) from which it came.
Images with tens of microns resolution.
TIR / SPR
SPRSurface Plasmon Resonance.
(Biacore)
Kinetic Rate Analysis: How FAST?
ka, kd KD = kd/ka, KA = ka/kd
Yes/No Data Ligand Fishing
Concentration Analysis:How MUCH?Active Concentration
Solution Equilibrium Inhibition
Affinity Analysis: HOWSTRONG?
KD, KARelative Ranking
Total internal reflectance (TIR) at interface of differingrefractive indices. Angle of incidence above a criticalvalue get TIR. Evanescent field (E) is setup.
Biacore’s proprietary SPRtechnology
• Non-label• Real-time• Unique, high quality data on molecular
interactions• Simple assay design• Robust and reproducible• Walk-away automation• Small amount of sample required
Biomolecular Binding in Real Time
Principle of Detection
D102
Flexibility in Assay Design• Multiple assay formats providing
complementary dataDirect measurement Indirect measurement
Inhibition in solution assay (ISA)
Surface competition assay (SCA)Direct Binding Assay (DBA)
QCM
Piezoelectric quartz microbalance: A quartz disk ~1cm in diameter and ~.1 mm thick with circular gold electrodes inthe center of each face. When an A.C. voltage is applied acrossthe electrodes the crystal oscillates in a thickness shear modein which the two faces move parallel to each other and inopposite directions.
Used in this way the quartz becomes a mechanicalresonator. Any adsorbed film on the electrodes will make theresonator heavier and so lower it’s resonant frequency. A filmthickness measurement is made by monitoring this frequencyshift. The crystals used for these experiments were usuallydriven at their third harmonic (fo,3 ~ 5.5 MHz).
Quartz crystal microbalance.
SERS:Surface Enhanced Raman Spectroscopy
The Raman Effect.When light is scattered from a molecule most photons are elastically scattered.The scattered photons have the same energy (frequency) and wavelength as the incident photons.However, a small fraction of light (approximately 1 in 107 photons) is scattered at optical frequenciesdifferent from, and usually lower than, the frequency of the incident photons. The process leading tothis inelastic scatter is the termed the Raman effect. Raman scattering can occur with a change invibrational, rotational or electronic energy of a molecule. Chemists are concerned primarily with thevibrational Raman effect. The difference in energy between the incident photon and the Ramanscattered photon is equal to the energy of a vibration of the scattering molecule. A plot of intensity ofscattered light versus energy difference is a Raman spectrum.
Resonance-Enhanced Raman Scattering. Raman spectroscopy is conventionally performed withgreen, red or near-infrared lasers. The wavelengths are below the first electronic transitions of mostmolecules, as assumed by scattering theory. The situation changes if the wavelength of the excitinglaser within the electronic spectrum of a molecule. In that case the intensity of some Raman-activevibrations increases by a factor of 102-104. This resonance enhancement or resonance Raman effectcan be quite useful.
Surface-Enhanced Raman Scattering.The Raman scattering from a molecule adsorbed on or evenwithin a few Angstroms of a structured metal surface can be 103-106X greater than in solution. Thissurface-enhanced Raman scattering is strongest on silver, but is observable on gold and copper.SERS arises from
1) enhanced electromagnetic field at the surface of the metal (wavelength of the incident light is close to theplasma wavelength of the metal, conduction electrons in the metal surface are excited into an extendedsurface electronic excited state called a surface plasmon resonance). Molecules adsorbed or in closeproximity to the surface experience an exceptionally large electromagnetic field. Vibrational modes normalto the surface are most strongly enhanced.
2) formation of a charge-transfer complex between the surface and analyte molecule. The electronictransitions of many charge transfer complexes are in the visible, so that resonance enhancement occurs.Molecules with lone pair electrons or pi clouds show the strongest SERS.
BioNano Methods & Materials
Methods Biology, Molecular biology Nano-scale Analysis & Manipulation
TEM, SEM, STM, AFM, SPM, QCM, SPR, SERS,NSOM, EDS, XPS
Materials (properties and synthesis) CNT, MWNT, SWNT, FWNT, C60
Nanoparticles Nanowires
NanoMaterials Carbon nanotech
CNT, MWCNT, SWCNT, FWNT C60 (buckyballs)
Nanoparticles Material: Metal, Semiconductor Size, shape, multi-layer
Crystalline nanowires Metal Semiconductor
Polymers
Carbon Nanostructures
C60, buckminsterfullerene, buckyball (1985) Kroto, Heath, O’Brien, Curl, Smalley, Nature 318, 162-163.
Carbon nanotubes (1991) Sumio Iijima, Nature 354, 56-58.
C60(1985) Kroto, Heath, O’Brien, Curl, Smalley, Nature 318, 162-163.
10 torr He
760 torr He
CNT, Iijima, 1991
(1991) Sumio Iijima, Nature 354, 56-58.
CNT smallest tubes
C20 tubes, 4Å wide, always armchair, always metallic
CNT Synthesis
Laser Electric arc Solar CVD
CNT synthesis mechanism
Large catalyst particles Surface bound NP catalyst
(from ferritin)
“Kiting” NP catalyst
Protein based catalyst - Ferritin
CNT, etc. Filling Organization
CNT , properties
CNT , other uses
Single-Wall Carbon Nanotubesfor Nanoelectronics & Biosensors SWNT devices SWNT circuits Interactions with proteins and DNA Self-assembly using DNA Biosensors from protein/CNT
(10,10) SWNT
SWNT, some properties
n,m vector n,0 zigzag n,n armchair Other = chiral n-m is divisible by 3
tube is metallic
http://www.pa.msu.edu/cmp/csc/nanotube.html
AFM manipulationof CNT
Targeted deposition of CNT
Targ Dep 2
Carbon Nanotubes, electronicsSynthesis: arc,CVD, laser
Doped CNT N doped B doped
CNT, electronics
CNT transistor 1
49-52
CNT transistor 2
49-52
CNT transistor 3
49-52
CNT logic circuits
1317-1320
CNT logic circuits 2
1317-1320
Crossed CNT junct
494-497
Crossed CNT junctions 2
494-497
Other CNT biosensor results: Vertically aligned CNT arrays. Antibodies raised against CNT and C60. Electropolymerization of conducting
polymers.
DNA on CNT (covalent)
DNA on CNT (adsorb)
1545-1548
DNA-CNT2
1545-1548
DNA-CNT 3338-342
NA: poly-T, in vitro evolved ssDNA,dsDNA or RNA from bacteria or yeast.
NA+surfactant+sonication. Near-IR fluorescence indicates well
dispersed SWNT. Anion-exchange chromatography
separates DNA-CNT by size andelectronic tube-type.
M
S
Nanoparticles, nanorods, nanowires
Nanoparticles, nanocrystals,nanospheres, quantum dots, etc. Drugs, proteins, etc.
Nanorods, nanowires. Optical and electronic properties. Organization using biomolecules. Future possibilities.
Nanoparticles
“0D nanostructures” Nanocrystals Nanospheres Quantum dots Core-shell nanoparticles
Nanoparticles Materials: QDs, magnets, noble metals Synthesis
Reduction of metal salt Production of insoluble salt Micelle confinement Microbial production Biomolecular nucleation
Control of: composition, size, shape, crystalstructure, and surface chemistry.
Properties: Optical, electrical, physical, chemical
Nanoparticles
Nanoparticles, gold Synthesis
Reduction of metal salt
Nanoparticles, metal replacement
Geometric crystals Metal replacement Solvothermal, etc.
Shape-Controlled Synthesis of Gold and SilverNanoparticles, Yugang Sun and Younan Xia,13 DECEMBER 2002 VOL 298 SCIENCE pp 2176
AuNP Properties
“Noble” metal catalyst. Nano size changes
properties.
Nanoparticles, silver Light dependent synthesis
QD Rainbow
Nanoparticles, organization
Nanoparticles and DNA
J. J. Storhoff, C. A. Mirkin, Chem. Rev. 1999, 99, 1849 - 1862.
Nanowires “1D nanostructures” Advantages of miniaturization
Lower cost, higher speed, lower powerconsumption, lower heat generation
New phenomena Ballistic conductance, size-dependent
excitation or emission, Coulomb blockade(SET), metal insulator transition
In situ fabrication (e-beam, FIB, X-ray orEUV litho.) vs chemical synthesis andassembly
NW, synthesis
Nanowires, crystal lattice
Nanowires, metal replacement
Nanowires
ECD (dc, ac, pulsed) Polycrystalline wires (some single-crystal)
Pressure injection into template pores. Single-crystal wires
Co/Cu layers from one solution byswitching cathodic potential.
Nanowires
Templates anodic alumina (Al2O3), nano-channel glass,
ion track-etched polymers, and mica films. 10-200 nm diameter pores. CNT in templates and as templates.
a) Anodic alumina from acid anodized Al film to givehexagonal array of cylindrical holes. b) particle track-etched polycarbonate membrane.
Protein templates
(also CNT synth, catalyst)
Nanowires
VLS - vapor, liquid, solid Mechanism first proposed for single-crystal Si whisker
synthesis (molten Au catalyst). Anisotropic crystal growth.
Nanowire networks Alignment by flow in channels. Alignment on surface patterns.
Amine terminated lines.
Nanowire devices Doped wires, logic gates.
Nanowires More complex structures by growth. Organization of fully formed rods. Ordered growth.
Nanowires
Nanowires Annealing