![Page 1: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/1.jpg)
Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites
Sung Yong Park and David Stroud
Department of Physics, Ohio State University, Columbus, OH 43210.
Work Supported by NSF DMR04-13395 and DMR01-04987. Calculations carried out using facilities of the Ohio Supercomputer Center
![Page 2: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/2.jpg)
1. Introduction
![Page 3: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/3.jpg)
DNA/Au nanoparticle colloids and linking strands
Linker DNA
R. Jin, et. al, J. Am. Chem. Soc. 125, 1643 (2003).
R. Elghanian, et. al., Science 277, 1078 (1997).
Linker DNA
![Page 4: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/4.jpg)
Recent Experiments
Particle-size dependence of Melting
Measured Melting Curves
R.Elghanian, et. al., Science 277, 1078 (1997). C.-H. Kiang, Physica A 321, 164 (2003).
Particlediameter
DNA only
DNA/Au
DNA/Au DNA only
![Page 5: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/5.jpg)
R. Jin, et. al, J. Am. Chem. Soc. 125, 1643 (2003).
Recent Experiments: Rebound Effect
![Page 6: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/6.jpg)
2. Calculation of Optical Properties
![Page 7: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/7.jpg)
Maxwell’s Equations Strategy: Consider each particle as a single dipole
Comparison DDA with more accurate method (89 13nm Au particle)
K.L. Kelly, et. al, CSE, (2001).
![Page 8: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/8.jpg)
3. Structure at low temperature
![Page 9: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/9.jpg)
Recipe for Reaction Limited Aggregations
1. Irrevesible process of bonding
2. Slow reaction (fractal dimension 2.1)
Cf. DLCA (lower fractal dimension)
At low T, this system satisfies these conditions.
![Page 10: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/10.jpg)
TEM Images of Linked DNA Gold Nanoparticles
http://www.chem.nwu.edu/~mkngrp/view1.html
Aggregate of 13 nm diameter DNA/gold nanocomposites Increased magnification image
Comparison with fast processGold-MUA nanoparticles(mercaptoundecanoic acid)
Y. Kim, et. al, Nano Lett. 1, 165 (2001).
![Page 11: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/11.jpg)
?
Morphology dependence of extinction cross section
Theory Experiment
![Page 12: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/12.jpg)
Comparison of size dependence of the extinction cross section
RLCA cluster Simple Cubic Cluster
![Page 13: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/13.jpg)
4. Melting Transition
![Page 14: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/14.jpg)
My strategy for explaining the results in experiments
1. DNA hybridizationo Two-state model
o “Multiple link per bond” effect
2. Cluster configuration at given temperature T
o Bond percolation model
o Model the system as simply as possible
3. Calculation of Extinction Cross Sectiono Discrete Dipole Approximation (Draine & Flatau, 1994)
o Dilute cluster limit
o Reaction limited cluster aggregation model
![Page 15: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/15.jpg)
DSS
KD
SS
][
]][[
Two State Model
)exp( TG
3)()( MM TTbTTaG
We treat p as static probability.
][D : Concentration of duplex
: Total concentration of DNA
probability that DNA pair remains hybidized is
1. DNA hybridization
![Page 16: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/16.jpg)
“multiple DNA per bond” effect
p p =1-(1-p)
n
eff
n
Particle-size dependence of avg. no of DNA per bond <n>
Temperature dependence of Peff
= Prob. that pair of Au particles have > 1 DNA links
Particle diameter
1. DNA hybridization
![Page 17: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/17.jpg)
My strategy for explaining the results in experiments
1. DNA hybridizationo Two-state model
o “Multiple link per bond” effect
2. Cluster configuration at given temperature T
o Bond percolation model
o Model the system as simply as possible
3. Calculation of Extinction Cross Sectiono Discrete Dipole Approximation (Draine & Flatau, 1994)
o Dilute cluster limit
o Reaction limited cluster aggregation model
![Page 18: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/18.jpg)
1. Prepare the low-T config.
Schematics of melting for a regular square lattice
2. Cut bonds with prob. 1-p
3. Place the connected clusters into
larger box with random position and random orientation.
![Page 19: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/19.jpg)
p=0.95 p=0.50
p=0.0
p=0.25>pc
Our model: melting of a regular simple cubic cluster
Bond percolationthreshold
p=0.15<pc
![Page 20: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/20.jpg)
My strategy for explaining the results in experiments
1. DNA hybridizationo Two-state model
o “Multiple link per bond” effect
2. Cluster configuration at given temperature T
o Bond percolation model
o Model the system as simply as possible
3. Calculation of Extinction Cross Sectiono Discrete Dipole Approximation (Draine & Flatau, 1994)
o Dilute cluster limit
o Reaction limited cluster aggregation model
![Page 21: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/21.jpg)
Calculation of extinction cross section
Using Discrete Dipole Approximation (DDA)
Dilute Cluster LimitTemperature dependence of extinction cross section at 520nm
DNA only
DNA only (higher concentration)
![Page 22: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/22.jpg)
DNA only
DNA/Au
DNA/Au
DNA only
Theory vs. Experiment
D
Temperature dependence of extinction cross section at 520nm
Theory Experiment
DNA only
DNA only (higher concentration)
![Page 23: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/23.jpg)
5. Effects of Restructuring
![Page 24: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/24.jpg)
If T increases, bonding becomes reversible.Thus it becomes compact cluster.
Thus, the model to mimic this feature is needed.
o Bond percolation model
+ Reaction limited cluster aggregation model
![Page 25: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/25.jpg)
Radius of gyration
RLCA case
Slope=fractal dimension =2.1
With RLCA + BP
Long time: 3.0
Short time=2.1
![Page 26: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/26.jpg)
P=0.9
N MC=0 N MC=7000
N MC=70000 MC=70000
N MC=7000
RLCA
![Page 27: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/27.jpg)
6. Summary
![Page 28: Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites Sung Yong Park and David Stroud Department of Physics, Ohio State University,](https://reader035.vdocuments.net/reader035/viewer/2022062517/56649f315503460f94c4d205/html5/thumbnails/28.jpg)
DNA/Au nanocomposite system
R. Jin, et. al, J. Am. Chem. Soc. 125, 1643 (2003).
R. Elghanian, et. al., Science 277, 1078 (1997).
Linker DNA
1. Expected phase diagram
2. Morphologies from a structural model
3. DDA calculation of extinction cross section
gel sol Ind. particles
Gel-sol transition
meltingtransition T0
gel sol
near melting transition
Gel-soltransition
meltingtransition
Experiment