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Biomolecule-Material Interface at the Nanoscale:

Colloquium Department of Physics and Astronomy, University of Mississippi. Biomolecule-Material Interface at the Nanoscale: atomic structure, electronic properties, and energy applications. Sheng Meng. Department of Physics and School of Engineering and Applied Sciences, Harvard University.

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Biomolecule-Material Interface at the Nanoscale:

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  1. Colloquium Department of Physics and Astronomy, University of Mississippi Biomolecule-Material Interface at the Nanoscale: atomic structure, electronic properties, and energy applications Sheng Meng Department of Physics and School of Engineering and Applied Sciences, Harvard University Jan. 31, 2008

  2. Biology is naturally nanoscale Spinach aquaporin

  3. A hybrid bio-nano machine? Schwegler, LLNL We need tools to manipulate … • Substrates for investigating biomolecules • Biosensor for recognition and diagnosis • Implants for medical operation & recovery • Drug delivery • Building up bio-chips • Bio-nanotechnology

  4. Bring Materials to Life In Contact With a Cell

  5. A closer look: BIO|materials interface at nanoscale Kasemo, Surf. Sci. (2002).

  6. Microscopic Understanding of BIO|materials Interface OUTLINE • Water-surface interaction and a molecular view of hydrophilicity • DNA-carbon nanotube interaction and identification 3. Melanin structure and implications in phototechnology

  7. I. Water at surfaces

  8. Structure→Properties Structure: monomer→multilayer H2O/Pt(111) Bonding Vibration H2O/metal Wetting H2O/non-metal Properties→Structure Superhydrophilic Our strategy for water/surface

  9. Theorem I. Theorem II. • Advantages: 1. First-principles (=“parameter free”) Input: atomic numbers 2. Practicality. N ~ 1000, accuracy ~ 0.01 eV. • Drawback: Unknown Vxc? Approximations: LDA GGA Calculation details: • Plane-waves • Pseudopotential(USPP,PAW)+GGA(PBE) • Ab initio molecular dynamics (MD) • Nudged Elastic Band for reaction barriers W. Kohn Nobel prize, 1998 Density functional theory (DFT) Many-electron Schrödinger equation Single-particle Kohn-Sham equation

  10. Time-dependent DFT (TDDFT) for electron dynamics TDDFT: Our implementation: • Real time • Local bases: numeric atomic orbitals • Parallelizable • Order (N) Biomolecules, nanomaterials Applications: • Optical absorption (linear response) • Excited state dynamics • Chemical reactions • Atom collision • Quantum control (strong laser field)

  11. TDDFT Ab initio MD Classic MD Multiscale modelling Adapted from DOE (2006) The scale we are working on: Length: 0.1 1 10100 1000 109 nm Time: 10-18 10-15 10-12 10-9 10-6 10-3 100 s Non-atomistic models

  12. Results A Model System: H2O/Pt(111) Metal surfaces: 1.Simple structure. 2.Wide applications. • Nearly atop, flat (14º), free rotation • dOH (0.98Å) elongated, HOH (105.6º) broadened • Electron transfer (O→Pt) 0.02e • Diffusion barrier: 0.13 eV Single water adsorption

  13. Water clusters 304 meV/H2O 359 520 433 H-bond energy in dimer: >260 meV > 240 meV (free). H-bonds enhanced upon adsorption.

  14. 2D bilayers to 3D multilayers up bottom • H-up: 512 meV • H-down: 524 meV • Half-dissociated: 291 meV H-up H-down 2 BL No dissociation on Pt(111).

  15. Chemical bonding Lone pair-surface d states Localized at bottom layer Nature of water-Pt bonds lone-pair Single molecule Dimer d-orbital H-up H-down

  16. Vibrational recognition Meng et al., Phys. Rev. Lett. (2002).

  17. Summary of water/Pt Structure • Top sites, nearly flatly, various structures • Water doesn’t dissociate • Local lone pair-dz2,dxz chemical bonds • H-bonds strengthened • OH stretches for vibration recognition • Two types of H-bonds Bonding Vibration

  18. General trends: water-surface distance Meng et al., Phys. Rev. B (2004); Phys. Rev. Lett (2003).

  19. d7s1 d8s1 d9s1 d10s1 Wetting order hydrophobic ω hydrophilic Wetting order: RuRh  Pd  Pt  Au

  20. 3.16 Ǻ 2.82 Ǻ Ice tessellation on silica Water/-cristobalite (100) Yang, Menget al., Phys. Rev. Lett. (2004).

  21. Na/K H/F Inverse Design: Properties →Structure A superhydrophilic biocompatible surface A superhydrophilic diamond surface Why diamond? • Lattice match: 2% • Carbon only—biocompatible • Affinity to proteins/DNA: better than Si, Au • Additional merits: hardness, low friction etc • Low cost: Nanocrystalline Applications • Self-cleaning • Scratch and fouling resistant • Heat transfer Meng, Zhang, Kaxiras, Phys. Rev. Lett.(2006).

  22. Eb=0.674 eV >Eice=0.670 eV Wettability before and after surface modification hydrophobic hydrophilic superhydrophilic

  23. Structure→Properties Structure: monomer→multilayer H2O/Pt(111) Bonding Vibration H2O/metal Wetting H2O/non-metal Properties→Structure Superhydrophilic Water/surface: Summary

  24. II. DNA nucleoside interaction and identification with carbon nanotubes Nano Letters 7, 45 (2007). Nano Letters 7, 663 (2007).

  25. Why DNA-carbon nanotube (CNT)? Similarities: • Prototypical one-dimensional • Conducting properties: metal, semiconductor, or insulator? Differences: (single-stranded) DNA: CNT: • extremely flexible stiff • strongly hydrophilic hydrophobic • central in biology central in nanotechnology Combine!

  26. Structure of the single-strand DNA wrapped CNT d(GT)30/CNT Poly(T)/CNT(10,0) Zheng et al., Science (2003); Nature Materials (2003). It is also possible to wrap CNT using long genomic ssDNA (>>100 bases). Gigliotti et al., Nano Lett. (2006).

  27. Label-free DNA detection by electronic signals Ultimate goal: Ultrafast DNA sequencing Jeng et al., Nano Lett. (2006).

  28. Our objective • Single nucleoside/CNT interaction • Discriminate nucleosides based on electronic features DNA detection by electronic means: Is that possible at single-base resolution? What’s missing? • The nature of DNA-CNT interaction • Its dependence on nucleoside identity Methodology Configuration space search: Force Fields Electronic features: Density Functional Theory Nucleoside identification: Artificial Neural Network

  29. DNA/CNT molecular dynamics DNA wraps around CNT in a short time ~ 2 ns.

  30. Proposed experimental setup i) Orientation ii) Electronic feature iii) STM image Meng, Maragakis, Papaloukas, Kaxiras, Nano Letters 7, 45 (2007).

  31. Most stable configurations 28.4% 27.6% 10.1% A/CNT ~1000 configurations (local minima) C/CNT • Interaction through base plane • van der Waals interaction: 0.7~0.8 eV (LDA~0.4 eV) • Electric field further stabilizes adsorption 25.2% 6.8% 4.3% 3.2%

  32. Reduced noises: favorable base orientations Free On CNT Our Theory: through very delicate simulations of electron dynamics (TDDFT), all features are reproduced if we align nanotube axis as indicated. Experiment Hughes et al. (Harvard)

  33. “Measured” vs. calculated orientation • Red line: “measured” CNT axis • Atomic models: Calculated Menget al., Nano Letters 7, 663 (2007).

  34. Electronic interaction: charge density Red: electron depletion Blue: electron accumulation • Mutual polarization • Slight electron transfer from base to CNT

  35. 100% accuracy Electronic features: density of states HOMO LUMO Six features F1: HOMO F2: LUMO F3: Band-gap F4: Number of occupied peaks F5: Highest occupied peak F6: Integral

  36. Experiment: CNT Odom et al., Nature (1998). Identification made easy: STM images Simulation Voltage: +1.4 V Ultrafast sequencing: currently availabe: 30, 000 bases/day (454 LifeSciences) 20 images/s: 1,728,000 bases/day!

  37. III. Melanin structure, flavonoids, and renewable energy applications

  38. Melanin is a ubiquitous pigment Existence • Human: skin, hair, eye, ear, brain • Animals • Plant • Microorganism Functions • Photoprotection • Camouflage • Vitamin D synthesis • Antioxidation • Hearing • Parkinson’s disease Meng & Kaxiras, Biophys. J. (2008).

  39. Molecular structure unknown Monomer units UV-vis spectra ? Chen et al., Pigment Cell Res. (1994). Meredith & Sarna, Pigment Cell Res. (2006).

  40. Our model: a porphyrin-like 2nd structure X-ray UV-vis Kaxiras, Tsolakidis, Zonios, Meng, Phys. Rev. Lett. 97, 128102 (2006).

  41. Hybrid melanin/solid structure for photo-technology

  42. B C A “Just for flavor”: Flavonoids as one of natural pigments Melanin Carotene Flavonoids Chlorophyll ? TiO2 Dye-sensitized TiO2

  43. Attach the pigment to TiO2 semiconductor Band structure wavefunction LUMO HOMO

  44. Optical absorption experiment dye/TiO2 dye Wongcharee et al. (2007).

  45. Charge injection dynamics excited electron LUMO HOMO T=350 K δt=0.02419 fs

  46. Pigment/semiconductor antenna system for solar cells e e

  47. Conclusions BIO|materials contact very promising. Basics: water/surface Sensor: Energy: pigment/TiO2 DNA/CNT • Design biocompatible, superphilic surface • DNA/CNT at different levels -Experimental determination of base orientation -Electronic characteristics in spectroscopy and images: ultrafast sequencing • Renewable energy applications -Porphorin-like melanin structure -light harvest

  48. Acknowledgment Theoretical: Prof. E.G. Wang (IoP,CAS) Dr. Jianjun Yang (IoP,CAS) Dr. Yong Yang (IoP,CAS) Prof. Efthimios Kaxiras Dr. Weili Wang Dr. Maria Fyta Dr. Yina Mo Dr. P. Maragakis (DE Shaw Co.) Dr. C. Papaloukas (Ioannina U) Experimental: Prof. Jene A. Golovchenko Prof. Daniel Branton Mary Hughes Prof. Michael Aziz Funded by: Prof. Shiwu Gao (GU/Chalmers) Prof. B. I. Lundqvist (Chalmers) Prof. Zhenyu Zhang (ORNL/UT) Dr. Wenguang Zhu (UT) Yang Lei (U. London) Prof. Bengt Kasemo (Chalmers) Prof. D. V. Chakarov (Chalmers) Prof. Martin Wolf (Freie U, Berlin) Dr. Ch. Frischkorn (Freie U, Berlin) Prof. Z.X. Guo (U. London) Prof. P. Meredith (U. Queensland) Jennifer Riesz (U. Queensland)

  49. Molecular dynamics (MD) simulation Vibrational spectrum Fourier transformation

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