Simulating living molecules - PowerPoint Presentation

Slide1

Simulating living molecules with quantum computers

Vlatko

Vedral

,

Oxford

&

Singapore

v

latko.vedral@qubit.orgSlide2

Talk Outline

A discussion regarding reductionism;

Quantum effects in biology;

Cold atoms quantum computers;

Simulating energy transfer with quantum computers;

Simulating life?Slide3

In collaboration with…

Ross

Dorner

, John

Goold

, Libby Heaney,

Felix Pollock, Felix Binder, Tristan Farrow,

Agata

Checinska

Mile

Gu

, Mark Williamson

Discussions with

: Martin

Aulbach

, Oscar

Dahlsten

, Andrew Garner,

Kavan

Modi

, Giovanni

Vacanti

.

Funding

: Ministry of Education and National Science Foundation,

Singapore,

Leverhulme

Trust, Templeton Foundation, James Martin School (Oxford).Slide4

Reductionism or not?

Macroscopic laws are compatible with the

microscopic ones, but can they be fully

d

erived from them?Slide5

“At each stage, entirely new

laws and

generalisations are necessary, requiring inspiration and creativity.”

Different Views

"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

Anderson

“

Everything is either Physics or Stamp

Collecting

”

Rutherford Slide6

Smallest Clock

Peter

Pesic

, 1993

Eur

. J. Phys.

14,

90

E-coli:

Reflects

Schroedinger’s

beliefs in “What is life?”

(Wigner)Slide7

Can we Derive Biological

Laws?

H

k

3

3

1

0

2

4

3

2

3

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

kSlide8

Conclusion of

Gu

et al.

Any averaging Macroscopic Properties of the Periodic

Ising

Lattice at Ground State are in general,

undecidable

.

H

k

3

3

1

0

2

4

3

2

3

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

H

k

k = 3Slide9

Towards Quantum Simulations of Biological Information Flow

Interface Focus Theme Issue

`Computability and the Turning centenary

'

Ross

Dorner

, John

Goold

and

VVQuantum coherent contributions in biological electron transferRoss

Dorner, John Goold, Libby Heaney, Tristan Farrow, V VSlide10

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)Slide11

Respiratory complex I

Left:. L. A. Sazanov,

Biochemistry

,

46,

2275 (2007).

Right: J. Hirst,

Biochem. J

.,

425, 327 (2010).Slide12

Marcus theorySlide13

Holstein HamiltonianSlide14

Optical excitation using arc lamp ramped

from λ = 350 to 550 nm

RC-I aliquot

conc

n

.

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 of

excitation wavelengths above

450nm

, where most the emission

signal is the contribution from arc lamp.

Room temperature emission from Respiratory Complex I (RCI)

Arc Lamp emission

RC I emission: FMN +

FeSSlide15

RC I

conc

n

.

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

Phonon frequency at Room TemperatureSlide16

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)Slide17
Slide18
Slide19

Can we simulate the salient aspects of a biological system

in a tunable laboratory setup?Slide20

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) Slide21

Greiner Lab – Harvard 2010

Bloch Lab – MPQ 2011Slide22

Simulation of Holstein Hamiltonian

With Two Component ultra cold atomic mixtures

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)

Dieter Jaksch Group

Trap single impurity on a lattice potential immersed in an auxiliary BEC!Slide23

Simulation of Biological Electron Transport

Tune interactions and correlation functions of auxiliary BEC bath to simulate noiseSlide24

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 organismsProperties of living systems:Slide25

The Colloid and the Crystal (Joseph Wood Krutch)

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. Slide26

Living

Systems = Maxwell’s demons

Jacques Monod “Chance and Necessity” (1970)

(

Democritus

, "Everything existing in the universe is the fruit of chance and

necessity

.“)Slide27

Questions

Are biomolecules capable of coherent quantum

behaviour

?

Are quantum effects just deliberately suppressed or is there any advantage

i

n 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?