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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.

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Structure Formation, Melting and the Optical Properties of Gold/DNA Nanocomposites

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  1. 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

  2. 1. Introduction

  3. DNA/Au nanoparticle colloids and linking strands Linker DNA Linker DNA R. Elghanian, et. al., Science277, 1078 (1997). R. Jin, et. al, J. Am. Chem. Soc. 125, 1643 (2003).

  4. Recent Experiments Measured Melting Curves Particle-size dependence of Melting DNA/Au DNA only Particle diameter DNA only DNA/Au R.Elghanian, et. al., Science277, 1078 (1997). C.-H. Kiang, Physica A 321, 164 (2003).

  5. Recent Experiments: Rebound Effect R. Jin, et. al, J. Am. Chem. Soc. 125, 1643 (2003).

  6. 2. Calculation of Optical Properties

  7. 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).

  8. 3. Structure at low temperature

  9. 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.

  10. TEM Images of Linked DNA Gold Nanoparticles Aggregate of 13 nm diameter DNA/gold nanocomposites Increased magnification image http://www.chem.nwu.edu/~mkngrp/view1.html Comparison with fast process Gold-MUA nanoparticles (mercaptoundecanoic acid) Y. Kim, et. al, Nano Lett. 1, 165 (2001).

  11. Morphology dependence of extinction cross section ? Experiment Theory

  12. Comparison of size dependence of the extinction cross section RLCA cluster Simple Cubic Cluster

  13. 4. Melting Transition

  14. My strategy for explaining the results in experiments • Model the system as simply as possible 1. DNA hybridization • Two-state model • “Multiple link per bond” effect 2. Cluster configuration at given temperature T • Bond percolation model • Reaction limited cluster aggregation model 3. Calculation of Extinction Cross Section • Discrete Dipole Approximation (Draine & Flatau, 1994) • Dilute cluster limit

  15. 1. DNA hybridization Two State Model probability that DNA pair remains hybidized is : Concentration of duplex : Total concentration of DNA We treat p as static probability.

  16. n n p p =1-(1-p) eff Particle-size dependence of avg. no of DNA per bond <n> 1. DNA hybridization “multiple DNA per bond” effect = Prob. that pair of Au particles have > 1 DNA links Particle diameter Temperature dependence of Peff

  17. My strategy for explaining the results in experiments • Model the system as simply as possible 1. DNA hybridization • Two-state model • “Multiple link per bond” effect 2. Cluster configuration at given temperature T • Bond percolation model • Reaction limited cluster aggregation model 3. Calculation of Extinction Cross Section • Discrete Dipole Approximation (Draine & Flatau, 1994) • Dilute cluster limit

  18. 2. Cut bonds with prob. 1-p 1. Prepare the low-T config. 3. Place the connected clusters into larger box with random position and random orientation. Schematics of melting for a regular square lattice

  19. p=0.95 p=0.50 p=0.25>p p=0.15<p c c p=0.0 Our model: melting of a regular simple cubic cluster Bond percolation threshold

  20. My strategy for explaining the results in experiments • Model the system as simply as possible 1. DNA hybridization • Two-state model • “Multiple link per bond” effect 2. Cluster configuration at given temperature T • Bond percolation model • Reaction limited cluster aggregation model 3. Calculation of Extinction Cross Section • Discrete Dipole Approximation (Draine & Flatau, 1994) • Dilute cluster limit

  21. Calculation of extinction cross section Using Discrete Dipole Approximation (DDA) Dilute Cluster Limit Temperature dependence of extinction cross section at 520nm DNA only DNA only (higher concentration)

  22. D Theory vs. Experiment Temperature dependence of extinction cross section at 520nm DNA only DNA/Au DNA only DNA only DNA/Au DNA only (higher concentration) Theory Experiment

  23. 5. Effects of Restructuring

  24. If T increases, bonding becomes reversible. Thus it becomes compact cluster. Thus, the model to mimic this feature is needed. • Bond percolation model + Reaction limited cluster aggregation model

  25. RLCA case Radius of gyration Slope=fractal dimension =2.1 With RLCA + BP Long time: 3.0 Short time=2.1

  26. P=0.9 N MC=7000 N MC=0 RLCA N MC=7000 MC=70000 N MC=70000

  27. 6. Summary

  28. Linker DNA R. Elghanian, et. al., Science277, 1078 (1997). DNA/Au nanocomposite system 1. Expected phase diagram Gel-sol transition melting transition 0 T gel sol Ind. particles 2. Morphologies from a structural model 3. DDA calculation of extinction cross section Experiment gel sol melting transition Gel-sol transition near melting transition R. Jin, et. al, J. Am. Chem. Soc. 125, 1643 (2003).

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