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Data Blitz

Data Blitz. John Fonner 4.05.2010. Overview. Experimental and Simulated Chain Packing X-ray diffraction (experimental) Radial distribution functions (simulated) PPyCl Matrix Formation T59 simulations. X-Ray Diffraction. Bragg’s Law: n λ =2d sin θ.

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Data Blitz

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  1. Data Blitz John Fonner 4.05.2010

  2. Overview • Experimental and Simulated Chain Packing • X-ray diffraction (experimental) • Radial distribution functions (simulated) • PPyCl Matrix Formation • T59 simulations

  3. X-Ray Diffraction Bragg’s Law: nλ=2dsinθ Image source: http://upload.wikimedia.org/wikipedia/commons/7/74/Loi_de_bragg.png

  4. X-Ray Diffraction Synthesis: PPyCl thick film (2C/cm2) on ITO XRD: 3-40° range, 0.02° step size, 10s dwell time

  5. Simulated X-Ray Diffraction

  6. N-CL Radial Distribution Function

  7. N-N Radial Distribution Function

  8. Density Values • Two Problems: • Experimentally “reported” density values are usually ~1.45 g/cm3 • Cascales, et al. report in silico density values between 1.33 and 1.47 using a primitive MD model

  9. Doped PPy Matrix Formation • “Gas phase” simulations do not properly sample PPy-dopant interactions • Start with final undoped PPy structures • Randomly add Cl- and slowly turn on interactions • Mutate PPy from undoped to doped electrostatics Mutate PPy→PPyCl Add Cl-

  10. Matrix Formation: 2 Alternate Approaches • Hypothesis: The large change in backbone flexibility between doped and undoped PPy may inhibit chain packing • Test: Use doped torsion parameter during undoped matrix formation • Hypothesis: The more crystalline starting structures of other MD studies may have improved chain packing • Test: Try “pre-packing” the PPy chains in a crystal pattern

  11. T59 Simulations Native T59: THRTSTLSYFVI-GGGSC • REMD simulations in water – radius of gyration, hydrogen bonding, phi-psi angles • Compare with mutants

  12. Replica Exchange Molecular Dynamics

  13. Questions? Feedback? This is how I explain computer problems to my cat. My cat usually seems happier than me.

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