structure formation, melting and the optical properties of gold/dna nanocomposites

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

1. Introduction

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

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

R. Jin, et. al, J. Am. Chem. Soc. 125, 1643 (2003).

Recent Experiments: Rebound Effect

2. Calculation of Optical Properties

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).

3. Structure at low temperature

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.

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).

?

Morphology dependence of extinction cross section

Theory Experiment

Comparison of size dependence of the extinction cross section

RLCA cluster Simple Cubic Cluster

4. Melting Transition

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

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

“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

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

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.

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

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

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)

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)

5. Effects of Restructuring

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

Radius of gyration

RLCA case

Slope=fractal dimension =2.1

With RLCA + BP

Long time: 3.0

Short time=2.1

P=0.9

N MC=0 N MC=7000

N MC=70000 MC=70000

N MC=7000

RLCA

6. Summary

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