Simulating living molecules
with quantum computers
Vlatko Vedral,
Oxford & Singapore
vlatko.vedral@qubit.org
Talk Outline
A discussion regarding reductionism;
Quantum effects in biology;
Cold atoms quantum computers;
Simulating energy transfer with quantum computers;
Simulating life?
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).
Reductionism or not?
Macroscopic laws are compatible with the
microscopic ones, but can they be fully
derived from them?
“Everything is either Physics or Stamp Collecting”
Rutherford
"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
“At each stage, entirely new laws and
generalisations are necessary, requiring
inspiration and creativity.”
Anderson
Smallest Clock
Peter Pesic, 1993 Eur. J. Phys. 14, 90
𝒍=
𝒉𝑻
𝑴
(Wigner)
E-coli: 𝒍 = 𝟎. 𝟑𝝁𝒎, 𝐦 = 𝟖𝒙𝟏𝟎−𝟏𝟑 𝒈, 𝑻 ~𝟓𝟎𝒎𝒊𝒏𝒔
Reflects Schroedinger’s beliefs in “What is life?”
Can we Derive Biological
Laws?
k=3
Any averaging Macroscopic Properties of the Periodic Ising
Lattice at Ground State are in general, undecidable.
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,
VV
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)
Respiratory complex I
Left:. L. A. Sazanov, Biochemistry, 46, 2275 (2007).
Right: J. Hirst, Biochem. J., 425, 327 (2010).
Marcus theory
Holstein Hamiltonian
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
3.0x10
1.5x10
Exci
550
tatio
1.0x10
500
n wa
5.0x10
450
ngth
vele
0.0
400
350
[nm]
600
550
500
Emis
sion
450
w
400
th [nm
g
n
e
l
ave
]
5
5
4
5
[arb. u.]
2.0x10
5
Intensity
2.5x10
5
•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 of excitation wavelengths
above 450nm , where most the emission signal is
the contribution from arc lamp.
Phonon frequency at Room Temperature
•RC I concn. of 2.5 mg/ml in MOPS solution
Intensity [arb. u.]
29.4 nm
1.0
Absorption
Emission
Lorentzian Fit
•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).
0.5
•Stokes shift => approximate phonon
0.0
380 400 420 440 460 480 500 520 540 560 frequency
Wavelength [nm]
•Multiple Lorentzian peak fitting =>
wavelength difference estimated between
the most intense peak in the two curves
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)
Can we simulate the salient aspects of a biological
system in a tunable laboratory setup?
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)
Greiner Lab – Harvard 2010
Bloch Lab – MPQ 2011
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!
Simulation of Biological Electron Transport
Tune interactions and correlation functions of auxiliary BEC bath to simulate noise
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
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.
Living Systems = Maxwell’s demons
Jacques Monod “Chance and Necessity” (1970)
(Democritus, "Everything existing in the universe is the fruit of chance and
necessity.“)
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?