Bioimaging; Biosensing; Nano-plasmonics; Optical microscopy; Ultrafast laser spectroscopy; Bio-imaging; Biomolecular interactions; Cross-disciplinary; Interaction phenomena; Life-sciences; Native environment; Physical science; Space and time; Electronic, Optical and Magnetic Materials; Atomic and Molecular Physics, and Optics
Abstract :
[en] In the quest to decipher the chain of life from molecules to cells, the biological and biophysical questions being asked increasingly demand techniques that are capable of identifying specific biomolecules in their native environment, and can measure biomolecular interactions quantitatively, at the smallest possible scale in space and time, without perturbing the system under observation. The interaction of light with biomolecules offers a wealth of phenomena and tools that can be exploited to drive this progress. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of bio-nano-photonics, spanning from the development of optical micro/nano-spectroscopy technologies for quantitative bioimaging and biosensing to the fundamental understanding of light–matter interaction phenomena with biomolecules at the nanoscale. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.
Disciplines :
Physics
Author, co-author :
Herkert, Ediz; ICFO—Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, Barcelona, Spain
Slesiona, Nicole; School of Biosciences, Cardiff University, Cardiff, United Kingdom
Recchia, Martina Elisena; School of Biosciences, Cardiff University, Cardiff, United Kingdom
DECKERT, Thomas ; University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Physics and Materials Science (DPHYMS)
Garcia-Parajo, Maria F. ; ICFO—Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, Barcelona, Spain ; ICREA, Barcelona, Spain
Fantuzzi, Eric Michele; Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
Pruccoli, Andrea; Department Chemie, Universität Konstanz, Konstanz, Germany
Ragupathy, Imaiyan Chitra; Department Chemie, Universität Konstanz, Konstanz, Germany
Gudavičius, Dominykas; Light Conversion, Vilnius, Lithuania ; School of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
Rigneault, Hervé ; Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
Majer, Jan; GSK Medicines Research Centre, Stevenage, United Kingdom
Zumbusch, Andreas; Department Chemie, Universität Konstanz, Konstanz, Germany
Munger, Eleanor; Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
Brasselet, Sophie ; Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
Jones, Arwyn T. ; GSK Medicines Research Centre, Stevenage, United Kingdom
Watson, Peter ; School of Biosciences, Cardiff University, Cardiff, United Kingdom
Boppart, Stephen A. ; University of Illinois at Urbana-Champaign, Champaign, United States
Singh, Vikramdeep; School of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
Borkar, Saurabh; ICFO—Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, Barcelona, Spain
Quintela Rodriguez, Frank E.; Dipartimento FIM, Università di Modena e Reggio Emilia, Modena, Italy ; Istituto Nanoscienze—CNR, Modena, Italy
Langbein, Wolfgang ; School of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
Petropoulos, Vasilis; IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Milano, Italy
van Hulst, Niek F. ; ICFO—Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, Barcelona, Spain ; ICREA, Barcelona, Spain
Maiuri, Margherita ; IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Milano, Italy
Cerullo, Giulio ; IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Milano, Italy
BRIDA, Daniele ; University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Physics and Materials Science (DPHYMS)
The authors would like to thank Dr Lukas Kontenis and Ignas Stasevičius for their helpful advice. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 812992.
Zhang C and Chen J-X 2018 Perspective: coherent Raman scattering microscopy, the future is bright APL Photonics 3 090901
Jonas D M 2003 Two-dimensional femtosecond spectroscopy Annu. Rev. Phys. Chem. 54 425–63
Stockman M I 2011 Nanoplasmonics: past, present, and glimpse into future Opt. Express 19 22029–106
Winkler P M, Regmi R, Flauraud V, Brugger J, Rigneault H, Wenger J and García-Parajo M F 2018 Optical antenna-based fluorescence correlation spectroscopy to probe the nanoscale dynamics of biological membranes J. Phys. Chem. Lett. 9 110–9
Neubrech F, Huck C, Weber K, Pucci A and Giessen H 2017 Surface-enhanced infrared spectroscopy using resonant nanoantennas Chem. Rev. 117 5110–45
Zhan P, Wen T, Wang Z-G, He Y, Shi J, Wang T, Liu X, Lu G and Ding B 2018 DNA origami directed assembly of gold bowtie nanoantennas for single-molecule surface-enhanced Raman scattering Angew. Chem., Int. Ed. 57 2846–50
Zhang Y, Zhen Y R, Neumann O, Day J K, Nordlander P and Halas N J 2014 Coherent anti-Stokes Raman scattering with single-molecule sensitivity using a plasmonic Fano resonance Nat. Commun. 5 4424
Fischer M P et al 2018 Plasmonic mid-infrared third harmonic generation in germanium nanoantennas Light Sci. Appl. 7 106
Zong C, Premasiri R, Lin H, Huang Y, Zhang C, Yang C, Ren B, Ziegler L D and Cheng J-X 2019 Plasmon-enhanced stimulated Raman scattering microscopy with single-molecule detection sensitivity Nat. Commun. 10 5318
Flauraud V, van Zanten T S, Mivelle M, Manzo C, Garcia Parajo M F and Brugger J 2015 Large-scale arrays of bowtie nanoaperture antennas for nanoscale dynamics in living cell membranes Nano Lett. 15 4176–82
Kuzyk A, Jungmann R, Acuna G P and Liu N 2018 DNA origami route for nanophotonics ACS Photonics 5 1151–63
Raab M, Vietz C, Stefani F D, Acuna G P and Tinnefeld P 2017 Shifting molecular localization by plasmonic coupling in a single-molecule mirage Nat. Commun. 8 13966
Tittl A, Leitis A, Liu M, Yesilkoy F, Choi D-Y, Neshev D N, Kivshar Y S and Altug H 2018 Imaging-based molecular barcoding with pixelated dielectric metasurfaces Science 360 1105–9
Polli D, Kumar V, Valensise C M, Marangoni M and Cerullo G 2018 Broadband coherent Raman scattering microscopy Laser Photonics Rev. 12 1800020
Sarri B, Poizat F, Heuke S, Wojak J, Franchi F, Caillol F, Giovannini M and Rigneault H 2019 Stimulated Raman histology: one to one comparison with standard hematoxylin and eosin staining Biomed. Opt. Express 10 5378–84
Freudiger C W, Min W, Saar B G, Lu S, Holtom G R, He C, Tsai J C, Kang J X and Xie X S 2008 Label-free biomedical imaging with high sensitivity by stimulated Raman scattering microscopy Science 322 1857–61
Freudiger C W, Yang W, Holtom G R, Peyghambarian N, Xie X S and Kieu K Q 2014 Stimulated Raman scattering microscopy with a robust fibre laser source Nat. Photon. 8 153–9
Mertz J 2019 Introduction to Optical Microscopy (Cambridge: Cambridge University Press)
Wei L, Chen Z, Shi L, Long R, Anzalone A V, Zhang L, Hu F, Yuste R, Cornish V W and Min W 2017 Super-multiplex vibrational imaging Nature 544 465
Xiong H, Shi L, Wei L, Shen Y, Long R, Zhao Z and Min W 2019 Stimulated Raman excited fluorescence spectroscopy and imaging Nat. Photon. 13 412–7
Hofer M, Shivkumar S, El Waly B and Brasselet S 2020 Coherent anti-Stokes Raman scattering through thick biological tissues by single-wavefront shaping Phys. Rev. Appl. 14 14
Lombardini A et al 2018 High-resolution multimodal flexible coherent Raman endoscope Light Sci. Appl. 7 10
Gasecka P, Jaouen A, Bioud F-Z F-Z, de Aguiar H, Duboisset J, Ferrand P, Rigneault H, Balla N K, Debarbieux F and Brasselet S 2017 Lipid order degradation in autoimmune demyelination probed by polarized coherent Raman microscopy Biophys. J. 113 1520–30
Heuke S, Unger K, Khadir S, Belkebir K, Chaumet P C, Rigneault H and Sentenac A 2019 Coherent anti-Stokes Raman Fourier ptychography Opt. Express 27 23497–514
Yamakoshi H, Dodo K, Palonpon A, Ando J, Fujita K, Kawata S and Sodeoka M 2012 Alkyne-Tag Raman imaging for visualization of mobile small molecules in live cells J. Am. Chem. Soc. 134 20681
Wei L, Hu F, Chen Z, Shen Y, Zhang L and Min W 2016 Live-cell bioorthogonal chemical imaging: stimulated Raman scattering microscopy of vibrational probes Acc. Chem. Res. 49 1494
Chung C-Y and Potma E O 2013 Biomolecular imaging with coherent nonlinear vibrational microscopy Annu. Rev. Phys. Chem. 64 77
Cheng J-X and Xie X S 2015 Vibrational spectroscopic imaging of living systems: an emerging platform for biology and medicine Science 350 1054
Zhang C, Zhang D and Cheng J-X 2015 Coherent Raman scattering microscopy in biology and medicine Annu. Rev. Biomed. Eng. 17 415
Tipping W J, Lee M, Serrels A, Brunton V G and Hulme A N 2016 Stimulated Raman scattering microscopy: an emerging tool for drug discovery Chem. Soc. Rev. 45 2075
Meldal M and Tornøe C W 2008 Cu-catalyzed azide−alkyne cycloaddition Chem. Rev. 108 2952
Bi Y L, Yang C, Chen Y, Yan S, Yang G, Wu Y, Zhang G and Wang P 2018 Near-resonance enhanced label-free stimulated Raman scattering microscopy with spatial resolution near 130 nm Light Sci. Appl. 7 81
Ebner L and Zumbusch A 2019 Yb fiber based laser source for tunable, narrow bandwidth picosecond pulses in the visible Opt. Lett. 44 2290
Brasselet S 2011 Polarization-resolved nonlinear microscopy: application to structural molecular and biological imaging Adv. Opt. Photonics 3 205–71
de Vito G, Cappello V, Tonazzini I, Cecchini M and Piazza V 2017 RP-CARS reveals molecular spatial order anomalies in myelin of an animal model of Krabbe disease J. Biophoton. 10 385–93
Campbell K R, Chaudhary R, Handel J, Patankar M and Campagnola P J 2018 Polarization-resolved second harmonic generation imaging of human ovarian cancer J. Biomed. Opt. 23 066501
Kumar Balla N, Rendón-Barraza N, C, Hoang C L M, Karpinski P, Bermúdez-Ureña E and Brasselet S 2017 Polarized nonlinear nanoscopy of metal nanostructures ACS Photonics 4 292–301
Kallioniemi L, Turquet L, Lipsanen H, Kauranen M and Bautista G 2020 Tailoring the longitudinal electric fields of high-order laser beams and their direct verification in three dimensions Opt. Commun. 459 124894
Hofer M, Balla N K and Brasselet S 2017 High-speed polarization-resolved coherent Raman scattering imaging Optica 4 795–801
Morizet J, Ducourthial G, Supatto W, Boutillon A, Legouis R, Schanne-Klein M-C, Stringari C and Beaurepaire E 2019 High-speed polarization-resolved third-harmonic microscopy Optica 6 385–8
de Aguiar H B, Gigan S and Brasselet S 2017 Polarization recovery through scattering media Sci. Adv. 3 e1600743
Hafi N et al 2016 Erratum: corrigendum: fluorescence nanoscopy by polarization modulation and polarization angle narrowing Nat. Methods 13 101
Ju Y, Guo H, Edman M and Hamm-Alvarez S F 2020 Application of advances in endocytosis and membrane trafficking to drug delivery Adv. Drug Deliv. Rev. 157 118-41
Yarwood R, Hellicar J, Woodman P G and Lowe M 2020 Membrane trafficking in health and disease Dis. Models Mech. 13 dmm043448
Stewart M P, Sharei A, Ding X, Sahay G, Langer R and Jensen K F 2016 In vitro and ex vivo strategies for intracellular delivery Nature 538 183–92
Laissue P P, Alghamdi R A, Tomancak P, Reynaud E G and Shroff H 2017 Assessing phototoxicity in live fluorescence imaging Nat. Methods 14 657–61
Birch D, Christensen M V, Staerk D, Franzyk H and Nielsen H M 2017 Fluorophore labeling of a cell-penetrating peptide induces differential effects on its cellular distribution and affects cell viability Biochim. Biophys. Acta Biomembr. 1859 2483–94
Gwosch K C, Pape J K, Balzarotti F, Hoess P, Ellenberg J, Ries J and Hell S W 2020 MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells Nat. Methods 17 217–24
Chen K, Gu Y, Sun W, Dong B, Wang G, Fan X, Xia T and Fang N 2017 Characteristic rotational behaviors of rod-shaped cargo revealed by automated five-dimensional single particle tracking Nat. Commun. 8 887
Liu Y-L et al 2020 Three-dimensional two-color dual-particle tracking microscope for monitoring DNA conformational changes and nanoparticle landings on live cells ACS Nano 14 7927–39
Giannakopoulou N et al 2020 Four-wave-mixing microscopy reveals non-colocalisation between gold nanoparticles and fluorophore conjugates inside cells Nanoscale 12 4622–35
Zoriniants G, Masia F, Giannakopoulou N, Langbein W and Borri P 2017 Background-free 3D nanometric localization and sub-nm asymmetry detection of single plasmonic nanoparticles by four-wave mixing interferometry with optical vortices Phys. Rev. X 7 041022
Mohammad-Beigi H, Hayashi Y, Zeuthen C M, Eskandari H, Scavenius C, Juul-Madsen K, Vorup-Jensen T, Enghild J J and Sutherland D S 2020 Mapping and identification of soft corona proteins at nanoparticles and their impact on cellular association Nat. Commun. 11 4535
Hu F, Zeng C, Long R, Miao Y, Wei L, Xu Q and Min W 2018 Supermultiplexed optical imaging and barcoding with engineered polyynes Nat. Methods 15 194–200
Miao Y, Shi L, Hu F and Min W 2019 Probe design for super-multiplexed vibrational imaging Phys. Biol. 16 041003
Hanahan D and Weinberg R A 2000 The hallmarks of cancer Cell 100 57–70 and 2011 Hallmarks of cancer: the next generation Cell 144 646–74
Wong T T W, Zhang R, Hai P, Zhang C, Pleitez M A, Aft R L, Novack D V and Wang L V 2017 Fast label-free multilayered histology-like imaging of human breast cancer by photoacoustic microscopy Sci. Adv. 3 e1602168
Liu Z, Pouli D, Alonzo C A, Varone A, Karaliota S, Quinn K P, Münger K, Karalis K P and Georgakoudi I 2018 Mapping metabolic changes by noninvasive, multiparametric, high-resolution imaging using endogenous contrast Sci. Adv. 4 eaap9302
Mittal S, Yeh K, Leslie L S, Kenkel S, Kajdacsy-Balla A and Bhargava R 2018 Simultaneous cancer and tumor microenvironment subtyping using confocal infrared microscopy for all-digital molecular histopathology Proc. Natl Acad. Sci. 115 E5651–60
Orringer D A et al 2017 Rapid intraoperative histology of unprocessed surgical specimens via fibre-laser-based stimulated Raman scattering microscopy Nat. Biomed. Eng. 1 27
Tu H, Liu Y, Marjanovic M, Chaney E J, You S, Zhao Y and Boppart S A 2017 Concurrence of extracellular vesicle enrichment and metabolic switch visualized label-free in the tumor microenvironment Sci. Adv. 3 e1600675
You S et al 2018 Intravital imaging by simultaneous label-free autofluorescence-multiharmonic microscopy Nat. Commun. 9 2125
You S et al 2019 Label-free visualization and characterization of extracellular vesicles in breast cancer Proc. Natl Acad. Sci. 116 24012–8
You S, Sun Y, Yang L, Park J, Tu H, Marjanovic M, Sinha S and Boppart S A 2019 Real-time intraoperative diagnosis by deep neural network driven multiphoton virtual histology npj Precis. Oncol. 3 33
Sun Y et al 2018 Intraoperative visualization of the tumor microenvironment and quantification of extracellular vesicles by label-free nonlinear imaging Sci. Adv. 4 eaau5603
Moerner W E and Kador L 1989 Optical detection and spectroscopy of single molecules in a solid Phys. Rev. Lett. 62 2535–8
Orrit M and Bernard J 1990 Single pentacene molecules detected by fluorescence excitation in a p-terphenyl crystal Phys. Rev. Lett. 65 2716–9
Nonn T and Plakhotnik T 2001 Fluorescence excitation spectroscopy of vibronic transitions in single molecules Chem. Phys. Lett. 336 97–104
Nonn T and Plakhotnik T 2000 Non-Lorentzian single-molecule line shape: pseudolocal phonons and coherence transfer Phys. Rev. Lett. 85 1556–9
Maser A, Gmeiner B, Utikal T, Götzinger S and Sandoghdar V 2016 Few-photon coherent nonlinear optics with a single molecule Nat. Photon. 10 450–4
Moradi A, Ristanović Z, Orrit M, Deperasi´nska I and Kozankiewicz B 2019 Matrix-induced linear Stark effect of single dibenzoterrylene molecules in 2,3-dibromonaphthalene crystal ChemPhysChem 20 55–61
Wang D, Kelkar H, Martin-Cano D, Rattenbacher D, Shkarin A, Utikal T, Götzinger S and Sandoghdar V 2019 Turning a molecule into a coherent two-level quantum system Nat. Phys. 15 483–9
Najer D et al 2019 A gated quantum dot strongly coupled to an optical microcavity Nature 575 622–7
Weisenburger S, Boening D, Schomburg B, Giller K, Becker S, Griesinger C and Sandoghdar V 2017 Cryogenic optical localization provides 3D protein structure data with Angstrom resolution Nat. Methods 14 141–4
Flauraud V, Regmi R, Winkler P M, Alexander D T L, Rigneault H, van Hulst N F, García-Parajo M F, Wenger J and Brugger J 2017 In-plane plasmonic antenna arrays with surface nanogaps for giant fluorescence enhancement Nano Lett. 17 1703–10
Baumberg J J, Aizpurua J, Mikkelsen M H and Smith D R 2019 Extreme nanophotonics from ultrathin metallic gaps Nat. Mater. 18 668–78
Bach H, Renn A and Wild U P 2000 Spectral imaging of single molecules Single Mol. 1 73–7
Hildner R, Brinks D, Nieder J B, Cogdell R J and van Hulst N F 2013 Quantum coherent energy transfer over varying pathways in single light-harvesting complexes Science 340 1448–51
Thyrhaug E, Krause S, Perri A, Cerullo G, Polli D, Vosch T and Hauer J 2019 Single-molecule excitation–emission spectroscopy Proc. Natl Acad. Sci. 116 4064–9
Coolen L, Brokmann X, Spinicelli P and Hermier J-P 2008 Emission characterization of a single CdSe-ZnS nanocrystal with high temporal and spectral resolution by photon-correlation Fourier spectroscopy Phys. Rev. Lett. 100 0274031–4
Maiuri M, Garavelli M and Cerullo G 2020 Ultrafast spectroscopy: state of the art and open challenges J. Am. Chem. Soc. 142 3–15
Langbein W and Patton B 2006 Heterodyne spectral interferometry for multidimensional nonlinear spectroscopy of individual quantum systems Opt. Lett. 31 1151–3
Kasprzak J, Patton B, Savona V and Langbein W 2011 Coherent coupling between distant excitons revealed by two-dimensional nonlinear hyperspectral imaging Nat. Photon. 5 57–63
Kasprzak J, Reitzenstein S, Muljarov E A, Kistner C, Schneider C, Strauss M, Höfling S, Forchel A and Langbein W 2010 Up on the Jaynes–Cummings ladder of a quantum-dot/microcavity system Nat. Mater. 9 304–8
Albert F et al 2013 Microcavity controlled coupling of excitonic qubits Nat. Commun. 4 1747
Delemonte V, Specht J F, Jakubczyk T, Höfling S, Kamp M, Schneider C, Langbein W, Nogues G, Richter M and Kasprzak J 2017 Coherent coupling of individual quantum dots measured with phase-referenced two-dimensional spectroscopy: photon echo versus double quantum coherence Phys. Rev. B 96 0411241–6
Furubayashi T, Ishida K, Kashida H, Nakata E, Morii T, Matsushita M and Fujiyoshi S 2019 Nanometer accuracy in cryogenic far-field localization microscopy of individual molecules J. Phys. Chem. Lett. 10 5841–6
Carnegie C et al 2017 Mapping SERS in CB:Au plasmonic nanoaggregates ACS Photonics 4 2681–6
Sigle D O, Kasera S, Herrmann L O, Palma A, de Nijs B, Benz F, Mahajan S, Baumberg J J and Scherman O A 2016 Observing single molecules complexing with Cucurbit[7]uril through nanogap surface-enhanced Raman spectroscopy J. Phys. Chem. Lett. 7 704–10
Grangier P, Levenson J A and Poizat J-P 1998 Quantum non-demolition measurements in optics Nature 396 537–42
Dorfman K E, Schlawin F and Mukamel S 2016 Nonlinear optical signals and spectroscopy with quantum light Rev. Mod. Phys. 88 0450081–67
Myers A B, Tchenio P, Zgierski M Z and Moerner W E 1994 Vibronic spectroscopy of individual molecules in solids J. Phys. Chem. 98 10377–90
Kukura P, Celebrano M, Renn A and Sandoghdar V 2010 Single-molecule sensitivity in optical absorption at room temperature J. Phys. Chem. Lett. 1 3323–7
Gaiduk A, Yorulmaz M, Ruijgrok P V and Orrit M 2010 Room-temperature detection of a single molecule’s absorption by photothermal contrast Science 330 353–6
van Dijk E M H P, Hernando J, García-López J-J, Crego-Calama M, Reinhoudt D N, Kuipers L, García-Parajó M F and van Hulst N F 2005 Single-molecule pump-probe detection resolves ultrafast pathways in individual and coupled quantum systems Phys. Rev. Lett. 94 078302
Piatkowski L, Accanto N, Calbris G, Christodoulou S, Moreels I and van Hulst N F 2019 Ultrafast stimulated emission microscopy of single nanocrystals Science 366 1240–3
Liebel M, Toninelli C and van Hulst N F 2018 Room-temperature ultrafast nonlinear spectroscopy of a single molecule Nat. Photon. 12 46–9
Brinks D, Stefani F D, Kulzer F, Hildner R, Taminiau T H, Avlasevich Y, Müllen K and van Hulst N F 2010 Visualizing and controlling vibrational wave packets of single molecules Nature 465 905–8
Weigel A, Sebesta A and Kukura P 2015 Shaped and feedback-controlled excitation of single molecules in the weak-field limit J. Phys. Chem. Lett. 6 4032–7
Stopel M H W, Blum C and Subramaniam V 2014 Excitation spectra and Stokes shift measurements of single organic dyes at room temperature J. Phys. Chem. Lett. 5 3259–64
Piatkowski L, Gellings E and van Hulst N F 2016 Broadband single-molecule excitation spectroscopy Nat. Commun. 7 10411
Jonas D M 2003 CHEMISTRY: optical analogs of 2D NMR Science 300 1515–7
Thyrhaug E, Tempelaar R, Alcocer M J P, Žídek K, Bína D, Knoester J, Jansen T L C and Zigmantas D 2018 Identification and characterization of diverse coherences in the Fenna–Matthews–Olson complex Nat. Chem. 10 780–6
Hamm P and Zanni M 2011 Concepts and Methods of 2D Infrared Spectroscopy (Cambridge: Cambridge University Press)
Mukamel S 2000 Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations Annu. Rev. Phys. Chem. 51 691–729
Fuller F D and Ogilvie J P 2015 Experimental implementations of two-dimensional fourier transform electronic spectroscopy Annu. Rev. Phys. Chem. 66 667–90
Oliver T A A 2018 Recent advances in multidimensional ultrafast spectroscopy R. Soc. Open Sci. 5 171425
Brixner T, Stenger J, Vaswani H M, Cho M, Blankenship R E and Fleming G R 2005 Two-dimensional spectroscopy of electronic couplings in photosynthesis Nature 434 625–8
Zigmantas D, Read E L, Mančal T A C, Brixner T, Gardiner A T and Fleming G R 2006 2D electronic spectroscopy of the B800-B820 LH3 light-harvesting complex Femtochemistry VII (Elsevier) pp 372–6
Ostroumov E E, Mulvaney R M, Cogdell R J and Scholes G D 2013 Broadband 2D electronic spectroscopy reveals a carotenoid dark state in purple bacteria Science 340 52–6
Duan H-G, Prokhorenko V I, Cogdell R J, Ashraf K, Stevens A L, Thorwart M and Miller R J D 2017 Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer Proc. Natl Acad. Sci. 114 8493–8
Cao J et al 2020 Quantum biology revisited Sci. Adv. 6 eaaz4888
Son M, Pinnola A, Gordon S C, Bassi R and Schlau-Cohen G S 2020 Observation of dissipative chlorophyll-to-carotenoid energy transfer in light-harvesting complex II in membrane nanodiscs Nat. Commun. 11 1295
Scholes G D et al 2017 Using coherence to enhance function in chemical and biophysical systems Nature 543 647–56
Engel G S, Calhoun T R, Read E L, Ahn T-K, Mančal T, Cheng Y-C, Blankenship R E and Fleming G R 2007 Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems Nature 446 782–6
Collini E, Wong C Y, Wilk K E, Curmi P M G, Brumer P and Scholes G D 2010 Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature Nature 463 644–7
Rolczynski B S et al 2018 Correlated protein environments drive quantum coherence lifetimes in photosynthetic pigment-protein complexes Chem 4 138–49
Fuller F D, Pan J, Gelzinis A, Butkus V, Senlik S S, Wilcox D E, Yocum C F, Valkunas L, Abramavicius D and Ogilvie J P 2014 Vibronic coherence in oxygenic photosynthesis Nat. Chem. 6 706–11
Romero E, Augulis R, Novoderezhkin V I, Ferretti M, Thieme J, Zigmantas D and van Grondelle R 2014 Quantum coherence in photosynthesis for efficient solar-energy conversion Nat. Phys. 10 676–82
Tekavec P F, Lott G A and Marcus A H 2007 Fluorescence-detected two-dimensional electronic coherence spectroscopy by acousto-optic phase modulation J. Chem. Phys. 127 214307
Goetz S, Li D, Kolb V, Pflaum J and Brixner T 2018 Coherent two-dimensional fluorescence micro-spectroscopy Opt. Express 26 3915
Tiwari V, Matutes Y A, Gardiner A T, Jansen T L C, Cogdell R J and Ogilvie J P 2018 Spatially-resolved fluorescence-detected two-dimensional electronic spectroscopy probes varying excitonic structure in photosynthetic bacteria Nat. Commun. 9 4219
Wientjes E, Renger J, Curto A G, Cogdell R and van Hulst N F 2014 Strong antenna-enhanced fluorescence of a single light-harvesting complex shows photon antibunching Nat. Commun. 5 4236
Kratochvil H T et al 2016 Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy Science 353 1040
Baldassarre L, Sakat E, Frigerio J, Samarelli A, Gallacher K, Calandrini E, Isella G, Paul D J, Ortolani M and Biagioni P 2015 Midinfrared plasmon-enhanced spectroscopy with germanium antennas on silicon substrates Nano Lett. 15 7225–31
Pellegrini G, Baldassare L, Giliberti V, Frigerio J, Gallacher K, Paul D J, Isella G, Ortolani M and Biagioni P 2018 Benchmarking the use of heavily doped Ge for plasmonics and sensing in the mid-infrared ACS Photonics 5 3601–7
Frigerio J et al 2016 Tunability of the dielectric function of heavily doped germanium thin films for mid-infrared plasmonics Phys. Rev. B 94 85202
Fischer M P et al 2016 Optical activation of germanium plasmonic antennas in the mid-infrared Phys. Rev. Lett. 117 47401
Oh S-H and Altug H 2018 Performance metrics and enabling technologies for nanoplasmonic biosensors Nat. Commun. 9 5263
Sell A, Scheu R, Leitenstorfer A and Huber R 2008 Field-resolved detection of phase-locked infrared transients from a compact Er:fiber system tunable between 55 and 107 THz Appl. Phys. Lett. 93 251107
Somma C, Folpini G, Reimann K, Woerner M and Elsaesser T 2016 Phase-resolved two-dimensional terahertz spectroscopy including off-resonant interactions beyond the χ(3) limit J. Chem. Phys. 144 184202
Chikkaraddy R, de Nijs B, Benz F, Barrow S J, Scherman O A, Rosta E, Demetriadou A, Fox P, Hess O and Baumberg J J 2016 Single-molecule strong coupling at room temperature in plasmonic nanocavities Nature 535 127–30
Curutchet C and Mennucci B 2017 Quantum chemical studies of light harvesting Chem. Rev. 117 294–343
de Sio A et al 2016 Tracking the coherent generation of polaron pairs in conjugated polymers Nat. Commun. 7 13742
Goulielmakis E et al 2010 Real-time observation of valence electron motion Nature 466 739–43
Rozzi C A, Troiani F and Tavernelli I 2018 Quantum modeling of ultrafast photoinduced charge separation J. Phys.: Condens. Matter 30 013002
Streltsov A, Adesso G and Plenio M B 2017 Colloquium: quantum coherence as a resource Rev. Mod. Phys. 89 041003
Scholes G D, Fleming G R, Olaya-Castro A and van Grondelle R 2011 Lessons from nature about solar light harvesting Nat. Chem. 3 763–74
Brédas J-L, Sargent E H and Scholes G D 2017 Photovoltaic concepts inspired by coherence effects in photosynthetic systems Nat. Mater. 16 35–44
Nelson T R, White A J, Bjorgaard J A, Sifain A E, Zhang Y, Nebgen B, Fernandez-Alberti S, Mozyrsky D, Roitberg A E and Tretiak S 2020 Non-adiabatic excited-state molecular dynamics: theory and applications for modeling photophysics in extended molecular materials Chem. Rev. 120 2215–87
Rozzi C A and Pittalis S 2018 Prototyping ultrafast charge separation by means of time-dependent density functional methods Handbook of Materials Modeling. Volume 2 Applications: Current and Emerging Materials ed W Andreoni and S Yip (Berlin: Springer)pp 325–43
Strickland D and Mourou G 1985 Compression of amplified chirped optical pulses Opt. Commun. 56 219–21
Petersen T, Zuegel J D and Bromage J 2017 Thermal effects in an ultrafast BiB3O6 optical parametric oscillator at high average powers Appl. Opt. 56 6923–9
Lefort C 2017 A review of biomedical multiphoton microscopy and its laser sources J. Phys. D: Appl. Phys. 50 423001
Brida D, Krauss G, Sell A and Leitenstorfer A 2014 Ultrabroadband Er:fiber lasers Laser Photonics Rev. 8 409–28
Wang H, Gao T and Xiong W 2017 Self-phase-stabilized heterodyne vibrational sum frequency generation microscopy ACS Photonics 4 1839–45
Upputuri P K, Wu Z, Gong L, Ong C K and Wang H 2014 Super-resolution coherent anti-Stokes Raman scattering microscopy with photonic nanojets Opt. Express 22 12890–9
Grupp A, Budweg A, Fischer M P, Allerbeck J, Soavi G, Leitenstorfer A and Brida D 2017 Broadly tunable ultrafast pump-probe system operating at multi-kHz repetition rate J. Opt. 20 014005
Miller D R et al 2017 In vivo multiphoton imaging of a diverse array of fluorophores to investigate deep neurovascular structure Biomed. Opt. Express 8 3470–81
Lamb E S, Lefrancois S, Ji M, Wadsworth W J, Xie X S and Wise F W 2013 Fiber optical parametric oscillator for coherent anti-Stokes Raman scattering microscopy Opt. Lett. 38 4154–7
Lefrancois S, Fu D, Holtom G R, Kong L, Wadsworth W J, Schneider P, Herda R, Zach A, Xie X S and Wise F W 2012 Fiber four-wave mixing source for coherent anti-Stokes Raman scattering microscopy Opt. Lett. 37 1652–4
Abdeladim L et al 2019 Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy Nat. Commun. 10 1662
Dubietis A, Jonusauskas G and Piskarskas A 1991 Powerful femtosecond pulse generation by chirped and stretched pulse parametric amplification in BBO crystal J. Opt. 88 437–40
Budriunas R, Stanislauskas T, Adamonis J, Aleknavicius A, Veitas G, Gadonas D, Balickas S, Michailovas A and Varanavicius A 1991 53 W average power CEP-stabilized OPCPA system delivering 5.5 TW few cycle pulses at 1 kHz repetition rate Opt. Express 25 5797–806
Wachulak P et al 2017 Bioimaging using full field and contact EUV and SXR microscopes with nanometer spatial resolution Appl. Sci. 7 548
Li B, Wu C, Wang M, Charan K and Xu C 2020 An adaptive excitation source for high-speed multiphoton microscopy Nat. Methods 17 163–6
Wise F W 2012 Femtosecond fiber lasers based on dissipative processes for nonlinear microscopy IEEE J. Sel. Top. Quantum Electron. 18 1412–21
Pegoraro A F, Ridsdale A, Moffatt D J, Pezacki J P, Thomas B K, Fu L, Dong L, Fermann M E and Stolow A 2009 All-fiber CARS microscopy of live cells Opt. Express 17 20700–6
Brustlein S, Berto P, Hostein R, Ferrand P, Billaudeau C, Marguet D, Muir A, Knight J and Rigneault H 2011 Double-clad hollow core photonic crystal fiber for coherent Raman endoscope Opt. Express 19 12562–8
