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

2

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Moresensi)vebiosensingdevices

Nanoscaleop)caldevices

Be4ersolarcells Fastercompu)ng

Nature uses precise chromophore architectures to absorb and funnel light to reaction centers

3

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: kschulte@ks.uiuc.edu.

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

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ctio

n (M

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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