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’

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5’ 3’

3’ 5’

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Ligation

5’ 3’ 5’ 3’

3’ 5’ 3’ 5’

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5’ 3’

3’ 5’

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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