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Modélisation mathématique pour l'analyse et la conception de dispositifs nanophotoniques
Étienne Boulais, Ph.D. Stagiaire postdoctoral Génie Physique – École Polytechnique de Montréal Chimie – Université de Montréal
Controlling photons at the nanoscale is a crucial aspect of modern technology
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≈l
Moresensi)vebiosensingdevices
Nanoscaleop)caldevices
Be4ersolarcells Fastercompu)ng
Nature uses precise chromophore architectures to absorb and funnel light to reaction centers
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Purple bacteria
LH1
Reaction CenterEnergy conversion
LH2
10 nmStrumpfer et al. Phys. Chem. Lett., 2012
DNA NANOTECHNOLOGY ENGINEERING 3D MOLECULAR SCAFFOLDS
DNA : a programmable building material
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Guanine Cytosine
Adenine ThymineG
A
T
A
C
C
T
A
T
G
5’
3’ 5’
3’
DNA forms engineered self-assembled programmable nanostructures
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P. Rothemund, Nature 2006 Credit : Wyss Institute
Complex nanoscale 3D structures can be engineered
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Y. Ke et al. Science 2012
Block structures Curved topology
K. Pan et al. Nat. Comm. 2014
Cages
C. Zhang et al. PNAS 2008LCBB@MIT
DNA can be used to program the assembly of chromophores and inorganic particles
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Sequence-specificgroovebinding
CovalentlymodifiedDNAbases
M. K. Teng et al. Nuc. Ac. Res. 1988. J. Barbaric et al. Org. Biomol. Chem. 2006.
I use DNA nanotechnology and computer-aided engineering to design nanophotonic devices
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Programmable DNAscaffoldsThe supramolecular assembly of membrane proteins thus
described is called the photosynthetic chromatophore. A purplebacterial cell may contain over 1000 chromatophores,65 eachcontaining over 3000 BChls.5 In many species, chromatophoresform spherical vesicles such as the one shown in Figure 5.8 The
chromatophore is an amazing biological device whose primaryfunction is light harvesting and the formation of a membranepotential. This function can be traced in great detail acrossmany time scales, beginning with the capture and subpico-second transfer of light energy among its constituent pigments.The overall efficiency of light harvesting in the chromato-
phore can be calculated by combining four processes in a so-called stochastic rate equation, (i) light absorption, (ii)excitation migration, as described by the FRET rates in eqs 1,3, and 4), (iii) electron transfer in the RC, and (iv) fluorescenceor so-called internal conversion that leads to the finitenanosecond lifetime of BChl electronic excitation. Process(iv) limits the efficiency of light harvesting; the longer the timefrom light absorption to electron transfer at the RC, the less theefficiency due to loss of excitation to fluorescence or internalconversion. The solution of the stochastic rate equation5,7,8
permits one to calculate various characteristics of thechromatophore, in particular, its light-harvesting efficiency of90%. It should be noted that optimal light-harvesting efficiency isnot the only relevant constraint to give a photosynthetic organisma competitive advantage. For example, the organism also needs toprotect itself from photo-oxidative damage, especially under highlight conditions, by dissipating excitation energy across its wholelight-harvesting apparatus rather than only in the RCs.The chromatophore of purple bacteria displays a remarkable
simplicity compared to its evolutionary competitors in cyano-bacteria, algae, and plants; the latter usurped the biosphere byevolving a more complex photosynthetic apparatus that feedsphotoexcited electrons into various cellular processes, for example,the synthesis of sugar, and replenishes electrons by splitting waterinto oxygen gas, electrons, and protons (the purple bacteria justcirculate electrons in the chromatophore). Nonetheless, bystudying the chromatophore, the simplest known incarnation ofbiological photosynthesis, the key features of the quantum biologyof light harvesting in all of biological photosynthesis are revealed,in particular, the role of quantum coherence.The role of quantum coherence in purple bacteria light
harvesting was first established in 1997.30 Quantum coherencemanifests itself in exciton states of BChl clusters that bunch up
transition dipole moments of individual BChls. Additionally,quantum coherence shifts energy levels and improvesresonance (spectral overlap) between BChl clusters. As aresult, quantum coherence critically increases FRET rates,which allows additional pigments, placed a distance away fromthe RC, to capture additional photons and rapidly feedexcitation energy to the SP for conversion into an electronicgradient before significant loss of energy occurs. Quantumcoherence thus also allows antenna protein complexes to bespaced far enough apart that other processes, such as diffusionof quinone molecules in the chromatophore membrane, canproceed unhindered while maintaining remarkably high light-harvesting efficiency.
The chromatophore is an amazing optoelectronic device.It amasses pigments in a hierarchical pattern, as shown inFigure 5b, exploiting quantum coherence in a beautiful andelegant manner.
■ AUTHOR INFORMATIONCorresponding Author*E-mail: [email protected].
BiographiesJ. Strumpfer received his M.Sc in Computational Chemistry from theUniversity of Cape Town in 2009 and is presently pursuing his Ph.D.studies in the Theoretical and Computational Biophysics Group.
M. S ener received his Ph. D. in Physics at the State University ofNew York at Stony Brook in 1999 and is presently a postdoctoralresearcher in the Theoretical and Computational Biophysics Group.
K. Schulten received his Ph.D. from Harvard University in 1974. He isSwanlund Professor of Physics and is also affiliated with theDepartment of Chemistry as well as with the Center for Biophysicsand Computational Biology. Prof. Schulten is a full-time facultymember in the Beckman Institute, co-director of the Center for thePhysics of Living Cells, and directs the Theoretical and ComputationalBiophysics Group (http://www.ks.uiuc.edu).
■ ACKNOWLEDGMENTSThe authors are supported by grants from the National ScienceFoundation (MCB-0744057 and PHY-0822613) as well as theNational Institutes of Health (P41-RR005969).
Figure 5. Spherical chromatophore from Rhodobacter sphaeroidesshowing (a) proteins and (b) bacteriochlorophylls. The RC is shownin red, LH1 is in blue, and LH2 is in green. LH1−RC complexes formfigure-eight-shaped dimers in Rhodobacter sphaeroides.8
Quantum coherence criticallyincreases FRET rates, which allowsadditional pigments, placed adistance away from the RC, to
capture additional photons and rap-idly feed excitation energy to the SPfor conversion into an electronicgradient before significant loss of
energy occurs.
The Journal of Physical Chemistry Letters Perspective
dx.doi.org/10.1021/jz201459c | J. Phys. Chem.Lett. 2012, 3, 536−542540
Fully-customizable polymeric 3D molecular nanopegboard
Set of photoactive building blocks QD, plasmonic NPs, molecules
Nanophotonic devices with tailored properties
4 AXIS OF RESEARCH I. Photonic 2D lattice II. Customizable excitonic circuits III. Customizable plasmonic particles IV. Plasmonic nanolenses for cell nanosurgery
Axis I : Engineering photonic 2D lattices
400 500 600 700 800 9000
1
2
3
0
2
4
6x 1018x 105
Wavelength (nm)
Mol
ar e
xtin
ctio
n (M
-1cm
-1)
Irrad
ianc
e (p
hoto
ns n
m-1 m
-2)
AF488
AF546
AF555
AF568
AF594
AF647
AF700
AF750
RC
Solar irradiance
Wavelength
Dye libraryAF546AF568
AF647
AF700
AF750
AF488
Reaction center
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Monte-Carlo optimization helps find the best lattice configuration
FRET (Markov chain) : dρi
dt= kjiρ j −
i≠ j∑ kijρi −
ρi
τ⎛⎝⎜
⎞⎠⎟j≠i
∑
Axis II : Engineering customizableexcitonic circuits
J-bit : A cyanine-based nanophotonic building block
Pseudoisocyanine (PIC)
E Boulais , …, A Aspuru-Guzik, M Bathe. In Preparation12
UV-Vis
Circular dichroism
Quantum coupling
J-bit
Monomer
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E Boulais , …, A Aspuru-Guzik, M Bathe. In Preparation
Axis II : Engineering customizableexcitonic circuits
Computational methods gives insight on the structure of the J-Bit
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E Boulais , …, A Aspuru-Guzik, M Bathe. In Preparation
Axis II : Engineering customizableexcitonic circuits
Computational methods gives insight on exciton transport
H = Hel + Hph + Hel-ph
ElectronHamiltonian
PhononHamiltonian
Electron-phononinterac)on
∂ρµν
∂t= −iω µνρµν + Rµν ,µ 'ν '
µ 'ν '∑ ρµ 'ν '
Axis III : Engineering customizableplasmonic particles
E. Boulais et al. J. Photochem. Photobiol C. 2013
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Extinction
Scattering
Absorption
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E. Boulais et al. J. Photochem. Photobiol C. 2013
Axis III : Engineering customizableplasmonic particles
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Axis III : Engineering customizableplasmonic particles
Disk Sphere Cylinder Prism Torus
Engineering plasmon resonance
At the macroscale…
Can we do something similar at the nanoscale ?
Box Sphere Prism
S. Wei, E. Boulais et al. Science, 201419
Axis III : Engineering customizableplasmonic particles
We design nanomold with DNA
S. Wei, E. Boulais et al. Science, 201420
Ag-Box Ag-Triangle Ag-NP Au-Box Composite structures
Axis III : Engineering customizableplasmonic particles
The particle replicate the mold
S. Wei, E. Boulais et al. Science, 201421
1.95 eV 2.45 eV
2.75 eV 3.10 eV
Axis III : Engineering customizableplasmonic particles
Target plasmonic properties - wavelength- near-field
Computational framework
- Tailored particle- Required mold
Synthesis
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Plasma Pressure wave Nanobubble
The membrane is perforated by plasma-mediated nanobubbles
E. Boulais et al. Nano Lett. 2012
How can we engineer optimized nanolenses for cell nanosurgery ?
Axis IV : Engineering plasmonic nanolenses for cell nanosurgery
E.Boulaisetal.NanoLe(.12(9),2012.Water § Fluid dynamics § Heat transfer § Phase change
Electromagnetic interaction
Nanostructure § Lattice temperature § Electron temperature
Plasma § Electron density § Temperature
E. Boulais et al. Nano Lett. 12(9), 2012.
Axis IV : Engineering plasmonic nanolenses for cell nanosurgery
Irradiation parameters
Plasmonic nanostructure
Modeling framework Bubble dynamics
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Conclusion Computer-aided engineering : from macro to nano
Photonic nanolattices
Programmable excitonics
Customizable plamonics
Plasmonic nanolense
Acknowledgment SmithFamilyGraduate
ScienceandEngineeringFellowship
ArmyResearchOfficeMURIW911NF1210420
DARPAYoungFacultyAwardN66001-11-1-4136
ONRYoungInvesFgatorProgramAwardN000141110914
NSFCareerAwardCCF1054898
NIHDirector’sNewInnovatorAward
IDP2OD007292
WyssInsFtuteFacultyStartupFund
ONRDURIPN00014130664
ONRDURIPN00014120621
NSF-DMREF1334109
Acknowledgment YinLab,Harvard
Aspuru-GuzikLab,Harvard
LCBB,MIT
LP2L,PolytechniqueMontréal
PengYin WeiSun WeiliWang
AlanAspuru-Guzik
NicolasSawaya
MarkBathe KeyaoPan RemiVeneziano
RemiLachaine DavidRiouxMichelMeunier JudithBaumgart