Photon correlation spectroscopy as a witness for quantum coherence

The development of spectroscopic techniques able to detect and verify quantum coherence is a goal of increasing importance given the rapid progress of new quantum technologies, the advances in the field of quantum thermodynamics, and the emergence of new questions in chemistry and biology regarding the possible relevance of quantum coherence in biochemical processes. Ideally, these tools should be able to detect and verify the presence of quantum coherence in both the transient dynamics and the steady state of driven-dissipative systems, such as light-harvesting complexes driven by thermal photons in natural conditions. This requirement poses a challenge for standard laser spectroscopy methods. Here, we propose photon correlation measurements as a new tool to analyse quantum dynamics in molecular aggregates in driven-dissipative situations. We show that the photon correlation statistics on the light emitted by a molecular dimer model can signal the presence of coherent dynamics. Deviations from the counting statistics of independent emitters constitute a direct fingerprint of quantum coherence in the steady state. Furthermore, the analysis of frequency resolved photon correlations can signal the presence of coherent dynamics even in the absence of steady state coherence, providing direct spectroscopic access to the much sought-after site energies in molecular aggregates

Maximizing the biochemical resolving power of fluorescence microscopy.

Most recent advances in fluorescence microscopy have focused on achieving spatial resolutions below the diffraction limit. However, the inherent capability of fluorescence microscopy to non-invasively resolve different biochemical or physical environments in biological samples has not yet been formally described, because an adequate and general theoretical framework is lacking. Here, we develop a mathematical characterization of the biochemical resolution in fluorescence detection with Fisher information analysis. To improve the precision and the resolution of quantitative imaging methods, we demonstrate strategies for the optimization of fluorescence lifetime, fluorescence anisotropy and hyperspectral detection, as well as different multi-dimensional techniques. We describe optimized imaging protocols, provide optimization algorithms and describe precision and resolving power in biochemical imaging thanks to the analysis of the general properties of Fisher information in fluorescence detection. These strategies enable the optimal use of the information content available within the limited photon-budget typically available in fluorescence microscopy. This theoretical foundation leads to a generalized strategy for the optimization of multi-dimensional optical detection, and demonstrates how the parallel detection of all properties of fluorescence can maximize the biochemical resolving power of fluorescence microscopy, an approach we term Hyper Dimensional Imaging Microscopy (HDIM). Our work provides a theoretical framework for the description of the biochemical resolution in fluorescence microscopy, irrespective of spatial resolution, and for the development of a new class of microscopes that exploit multi-parametric detection systems

Cosmic Rays from the Knee to the Highest Energies

This review summarizes recent developments in the understanding of high-energy cosmic rays. It focuses on galactic and presumably extragalactic particles in the energy range from the knee (10^15 eV) up to the highest energies observed (>10^20 eV). Emphasis is put on observational results, their interpretation, and the global picture of cosmic rays that has emerged during the last decade.Comment: Invited review, submitted to Progress in Particle and Nuclear Physic

Quantum plasmonics: second-order coherence of surface plasmons launched by quantum emitters into a metallic film

We address the issue of the second-order coherence of single surface plasmons launched by a quantum source of light into extended gold films. The quantum source of light is made of a scanning fluorescent nanodiamond hosting five nitrogen-vacancy (NV) color centers. By using a specially designed microscopy that combines near-field optics with far-field leakage-radiation microscopy in the Fourier space and adapted spatial filtering, we find that the quantum statistics of the initial source of light is preserved after conversion to surface plasmons and propagation along the polycrystalline gold film.Comment: Second version with minor changes made to comply with Referees' comments. Editorially approved for publication in Phys. Rev. B on 22 June 201

Acquisition and analysis of steady-state and time-resolved fluorescence data for applications in materials science, bioanalytical chemistry, and super-resolution microscopy

Steady-state and time-resolved fluorescence techniques enjoy widespread applicability in domains ranging from biology to materials science owing to their extraordinary sensitivity and dynamic range. Among the most useful of these techniques is time-correlated, single-photon counting, which forms the basis of another: fluorescence lifetime imaging using stimulated emission depletion microscopy (FLIM-STED), which is used to obtain structural information on a subdiffraction-limited level (i.e., 40 nm or less). The high spatial resolution afforded by this technique is, however, accompanied by a reduction in the number of photons collected. Thus, its utility can only be exploited when meaningful information can be retrieved from sparse data sets. This retrieval requires the use of proper modeling and efficient analysis techniques. In this dissertation, several such techniques and their significance in super-resolution imaging are discussed in the context of extracting excited state fluorescence lifetime of one or more fluorophores. Probability-based, maximum-likelihood (ML) methods are compared with residual minimization (RM) methods in order to determine the limiting number of photons that are required to provide a meaningful analysis of the data. The ML methods are more robust and show considerable improvement over RM methods. The ML methods are further improved by implementing a Bayesian framework, where a nonuniform prior distribution of the parameters is included in the form of a Gaussian, an exponential, or a Dirichlet distribution. Two examples of the applications of the steady-state and time-resolved techniques are provided: the characterization of the properties of magnetic ionic liquids (MILs) and those of poly (3-hexylthiophene) (P3HT). MILs facilitate the solvent extraction of bioanalytes, e.g. DNA extraction from an aqueous solvent, with the help of an external magnetic field. The presence of paramagnetic ions, however, introduces several mechanisms of nonradiative quenching for the fluorescence of the label. Several MILs are screened to find a suitable candidate for DNA extraction using fluorescence spectroscopy. P3HT is used as the active donor layer of organic photovoltaics owing to their high photon-conversion efficiency. The structural details of the polymer aggregates of a thin film of P3HT exposed to electric filed are studied using steady-state and time-resolved anisotropy. Preferential orientations of the polymer backbone are observed if the thin film is exposed to an electric field during preparation

Resolving the emission transition dipole moments of single doubly-excited seeded nanorods via heralded defocused imaging

Semiconductor nanocrystal emission polarization is a crucial probe of nanocrystal physics and an essential factor for nanocrystal-based technologies. While the transition dipole moment of the lowest excited state to ground state transition is well characterized, the dipole moment of higher multiexcitonic transitions is inaccessible via most spectroscopy techniques. Here, we realize direct characterization of the doubly-excited state relaxation transition dipole by heralded defocused imaging. Defocused imaging maps the dipole emission pattern onto a fast single-photon avalanche diode detector array, allowing the post-selection of photon pairs emitted from the biexciton-exciton emission cascade and resolving the differences in transition dipole moments. Type-I1/2 seeded nanorods exhibit higher anisotropy of the biexciton-to-exciton transition compared to the exciton-to-ground state transition. In contrast, type-II seeded nanorods display a reduction of biexciton emission anisotropy. These findings are rationalized in terms of an interplay between transient dynamics of the refractive index and the excitonic fine structure

Effects of excitation light polarization on fluorescence emission in two-photon light-sheet microscopy

Light-sheet microscopy (LSM) is a powerful imaging technique that uses a planar illumination oriented orthogonally to the detection axis. Two-photon (2P) LSM is a variant of LSM that exploits the 2P absorption effect for sample excitation. The light polarization state plays a significant, and often overlooked, role in 2P absorption processes. The scope of this work is to test whether using different polarization states for excitation light can affect the detected signal levels in 2P LSM imaging of typical biological samples with a spatially unordered dye population. Supported by a theoretical model, we compared the fluorescence signals obtained using different polarization states with various fluorophores (fluorescein, EGFP and GCaMP6s) and different samples (liquid solution and fixed or living zebrafish larvae). In all conditions, in agreement with our theoretical expectations, linear polarization oriented parallel to the detection plane provided the largest signal levels, while perpendicularly-oriented polarization gave low fluorescence signal with the biological samples, but a large signal for the fluorescein solution. Finally, circular polarization generally provided lower signal levels. These results highlight the importance of controlling the light polarization state in 2P LSM of biological samples. Furthermore, this characterization represents a useful guide to choose the best light polarization state when maximization of signal levels is needed, e.g. in high-speed 2P LSM.Comment: 16 pages, 4 figures. Version of the manuscript accepted for publication on Biomedical Optics Expres

Single-molecule fluorescence spectroscopy

Single-molecule fluorescence spectroscopy is a powerful tool for the study of physical and biological processes through the use of fluorescent probes. By combining the femtoliter-sized observation volume of a confocal microscope with low concentrations of analytes, single fluorescent molecules can be observed as they freely diffuse in solution. From the many parameters of the fluorescence signal, a wealth of information is obtained about the structure, dynamics and interactions of the studied system. The objective of this thesis was the development, implementation and application of quantitative single-molecule fluorescence methods. To this end, a software framework for the analysis of solution-based single-molecule measurements of Förster resonance energy transfer (FRET) has been developed as part of the PAM software package. In addition, the new method of three-color photon distribution analysis (3C-PDA) is introduced in this thesis, enabling a quantitative analysis of single-molecule three-color FRET experiments. The developed analysis framework has been applied to elucidate coordinated conformational changes in the Hsp70 chaperone protein BiP, to study the conformational dynamics of a small fragment of the cellulosome, to investigate energy transfer pathways in complex artificial dye arrangements and to quantify the nanosecond dynamics of an intrinsically disordered peptide. For several studies, molecular dynamics (MD) simulations have also been used to support and cross-validate the experimental results. Here, the focus is to provide a comprehensive overview of the used methodologies, their theoretical background and their application to the various experimental systems