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Simulating living molecules with quantum computers

Simulating living molecules with quantum computers. Vlatko Vedral , Oxford & Singapore v latko.vedral@qubit.org. A discussion regarding reductionism; Quantum effects in biology; Cold atoms quantum computers; Simulating energy transfer with quantum computers; Simulating life?.

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Simulating living molecules with quantum computers

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  1. Simulating living molecules with quantum computers VlatkoVedral, Oxford & Singapore vlatko.vedral@qubit.org

  2. A discussion regarding reductionism; Quantum effects in biology; Cold atoms quantum computers; Simulating energy transfer with quantum computers; Simulating life? Talk Outline

  3. In collaboration with… • Ross Dorner, John Goold, Libby Heaney, • Felix Pollock, Felix Binder, Tristan Farrow, AgataChecinska • Mile Gu, Mark Williamson • Discussions with: Martin Aulbach, Oscar Dahlsten, Andrew Garner, • KavanModi, Giovanni Vacanti. • Funding: Ministry of Education and National Science Foundation, • Singapore, • Leverhulme Trust, Templeton Foundation, James Martin School (Oxford).

  4. Macroscopic laws are compatible with the microscopic ones, but can they be fully derived from them? Reductionism or not?

  5. Different Views “Everything is either Physics or Stamp Collecting” "The ability to reduce everything to simple fundamental laws does not imply the ability to start from those laws and reconstruct the universe.” –”More is Different” Science 1972 Rutherford “At each stage, entirely new laws and generalisations are necessary, requiring inspiration and creativity.” Anderson

  6. SmallestClock Peter Pesic, 1993 Eur. J. Phys. 14, 90 (Wigner) E-coli: Reflects Schroedinger’s beliefs in “What is life?”

  7. Can we Derive Biological Laws? Hk Hk Hk Hk Hk Hk 3 3 2 Hk Hk Hk Hk Hk Hk Hk Hk Hk Hk 1 0 4 3 2 3

  8. Conclusion of Gu et al. Hk Hk Hk Hk Hk Hk 3 3 2 Hk Hk Hk Hk Hk Hk Hk Hk Hk Hk 1 0 4 k = 3 3 2 3 Any averaging Macroscopic Properties of the Periodic Ising Lattice at Ground State are in general, undecidable.

  9. Towards Quantum Simulations of Biological Information Flow Interface Focus Theme Issue `Computability and the Turning centenary' Ross Dorner, John Goold and VV Quantum coherent contributions in biological electron transfer Ross Dorner, John Goold, Libby Heaney, Tristan Farrow, V V

  10. Electron transfer in biology • The basis of all oxidation-reduction reactions in an • organism; photosynthesis, vision, respiration... • Current/future technologies: Molecular electronic • devices, organic LEDs Figure: M. Brownlee, Nature 414, 813 (2001)

  11. Respiratory complex I Left:. L. A. Sazanov, Biochemistry, 46, 2275 (2007). Right: J. Hirst, Biochem. J., 425, 327 (2010).

  12. Marcus theory

  13. Holstein Hamiltonian

  14. Room temperature emission from Respiratory Complex I (RCI) • Arc Lamp emission RC I emission: FMN + FeS • Optical excitation using arc lamp ramped • from λ = 350 to 550 nm • RC-I aliquot concn. 1mg/ml in MOPS (at RTP) • A grating spectrometer was used to analyse the emission then recorded with a Silicon CCD array. • Sharp rise in emission intensity in the excitation range λ = 350 to 450 nm, peaking at 410nm. • This coincides with the wavelength range where the FeS clusters and the FMN molecule in RC I absorb strongly. • Low RC I absorption ofexcitation wavelengths above 450nm , where most the emissionsignal is the contribution from arc lamp.

  15. Phonon frequency at Room Temperature • RC I concn. of 2.5 mg/ml in MOPS solution • Room temperature excitation using arc lamp centred λ = 389.5nm; Grating spectrometer was used to select the excitation line (FWHM ~12nm) • Absorption measured with Perkin-Elmer spectrometer • Red-shifted emission spectrum from RC I (red curve) with respect to the absorption spectrum (blue curve). • Stokes shift =>approximate phonon frequency • Multiple Lorentzian peak fitting => wavelength difference estimated between the most intense peak in the two curves

  16. Parameters • On-site energies from reduction potential data1 • Vibronic coupling strength from DFT simulations of inner sphere reorganisation energy2: g = 10 – 30 THz • Vibronic frequencies from NRVS, resonance Raman • spectroscopy and DFT2: ω = 5 - 10 THz • Tunnelling rates fitted from DFT simulations of in situ electron tunnelling within RC-I1: t = 1 - 10 GHz 1. T. Hayashi and A. A. Stuchebrukhov, PNAS 45, 19157 (2010). 2. D. Mitra et al, Biochem.US. 50, 5220 (2011)

  17. Can we simulate the salient aspects of a biological system in a tunable laboratory setup?

  18. Ultra-cold atoms as open system quantum simulators A trapped single ion inside a Bose Einstein Condensate C. Zipkes, S. Palzer, C. Sias and M. Kohl Nature. 464, 388 (2010) Polaron Problem C.H. Wu, A. Sommer, and A.W. Zwierlien PRL. 464, 102 230402 (2011)

  19. Greiner Lab – Harvard 2010 Bloch Lab – MPQ 2011

  20. Simulation of Holstein Hamiltonian With Two Component ultra cold atomic mixtures Dieter Jaksch Group Polaron Physics in Optical Lattices Phys. Rev. A 76, 011605(R) (2007) Transport of strong-coupling polarons in optical lattices New J. Phys. 10, 033015 (2008) Trap single impurity on a lattice potential immersed in an auxiliary BEC!

  21. Simulation of Biological Electron Transport Tune interactions and correlation functions of auxiliary BEC bath to simulate noise

  22. Properties of living systems: Homeostasis: Regulation of the internal environment to maintain a constant state; Organization: Being structurally composed of one or more cells, which are the basic units of life. Metabolism: Transformation of energy by converting chemicals and energy into cellular components and decomposing organic matter. Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter. Adaptation: The ability to change over a period of time in response to the environment. Reproduction: The ability to produce new individual organisms

  23. No wonder that enthusiastic biologists in the nineteenth century, anxious to conclude that there was no qualitative difference between life and chemical processes, tried to believe that the crystal furnished the link, that its growth was actually the same as the growth of a living organism. But excusable though the fancy was, no one, I think, believes anything of the sort today. Protoplasm is a colloid and the colloids are fundamentally different from the crystalline substances. Instead of crystallizing they jell, and life in its simplest known form is a shapeless blob of rebellious jelly rather than a crystal eternally obeying the most ancient law. The Colloid and the Crystal (Joseph Wood Krutch)

  24. Living Systems = Maxwell’s demons Jacques Monod “Chance and Necessity” (1970) (Democritus, "Everything existing in the universe is the fruit of chance and necessity.“)

  25. Questions • Are biomolecules capable of coherent quantum behaviour? • Are quantum effects just deliberately suppressed or is there any advantage • in having a fully quantum energy and matter transport? • How far can quantum computers simulate bio-molecules? • Can we understand laws of chemistry and biology as being consequencs of • microsopic quantum physics? (Do physical facts fix all facts?) • Can we build living systems bottom up?

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