Single-Molecule Fluorescence Spectroscopy of Photosynthetic Systems

Discovery of Multiple Light-Harvesting States of the Photosynthetic Protein PE545

Cryptophytes are photosynthetic microalga that flourish in a remarkable diversity of natural environments by using pigment-containing proteins with absorption maxima tuned to each ecological niche. While this diversity in the absorption has been well established, the subsequent photophysics is highly sensitive to the local protein environment and so may exhibit similar variation. Thermal fluctuations of the protein conformation are expected to introduce photophysical heterogeneity of the pigments that may have evolved important functional properties in a manner similar to that of the absorption. However, such heterogeneity is averaged out in ensemble measurements and, therefore, has not yet been probed. Here, we report single-molecule measurements of phycoerythrin 545 (PE545), the prototypical cryptophyte antenna protein, in its native dimeric form. A conformational ensemble was resolved consisting of distinct photophysical states with different light-harvesting properties. Proteins that did not quench, partially quenched, or fully quenched absorbed light were observed. Light intensity increased the quenched-state population of the dimer, potentially as a mechanism to deal with the extreme light intensities found in aqueous environments. Cross-linking, which mimics local interactions, introduces this light-dependent functionality while also suppressing other conformational dynamics. The cellular organization can, therefore, actively modulate the protein conformation and dynamics, selecting for distinct levels of light harvesting. Thus, the complex conformational equilibrium provides an additional mechanism for cryptophytes and likely other photosynthetic organisms to optimize solar energy capture and conversion.

Advanced analysis of single-molecule spectroscopic data

We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analyzing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data-such as fluorescence brightness, lifetime, and spectra-of molecular- or nanometer-scale particles such as single dye molecules, quantum dots, or fluorescently labeled biological macromolecules. Full SMS allows an unbiased statistical analysis of fluorescence brightness through level resolution and clustering, analysis of fluorescence lifetimes through decay fitting, as well as the calculation of second-order correlation functions and the display of fluorescence spectra and raster-scan images. Additional features include extensive data filtering options, a custom HDF5-based file format, and flexible data export options. The software is open source and written in Python but GUI based so it may be used without any programming knowledge. A multiprocess architecture was employed for computational efficiency. The software is also designed to be easily extendable to include additional import data types and analysis capabilities.

Efficient, nonparametric removal of noise and recovery of probability distributions from time series using nonlinear-correlation functions: Photon and photon-counting noise

A preceding paper [M. Dhar, J. A. Dickinson, and M. A. Berg, J. Chem. Phys. 159, 054110 (2023)] shows how to remove additive noise from an experimental time series, allowing both the equilibrium distribution of the system and its Green's function to be recovered. The approach is based on nonlinear-correlation functions and is fully nonparametric: no initial model of the system or of the noise is needed. However, single-molecule spectroscopy often produces time series with either photon or photon-counting noise. Unlike additive noise, photon noise is signal-size correlated and quantized. Photon counting adds the potential for bias. This paper extends noise-corrected-correlation methods to these cases and tests them on synthetic datasets. Neither signal-size correlation nor quantization is a significant complication. Analysis of the sampling error yields guidelines for the data quality needed to recover the properties of a system with a given complexity. We show that bias in photon-counting data can be corrected, even at the high count rates needed to optimize the time resolution. Using all these results, we discuss the factors that limit the time resolution of single-molecule spectroscopy and the conditions that would be needed to push measurements into the submicrosecond region.

Minimizing Structural Heterogeneity in DNA Self-Assembled Dye Templating via DNA Origami-Tuned Conformations

With recent advances in DNA-templated dye aggregation for leveraging and engineering molecular excitons, a need exists for minimizing structural heterogeneity. Holliday Junction complexes (HJ) are commonly used to covalently template dye aggregates on their core; however, the global conformation of HJ is detrimentally dynamic. Here, the global conformation of the HJ is selectively tuned by restricting its position and orientation by using a sheet-like DNA origami construct (DOC) physisorbed on glass. The HJ arms are fixed with four different designed interduplex angles (IDAs). Atomic force microscopy confirmed that the HJs are bound to the surface of DOC with tuned IDAs. Dye orientation distributions were determined by combining dipole imaging and super-resolution microscopy. All IDAs led to dye orientations having dispersed distributions along planes perpendicular to the HJ plane, suggesting that stacking occurred between the dye and the neighboring DNA bases. The dye-base stacking interpretation was supported by increasing the size of the core cavity. The narrowest IDA minimizes structural heterogeneity and suggests dye intercalation. A strong correlation is found between the IDA and the orientation of the dye along the HJ plane. These results show that the HJ imposes restrictions on the dye and that the dye-DNA interactions are always present regardless of global conformation. The implications of our results are discussed for the scalability of dye aggregates using DNA self-assembly. Our methodology provides an avenue for the solid-supported single-molecule characterization of molecular assemblies templated on biomolecules─such as DNA and protein templates involved in light-harvesting and catalysis─with tuned conformations and restricted in position and orientation.

Thermoelectric Properties of Porphyrin Nano Rings: A Theoretical and Modelling Investigation

Propagation of De Broglie waves through nanomolecular junctions is greatly affected by molecular topology changes, which in turn plays a key role in determining the electronic and thermoelectric properties of source|molecule|drain junctions. The probing and realization of the constructive quantum interference (CQI) and a destructive quantum interference (DQI) are well established in this work. The critical role of quantum interference (QI) in governing and enhancing the transmission coefficient T(E), thermopower (S), power factor (P) and electronic figure of merit (ZelT) of porphyrin nanorings has been investigated using a combination of density functional theory (DFT) methods, a tight binding (Hückel) modelling (TBHM) and quantum transport theory (QTT). Remarkably, DQI not only dominates the asymmetric molecular pathways and lowering T(E), but also improves the thermoelectric properties.

ApcE plays an important role in light-induced excitation energy dissipation in the Synechocystis PCC6803 phycobilisomes

Phycobilisomes (PBs) play an important role in cyanobacterial photosynthesis. They capture light and transfer excitation energy to the photosynthetic reaction centres. PBs are also central to some photoprotective and photoregulatory mechanisms that help sustain photosynthesis under non-optimal conditions. Amongst the mechanisms involved in excitation energy dissipation that are activated in response to excessive illumination is a recently discovered light-induced mechanism that is intrinsic to PBs and has been the least studied. Here, we used single-molecule spectroscopy and developed robust data analysis methods to explore the role of a terminal emitter subunit, ApcE, in this intrinsic, light-induced mechanism. We isolated the PBs from WT Synechocystis PCC 6803 as well as from the ApcE-C190S mutant of this strain and compared the dynamics of their fluorescence emission. PBs isolated from the mutant (i.e., ApcE-C190S-PBs), despite not binding some of the red-shifted pigments in the complex, showed similar global emission dynamics to WT-PBs. However, a detailed analysis of dynamics in the core revealed that the ApcE-C190S-PBs are less likely than WT-PBs to enter quenched states under illumination but still fully capable of doing so. This result points to an important but not exclusive role of the ApcE pigments in the light-induced intrinsic excitation energy dissipation mechanism in PBs.

High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes

Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.

Access to the Antenna System of Photosystem I via Single-Molecule Excitation-Emission Spectroscopy

In the development of single-molecule spectroscopy, the simultaneous detection of the excitation and emission spectra has been limited. The fluorescence excitation spectrum based on background-free signals is compatible with the fluorescence-emission-based detection of single molecules and can provide insight into the variations in the input energy of the different terminal emitters. Here, we implement single-molecule excitation-emission spectroscopy (SMEES) for photosystem I (PSI) via a cryogenic optical microscope. To this end, we extended our line-focus-based excitation-spectral microscope system to the cryogenic temperature-compatible version. PSI is one of the two photosystems embedded in the thylakoid membrane in oxygen-free photosynthetic organisms. PSI plays an essential role in electron transfer in the photosynthesis reaction. PSIs of many organisms contain a few red-shifted chlorophylls (Chls) with much lower excitation energies than ordinary antenna Chls. The fluorescence emission spectrum originates primarily from the red-shifted Chls, whereas the excitation spectrum is sensitive to the antenna Chls that are upstream of red-shifted Chls. Using SMEES, we obtained the inclining two-dimensional excitation-emission matrix (2D-EEM) of PSI particles isolated from a cyanobacterium, Thermosynechococcus vestitus (equivalent to elongatus), at about 80 K. Interestingly, by decomposing the inclining 2D-EEMs within time course observation, we found prominent variations in the excitation spectra of the red-shifted Chl pools with different emission wavelengths, strongly indicating the variable excitation energy transfer (EET) pathway from the antenna to the terminal emitting pools. SMEES helps us to directly gain information about the antenna system, which is fundamental to depicting the EET within pigment-protein complexes.

Quantum plasmonics pushes chiral sensing limit to single molecules: a paradigm for chiral biodetections

Chiral sensing of single molecules is vital for the understanding of chirality and their applications in biomedicine. However, current technologies face severe limitations in achieving single-molecule sensitivity. Here we overcome these limitations by designing a tunable chiral supramolecular plasmonic system made of helical oligoamide sequences (OS) and nanoparticle-on-mirror (NPoM) resonator, which works across the classical and quantum regimes. Our design enhances the chiral sensitivity in the quantum tunnelling regime despite of the reduced local E-field, which is due to the strong Coulomb interactions between the chiral OSs and the achiral NPoMs and the additional enhancement from tunnelling electrons. A minimum of four molecules per single-Au particle can be detected, which allows for the detection of an enantiomeric excess within a monolayer, manifesting great potential for the chiral sensing of single molecules.

Insights into protein structure using cryogenic light microscopy

Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.

Current trends in the detection and removal of heavy metal ions using functional materials

The shortage of freshwater resources caused by heavy metal pollution is an acute global issue, which has a great impact on environmental protection and human health. Therefore, the exploitation of new strategies for designing and synthesizing green, efficient, and economical materials for the detection and removal of heavy metal ions is crucial. Among the various methods for the detection and removal of heavy ions, advanced functional systems including nanomaterials, polymers, porous materials, and biomaterials have attracted considerable attention over the past several years due to their capabilities of real-time detection, excellent removal efficiency, anti-interference, quick response, high selectivity, and low limit of detection. In this tutorial review, we review the general design principles underlying the aforementioned functional materials, and in particular highlight the fundamental mechanisms and specific examples of detecting and removing heavy metal ions. Additionally, the methods which enhance water purification quality using these functional materials have been reviewed, also current challenges and opportunities in this exciting field have been highlighted, including the fabrication, subsequent treatment, and potential future applications of such functional materials. We envision that this tutorial review will provide invaluable guidance for the design of functional materials tailored towards the detection and removal of heavy metals, thereby expediting the development of high-performance materials and fostering the development of more efficient approaches to water pollution remediation.

A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins

Photosynthetic light harvesting requires efficient energy transfer within dynamic networks of light-harvesting complexes embedded within phospholipid membranes. Artificial light-harvesting models are valuable tools for understanding the structural features underpinning energy absorption and transfer within chromophore arrays. Here, a method for attaching a protein-based light-harvesting model to a planar, fluid supported lipid bilayer (SLB) is developed.  The protein model consists of the tobacco mosaic viral capsid proteins that are gene-doubled to create a tandem dimer (dTMV). Assemblies of dTMV break the facial symmetry of the double disk to allow for differentiation between the disk faces. A single reactive lysine residue is incorporated into the dTMV assemblies for the site-selective attachment of chromophores for light absorption. On the opposing dTMV face, a cysteine residue is incorporated for the bioconjugation of a peptide containing a polyhistidine tag for association with SLBs. The dual-modified dTMV complexes show significant association with SLBs and exhibit mobility on the bilayer. The techniques used herein offer a new method for protein-surface attachment and provide a platform for evaluating excited state energy transfer events in a dynamic, fully synthetic artificial light-harvesting system.

Probing the interactions between amyloidogenic proteins and bio-membranes

Protein misfolding diseases (PMDs) in humans are characterized by the deposition of protein aggregates in tissues, including Alzheimer's disease, Parkinson's disease, type 2 diabetes, and amyotrophic lateral sclerosis. Misfolding and aggregation of amyloidogenic proteins play a central role in the onset and progression of PMDs, and these processes are regulated by multiple factors, especially the interaction between proteins and bio-membranes. Bio-membranes induce conformational changes in amyloidogenic proteins and affect their aggregation; on the other hand, the aggregates of amyloidogenic proteins may cause membrane damage or dysfunction leading to cytotoxicity. In this review, we summarize the factors that affect the binding of amyloidogenic proteins and membranes, the effects of bio-membranes on the aggregation of amyloidogenic proteins, mechanisms of membrane disruption by amyloidogenic aggregates, technical approaches for detecting these interactions, and finally therapeutic strategies targeting membrane damage caused by amyloidogenic proteins.

Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles

Single-molecule microscopic techniques allow the counting of successive turnover events and the study of the time-dependent fluctuations of the catalytic activities of individual enzymes and different sites on a single heterogeneous nanocatalyst. It is important to establish theoretical methods to obtain the statistical measurements of such stochastic fluctuations that provide insight into the catalytic mechanism. In this review, we discuss a few theoretical frameworks for evaluating the first passage time distribution functions using a self-consistent pathway approach and chemical master equations, to establish a connection with experimental observables. The measurable probability distribution functions and their moments depend on the molecular details of the reaction and provide a way to quantify the molecular mechanisms of the reaction process. The statistical measurements of these fluctuations should provide insight into the enzymatic mechanism.

Surface Preparation for Single-Molecule Fluorescence Imaging in Organic Solvents

The development of single-molecule techniques provides opportunities to investigate the properties and heterogeneities of individual molecules, which are almost impossible to be obtained in ensemble measurements. Recently, single-molecule fluorescence microscopy is being applied more and more to study chemical reactions in organic solvents. However, little has been done to optimize the surface preparation procedures for single-molecule fluorescence imaging in organic solvents. In this work, we developed a method to prepare the surface for single-molecule fluorescence imaging in organic solvents with a well-controlled surface density of chemically immobilized dye molecules and a low density of nonspecifically adsorbed impurities. We also compared the surfaces prepared by two different procedures and studied the impacts of the polarities of the solvent and the surface functionality on the quality of prepared surface. We found that higher polarities of both the solvent and the surface functionality provided better control of the surface density of chemically immobilized dyes and helped reduce the nonspecific adsorption of both dyes and fluorescent impurities in organic solvents. We further performed single-molecule fluorescence imaging in DMF and investigated the photophysical properties of dyes and fluorescent impurities, which could be used to filter out false counts in single-molecule fluorescence measurements.

Infrared nanospectroscopic imaging of DNA molecules on mica surface

Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying IR-AFM technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the AFM-IR investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of AFM-IR mapping modalities with corresponding absorption spectra based on two different DNA deposition protocols on spermidine and Ni²⁺ pretreated mica surface. The nanoscale IR absorbance of distinctly formed DNA morphologies on mica are demonstrated through series of AFM-IR absorption maps with corresponding IR spectrum. Our results thus demonstrate the sensitivity of AFM-IR nanospectroscopy for a nucleic acid research with an open potential to be employed in further investigation of nucleoprotein complexes.

Dual-function artificial molecular motors performing rotation and photoluminescence

Molecular machines have caused one of the greatest paradigm shifts in chemistry, and by powering artificial mechanical molecular systems and enabling autonomous motion, they are expected to be at the heart of exciting new technologies. One of the biggest challenges that still needs to be addressed is designing the involved molecules to combine different orthogonally controllable functions. Here, we present a prototype of artificial molecular motors exhibiting the dual function of rotary motion and photoluminescence. Both properties are controlled by light of different wavelengths or by exploiting motors' outstanding two-photon absorption properties using low-intensity near-infrared light. This provides a noninvasive way to both locate and operate these motors in situ, essential for the application of molecular machines in complex (bio)environments.

Optical Detection and Imaging of Nonfluorescent Matter at the Single-Molecule/Particle Level

Since the first optical detection of single molecules in 1989, single-molecule spectroscopy has developed rapidly and been widely applied in many areas. However, the vast majority of matter is extremely inefficient at emitting photons in our physical world, which seriously limits the applications of optical methods based on photoluminescence. In addition to indirect detection by fluorescence labeling, many efforts have been made to directly image nonfluorescent matter at the single-particle or single-molecule level in different ways based on the absorption or scattering interaction between light and matter. Herein, we review five popular methods for imaging nonfluorescent particles/molecules, including dark-field microscopy (DFM), surface plasmon resonance microscopy (SPRM), surface enhanced Raman microscopy (SERM), interferometric scattering microscopy (iSCAT), and photothermal microscopy (PTM). After summarizing the principles and applications of these methods, we compare the advantages and disadvantages of each method and describe further potential development and applications.

Observation of conformational dynamics in single light-harvesting proteins from cryptophyte algae

Photosynthetic organisms use pigment-protein complexes to capture the sunlight that powers most life on earth. Within these complexes, the position of the embedded pigments is all optimized for light harvesting. At the same time, the protein scaffold undergoes thermal fluctuations that vary the structure, and, thus, photophysics, of the complexes. While these variations are averaged out in ensemble measurements, single-molecule spectroscopy provides the ability to probe these conformational changes. We used single-molecule fluorescence spectroscopy to identify the photophysical substates reflective of distinct conformations and the associated conformational dynamics in phycoerythrin 545 (PE545), a pigment-protein complex from cryptophyte algae. Rapid switching between photophysical states was observed, indicating that ensemble measurements average over a conformational equilibrium. A highly quenched conformation was also identified, and its population increased under high light. This discovery establishes that PE545 has the characteristics to serve as a photoprotective site. Finally, unlike homologous proteins from the evolutionarily related cyanobacteria and red algae, quenching was not observed upon photobleaching, which may allow for robust photophysics without the need for rapid repair or replacement machinery. Collectively, these observations establish the presence of a rich and robust set of conformational states of PE545. Cryptophytes exhibit particularly diverse energetics owing to the variety of microenvironments in which they survive, and the conformational states and dynamics reported here may provide photophysical flexibility that contributes to their remarkable ability to flourish under diverse conditions.

Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective

Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.

Preprocess dependence of optical properties of ensembles and single siphonaxanthin-containing major antenna from the marine green alga Codium fragile

The siphonaxanthin-siphonein-Chl-a/b-protein (SCP) is the light-harvesting complex of the marine alga Codium fragile. Its structure resembles that of the major light-harvesting complexes of higher plants, LHC II, yet it features a reversed Chl a:Chl b ratio and it accommodates other variants of carotenoids. We have recorded the fluorescence emission spectra and fluorescence lifetimes from ensembles and single SCP complexes for three different scenarios of handling the samples. While the data obtained from ensembles of SCP complexes yield equivalent results, those obtained from single SCP complexes featured significant differences as a function of the sample history. We ascribe this discrepancy to the different excitation intensities that have been used for ensemble and single complex spectroscopy, and conclude that the SCP complexes undergo an aging process during storage. This process is manifested as a lowering of energetic barriers within the protein, enabling thermal activation of conformational changes at room temperature. This in turn leads to the preferential population of a red-shifted state that features a significant decrease of the fluorescence lifetime.

Photoprotective conformational dynamics of photosynthetic light-harvesting proteins

Under high light conditions, excess energy can damage the machinery of oxygenic photosynthesis. Plants have evolved a series of photoprotective processes, including conformational changes of the light-harvesting complexes that activate dissipation of energy as heat. In this mini-review, we will summarize our recent work developing and applying single-molecule methods to investigate the conformational states of the light-harvesting complexes. Through these measurements, we identified dissipative conformations and how they depend on conditions that mimic high light. Our studies revealed an equilibrium between the light-harvesting and dissipative conformations, and that the nature of the equilibrium varies with cellular environment, between proteins, and between species. Finally, we conclude with an outlook on open questions and implications for photosynthetic yields.

The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol

The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.

Determination of two-photon absorption in nucleobase analogues: a QR-DFT perspective

With the prevalence of fluorescence spectroscopy in biological systems, and the benefits of two-photon absorption techniques, presented here is an assessment of the two-photon accessibility of modern fluorescent nucleobase analogues utilising quadratic response DFT. Due to the complex environment experienced by these nucleobases, the two-photon spectra of each analogue has been assessed in the presence of both [Formula: see text]-stacked and hydrogen-bonding interactions involving the canonical nucleobases. Findings suggest that the [Formula: see text]-stacking environment provides a more significant effect on the spectra of the analogues studies than a hydrogen-bonding environment; analogue structures presenting high two-photon cross-section values for one or more states coincide with polycyclic extensions to preserved canonical base structure, as observed in the qA family of analogues, while analogue structures more closely resembling the structure of the base in question present a much more muted spectra in comparison. Results from this investigation have also allowed for the derivation of a number of design rules for the development of potential, two-photon specific, analogues for future use in both imaging and potential photochemical activation.

Observation of robust energy transfer in the photosynthetic protein allophycocyanin using single-molecule pump-probe spectroscopy

Photosynthetic organisms convert sunlight to electricity with near unity quantum efficiency. Absorbed photoenergy transfers through a network of chromophores positioned within protein scaffolds, which fluctuate due to thermal motion. The resultant variation in the individual energy transfer steps has not yet been measured, and so how the efficiency is robust to this variation has not been determined. Here, we describe single-molecule pump-probe spectroscopy with facile spectral tuning and its application to the ultrafast dynamics of single allophycocyanin, a light-harvesting protein from cyanobacteria. We disentangled the energy transfer and energetic relaxation from nuclear motion using the spectral dependence of the dynamics. We observed an asymmetric distribution of timescales for energy transfer and a slower and more heterogeneous distribution of timescales for energetic relaxation, which was due to the impact of the protein environment. Collectively, these results suggest that energy transfer is robust to protein fluctuations, a prerequisite for efficient light harvesting.

Monitoring tautomerization of single hypericin molecules in a tunable optical λ/2 microcavity

Hypericin tautomerization that involves the migration of the labile protons is believed to be the primary photophysical process relevant to its light-activated antiviral activity. Despite the difficulty in isolating individual tautomers, it can be directly observed in single-molecule experiments. We show that the tautomerization of single hypericin molecules in free space is observed as an abrupt flipping of the image pattern accompanied with fluorescence intensity fluctuations, which are not correlated with lifetime changes. Moreover, the study can be extended to a λ/2 Fabry-Pérot microcavity. The modification of the local photonic environment by a microcavity is well simulated with a theoretical model that shows good agreement with the experimental data. Inside a microcavity, the excited state lifetime and fluorescence intensity of single hypericin molecules are correlated, and a distinct jump of the lifetime and fluorescence intensity reveals the temporal behavior of the tautomerization with high sensitivity and high temporal resolution. The observed changes are also consistent with time-dependent density functional theory calculations. Our approach paves the way to monitor and even control reactions for a wider range of molecules at the single molecule level.

Recent advances in single-molecule spectroscopy studies on light-harvesting processes in oxygenic photosynthesis

Photosynthetic light-harvesting complexes (LHCs) play a crucial role in concentrating the photon energy from the sun that otherwise excites a typical pigment molecule, such as chlorophyll-a, only several times a second. Densely packed pigments in the complexes ensure efficient energy transfer to the reaction center. At the same time, LHCs have the ability to switch to an energy-quenching state and thus play a photoprotective role under excessive light conditions. Photoprotection is especially important for oxygenic photosynthetic organisms because toxic reactive oxygen species can be generated through photochemistry under aerobic conditions. Because of the extreme complexity of the systems in which various types of pigment molecules strongly interact with each other and with the surrounding protein matrixes, there has been long-standing difficulty in understanding the molecular mechanisms underlying the flexible switching between the light-harvesting and quenching states. Single-molecule spectroscopy studies are suitable to reveal the conformational dynamics of LHCs reflected in the fluorescence properties that are obscured in ordinary ensemble measurements. Recent advanced single-molecule spectroscopy studies have revealed the dynamical fluctuations of LHCs in their fluorescence peak position, intensity, and lifetime. The observed dynamics seem relevant to the conformational plasticity required for the flexible activations of photoprotective energy quenching. In this review, we survey recent advances in the single-molecule spectroscopy study of the light-harvesting systems of oxygenic photosynthesis.

Untargeted LC-MS-based metabonomic analysis of the effect of photoperiod on the testes of broiler roosters

Photoperiod is an important factor that stimulates the reproductive performance of broiler breeder roosters. However, the mechanism by which photoperiod affects the reproductive performance of broiler breeder roosters has not been fully studied. To study the effects of different photoperiods on the reproductive performance of broiler breeder roosters, 120 Arbor Acres broiler breeder roosters aged 20 weeks were randomly assigned to three groups (n = 40), and the three groups were treated with different photoperiod regimes: control (CTR; 12.5 h of light and 11.5 h of dark, 12.5 L: 11.5 D), short day (SD; 16 L: 8 D) and long day (LD; 8 L: 16 D). Serum and testes were collected after 4 weeks of feeding, and testosterone-related indices were detected. We found that testosterone synthesis in the testes of broiler roosters was boosted with prolonged of photoperiod. Subsequently, metabonomics was used to identify the differential endogenous metabolites that may affect the function of the testes in breeder roosters. We found compared with other groups, the concentrations of creatine, uridine monophosphate, phosphoribosyl pyrophosphate, dCMP, α-D-glucose and citric acid in the SD group decreased significantly (p < 0.05), and glyoxylic acid, D-ribose 5-phosphate, deoxyuridine and orotic acid in the SD group increased significantly (p < 0.05), while the CTR group and LD group showed no significant difference (p > 0.05). The concentrations of linoleic acid and α-linolenic acid in the LD group were increased significantly (p < 0.05) than those in the CTR and SD groups. Compared with the CTR group, the concentrations of histamine in the SD and LD groups were significant increased (p < 0.05). The 13 of the different metabolites could be used as candidate biomarkers for different photoperiods affecting testosterone synthesis, may be used to molecular breeding of high reproductive performance broiler roosters.

Spectrally-tunable femtosecond single-molecule pump-probe spectroscopy

Single-molecule spectroscopy has been extensively used to investigate heterogeneity in static and dynamic behaviors on millisecond and second timescales. More recently, single-molecule pump-probe spectroscopy emerged as a method to access heterogeneity on the femtosecond and picosecond timescales. Here, we develop a single-molecule pump-probe apparatus that is easily tunable across the visible region and demonstrate its utility on the widely-used fluorescent dye, Atto647N. A spectrally-independent, bimodal distribution of energetic relaxation time constants is found, where one peak corresponds to electronic dephasing (∼ 100 fs) and the other to intravibrational relaxation (∼ 300 fs). The bimodal nature indicates that relaxation within each individual molecule is dominated by only one of these processes. Both peaks of the distribution are narrow, suggesting little heterogeneity is present for either process. As illustrated here, spectrally-tunable single-molecule pump-probe spectroscopy will enable investigation of the heterogeneity in a wide range of biological and material systems.

Membrane-dependent heterogeneity of LHCII characterized using single-molecule spectroscopy

In green plants, light harvesting complex of Photosystem II (LHCII) absorbs and transports excitation energy toward the photosynthetic reaction centers and serves as a site for energy-dependent nonphotochemical quenching (qE), the photoprotective dissipation of energy as heat. LHCII is thought to activate dissipation through conformational changes that change the photophysical behaviors. Understanding this balance requires a characterization of how the conformations of LHCII, and thus its photophysics, are influenced by individual factors within the membrane environment. Here, we used ensemble and single-molecule fluorescence to characterize the excited-state lifetimes and switching kinetics of LHCII embedded in nanodisc- and liposome-based model membranes of various sizes and lipid compositions. As the membrane area decreased, the quenched population and the rate of conformational dynamics both increased because of interactions with other proteins, the aqueous solution, and/or disordered lipids. Although the conformational states and dynamics were similar in both thylakoid and asolectin lipids, photodegradation increased with thylakoid lipids, likely because of their charge and pressure properties. Collectively, these findings demonstrate the ability of membrane environments to tune the conformations and photophysics of LHCII.

Stochastic Collision Electrochemistry from Single G-Quadruplex/Hemin: Electrochemical Amplification and MicroRNA Sensing

Stochastic collision electrochemistry is a hot topic in single molecule/particle research, which provides an opportunity to investigate the details of the single molecule/particle reaction mechanism that is always masked in ensemble-averaged measurements. In this work, we develop an electrochemical amplification strategy to monitor the electrocatalytic behavior of single G-quadruplex/hemin (GQH) for the reaction between hydrogen peroxide and hydroquinone (HQ) through the collision upon a gold nanoelectrode. The intrinsic peroxidase activities of single GQH were investigated by stochastic collision electrochemical measurements, giving further insights into understanding biocatalytic processes. Based on the unique catalytic activity of GQH, we have also designed a hybridization chain reaction strategy to detect miRNA-15 with good selectivity and sensitivity. This work provided a meaningful strategy to investigate the electrochemical amplification and the broad application for nucleic acid sensing at the single molecule/particle level.

Production and monitoring of biomass and fucoxanthin with brown microalgae under outdoor conditions

The effect of light on biomass and fucoxanthin (Fx) productivities was studied in two microalgae, Tisochrysis lutea and Phaeodactylum tricornutum. High and low biomass concentrations (1.1 and 0.4 g L-1 ) were tested in outdoor pilot-scale flat-panel photobioreactors at semi-continuous cultivation mode. Fluorescence spectroscopy coupled with chemometric modeling was used to develop prediction models for Fx content and for biomass concentration to be applied for both microalgae species. Prediction models showed high R2 for cell concentration (.93) and Fx content (.77). Biomass productivity was lower for high biomass concentration than low biomass concentration, for both microalgae (1.1 g L-1 : 75.66 and 98.14 mg L-1  d-1 , for T. lutea and P. tricornutum, respectively; 0.4 g L-1 : 129.9 and 158.47 mg L-1  d-1 , T. lutea and P. tricornutum). The same trend was observed in Fx productivity (1.1 g L-1 : 1.14 and 1.41 mg L-1 d-1 , T. lutea and P. tricornutum; 0.4 g L-1 : 2.09 and 1.73 mg L-1  d-1 , T. lutea and P. tricornutum). These results show that biomass and Fx productivities can be set by controlling biomass concentration under outdoor conditions and can be predicted using fluorescence spectroscopy. This monitoring tool opens new possibilities for online process control and optimization.

Visualizing Quantum Coherence Based on Single-Molecule Coherent Modulation Microscopy

Massive magical phenomena in nature are closely related to quantum effects at the microscopic scale. However, the lack of straightforward methods to observe the quantum coherent dynamics in integrated biological systems limits the study of essential biological mechanisms. In this work, we developed a single-molecule coherent modulation (SMCM) microscopy by combining the superior features of single-molecule microscopy with ultrafast spectroscopy. By introducing the modem technology and defining the coherent visibility, we realized visualization and real-time observation of the decoherence process of a single molecule influenced by the microenvironment for the first time. In particular, we applied this technique to observe the quantum coherent properties of the entire chlorella cells and found the correlation between the coherent visibility and metabolic activities, which may have potential applications in molecular diagnostics and precision medicine.

Fluorescence Quantum Yields in Complex Environments from QM-MM TDDFT Simulations: The Case of Indole in Different Solvents

Fluorescence is commonly exploited to probe microscopic properties. An important example is tryptophan in protein environments, where variations in fluorescence quantum yield, and in absorption and emission maxima, are used as indicators of changes in the environment. Modeling the fluorescence quantum yield requires the determination of both radiative and nonradiative decay constants, both on the potential energy surface of the excited fluorophore. Furthermore, the inclusion of complex environments implies their accurate representation as well as extensive configurational sampling. In this work, we present and test various methodologies based on time-dependent density functional theory (TDDFT) and quantum mechanics/molecular mechanics (QM/MM) dynamics that take all of these requirements into account to provide a quantitative prediction of the effect of the environment on the fluorescence quantum yield of indole, a tryptophan fluorophore. This investigation paves the way for applications to the realistic spectroscopic characterization of the local protein environment of tryptophan from computer simulations.

Molecular versus Excitonic Disorder in Individual Artificial Light-Harvesting Systems

Natural light-harvesting antennae employ a dense array of chromophores to optimize energy transport via the formation of delocalized excited states (excitons), which are critically sensitive to spatio-energetic variations of the molecular structure. Identifying the origin and impact of such variations is highly desirable for understanding and predicting functional properties yet hard to achieve due to averaging of many overlapping responses from individual systems. Here, we overcome this problem by measuring the heterogeneity of synthetic analogues of natural antennae-self-assembled molecular nanotubes-by two complementary approaches: single-nanotube photoluminescence spectroscopy and ultrafast 2D correlation. We demonstrate remarkable homogeneity of the nanotube ensemble and reveal that ultrafast (∼50 fs) modulation of the exciton frequencies governs spectral broadening. Using multiscale exciton modeling, we show that the dominance of homogeneous broadening at the exciton level results from exchange narrowing of strong static disorder found for individual molecules within the nanotube. The detailed characterization of static and dynamic disorder at the exciton as well as the molecular level presented here opens new avenues in analyzing and predicting dynamic exciton properties, such as excitation energy transport.

Optical scanning tunneling microscopy based chemical imaging and spectroscopy

Through coupling optical processes with the scanning tunneling microscope (STM), single-molecule chemistry and physics have been investigated at the ultimate spatial and temporal limit. Electrons and photons can be used to drive interactions and reactions in chemical systems and simultaneously probe their characteristics and consequences. In this review we introduce and review methods to couple optical imaging and spectroscopy with scanning tunneling microscopy. The integration of the STM and optical spectroscopy provides new insights into individual molecular adsorbates, surface-supported molecular assemblies, and two-dimensional materials with subnanoscale resolution, enabling the fundamental study of chemistry at the spatial and temporal limit. The inelastic scattering of photons by molecules and materials, that results in unique and sensitive vibrational fingerprints, will be considered with tip-enhanced Raman spectroscopy. STM-induced luminescence examines the intrinsic luminescence of organic adsorbates and their energy transfer and charge transfer processes with their surroundings. We also provide a survey of recent efforts to probe the dynamics of optical excitation at the molecular level with scanning tunneling microscopy in the context of light-induced photophysical and photochemical transformations.

Coherent-to-Incoherent Transition of Molecular Fluorescence Controlled by Surface Plasmon Polaritons

We investigate the coherent-to-incoherent transition of molecular fluorescence of a chromophore above a silver surface (including bulk and thin-film systems) and explore the distance dependence of fluorescence rate enhancement. In the framework of macroscopic quantum electrodynamics, we generalize our previous theory to include multiple vibrational modes. The present theory can accurately describe quantum dynamics from the coherent limit to the incoherent limit. Moreover, we introduce a new concept Incoherent Index to quantify the degree of quantum coherence and demonstrate that the coherent-to-incoherent transition can be controlled by the dielectric environment and the molecule-silver distance. In addition, our theory indicates that strong molecule-photon (polariton) coupling can be achieved by virtue of small Huang-Rhys factors, large transition dipole moments, and appropriate dielectric material design. The present study provides a new direction for engineering light-matter interactions in polaritonic chemistry.

Recent Trends in Electrochemical Sensors for Vital Biomedical Markers Using Hybrid Nanostructured Materials

This work provides a succinct insight into the recent developments in electrochemical quantification of vital biomedical markers using hybrid metallic composite nanostructures. After a brief introduction to the biomarkers, five types of crucial biomarkers, which require timely and periodical monitoring, are shortlisted, namely, cancer, cardiac, inflammatory, diabetic and renal biomarkers. This review emphasizes the usage and advantages of hybrid nanostructured materials as the recognition matrices toward the detection of vital biomarkers. Different transduction methods (fluorescence, electrophoresis, chemiluminescence, electrochemiluminescence, surface plasmon resonance, surface-enhanced Raman spectroscopy) reported for the biomarkers are discussed comprehensively to present an overview of the current research works. Recent advancements in the electrochemical (amperometric, voltammetric, and impedimetric) sensor systems constructed with metal nanoparticle-derived hybrid composite nanostructures toward the selective detection of chosen vital biomarkers are specifically analyzed. It describes the challenges involved and the strategies reported for the development of selective, sensitive, and disposable electrochemical biosensors with the details of fabrication, functionalization, and applications of hybrid metallic composite nanostructures.

Cryogenic Single-Molecule Spectroscopy of the Primary Electron Acceptor in the Photosynthetic Reaction Center

The photosynthetic reaction center (RC) converts light energy into electrochemical energy. The RC of heliobacteria (hRC) is a primitive homodimeric RC containing 58 bacteriochlorophylls and 2 chlorophyll as. The chlorophyll serves as the primary electron acceptor (Chl a-A₀) responsible for light harvesting and charge separation. The single-molecule spectroscopy of Chl a-A₀ can be used to investigate heterogeneities of the RC photochemical function, though the low fluorescence quantum yield (0.1%) makes it difficult. Here, we show the fluorescence excitation spectroscopy of individual Chl a-A₀s in single hRCs at 6 K. The fluorescence quantum yield and absorption cross section of Chl a-A₀ increase 2- and 4-fold, respectively, compared to those at room temperature. The two Chl a-A₀s in single hRCs are identified as two distinct peaks in the fluorescence excitation spectrum, exhibiting different excitation polarization dependences. The spectral changes caused by photobleaching indicate the energy transfer across subunits in the hRC.

Advanced space- and time-resolved techniques for photocatalyst studies

Nanoparticle photocatalysts present the obvious characteristic of heterogeneity in structure, energy, and function at spatial and temporal scales.

Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation

Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light-harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins.

Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy

Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is essential for survival. Protein dynamics are often local conformational changes, which allows multiple dynamical processes to occur simultaneously and rapidly in individual proteins. Experiments often average over these dynamics and their multiplicity, preventing identification of the molecular origin and impact on biological function. Green plants survive under high light by quenching excess energy, and Light-Harvesting Complex Stress Related 1 (LHCSR1) is the protein responsible for quenching in moss. Here, we expand an analysis of the correlation function of the fluorescence lifetime by improving the estimation of the lifetime states and by developing a multicomponent model correlation function, and we apply this analysis at the single-molecule level. Through these advances, we resolve previously hidden rapid dynamics, including multiple parallel processes. By applying this technique to LHCSR1, we identify and quantitate parallel dynamics on hundreds of microseconds and tens of milliseconds timescales, likely at two quenching sites within the protein. These sites are individually controlled in response to fluctuations in sunlight, which provides robust regulation of the light-harvesting machinery. Considering our results in combination with previous structural, spectroscopic, and computational data, we propose specific pigments that serve as the quenching sites. These findings, therefore, provide a mechanistic basis for quenching, illustrating the ability of this method to uncover protein function.

Waveguide-based chemo- and biosensors: complex emulsions for the detection of caffeine and proteins

We report on a new modular sensing approach in which complex emulsions serve as efficient transducers in optical evanescent field-based sensing devices. Specifically, we leverage the tunable refractive index upon chemically triggered changes in droplet morphology or orientation. Variations in the optical coupling result in readily detectable changes in the light transmitted from a waveguide.

Robust and Fragile Quantum Effects in the Transfer Kinetics of Delocalized Excitons between B850 Units of LH2 Complexes

Aggregates of light harvesting 2 (LH2) complexes form the major exciton-relaying domain in the photosynthetic unit of purple bacteria. Application of a generalized master equation to pairs of the B850 units of LH2 complexes, where excitons predominantly reside, provides quantitative information on how the inter-LH2 exciton transfer depends on the distance, relative rotational angle, and the relative energies of the two LH2s. The distance dependence demonstrates significant enhancement of the rate due to quantum delocalization of excitons, the qualitative nature of which remains robust against the disorder. The angle dependence reflects isotropic nature of exciton transfer, which remains similar for the ensemble of disorder. The variation of the rate on relative excitation energies of LH2 exhibits resonance peaks, which, however, is fragile as the disorder becomes significant. Overall, the average transfer times between two LH2s are estimated to be in the range of 4-25 ps for physically plausible inter-LH2 distances.