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Malevich P, Heshmatpour C, Lincoln CN, Ceymann H, Schreck MH, Hauer J. Ultrafast bi-excitonic dynamics and annihilation in molecular and mesoscopic systems. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920506013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present 5th and 3rd order 2D spectra of a squarine trimer. Slowly decaying (τ = 0.8 ps) and intensity dependent features unique to the 5th order signal are attributed to exciton-exciton annihilation.
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2
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Heshmatpour C, Šanda F, Lincoln CN, Perlík V, Malevich P, Hauer J. Simulating exciton migration and annihilation dynamics in higher order spectroscopies of a molecular trimer. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920506016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present simulations of 3rd and 5th order multidimensional time-dependent signals of a molecular trimer. The developed model allows for the simulation of both signal types within one theoretical framework. We therefore extended standard Redfield theory of exciton migration by a new term to include the process of exciton-exciton annihilation.
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3
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Lincoln CN, Block M, Baudisch B, Malevich P, von Berlepsch H, Riedle E, Hauer J. Exciton-Exciton Annihilation as a Mechanism for Uphill Transfer in a Molecular Excitonic System. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920506017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Exciton dynamics in a HJ-aggregate of cyanine dye TTBC are investigated by transient absorption with a time resolution of <60 fs and power-dependent emission spectroscopies. Both measurements are consistent with an exciton delocalization length of ~28 monomers. A model assuming diffusive exciton motion reveals that the exciton mobility is at least bimodal and restricted to one spatial dimension. J-band diffusion rates of 2.69 and 2.79e-3 cm2s-1 are found, leading to maximal diffusion lengths of 449 and 14.5 nm. The findings indicate that exciton-exciton annihilation is the origin of effective uphill transfer. This mechanism, if present under solar radiation, maybe useful for organic photovoltaic systems.
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Thyrhaug E, Lincoln CN, Branchi F, Cerullo G, Perlík V, Šanda F, Lokstein H, Hauer J. Carotenoid-to-bacteriochlorophyll energy transfer through vibronic coupling in LH2 from Phaeosprillum molischianum. Photosynth Res 2018; 135:45-54. [PMID: 28523607 PMCID: PMC5783993 DOI: 10.1007/s11120-017-0398-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
The peripheral light-harvesting antenna complex (LH2) of purple photosynthetic bacteria is an ideal testing ground for models of structure-function relationships due to its well-determined molecular structure and ultrafast energy deactivation. It has been the target for numerous studies in both theory and ultrafast spectroscopy; nevertheless, certain aspects of the convoluted relaxation network of LH2 lack a satisfactory explanation by conventional theories. For example, the initial carotenoid-to-bacteriochlorophyll energy transfer step necessary on visible light excitation was long considered to follow the Förster mechanism, even though transfer times as short as 40 femtoseconds (fs) have been observed. Such transfer times are hard to accommodate by Förster theory, as the moderate coupling strengths found in LH2 suggest much slower transfer within this framework. In this study, we investigate LH2 from Phaeospirillum (Ph.) molischianum in two types of transient absorption experiments-with narrowband pump and white-light probe resulting in 100 fs time resolution, and with degenerate broadband 10 fs pump and probe pulses. With regard to the split Qx band in this system, we show that vibronically mediated transfer explains both the ultrafast carotenoid-to-B850 transfer, and the almost complete lack of transfer to B800. These results are beyond Förster theory, which predicts an almost equal partition between the two channels.
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Affiliation(s)
- Erling Thyrhaug
- Photonics Institute, TU Wien, Gußhausstraße 27, 1040, Vienna, Austria
| | - Craig N Lincoln
- Photonics Institute, TU Wien, Gußhausstraße 27, 1040, Vienna, Austria
| | - Federico Branchi
- Dipartimento di Fisica, IFN-CNR, Politecnico di Milano, Piazza L. da Vinci, 32, 20133, Milan, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, IFN-CNR, Politecnico di Milano, Piazza L. da Vinci, 32, 20133, Milan, Italy
| | - Václav Perlík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - František Šanda
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 12116, Praha 2, Czech Republic
| | - Jürgen Hauer
- Photonics Institute, TU Wien, Gußhausstraße 27, 1040, Vienna, Austria.
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5
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Balevičius V, Lincoln CN, Viola D, Cerullo G, Hauer J, Abramavicius D. Effects of tunable excitation in carotenoids explained by the vibrational energy relaxation approach. Photosynth Res 2018; 135:55-64. [PMID: 28741055 DOI: 10.1007/s11120-017-0423-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/09/2017] [Indexed: 05/20/2023]
Abstract
Carotenoids are fundamental building blocks of natural light harvesters with convoluted and ultrafast energy deactivation networks. In order to disentangle such complex relaxation dynamics, several studies focused on transient absorption measurements and their dependence on the pump wavelength. However, such findings are inconclusive and sometimes contradictory. In this study, we compare internal conversion dynamics in [Formula: see text]-carotene, pumped at the first, second, and third vibronic progression peak. Instead of employing data fitting algorithms based on global analysis of the transient absorption spectra, we apply a fully quantum mechanical model to treat the high-frequency symmetric carbon-carbon (C=C and C-C) stretching modes explicitly. This model successfully describes observed population dynamics as well as spectral line shapes in their time-dependence and allows us to reach two conclusions: Firstly, the broadening of the induced absorption upon excess excitation is an effect of vibrational cooling in the first excited state ([Formula: see text]). Secondly, the internal conversion rate between the second excited state ([Formula: see text]) and [Formula: see text] crucially depends on the relative curve displacement. The latter point serves as a new perspective on solvent- and excitation wavelength-dependent experiments and lifts contradictions between several studies found in literature.
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Affiliation(s)
- Vytautas Balevičius
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Craig N Lincoln
- Photonics Institute, TU Wien, Gusshausstr. 27, 1040, Vienna, Austria
| | - Daniele Viola
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
| | - Jürgen Hauer
- Photonics Institute, TU Wien, Gusshausstr. 27, 1040, Vienna, Austria
| | - Darius Abramavicius
- Department of Theoretical Physics, Vilnius University, Sauletekio al. 9-III, 10222, Vilnius, Lithuania.
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6
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Perlík V, Seibt J, Cranston LJ, Cogdell RJ, Lincoln CN, Savolainen J, Šanda F, Mančal T, Hauer J. Vibronic coupling explains the ultrafast carotenoid-to-bacteriochlorophyll energy transfer in natural and artificial light harvesters. J Chem Phys 2016; 142:212434. [PMID: 26049454 DOI: 10.1063/1.4919548] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The initial energy transfer steps in photosynthesis occur on ultrafast timescales. We analyze the carotenoid to bacteriochlorophyll energy transfer in LH2 Marichromatium purpuratum as well as in an artificial light-harvesting dyad system by using transient grating and two-dimensional electronic spectroscopy with 10 fs time resolution. We find that Förster-type models reproduce the experimentally observed 60 fs transfer times, but overestimate coupling constants, which lead to a disagreement with both linear absorption and electronic 2D-spectra. We show that a vibronic model, which treats carotenoid vibrations on both electronic ground and excited states as part of the system's Hamiltonian, reproduces all measured quantities. Importantly, the vibronic model presented here can explain the fast energy transfer rates with only moderate coupling constants, which are in agreement with structure based calculations. Counterintuitively, the vibrational levels on the carotenoid electronic ground state play the central role in the excited state population transfer to bacteriochlorophyll; resonance between the donor-acceptor energy gap and the vibrational ground state energies is the physical basis of the ultrafast energy transfer rates in these systems.
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Affiliation(s)
- Václav Perlík
- Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, Prague 121 16, Czech Republic
| | - Joachim Seibt
- Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, Prague 121 16, Czech Republic
| | - Laura J Cranston
- Institute of Molecular Cell and System Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Biomedical Research Centre, 120 University Place, Glasgow G12 8TA, Scotland
| | - Richard J Cogdell
- Institute of Molecular Cell and System Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Biomedical Research Centre, 120 University Place, Glasgow G12 8TA, Scotland
| | - Craig N Lincoln
- Photonics Institute, Vienna University of Technology, Gusshausstrasse 27, 1040 Vienna, Austria
| | - Janne Savolainen
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany
| | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, Prague 121 16, Czech Republic
| | - Tomáš Mančal
- Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, Prague 121 16, Czech Republic
| | - Jürgen Hauer
- Photonics Institute, Vienna University of Technology, Gusshausstrasse 27, 1040 Vienna, Austria
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7
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Abstract
![]()
Center line slope (CLS) analysis
in 2D infrared spectroscopy has been extensively used to extract frequency–frequency
correlation functions of vibrational transitions. We apply this concept
to 2D electronic spectroscopy, where CLS is a measure of electronic
gap fluctuations. The two domains, infrared and electronic, possess
differences: In the infrared, the frequency fluctuations are classical,
often slow and Gaussian. In contrast, electronic spectra are subject
to fast spectral diffusion and affected by underdamped vibrational
wavepackets in addition to Stokes shift. All these effects result
in non-Gaussian peak profiles. Here, we extend CLS-analysis beyond
Gaussian line shapes and test the developed methodology on a solvated
molecule, zinc phthalocyanine. We find that CLS facilitates the interpretation
of 2D electronic spectra by reducing their complexity to one dimension.
In this way, CLS provides a highly sensitive measure of model parameters
describing electronic–vibrational and electronic–solvent
interaction.
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Affiliation(s)
- František Šanda
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, Prague, 121 16 Czech Republic
| | - Václav Perlík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, Prague, 121 16 Czech Republic
| | - Craig N Lincoln
- Photonics Institute, TU Wien , Gusshausstrasse 27, 1040 Vienna, Austria
| | - Jürgen Hauer
- Photonics Institute, TU Wien , Gusshausstrasse 27, 1040 Vienna, Austria
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Balevičius V, Pour AG, Savolainen J, Lincoln CN, Lukeš V, Riedle E, Valkunas L, Abramavicius D, Hauer J. Vibronic energy relaxation approach highlighting deactivation pathways in carotenoids. Phys Chem Chem Phys 2015; 17:19491-9. [DOI: 10.1039/c5cp00856e] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Energy relaxation between two electronic states of a molecule is mediated by a set of relevant vibrational states.
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Affiliation(s)
- Vytautas Balevičius
- Department of Theoretical Physics
- Faculty of Physics
- Vilnius University
- LT-10222 Vilnius
- Lithuania
| | | | - Janne Savolainen
- Department of Physical Chemistry II
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - Craig N. Lincoln
- Photonics Institute
- Vienna University of Technology
- 1040 Vienna
- Austria
| | - Vladimír Lukeš
- Department of Chemical Physics
- Slovak University of Technology
- 81237 Bratislava
- Slovakia
| | - Eberhard Riedle
- Lehrstuhl für BioMolekulare Optik
- Ludwig-Maximilians-University
- 80538 Munich
- Germany
| | - Leonas Valkunas
- Department of Theoretical Physics
- Faculty of Physics
- Vilnius University
- LT-10222 Vilnius
- Lithuania
| | - Darius Abramavicius
- Department of Theoretical Physics
- Faculty of Physics
- Vilnius University
- LT-10222 Vilnius
- Lithuania
| | - Jürgen Hauer
- Photonics Institute
- Vienna University of Technology
- 1040 Vienna
- Austria
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van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber T. Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein. Faraday Discuss 2014; 171:439-55. [PMID: 25415305 DOI: 10.1039/c4fd00011k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Femtosecond time resolved pump-probe protein X-ray crystallography requires highly accurate measurements of the photoinduced structure factor amplitude differences. In the case of femtosecond photolysis of single P63 crystals of the Photoactive Yellow Protein, it is shown that photochemical dynamics place a considerable restraint on the achievable time resolution due to the requirement to stretch and add second order dispersion in order to generate threshold concentration levels in the interaction region. Here, we report on using a 'quasi-cw' approach to use the rotation method with monochromatic radiation and 2 eV bandwidth at 9.465 keV at the Linac Coherent Light Source operated in SASE mode. A source of significant Bragg reflection intensity noise is identified from the combination of mode structure and jitter with very small mosaic spread of the crystals and very low convergence of the XFEL source. The accuracy with which the three dimensional reflection is approximated by the 'quasi-cw' rotation method with the pulsed source is modelled from the experimentally collected X-ray pulse intensities together with the measured rocking curves. This model is extended to predict merging statistics for recently demonstrated self seeded mode generated pulse train with improved stability, in addition to extrapolating to single crystal experiments with increased mosaic spread. The results show that the noise level can be adequately modelled in this manner, indicating that the large intensity fluctuations dominate the merged signal-to-noise (I/σI) value. Furthermore, these results predict that using the self seeded mode together with more mosaic crystals, sufficient accuracy may be obtained in order to resolve typical photoinduced structure factor amplitude differences, as taken from representative synchrotron results.
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Affiliation(s)
- Jasper J van Thor
- Imperial College London, Division of Molecular Biosciences, South Kensington Campus, London SW7 2AZ, UK.
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Milota F, Lincoln CN, Hauer J. Precise phasing of 2D-electronic spectra in a fully non-collinear phase-matching geometry. Opt Express 2013; 21:15904-15911. [PMID: 23842377 DOI: 10.1364/oe.21.015904] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report an experimental design for two-dimensional electronic spectroscopy (2D-ES) that avoids the need to measure notoriously weak pump-probe spectra. Retaining a fully non-collinear folded boxcar geometry, the described layout replaces pump-probe with heterodyned transient grating (het-TG). The absorptive component of the het-TG signal is measured directly, following a straightforward optimization routine. The use of het-TG achieves an improvement in signal to noise ratio by almost two orders of magnitude. As a result, 2D-ES-signals down to 0.5% can be clearly resolved.
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Affiliation(s)
- Franz Milota
- Photonics Institute, Vienna University of Technology, Gusshausstrasse 27, 1040 Vienna, Austria
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11
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Lincoln CN, Fitzpatrick AE, van Thor JJ. Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein. Phys Chem Chem Phys 2012; 14:15752-64. [PMID: 23090503 DOI: 10.1039/c2cp41718a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quantum yield of photoisomerisation of the photoactive yellow protein (PYP) strongly depends on peak power and wavelength with femtosecond optical excitation. Using systematic power titrations and addition of second order dispersion resulting in 140, 300 and 600 fs pulse durations, the one and multi-photon cross-sections at 400, 450 and 490 nm have been assessed from transient absorption spectroscopy and additionally the Z-scan technique. Applying a target model that incorporates photoselection theory, estimates for the cross-sections for stimulated emission and absorption of the first excited state, the amount of ultrafast internal conversion and the underlying species associated dynamics have been determined. The final quantum yields for photoisomerisation were found to be 0.06, 0.14-0.19 and 0.02 for excitation wavelengths 400, 450 and 490 nm and found to increase with increasing pulse durations. Transient absorption measurements and Z-scan measurements at 450 nm, coinciding with the maximum wavelength of the ground state absorption, indicate that the photochemical quantum yield is intrinsically limited by an ultrafast internal conversion reaction as well as by stimulated emission cross-section. With excitation at 400 nm photoisomerisation quantum yield is further significantly limited by competing multi-photon excitation into excited state absorption at 385 nm previously proposed to result in photoionisation. With excitation at 490 nm the photoisomerisation quantum yield is predominantly limited further by the significantly higher stimulated emission cross-section compared to ground state cross-section as well as multi-photon processes. In addition to photoionisation, a second product of multi-photon excitation is identified and characterised by an induced absorption at 500 nm and a time constant of 2 ps for relaxation. With power densities up to 138 GW cm(-2) the measurements have not provided indication for coherent multi-photon absorption of PYP. In the saturation regime with 450 nm excitation, the limit for the photoisomerisation quantum yield was found to be 0.14-0.19 and the excited state absorption cross-section 6.1 × 10(-17) cm(2) or 0.36 times the ground state cross-section of 1.68 × 10(-16) cm(2) per molecule. This places a fundamental restriction on the maximum populations and sample penetration that may be achieved for instance in femtosecond pump-probe experiments with molecular crystals of PYP.
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Affiliation(s)
- Craig N Lincoln
- Imperial College London, Division of Molecular Biosciences, South Kensington campus, SW7 2AZ, London, UK
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Heskes AM, Lincoln CN, Goodger JQD, Woodrow IE, Smith TA. Multiphoton fluorescence lifetime imaging shows spatial segregation of secondary metabolites in Eucalyptus secretory cavities. J Microsc 2012; 247:33-42. [PMID: 22394321 DOI: 10.1111/j.1365-2818.2011.03593.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Multiphoton fluorescence lifetime imaging provides an excellent tool for imaging deep within plant tissues while providing a means to distinguish between fluorophores with high spatial and temporal resolution. Ideal candidates for the application of multiphoton fluorescence lifetime imaging to plants are the embedded secretory cavities found in numerous species because they house complex mixtures of secondary metabolites within extracellular lumina. Previous investigations of this type of structure have been restricted by the use of sectioned material resulting in the loss of lumen contents and often disorganization of the delicate secretory cells; thus it is not known if there is spatial segregation of secondary metabolites within these structures. In this paper, we apply multiphoton fluorescence lifetime imaging to investigate the spatial arrangement of metabolites within intact secretory cavities isolated from Eucalyptus polybractea R.T. Baker leaves. The secretory cavities of this species are abundant (up to 10 000 per leaf), large (up to 6 nL) and importantly house volatile essential oil rich in the monoterpene 1,8-cineole, together with an immiscible, non-volatile component comprised largely of autofluorescent oleuropeic acid glucose esters. We have been able to optically section into the lumina of secretory cavities to a depth of ∼80 μm, revealing a unique spatial organization of cavity metabolites whereby the non-volatile component forms a layer between the secretory cells lining the lumen and the essential oil. This finding could be indicative of a functional role of the non-volatile component in providing a protective region of low diffusivity between the secretory cells and potentially autotoxic essential oil.
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Affiliation(s)
- A M Heskes
- School of Botany, University of Melbourne, Australia.
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13
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Fitzpatrick AE, Lincoln CN, van Wilderen LJGW, van Thor JJ. Pump–Dump–Probe and Pump–Repump–Probe Ultrafast Spectroscopy Resolves Cross Section of an Early Ground State Intermediate and Stimulated Emission in the Photoreactions of the Pr Ground State of the Cyanobacterial Phytochrome Cph1. J Phys Chem B 2012; 116:1077-88. [DOI: 10.1021/jp206298n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ann E. Fitzpatrick
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
| | - Craig N. Lincoln
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
| | | | - Jasper J. van Thor
- Division of Molecular Biosciences, Imperial College London, South Kensington, SW7 2AZ
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14
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Abstract
Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments.
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Affiliation(s)
- Luuk J. G. W. van Wilderen
- Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London, United Kingdom
| | - Craig N. Lincoln
- Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London, United Kingdom
| | - Jasper J. van Thor
- Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London, United Kingdom
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15
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Teoh CL, Pham CLL, Todorova N, Hung A, Lincoln CN, Lees E, Lam YH, Binger KJ, Thomson NH, Radford SE, Smith TA, Müller SA, Engel A, Griffin MDW, Yarovsky I, Gooley PR, Howlett GJ. A structural model for apolipoprotein C-II amyloid fibrils: experimental characterization and molecular dynamics simulations. J Mol Biol 2010; 405:1246-66. [PMID: 21146539 DOI: 10.1016/j.jmb.2010.12.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops.
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Affiliation(s)
- Chai Lean Teoh
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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