UIC NanoEngineering Research Laboratory University of Illinois at Chicago College of Engineering N...

UIC NanoEngineering Research Laboratory

University of Illinois at Chicago College of Engineering

NNanoEngineeringResearch Lab

Applications of Colloidal Quantum Dots and Carbon Nanostructures

Michael A. Stroscioa,b,c, and Mitra Duttaa,b

Sun Ke,a Milana Vasudev,c Jun Qian,a Sicheng Liao,b Takayuki Yamanaka,a,* D. Ramadurai,c,** Hye-Son Jung,a Jianyong Yang,a A.

Rauchura,a Yang Li,a

University of Kentucky, September 24, 2008

aElectrical and Computer Engineering Department, U. of Illinois at Chicago (UIC), 851 S. Morgan Street, Chicago, Illinois 60607

bPhysics Department, U. of Illinois at Chicago, 851 S. Morgan Street, Chicago, Illinois 60607

cBioengineering Department, U. of Illinois at Chicago, 851 S. Morgan Street, Chicago, Illinois 60607

*Now at Northwestern U., M. Razeghi Group, **Now at EPIR, S. Sivananthan



NNano EngineeringResearch Laboratory

Integrating Nanostructures with Biomolecules: Tool for Studying Biomolecular Architectures

Capabilities for Integrating Nanostructures with Biomolecule

- Synthesis of Biomolecule-Nanostructure Complexes

- Nanostructures used --- CNTs and Quantum Dots (QDs in our arsenal --- Au, CdS, CdSe, CdSe-ZnS, CdTe, ZnO, PbSe, and TiO2)

- Biomolecules studies in our lab by linking with manmade nanostructures include a wide variety peptides (CGGGLDV, CGGGIKVAV, CGGGRGD, CGGGRGDS, CGGGDGEA, GRKKRRQRRR (TAT), CGGGRVDS, GGGC, and many more) and a large variety of single- and double-stranded DNA molecules including ---molecular beacons, short sequences such as TTTTTT, molecular junctions, and specialized sequences such as:Sequence # 1: 5'-Carboxy dT GTATGATATGTTCCCTGGCTCTACTACTGGAGT -3'Sequence # 2: 5'- ACTCCAGTAGAGCCTGGGAA -3'Second sequence (20 bases) is complementary to the first one (30 bases) from 3‘ end.WE WILL MAKE THESE CAPABILITIES AND OTHERS AVAILABLE

TO MEMBERS OF THE BIOMOLECULAR ARCHITECTURE TEAM

Biomolecule

Biomolecules

Biomolecules




Integrating Nanostructures with Biomolecules: Relevances tp Biomolecular Architectures

Essential for understanding how environmental effect modify the vibrational, optical, and electronic properties of biomolecules - as an example vibrational modes are modified at boundaries between biomolecules and surfaces in contact with biomolecules (for optical modes boundary conditions such as electrostatic boundary conditions apply and for acoustic modes continuity of displacements and/or normal components of stress tensors) Integrating nanostructures and biomolecules makes it possible to assemble

arrays of structures --- possible coherence enhancements in scattering signatures Our past work has exploited biomolecules to make ordered arrays of man-made nanostructures --- alternatively, nanostructures may be used to make arrays of biomolecules (possible enhancements of scattering signatures) New

CdS CdSe-ZnS-GGGCCdSe-ZnS

Au wire

WE WILL MAKE THESE CAPABILITIES AND OTHERS AVAILABLE TO MEMBERS OF THE BIOMOLECULAR ARCHITECTURE TEAM

Background


Schematic representation of PMMA slides modified chemically to have –NH2 end groups and the DNA strands are attached via glutaraldehyde

Glutaraldehyde, cross-linker

PMMA substrate modified with –NH2 group

NH2 NH2 NH2 NH2 NH2 NH2 NH2 NH2 NH2

DNA strand

NH2 NH2 NH2 NH2NH2 NH2 NH2 NH2 NH2

TiO2 Nanoparticles

Schematic of Immobilized DNA


Schematic of the DNA chemically bound to the PMMA sheets



DNA strand


N N N N N N N N N

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C


Illustration of DNA-based SAM fabricated for U. Va. The DNA strands for the formation of the monolayer on PMMA are: 5’- Amino AC TCG AGT ACA GCG ACC CAA CAT GAG AGA AC-‘3 and3’- TG AGC TCA TGT CGC TGG GTT GTA CTC TCT TG carboxy Dt-‘5

The DNA strand with the amino modification on the 5’ end is the one attached to the PMMA substrate modified by hexamethylene diamine to have a-NH2 group and glutaraldehyde is used as the cross-linking agent.

Carboxyl modified DNA was bound to the TiO2 particles via the dopamine modification. The two DNA strands are complementary to each other so they are hybridized to form a double stranded DNA monolayer.



DNA strand


N N N N N N N N N

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

AC

TC

GA

GT

AC

AG

CG

AC

CC

AA

CA

TG

AG

AG

AA

C

Yale-UIC Collaboration


1450

1600

1750

1900

2050

2200

400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000

814

931

1101

1449

1732

514.5 nm laser Raman from RRC

Slit: 50 μm grating: 1800 gr/mm Time: 60sec

Sample #2: Double-stranded DNA /TiO2 (4.5μm)

Raman spectrum from PMMA sample with double stranded DNA bound to TiO2 nanoparticles

PMMA has its major peaks at 1100, 1430, 1780 cm-1

TiO(2) below 620 cm-1


Raman Spectrum of Single-stranded DNA on PMMA

PMMA sample with single stranded DNA

* Spectral measurements by Jianyong Yang

PMMA has its major peaks at 1100, 1430, 1780 cm-1


Raman Spectra were obtained using the Renishaw Raman imaging microscope with an argon ion (514.5 nm) laser and the data is recorded using a CCD camera.

Raman spectra of DNA immobilized on PMMA substrate (a) single stranded amine modified DNA (35 bases) (b). Amine modified GAPDH DNA (850 bp)

Raman Spectroscopy

1250

1500

1750

2000

2250

2500

300 500 700 900 1100 1300 1500 1700 1900

wavelength (cm-1)

Inte

nsi

ty (a

.u.)

563

815

940

1098

1448

1728

A

984

500

700

900

1100

1300

1500

1700

1900

2100

400 600 800 1000 1200 1400 1600 1800 2000

wavelength (cm-1)

Inte

nsity

(a.u

.)

1746

1615

1454

1310

11901075

959

810

835

598560

1240

1110

B


Raman Spectra were obtained using an (325 nm) laser and the data is recorded using a CCD camera.

300

400

500

600

700

800

900

1000

1100

1200

400 600 800 1000 1200 1400 1600 1800 2000

Raman spectra of DNA immobilized on PMMA substrate with a SAM of amine modified GAPDH DNA (850 bp)

Raman Spectroscopy

1000

1500

2000

2500

3000

3500

400 600 800 1000 1200 1400 1600 1800 2000


Raman Spectra were obtained using an (325 nm) laser and the data is recorded using a CCD camera.

500

700

900

1100

1300

1500

1700

1900

2100

400 600 800 1000 1200 1400 1600 1800 2000

rel. (cm-1)

Inte

ns

ity

(a

.u.)

Raman spectra of DNA immobilized on PMMA substrate with a SAM of amine modified GAPDH DNA (850 bp)

Raman Spectroscopy

200

250

300

350

400

450

500

550

600

400 600 800 1000 1200 1400 1600 1800 2000


Raman Lines from DNA samples

DNA DNA TiO2

(A)

TiO2

(A)

TiO2

(A)

DNA DNA DNA PMMA DNA PMMA PMMA

Single stranded DNA

563 - 815 940 1098 1448 1728

Double stranded DNA

115 365 602 812 946 1064 1240 1451 1728

GAPDH DNA (850 bp)

560 598 810 959 1075 1310 1454 1746

DNA with TiO2

before exposure to UV light

188 610 814 930 - 1101 1449 1732

DNA with TiO2

after exposure to UV light

- 610 811 915 954 1103 1450 1730

Summary

The table shows the Raman lines from the various samples. Ar-ion-laser plasma lines and background have not been removed.


Molecular beacon

Quantum dotGold NP, quencher

Molecular beacon

Quantum dotGold NP, quencher

Quantum Dot

Molecular Beacon with target DNA strand

Gold NPsGlass substrate

Quantum Dot

Molecular Beacon with target DNA strand

Gold NPsGlass substrate



DNA Identification with Molecular Beacons




DNA Identification with Molecular Beacons

• This concentration can be increased to 10:1 of gold NP to quantum dots

• The concentration of the beacons to the quantum is adjusted to be 3:1 so that the quenchers can effectively quench the fluorescence from the dots

• The control experiment with a different DNA strand needs to be performed

0.00E+00

1.00E+04

2.00E+04

3.00E+04

4.00E+04

5.00E+04

480 500 520 540 560 580 600

w avelength (nm )

inte

nsity

(a.u

.)

MB with 560nm QD andgold NP quenched

MB with 560nm QD andgold NP unquenched


Left-handed Z-DNA is a higher-energy form of the double helix. Each time a right-handed DNA segment turns into Z-DNA, two B–Z junctions form.


I shaped DNA Structure for the study of B-Z DNA transitions

• DNA strands partially complementary to each other are used to form I DNA structure for the study of B-Z transitions.

• When B-Z transition occurs in presence of higher salt concentrations, the quantum dot fluorescence is quenched due to the contact with the quencher, BHQ1; quenching range of the BHQ1 is 480-580 nm

Representation of I DNA structure with the Quantum dot and quencher attached to opposite ends

TCTTGCTCTC TCTTGCTCTC

CACACGAACACACACGAACABHQ1, Quencher

QDAGAACGAGAG

GTGTGCTTGT

GCCG

TCTTGCTCTC TCTTGCTCTC

CACACGAACACACACGAACA BHQ1, Quencher

QDAGAACGAGAG

GTGTGCTTGT

GCCGGC


I shaped DNA Structure for the Study of B-Z DNA Transitions

• DNA strands partially complementary to each other are used to form I DNA structure for the study of B-Z transitions.

• When B-Z transition occurs in presence of higher salt concentrations, the quantum dot fluorescence is quenched due to the contact with the quencher, BHQ1; quenching range of the BHQ1 is 480-580 nm

Representation of I DNA structure with the Quantum dot and quencher attached to opposite ends

TCCTGCTCTCAGGACGAGAG GC CGGTGTGCTTGTCACACGAACA

TiO2QD, Luminescent

Quencher


0.00E +00

2.00E +03

4.00E +03

6.00E +03

8.00E +03

1.00E +04

1.20E +04

1.40E +04

1.60E +04

482 492 502 512 522 532 542 552 562 572

I2.DNA.unquenched

I2.DNA.quenched

I2.DNA.L C .unquenched

I2.DNA.L C .quenched

TCTTGCTCTC--QUENCHERAGAACGAGAG GC CG GCGTGTCGTTGTCACAGCAACA—QD

I-shaped DNA structures with a quencher and a quantum dot (QD) bound to adjacent arms of the structure. The GC-GC-GC linkers undergo pH control- led B- to Z-DNA transitions and move quenchers relative to quantum dots

I. Red Curve in Figure 2; B DNA in cacodylate buffer 50 mM NaCl 2.5 mM MgCl2II. Purple Curve in Figure 2; Z DNA in cacodylate buffer 50 mM NaCl 10 mM MgCl2 0.125 mM Co(NH3)6Cl3III. Green Curve in Figure 2; B DNA in cacodylate buffer 25 mM NaCl 1.0 mM MgCl2IV. Blue Curve in Figure 2; Z DNA in cacodylate buffer 25 mM NaCl 5 mM MgCl2 0.0625 mM Co(NH3)6Cl3


Raman spectra in the region 300-1800 cm-1 of B and Z formsof poly(dG-dC).poly(dG-dC) and their difference spectrum.

Benevides and Thomas, Nucleic Acids Research, 1983




Study of DNA Using Indirect Bandgap Semiconductor Quantum Dots

T. Yamanaka, M. Dutta, T. Rajh, and M. A. Stroscio, “Phonon Absorption and Emission by Holes in the HOMO Bands of Duplex DNA,” Proceedings of the International Conference on Hot Carriers in Semiconductors, Proceedings of the International Conference on Hot Carriers in Semiconductors, in Nonequilibrium Carrier Dynamicsin Semiconductors, Springer Proceedings 110, 225-228

(2006). 1D Model for Deformation Potential Scattering of Holes in DNA

• Michael A. Stroscio and Mitra Dutta, “Biologically-inspired Chemically-directed Self-assembly of Semiconductor Quantum-dot-based Systems: Phonon-hole Scattering in DNA Bound to DNA-quantum-dot Complexes,” International Journal of High Speed Electronics, 16(2), 659-668 (2006).• Bykhovskaia, Gelmont, Globus, Woolard et al., Prediction of DNA Far-IR Absorption Spectra based on Normal Mode Analysis, Theor. Chem. Acc., 106, 22 (2001).• Dimitri Alexson, Hongfeng Chen, Michael Cho, Mitra Dutta, Yang Li, Peng Shi, Amit Raichura, Dinakar Ramadurai, Shaunak Parikh, Michael A. Stroscio, and Milana Vasudev, “Semiconductor Nanostructures in Biological Applications,” Journal of Physics: Condensed Matter, 17, R637-R656 (2005)

E

N

m

D

E q

h

1

2

1

2

1

2

1

3

8162

24)(

1

*

2

42

2

2

Experimental Studies of Carrier-Phonon Interactions in DNA


It has been reported that a polaron in DNA is spread over 6~7 base-pairs.

E. M. Conwell and S. V. Rakhmanova, Proc. Natl. Acad. Sci. USA, 97, 4556 (2000); Michael A. Stroscio and Mitra Dutta, “Biologically-inspired Chemically-directed Self-assembly of Semiconductor Quantum-dot-based Systems: Phonon-hole Scattering in DNA Bound to DNA-quantum-dot Complexes,” International Journal of High Speed Electronics, 16(2), 659-668 (2006).

DNA might be characterized as a continuous media.

Polaron Drift

Introduction~ Polaron drift model in DNA ~


Phonon scattering rates are calculated for 1D wire model based on the optical deformation potential.It means

1D quantum wire modelbased on the optical deformation potential

Assumptions

DNA is a 1D chain which consists of base pairs.

All bases have same mass.

The cross section is a rectangle shape.

The elastic constant is identical along the chain.

)(int ruDH op


Phonon-like mode in DNA

Sound velocity along DNA was reported : 1.9 km/sec

This energy looks so small.But, from the basic model of 1D chain

M. B. Hakim, S. M. Lindsay, and J. Powell, Biopolymers., 23, 1185 (1984)

2

at 0s

Cav k

M

If is uniform,

22 = at s

M

vCk

M a a

3.68 meV

Some researchers have reported phonon-like modein the region of ~20 cm-1. For example, Urabe et al. reported 14 cm-1 . 1.74 meV

H. Urabe and Y. Tominaga, Biopolymers., 21, 2477 (1982)

1.74 meV is also a reasonable value.


DNA IP and Semiconductor EvIonization Potential of semiconductor-DNA complexes

-10

-8

-6

-4

-2

0

IP (

eV)

Conduction Band Band GapValence Band 5'GCGTGCGTGGTGC'3

Quantum Dot Interactions with DNA


Energy of carriers [meV]

Em

issi

on r

ate

[sec

-1]

no broadnings= 0.87 meVs= 1.74 meVs= 3.5 meV

(1014)

0 2 4 6 8 10 12

2.0

4.0

6.0

8.0

10.0

12.0

Phonon scattering rates with broadening.

E

N

m

D

E q

1

2

1

2

1

2

1

3

8162

24)(

12

42

2

2

Polaron scattering with the expected longitudinal acoustic phonon mode with a frequency of

14 cm-1 ( = 1.74 meV) evaluated in the Fermi Golden Rule approximation


Scattering Rates for Different Effective Mass

meff = 100 meff = 40 meff = 10 meff = 1

Abs

orpt

ion

rate

[se

c-1]

Carrier energy [meV]0 5 10 15 20

1.0

2.0

3.0(1014)

Em

issi

on r

ate

[sec

-1]

Carrier energy [meV]

meff = 100meff = 40meff = 10meff = 1

0 5 10 15 20

1

2

3

4

(1014)

Absorption Rate Emission RateEphonon = 1.74 meVDop = 0.03x1010 eV/m = 1.0 meV


Theoretical model

• Characterization of the charge transport in DNA based on phonon scatterings.

• Phonon scattering rates are calculated by the Fermi golden rule and the deformation potential.

• Especially in DNA, phonon scatterings are important on being trapped by an energy valley, typically, G, GG, or GGG site.

Ave

rage

pos

ition

of

char

ges

[nm

]

Time [sec]

Meff = 40

Meff = 60

Meff = 80

Meff = 100

29.2 m/sec

17.5 m/sec

9.29 m/sec

6.84 m/sec

(The electric field : 5.8x105 V/m)

0 0.2 0.4 0.6 0.8 1(10-9)

5

10

15

20

25

The charge movement through DNA starting at position x=0 and illustrates the distance over which

charges are transferred.


Monte Carlo Simulation 1

Simulation of drift

hx

x = 0

V/m108.5 5F

The space is simply one-dimensional without boundaries.

The initial energy is 25.9 meV.

Simulation setup 1


Simulation Result 1

Average position

Eini = 25.9 meVF = 5.8x105 V/mNo boundary

Evaluation ofthe drift velocity

Time [sec]

Ave

rage

pos

ition

of

char

ges

[nm

]

Simulation resultFitted line

meff = 40

meff = 60

meff = 80

meff = 100

29.2 m/sec

17.5 m/sec

9.29 m/sec

6.84 m/sec

0.0 0.2 0.4 0.6 0.8 1.0(10-9)

5

10

15

20

25


Simulation Result 2 (Evaluation of meff)

Saturation velocity due to the effective massEffective mass

Satu

ratio

n ve

loci

ty [

m/s

ec]

0 50 100 150 200

5

10

15

20

25

30

35

40

45

Drift velocity calculated by Conwell is 17.4 m/sec.

meff = 50 ~ 60 is very general value.

S. V. Rakhmanova and E. M. Conwell, J. Phys. Chem. B., 105, 2056 (2001)


Monte Carlo Simulation 2

Simulation of diffusive behavior

The space is 1D with the boundary at x = 0.

The initial energy is 25.9 meV.

Simulation setup 2

hx

x = 0

No electric field

meff is assumed to be 50.


Simulation Result 3

Demonstration of diffusive behavior

1 2 3 4 5 6 7 8 9 10 11 12

80 %

60 %

40 %

20 %

0 %

80 %

60 %

40 %

20 %

0 %

80 %

60 %

40 %

20 %

0 %

at 0.02 psec

at 0.1 psec

at 0.5 psec

Distance from the origin [base pairs]

Dis

trib

utio

n of

charg

es

Eini = 25.9 meVNo electric fieldBoundary at x = 0meff = 50

Rapid transfer for a long range was demonstrated.


Comparison to the Reported Experimental Result

One of the representative resultsGiese et al., Nature, 412, 318 (2001)

This weak distance dependency implies rapid charge transfer.

Unfortunately, it is difficult to evaluate carrier dynamics directly from experiments.

This agrees with our demonstration


Charge Transfer in DNA

• Charge transfer through DNA via TiO2(titanium dioxide) nanoparticles has been studied in the past.

• TiO2 is a IV-VI semiconductor which has its excitation and emission frequencies in the UV range.

Tijana Rajh et al., J Phys. Chem. B, 2002.

When excited via UV light, TiO2 has excess of holes (charges) which can be transferred to DNA due to the match in their energy levels


Gel Electrophoresis to Detect Cleavage

Lane 1: DNA/TiO2 before illumination with UV light

Lane 2: DNA/TiO2 illuminated with 365 nm UV for 15 min. The Gel clearly shows two separate bands and suggests that cleavage has occurred

Lane 3: Unconjugated DNA oligo (Control). It is evident from the Gel that Lane 1 and 3 have the same molecular weight and hence proves that the TiO2 does not get into the gel and affect the DNA.

Lane 5: 25 bp DNA ladder: 500, 200 125, 75, 50, and 25 bp

1 2 3 5

Nanocomposites used for oligonucleotide cleavage experiments were TiO2/30 sense 5’ Carboxy dT GTATGATATGTTCCCAGGCTCTACTGGAGT and antisense oligo TiO2/30 antisense 5’ ACTCCAGTAGAGCCTGGGAA

5’ COOH TGTATGATATGTTCCCAGGCTCTACTGGAGT AAGGGTCCGAGATDACCTCA 5’


Three-Dimensional DNA Networks

• The three sequences used to form the junction are:

# 1 : 5’-COOH TCTGAGGA

# 2 : 5’ GAGACAGA

# 3 : 5’ TCCTCGTCTC

The TiO2 is attached to the 5’ end of sequence #1.

Should be noted that the three-way junction is a T junction . Two arms are symmetric about the junction

TiO2


Theoretical model

• Characterization of the charge transport in DNA based on phonon scatterings.

• Phonon scattering rates are calculated by the Fermi golden rule and the deformation potential.

• Especially in DNA, phonon scatterings are important on being trapped by an energy valley, typically, G, GG, or GGG site.


u1 = u2 T1normal = T2normal

u = 0 clamped

Tnormal = 0 free-standing

a

M

1M 2M )( 21 MM

a

a '

k

a

M

C4

k

'a

1

2

M

C

2

2

M

C

21

112

MMC

Monoatomic chain Diatomic chain

Dispersion --- monoatomic chain Dispersion --- diatomic chain

k

'a

M

C2

M

C4

k

'a

M

C4

aa

'

2

Dispersion curvefor M1=M2=M

Folding the dispersion curve


DNA is considered as a one-dimensional chain.

If the base sequence is completely random, the number of phonon modes should become a number of base pairs. However, each base pair have almost same mass and it is considered that phonon modes in DNA can be discussed based on a monoatomic chain model.

In monoatomic chains,

at the zone edge.

At the same time, the sound velocity is represented by

at k = 0As a result, the angular frequency becomes

M

C4

M

Cavg

a

vg2


The sound velocity of B-DNA has been measured as 1.9 km/sec [1], and the period of bases is 3.4 Å. Therefore,

3.68 meV corresponds to 29.61 cm-1. This value is the energy of the phonon mode at the zone edge in the case of a uniform one-dimensional chain. However, if the periodic perturbation is assumed with a period of 2a, this energy becomes the energy of the optical mode at the zone center as discussed above. And if the perturbation is more complicated but still weak at the same time, which means that the discussion based on monoatomic chains is still valid, it is expected that another optical modes appear below this energy.

In fact, it has been reported that the lowest lying mode in B-DNA is 14 cm-1 (=1.74 meV) [2]. As a result, it can be said that there is the mode in DNA with only a few meV.

[1] M. B. Hakim, S. M. Lindsay, and J. Powell, ‘The Speed of Sound in DNA’, Biopolymers, 23, pp. 1185-1192, 1984[2] H. Urabe and Y. Tominaga, ‘Low-Lying Collective Modes of DNA Double Helix by Raman Spectroscopy’, Biopolymers, 21, pp. 2477-2481, 1982

[meV] 68.3[rad/sec] 1059.5[rad/sec] 103.4

109.12212

10-

3

a

vg


e-

h+

h+h+

Light

Quantum Dot DNA

TiO2

h+ h+ h+

AuAu

AFM

Glass

TiO2

Au

ssDNA

Measuring I-V Characteristics in ssDNA

Dopamine or 3,4 dihydroxyphenylethylamine

- cd TTTTTT


Au-TiO2-Au without UV Light Au-TiO2-Au with UV Light

e-

h+

h+h+Light

Quantum Dot

TiO2

Au

Au

Current sensing AFM For EF at mid-gap

For FN near Ec

For FP near Ev

I-V Characteristics of Nanostructure Interface


E0 = - 7.4 eVE0 = - 7.0 eV

E0 = - 6.6 eVE0 = - 6.2 eV

I-V Curves for a Au-Ti02-AuEc = - 4.2 eVEv = - 7.4 eV


u1 = u2 T1normal = T2normal

u = 0 clamped

Tnormal = 0 free-standing

a

M

1M 2M )( 21 MM

a

a '

k

a

M

C4

k

'a

1

2

M

C

2

2

M

C

21

112

MMC

Monoatomic chain Diatomic chain

Dispersion --- monoatomic chain Dispersion --- diatomic chain

k

'a

M

C2

M

C4

k

'a

M

C4

aa

'

2

Dispersion curvefor M1=M2=M

Folding the dispersion curve


DNA is considered as a one-dimensional chain.

If the base sequence is completely random, the number of phonon modes should become a number of base pairs. However, each base pair have almost same mass and it is considered that phonon modes in DNA can be discussed based on a monoatomic chain model.

In monoatomic chains,

at the zone edge.

At the same time, the sound velocity is represented by

at k = 0As a result, the angular frequency becomes

M

C4

M

Cavg

a

vg2


The sound velocity of B-DNA has been measured as 1.9 km/sec [1], and the period of bases is 3.4 Å. Therefore,

3.68 meV corresponds to 29.61 cm-1. This value is the energy of the phonon mode at the zone edge in the case of a uniform one-dimensional chain. However, if the periodic perturbation is assumed with a period of 2a, this energy becomes the energy of the optical mode at the zone center as discussed above. And if the perturbation is more complicated but still weak at the same time, which means that the discussion based on monoatomic chains is still valid, it is expected that another optical modes appear below this energy.

In fact, it has been reported that the lowest lying mode in B-DNA is 14 cm-1 (=1.74 meV) [2]. As a result, it can be said that there is the mode in DNA with only a few meV.

[1] M. B. Hakim, S. M. Lindsay, and J. Powell, ‘The Speed of Sound in DNA’, Biopolymers, 23, pp. 1185-1192, 1984[2] H. Urabe and Y. Tominaga, ‘Low-Lying Collective Modes of DNA Double Helix by Raman Spectroscopy’, Biopolymers, 21, pp. 2477-2481, 1982

[meV] 68.3[rad/sec] 1059.5[rad/sec] 103.4

109.12212

10-

3

a

vg


Energy of carriers [meV]

Em

issi

on r

ate

[sec

-1]

no broadnings= 0.87 meVs= 1.74 meVs= 3.5 meV

(1014)

0 2 4 6 8 10 12

2.0

4.0

6.0

8.0

10.0

12.0

Phonon scattering rates with broadening.

E

N

m

D

E q

1

2

1

2

1

2

1

3

8162

24)(

12

42

2

2

Polaron scattering with the expected longitudinal acoustic phonon mode with a frequency of

14 cm-1 ( = 1.74 meV) evaluated in the Fermi Golden Rule approximation


Intrasubband Intersubband

(a) Slab, (b) Reformulated, (c ) Guided, (d) Bulk


and u boundary conditions in and mechanical models of optical modes, and continuity of u and normal component of stress tensor for acoustic modes


Nano Engineering Research Lab

Univ. of Illinois at Chicago Chicago, USA

Su-Schrieffer-Heeger Hamiltonian

*Sugiyama H. & Saito, I. (1996) J. Am. Chem. Soc. 118, 7063-7068.

M = 4.35 x 10-22 g, K = 0.85 eV/A2 (K= Mvsound2/a2), vsound = 1.9 km/s, a = 0.34 nm,

to = 0.36 eV* , determined by interactions of –wavefunctions of adjacent bases* = t/u = 0.6 eV/Angstrom* G = 1.4 eV, A = 0.9 eV, C = .27 eV, T = 0 eV

on-site energy, transfer intergal (to) atthermal equilibrium, change in transfer integral due to displacements = carrier-phonon coupling

potential and kinetic energies ofvibrational modes --- phonons

SSH is used widely to describe polaron transport on polymers


Discussion

• From some of the Raman spectra, we notice that the PMMA has its major peaks at 1100, 1430, 1780 cm-1

• The contribution of the background signal from PMMA is high and may be blocking the weak DNA Raman signatures

• For future experiments– Use longer strands of DNA upto 2K BP obtained from PCR

reactions– Use other methods of tracking double stranded DNA such

as DAPI dye (commonly used biological dye)– Use gel electrophoresis to verify that the exposure to UV

light cleaves the DNA strands bound to TiO2 nanoparticles


Energy transfer between quantum dots and gold nanoparticles

• The transfer of energy is studied between the quantum dots (donors) and gold nanoparticles (acceptors) which leads to quenching of quantum dots

• This energy transfer could be explained as – FRET (fluorescence resonance energy transfer) process and the

efficiency of energy transfer is inversely proportional to d6

– Contact Quenching, which leads to the formation of non-fluorescent complex between the gold nanoparticles and QDs

– SET (Surface energy transfer) where the gold nanoparticles are assumed to behave as a mirror and the efficiency of energy transfer is inversely proportional to d4


• Fort orange dots (605 nm) are conjugated with short peptides (GGGC) using the standard procedures

• Following this, the cysteine group on the peptide is attached to monomaleimido nanogold particles via disulfide bonds

• PL spectra was measured before and after forming the quantum dot/gold nanoparticle complex using the 325 nm Ar+ laser

Procedure


Inte

nsity

(ar

b. U

nits

)

Wavelength in nm

540 565 590 615 640

Wavelength in nm

5000

10000

15000

20000

25000

30000

35000

40000

Inte

nsity

(ar

b. U

nits

)

45000

Backscattering from monomaleimido nanogold particles measured using 325 nm Ar+ Laser

PL spectrum of CdSe-ZnS fort orange quantum dots (E605nm) conjugated with GGGC using 325 nm Ar+ Laser

Emission spectra of Fort orange quantum dots and nanogold particles before forming

complex


Wavelength in nm

Inte

nsity

(ar

b. U

nits

)

Inte

nsity

(ar

b. U

nits

)

Wavelength in nm

PL Spectrum of fort orange quantum dots bound to GGGC and fort orange quantum dots with GGGC in

presence of nanogold particles

PL spectrum of the fort orange dots conjugated with GGGC bound to the monomaleimido nanogold particles

Emission spectra of Fort orange dots and gold nanoparticle complex


FRET and beyond…

• There is an observed 10-fold decrease in intensity of emission of QDs and blue-shift in the emission wavelength and this can possibly be explained by calculations

• The FRET demonstrated between the quantum dots and the nanogold particles can be used for mRNA detection in live cells using molecular beacons

• Molecular beacons are single stranded DNA which can form hair-pin loops to bring the fluorescent moiety close to the quenching molecule to facilitate FRET

Questions??


Phonon Bottleneck in Carbon Nanotubes

Applications of Short Nanotubes :Applications of Short Nanotubes :

Carbon Nanotube Field Effect Transistors Carbon Nanotube Field Effect Transistors

Field-Emission DisplaysField-Emission Displays

Biomedical SensorsBiomedical Sensors

Light Emitting DiodesLight Emitting Diodes

Molecular ElectronicsMolecular Electronics

Guo and Lundstrom, APL, 86, 193103 (2005)

The role of phonon scattering in carbon nanotube field-effect transistors (CNTFETs) is explored by solving the Boltzmann transport equation using the Monte Carlo method. The results show that elastic scattering in a short-channel CNTFET has a small effect on the source-drain current due to the long elastic mean-free path (mfp) ( 1 μm). If elastic scattering with a short mfp were to exist in a CNTFET, the on current would be severely degraded due to the one-dimensional channel geometry. At high drain bias, optical phonon scattering, which has a much shorter ( 1 μm), is expected to dominate, even in a short-channel CNTFET. Guo and Lundstrom find, however, that inelastic optical scattering has a small effect in CNTFETs under modest gate bias.



Acoustic Modes in Single Wall Nanotubes (SWNTs)

Amit Raichura, Mitra Dutta, and Michael A. Stroscio, “Continuum Model for Acoustic Phonons and Phonon Bottleneck in Amit Raichura, Mitra Dutta, and Michael A. Stroscio, “Continuum Model for Acoustic Phonons and Phonon Bottleneck in Single Wall Nanotubes,”Single Wall Nanotubes,” J. of Computational ElectronicsJ. of Computational Electronics, Vol. 4, Num 1-2, 91-95; Amit Raichura, Mitra Dutta, and Michael, Vol. 4, Num 1-2, 91-95; Amit Raichura, Mitra Dutta, and MichaelA. Stroscio, “Continuum Model for Acoustic Phonons in Nanotubes: Phonon Bottleneck,”A. Stroscio, “Continuum Model for Acoustic Phonons in Nanotubes: Phonon Bottleneck,” Phys. Stat. Sol.Phys. Stat. Sol. 241; 3448-53241; 3448-53..

Odd Modes:sin sinh cos( )cos( )

2 2

cos cosh sin( )cos( )2 2

cos cosh cos( )cos( )2 2

x

l lu A x k x n t

a a

l lu B x k x n t

a a

l lw C x k x n t

a a

sin2

sinh2

la

kla

tan tanh 02 2

l l

a a

Boundary Conditions

corresponding to 1, 3, 5,… axial half waves = 1.5π, 3.5π, 5.5π,… a

l



22 2 2 22 2

1 12

2 2 2 2 2 21 2 2

2 1 1

1 12 2

1 1 12 2 2

v vv n n

A

C v v vn n n

2 2 22 1

1 22

2 2 2 2 2 22 1 2

1 2 1

1 12 2

1 1 12 2 2

v vv n n n

B

C v v vn n n

2 2

1

21

lhC

M A BI I

C C

1

2x xu u u u ww dVV M

Amplitude Normalization

4

l

aeI

24cos sin 4 cos2 2 2

l l

a al l lae ka e

a a a

2 32 2 22 2 4 cos

2

l l l l

a a a alk ae le k le ka e

a

322 24 sin 4 sin

2 2

l l

a al l

ka e k a ka ea a

(

)



0

400

800

1200

1600

0 5 10 15 20

Wav

e N

umbe

r (c

m-1

)

Normalized Wave Vector

Radial

Torsional

Axial

0

200

400

600

800

0 5 10 15 20

Wav

e N

umbe

r (c

m-1

)

Normalized Wave Vector

Radial

Torsional

Axial

(10,10) nanotube with a length of 2.8 nm (10,10) nanotube with a length of 7 nm

Breathing Mode Frequency = 4.93 THz (k = 165 cm-1) Ando et al.., PRB 65, 235412


Phonon Bottleneck in Carbon Nanotubes: Deformation Potential

cos cosh cos2 2

nB l lx k x n

r a a

cos cosh cos2 2

C l lx k x n

r a a

cos cosh cos2 2

A l lu x k x n

a a a

ODD CASE:

EVEN CASE:

sin sinh cos2 2

nB l lx k x n

r a a

sin sinh cos2 2

C l lx k x n

r a a

sin sinh cos2 2

A l lu x k x n

a a a

uD = 24 eVD = 24 eV

HHdefdef = D D

Bardeen AnsatzBardeen AnsatzPRB 65, 235412


Phonon Bottleneck in Carbon Nanotubes --- Energy Subbands (10,0), length = 4 nm

kz = nπ/LL = length of the nanotube

(10,0) tube:Tc = π(2a)/L & T = 0.43 nmL = 9Tkz = nπ/9T

Ref: G. Pennington, PRB 68: 045426

-8

-4

0

4

8

-1 -0.5 0 0.5 1 Tight-Binding Bands Quantizedin Finite-Length NanotubesWave Vector (kz)

En

ergy

(eV

)


Phonon Bottleneck in Carbon Nanotubes: Phonon Assisted Electron Transitions

Axial Phonon at 55 meV

Intravalley Intersubband 2 1 n=1

-6

-3

0

3

6

-1 -0.5 0 0.5 1

Wave Vector (kz)

En

ergy

(eV

)


Phonon Bottleneck in Carbon Nanotubes: Phonon Assisted Electron Transitions

-8

-4

0

4

8

-1 -0.5 0 0.5 1

Intravalley Intersubband 3 1 n=1

Torsional Phonon at 37 meV

Wave Vector (kz)

En

ergy

(eV

)


Close-packed PbSe colloidal quantum dots

6.4 nm

weaker coupling

stronger coupling

Au

Au

Si3

N4

1.0 nm

2.3 nm

M.D. Fischbein and M. Drndic, U. Penn. Applied Physics Letters, 2006


A: Minibands in PbSe QD Superlattice: 4.9-nm diameter, 0.1-nm spacing

0 500 1000 1500 2000 2500 3000 3500 400010

-12

10-10

10-8

10-6

10-4

10-2

100

Energy (meV)

Tra

nsm

issi

on

Co

effi

cie

nt

Transmission Coefficient - Energy

A: Ec = 2.27 eV L1 = 0.1 L2 = 4.9 Barrier at -1 eV

a

a

b

b c

c

d

d

e e


B: Minibands in PbSe QD Superlattice: 4.8-nm diameter, 0.2-nm spacing

0 500 1000 1500 2000 2500 3000 3500 400010

-16

10-14

10-12

10-10

10-8

10-6

10-4

10-2

100

Energy (meV)

Tra

nsm

issi

on

Co

effi

cie

nt


B: Ec = 2.27 eV L1 = 0.2 L2 = 4.8 Barrier at -1 eV


C: Minibands in PbSe QD Superlattice: 6.4-nm diameter, 0.1-nm spacing

0 500 1000 1500 2000 2500 3000 3500 400010

-12

10-10

10-8

10-6

10-4

10-2

100

Energy (meV)

Tra

nsm

issi

on

Co

effi

cie

nt


C: Ec = 2.27 eV L1 = 0.1 L2 = 6.4Barrier at -1 eV


D: Minibands in PbSe QD Superlattice: 6.3-nm diameter, 0.2-nm spacing

0 500 1000 1500 2000 2500 3000 3500 400010

-14

10-12

10-10

10-8

10-6

10-4

10-2

100

Energy (meV)

Tra

nsm

issi

on

Co

effi

cie

nt


D: Ec = 2.27 eV L1 = 0.2 L2 = 6.3Barrier at -1 eV


Forward bias: V > 0

AuITO

MEH-PPV

CdSe

V+ -

MEH-PPV

e-

Ef of ITO

Ef of Au

ITO

MEH-PPVCdSe Au

h+

Current

MEH-PPVP3HT as electron donor

PCBM as electron acceptor

QD

Might also insert QDs into the highly crystalline polymer interpenetrating network for efficient charge separation and transport in one direction.

P3HT as electron donor

PCBM as electron acceptor

QD

Might also insert QDs into the highly crystalline polymer interpenetrating network for efficient charge separation and transport in one direction.


0

1

2

3

4

5

6

7

8

Evac

PDCTh

PPVPDS PVPy

P3HT

MEH-PPV

HOMO

LUMO

(eV)

PTCDAα -NPD

CuPC

0

1

2

3

4

5

6

7

8

Evac

CdSeGaN

SnO2Fe2O3

TiO2ZnOCdS

ZnS

PbSe

GaAsWO3

Ec

Ev

(eV)

InP

The Large Number of QDs and Conductive Polymers FacilitateDesign of Many Devices

PbS

0

1

2

3

4

5

6

7

8

Evac

PDCTh

PPVPDS PVPy

P3HT

MEH-PPV

HOMO

LUMO

(eV)

PTCDAα -NPD

CuPC

0

1

2

3

4

5

6

7

8

Evac

CdSeGaN

SnO2Fe2O3

TiO2ZnOCdS

ZnS

PbSe

GaAsWO3

Ec

Ev

(eV)

InP

The Large Number of QDs and Conductive Polymers FacilitateDesign of Many Devices

PbS

Conductive Polymers and Quantum Dots


Thermal transport in graphite and carbon nanotubes and the effects of point defect

scattering and boundary scattering mechanisms

Contacts

CNT

Contacts

CNT


( )42.36 10 m/s´

( )41.59 10 m/s´

vLA

vTA

2 2 2

2 1 1

LA TAv v v= +

41.86 10 m/sv = ´c-axis


2D intrinsic thermal conductivity of graphite

Two-dimensional intrinsic thermal conductivity of graphite as a function of temperature.

( )2 3 2

4

d

kfC f

a f=

( )3

2 2,4

di

Mv fl f T

kTfpg=


Effective average point defect concentration

…

Tub

e Dire

ction

…

Tub

e Dire

ction

Row 1st

2nd

nth

…

Tub

e Dire

ction

…

Tub

e Dire

ction

Row 1st

2nd

nth

N: number of circumferential atomsn: number of rowsln: length of CNTd: distance between 2 nearest atoms

Contacts

CNT

Contacts

CNT

For enlightening discussion on end effects see G. Mpourmpakis, G. Froudakis, A. N. Andriotis, M. Menon,

Carbon-nanotube Tips with Edge Made of a Transition Metal, APL, 87, 193105 (2005).


Effective average point defect concentration

…

Tub

e Direction

…

Tub

e Direction

Row 1st

2nd

nth

…

Tub

e Direction

…

Tub

e Direction

Row 1st

2nd

nth

N: number of circumferential atomsn: number of rowsln: length of CNTd: distance between 2 nearest atoms

Contacts

CNT

Contacts

CNT


End effects of point defects

End effects of point defects on CNT thermal conductivity:

solid line is at 300 K, dotted line is at 500 K dashed line is at 800 K


Compare point defect scattering and boundary scattering

Thermal conductivity as a function of CNT tube length at 300 K.

Thermal conductivity as a function of temperature for a single-wall CNT of about 21.2 nm in length:

- solid line is for boundary scattering - dotted line is for point-defect

scattering.


Thermoelectric figure of merit

Thermoelectric figure of merit as a function of temperature for a single-wall CNT of about 4.1 nm in length.

S is the Seebeck coefficient, σ is the electric conductivity, T is the absolute temperature and λ is the thermal conductivity

High ZT values achieved in other systems include AgPbmSbTe2+m reported to exhibit a ZT of ~2.2 at 800 K. ZT values of 2.0 at 300 K have been obtained for PbSnSeTe alloy materials and ~0.8 for the material CsBi4Te6 produced at 225 K.

ZT = S2σT/λ

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