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DOE OSTI2024

Coupling a recurrent neural network to SPAD TCSPC systems for real-time fluorescence lifetime imaging

Fluorescence lifetime imaging (FLI) has been receiving increased attention in recent years as a powerful diagnostic technique in biological and medical research. However, existing FLI systems often suffer from a tradeoff between processing speed, accuracy, and robustness. Inspired by the concept of Edge Artificial Intelligence (Edge AI), we propose a robust approach that enables fast FLI with no degradation of accuracy. This approach couples a recurrent neural network (RNN), which is trained to estimate the fluorescence lifetime directly from raw timestamps without building histograms, to SPAD TCSPC systems, thereby drastically reducing transfer data volumes and hardware resource utilization, and enabling real-time FLI acquisition. We train two variants of the RNN on a synthetic dataset and compare the results to those obtained using center-of-mass method (CMM) and least squares fitting (LS fitting). Results demonstrate that two RNN variants, gated recurrent unit (GRU) and long short-term memory (LSTM), are comparable to CMM and LS fitting in terms of accuracy, while outperforming them in the presence of background noise by a large margin. To explore the ultimate limits of the approach, we derive the Cramer-Rao lower bound of the measurement, showing that RNN yields lifetime estimations with near-optimal precision. To demonstrate real-time operation, we build a FLI microscope based on an existing SPAD TCSPC system comprising a 32 x 32 SPAD sensor named Piccolo. Four quantized GRU cores, capable of processing up to 4 million photons per second, are deployed on the Xilinx Kintex-7 FPGA that controls the Piccolo. Powered by the GRU, the FLI setup can retrieve real-time fluorescence lifetime images at up to 10 frames per second. The proposed FLI system is promising and ideally suited for biomedical applications, including biological imaging, biomedical diagnostics, and fluorescence-assisted surgery, etc.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence

Multicolor carbon dots (CDs) have been developed recently and demonstrate great potential in bio-imaging, sensing, and LEDs. However, the fluorescence mechanism of their tunable colors is still under debate, and efficient separation methods are still challenging. Herein, we synthesized multicolor polymeric CDs through solvothermal treatment of citric acid and urea in formamide. Automated reversed-phase column separation was used to achieve fractions with distinct colors, including blue, cyan, green, yellow, orange and red. This work explores the physicochemical properties and fluorescence origins of the red, green, and blue fractions in depth with combined experimental and computational methods. Three dominant fluorescence mechanism hypotheses were evaluated by comparing time-dependent density functional theory and molecular dynamics calculation results to measured characteristics. We find that blue fluorescence likely comes from embedded small molecules trapped in carbonaceous cages, while pyrene analogs are the most likely origin for emission at other wavelengths, especially in the red. Also important, upon interaction with live cells, different CD color fractions are trafficked to different sub-cellular locations. Super-resolution imaging shows that the blue CDs were found in a variety of organelles, such as mitochondria and lysosomes, while the red CDs were primarily localized in lysosomes. These findings significantly advance our understanding of the photoluminescence mechanism of multicolor CDs and help to guide future design and applications of these promising nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Report on laser-induced fluorescence transitions relevant for the microelectronics industry and sustainability applications

A wide variety of feed gases are used to generate low-temperature plasmas for the microelectronics and sustainability applications. These plasmas often have a complex combination of reactive and nonreactive species which may have spatial and temporal variations in density, temperature, and energy. Accurate knowledge of these parameters and their variations is critically important for understanding and advancing these applications through validated and predictive modeling and the design of relevant devices. Laser-induced fluorescence (LIF) provides both spatial and temporally resolved information about the plasma-produced radicals, ions, and metastables. However, the use of this powerful diagnostic tool requires the knowledge of optical transitions including excitation and fluorescence wavelengths which may not be available or scattered through a huge literature domain. In this paper, we collected, analyzed, and compiled the available transitions for laser-induced fluorescence for more than 160 chemical species relevant to the microelectronics industry and the sustainability applications. A list of species with overlapping LIF excitations and fluorescence wavelengths have been identified. Finally, this summary is intended to serve as a data reference for LIF transitions and should be updated in the future.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Construction, characterization and crystal structure of a fluorescent single-chain Fv chimera [Slides]

Conclusions of the presentation were: The scTGPs are recombinant intrinsically fluorescent antibodies, ready for use in traditional fluorescent antibody based assays; The scFPs can be constructed as vL-FP-vH format, TGP an extremely stable monomeric fluorescent protein is suitable FP; The scFPs can be effectively displayed on yeast, where they function similarly to their corresponding scFv counterparts, recognize specific antigen similar affinity; Functional expression levels of scFPs in the bacterial cytoplasm are relatively high and can rescue some scFvs otherwise expressed at low levels in the periplasm; Straightforward assessment of expression levels and monitoring of protein purification steps; Antigen recognition in one step binding assays, novel assays such as epitope binning TGP is a monomeric fluorescent protein amenable to crystallization. These features provide unique and valuable characteristics to scTGP molecules for their use in protein chemistry; and, We present unique antibody format with wide variety of use in research and clinical setting

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Chlorophyll fluorescence is a potential indicator to measure photochemical efficiency in early to late soybean maturity groups under changing day lengths and temperatures

In this study, we employed chlorophyll a fluorescence technique, to indicate plant health and status in response to changing day lengths (photoperiods) and temperatures in soybean early and late maturity groups. Chlorophyll a fluorescence study indicates changes in light reactions in photosystem II. Experiments were performed for 3-day lengths (12.5, 13.5, and 14.5 h) and five temperatures (22/14°C, 26/18°C, 30/22°C, 34/26°C, and 40/32°C), respectively. The I-P phase declined for changing day lengths. Active reaction centers decreased at long day length for maturity group III. We observed that low temperatures impacted the acceptor side of photosystem II and partially impacted electron transport toward the photosystem I end electron acceptor. Results emphasized that higher temperatures (40/32°C) triggered damage at the oxygen-evolving complex and decreased electron transport and photosynthesis. We studied specific leaf areas and aboveground mass. Aboveground parameters were consistent with the fluorescence study. Chlorophyll a fluorescence can be used as a potential technique for high-throughput phenotyping methods. The traits selected in the study proved to be possible indicators to provide information on the health status of various maturity groups under changing temperatures and day lengths. These traits can also be deciding criteria for breeding programs to develop inbreed soybean lines for stress tolerance and sensitivity based on latitudinal variations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Fluorescent bioaerosol particle concentrations measured by the DU WIBS during the AGINSGP field experiment

Real-time, immersion mode ambient fluorescent bioaerosol concentrations were measured at ARM’s Southern Great Plains (SGP) site during the AGINSGP field experiment using a Wideband Integrated Bioaerosol Sensor (DMT Inc.; WIBS-4A). The WIBS-4A is an optical particle counter that also measures single particle fluorescence in three channels, along with particle asymmetry. Particles are grouped into different types depending on which channels they fluoresce in. The instrument was located in the guest instrument facility (GIF) and measured fluorescent particle concentrations from April 7th to April 29th. Data presented here are the concentrations for each particle type, binned in 5 minute increments. Air was drawn into the GIF through custom aluminum stack inlets (6” inner diameter) attached vertically to the outer GIF wall and the GIF outside platform. A blower pulled air through the stacks at a velocity of 1 m/s. Aerosol instruments subsampled via wall ports, through either 3/8” or 1/4" copper lines, depending on sample flow of the instrument. Particles were dried using a silica diffusion dryer prior to analysis.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

A Comparison of NO Laser-Induced Fluorescence Models at Conditions Relevant to Supersonic and Hypersonic Flows

Planar laser-induced fluorescence (PLIF) of the nitric oxide (NO) molecule has been widely used in wind tunnel facilities for flow visualization, velocity, and temperature measurements. The experimental PLIF measurements are often compared with synthetic PLIF images using computationally derived temperatures, pressures, velocities, and species mole fractions. This approach is commonly referred to as computational flow imaging (CFI). In the present work, we compare signal intensity from PLIF models with experimental PLIF measurements obtained within a low pressure gas cell system at pressures and NO mole fractions relevant to supersonic and hypersonic flowfields. Experimental measurements were compared to several different laser induced-fluorescence models reported in the literature including LIFBASE, LINUS, and a NASA two-level model. The experimental measurements agreed well with all of the models at lower pressures and lower NO mole fractions; the fluorescence there is linear with both of these parameters. However, at higher pressures and mole fractions, the signal becomes nonlinear with respect to these parameters as self-quenching limits the signal and absorption further limits the signal. In fact, for the experimental path length of the experiment, the combination of high pressure and high NO mole fraction causes the experimental results to deviate significantly from the predicted results that neglect absorption of the incident laser sheet. The LINUS model, which allows absorption to be calculated, provided results that agreed better with the experimental measurements. Since supersonic and hypersonic flowfields may contain a region of the flow with high pressures and measurements in large-scale facilities often include a long path length, neglecting absorption may have a significantly negative effect on the CFI comparison to experimental PLIF images. As a result, PLIF models that account for absorption should be included in computational flow imaging approaches for laser induced fluorescence.

laser-induced fluorescence↗

NASA NTRSDate not supplied

Towards Simultaneous Multi-Parameter Measurements Using Burst-Mode Frequency-Scanning Planar Laser-Induced Fluorescence

While planar laser-induced fluorescence (PLIF) can provide valuable flow visualization, there are many challenges in extracting quantitative measurements from the fluorescence intensity. To overcome the multi-parameter dependence of the signal intensity, frequency scanning planar laser-induced fluorescence (FS-PLIF) provides the potential for 2D temperature, pressure, and velocity measurements by spectrally resolving the excitation spectrum of one or more fluorescence transitions to extract the Doppler shift, Doppler- and collisional-broadening of absorption lines, and the relative signal intensities of multiple transitions. This work aims to characterize a burst-mode FS-PLIF system consisting of a Spectral Energies, LLC burst-mode laser coupled with a Spectral Energies, LLC optical parametric oscillator using nitric oxide (NO) static pressure cell measurements. The effect of the OPO cavity on intensity fluctuations during frequency-scanning is investigated. A NO PLIF model is implemented to investigate the feasibility of property measurements using single- and two-NO-line scans.

burst-mode laser↗

DOE OSTI2020

Stepwise Assembly of Turn‐on Fluorescence Sensors in Multicomponent Metal–Organic Frameworks for in Vitro Cyanide Detection

Abstract The controlled synthesis of multicomponent metal–organic frameworks (MOFs) allows for the precise placement of multiple cooperative functional groups within a framework, leading to emergent synergistic effects. Herein, we demonstrate that turn‐on fluorescence sensors can be assembled by combining a fluorophore and a recognition moiety within a complex cavity of a multicomponent MOF. An anthracene‐based fluorescent linker and a hemicyanine‐containing CN − ‐responsive linker were sequentially installed into the lattice of PCN‐700. The selective binding of CN − to hemicyanine inhibited the energy transfer between the two moieties, resulting in a fluorescence turn‐on effect. Taking advantage of the high tunability of the MOF platform, the ratio between anthracene and the hemicyanine moiety could be fine‐tuned in order to maximize the sensitivity of the overall framework. The optimized MOF‐sensor had a CN − ‐detection limit of 0.05 μ m , which is much lower than traditional CN − fluorescent sensors (about 0.2 μ m ).

Li, Jialuo↗

DOE OSTI2024

Designer Fluorescent Redoxmer Self‐Reports Side Reactions in Nonaqueous Redox Flow Batteries

The state of health (SOH) is a critical measure for evaluating and predicting performance of redox flow batteries (RFBs). However, diagnosing SOH of RFBs is often challenging due to the overwhelming complexity of the electrolytes and associated electrochemical reactions. Designing active molecules or redoxmers that can autonomously exhibit property changes upon specific stimuli may provide a viable way for early diagnosis of SOH. Herein, a dimerized redoxmer, DGL-N-CH 3 , was designed and synthesized by linking blue-green fluorescent monomers through a diglycolamide linker. While DGL-N-CH 3 still maintains similar electrochemical behavior and strong fluorescence, we observe a unique side reaction when cycling DGL-N-CH 3 in H-cells, which leads to a side product, NHCH 3 -BzNSN via linker cleavage. Interestingly, NHCH 3 -BzNSN also emits fluorescence but at a longer wavelength. By taking advantage of this unique fluorescent change that corresponds to the growth of NHCH 3 -BzNSN, we successfully established the capacity decay of DGL-N-CH 3 H-cell cycling, exemplifying a proof-of-concept self-reporting redoxmer design towards in situ SOH monitoring.

25 ENERGY STORAGE↗

DOE OSTI2023

Lignin-based carbon quantum dots with high fluorescence performance prepared by supercritical catalysis and solvothermal treatment for tumor-targeted labeling

The poor fluorescence performance of lignin-based carbon quantum dots (L-CQDs) prepared using the bottom-up method has hindered their development. Here, in this study, a two-step strategy was proposed to efficiently enhance the fluorescence properties of L-CQDs. Lignin was first cracked using an ethanol supercritical/noble metal catalyst; then, the L-CQDs were prepared with the cracked lignin fragments as carbon precursors without adding any modified reagents. Compared with the OL-CQDs prepared by the traditional one-pot hydrothermal method, the L-CQDs-1 prepared from CL-1 containing much low molecular weight compounds, and have photoluminescence (increased from 63 to 975) and excellent up-conversion photoluminescence (enhanced by 16.3 to 963), which significantly enhanced by about 15 times and 60 times, respectively. They can emit bright blue fluorescence under both ultraviolet and near-infrared light irradiation owing to a large amount of surface defects caused by the rich compound composition. When L-CQDs-1 were combined with, and quenched by folic acid (FA), the prepared FA@L-CQDs-1 show the ability to target and label tumor cells. This study opens new avenues for the preparation of L-CQDs with high fluorescence performance using lignocellulosic material without heteroatom additives.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

A radiative transfer model for solar induced fluorescence using spectral invariants theory

Solar Induced chlorophyll Fluorescence (SIF) shows promise as an approach for estimating gross primary production (GPP) remotely. However, sun-target-sensor geometry and within-canopy absorption of SIF can alter the relationship between measured SIF and GPP, because sensors can only retrieve some unknown fraction of the total emitted SIF. Radiative transfer models that allow for variation in canopy structure and sensor angles are therefore needed to properly interpret SIF measurements. Spectral invariants allow decoupling of the wavelength-independent canopy structure and the wavelength-dependent leaf and soil spectrum in the radiative transfer process. Here we develop a simple analytical Fluorescence Radiative Transfer model based on Escape and Recollision probability (FluorRTER) to investigate the impact of canopy structure and sun-target-sensor geometry on SIF emissions. SIF simulations using the FluorRTER model agreed well the one-dimensional Soil-Canopy Observation of Photochemistry and Energy balance (SCOPE) model and the three-dimensional Fluorescence model with Weighted Photon Spread (FluorWPS) model. The fractional vegetation cover (FVC) and clumping effect have a large influence the SIF emission of 3D discontinuous canopies. For a moderate solar zenith angle (30°) and a clumped canopy (FVC?=?0.6), the difference between the directional observed SIF of a 3D discontinuous canopy and a 1D homogeneous canopy was as large as 43.2% and 38.4% for Photosystem I?+?II fluorescence at 685?nm and at 740?nm, respectively. By bridging the gap between observed SIF and total emitted SIF over 3D heterogeneous vegetation canopies, the FluorRTER model can assist with the angular normalization of SIF measurements and enable the more robust interpretation of how variations in SIF from directional and hemispherical in-situ, airborne and satellite observations relate to leaf and whole-canopy physiological processes.

Zeng, Yelu↗

DOE OSTI2020

Electrochemical Switching of a Fluorescent Molecular Rotor Embedded within a Bistable Rotaxane

We report how the nanoconfined environment, introduced by the mechanical bonds within an electrochemically switchable bistable [2]rotaxane, controls the rotation of a fluorescent molecular rotor, namely, an 8-phenyl-substituted boron dipyrromethene (BODIPY). The electrochemical switching of the bistable [2]rotaxane induces changes in the ground-state coconformation and in the corresponding excited-state properties of the BODIPY rotor. In the starting redox state, when no external potential is applied, the cyclobis(paraquat-p-phenylene) (CBPQT4+) ring component encircles the tetrathiafulvalene (TTF) unit on the dumbbell component, leaving the BODIPY rotor unhindered and exhibiting low fluorescence. Upon oxidation of the TTF unit to a TTF2+ dication, the CBPQT4+ ring is forced toward the molecular rotor, leading to an increased energy barrier for the excited state to rotate the rotor into the state with a high nonradiative rate constant, resulting in an overall 3.4-fold fluorescence enhancement. On the other hand, when the solvent polarity is high enough to stabilize the excited charge-transfer state between the BODIPY rotor and the CBPQT4+ ring, movement of the ring toward the BODIPY rotor produces an unexpectedly strong fluorescence signal decrease as the result of photoinduced electron transfer from the BODIPY rotor to the CBPQT4+ ring. The nanoconfinement effect introduced by mechanical bonding can effectively lead to modulation of the physicochemical properties as observed in this bistable [2]rotaxane. On account of the straightforward synthetic strategy and the facile modulation of switchable electrochromic behavior, our approach could pave the way for the development of new stimuli-responsive materials based on mechanically interlocked molecules for future electro-optical applications, such as sensors, molecular memories, and molecular logic gates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Engineering an efficient and bright split Corynactis californica green fluorescent protein

Split green fluorescent protein (GFP) has been used in a panoply of cellular biology applications to study protein translocation, monitor protein solubility and aggregation, detect protein–protein interactions, enhance protein crystallization, and even map neuron contacts. Recent work shows the utility of split fluorescent proteins for large scale labeling of proteins in cells using CRISPR, but sets of efficient split fluorescent proteins that do not cross-react are needed for multiplexing experiments. We present a new monomeric split green fluorescent protein (ccGFP) engineered from a tetrameric GFP found in Corynactis californica, a bright red colonial anthozoan similar to sea anemones and scleractinian stony corals. Split ccGFP from C. californica complements up to threefold faster compared to the original Aequorea victoria split GFP and enable multiplexed labeling with existing A. victoria split YFP and CFP.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Uranyl fluorescence in acidic solution: quenching effects by tetramethylammonium (TMA + )

The quenching of uranyl luminescence by various cation species was studied in aqueous media at low pH. Solutions with different nitrate salts, held at constant uranyl nitrate, nitric acid, and ion concentration, were tested to examine the quenching effects of the cations from the nitrate salts. Alkali metal (Li + , Na + , Rb + ) and quaternary ammonium cations (NH 4 + ), (CH 3 ) 4 N + (TMA + ), (C 2 H 5 ) 4 N + (TEA + ) were investigated. Solutions containing TMA + reduced the lifetime of uranyl fluorescence significantly more than the other cations. Uranyl emission spectra also showed that TMA + increased the complex formation between uranyl and nitrate ions. Fluorescence decay lifetime measurements for most solutions yielded values between 1.4–1.9 μs at 20 °C, while 1.8 M TMA + reduced the lifetime of uranyl fluorescence to 0.6 μs. Decay rate versus concentration data (Stern–Volmer plots) indicated a dynamic quenching process with increasing fluorescence decay rates at higher cation concentrations for Li + , TMA + , and TEA + . The temperature dependencies of the decay rates and the kinetics in D 2 O were also examined.

Persinger, Thomas D. [Argonne National Laboratory ↗

DOE OSTI2025

Brush-modified fluorescent organic nanoparticles by ATRP with rigidity-regulated emission

Organic nanoparticles provide exceptional intraparticle tailorability, enabling the incorporation of functional molecules for diverse applications. In this study, we present the synthesis and characterization of fluorescent organic nanoparticles (FoNPs) with encapsulated aggregation-induced emission (AIE) luminogens with emission properties regulated by particle rigidity. Atom transfer radical polymerization (ATRP) was employed in dispersed media to develop various fluorescence colors tuned by precise control over particle rigidity. Comprehensive analyses revealed that increased particle rigidity significantly enhanced photoluminescence, achieving quantum yields of up to 22% in selected solvents. The high chain-end fidelity facilitated the grafting of hydrophilic polymer brushes from surfaces of FoNPs used as macroinitiators, enabling their dispersion in aqueous media while maintaining bright fluorescence. These findings highlight the potential of rigidity-regulated FoNPs as versatile platforms for advanced material applications, particularly in fluorescent waterborne films and aqueous-phase sensing systems.

Yin, Rongguan [Carnegie Mellon Univ., Pittsburgh, ↗

DOE OSTI2021

The fluorescence quantum yield parameter in Förster resonance energy transfer (FRET)—Meaning, misperception, and molecular design

The fluorescence quantum yield parameter in Förster resonance energy transfer (FRET) processes underpins vital phenomena ranging from light harvesting in photosynthesis to design of sensors for monitoring physiological processes. The criteria for choosing a donor for use in FRET processes include chemical features (solubility, bioconjugatability, synthetic accessibility, and stability) as well as photophysical properties pertaining to absorption (wavelength and molar absorption coefficient) and fluorescence (wavelength and fluorescence quantum yield). The value of the donor fluorescence quantum yield (Φf, or emphatically, Φf(D)) alone has sometimes been thought (erroneously) to place a ceiling on the possible quantum yield of energy transfer (Φtrans). A high value of the donor Φf, while attractive, is not at all essential; indeed, many valuable candidates for use as FRET donors have likely been excluded on the basis of this injudiciously applied filter. Such disregard is unwarranted. In this tutorial overview, the equations for FRET are reviewed along with pertinent core concepts in photophysics. An analogy using simple hydraulics provides a pedagogical tool for the non-aficionado to better understand photochemical kinetics. Ten examples are presented of donor–acceptor systems with donors that exhibit a range of Φf values (0.60, 0.59. 0.21, 0.17, 0.12, 0.118, 0.04, 0.018, 0.007, and 0.003; i.e., 60%–0.3%), yet for each corresponding donor–acceptor pair, the value of Φtrans is at least 0.70 and in some cases nearly 1.00 (i.e., 70%–100%). The systems encompass protein, synthetic inorganic, and synthetic organic architectures. The objectives of this illustrative review are to deepen understanding of FRET and to broaden molecular design considerations by enabling selection from among a far richer set of donors for use in FRET processes.

Lindsey, Jonathan S. (ORCID:0000000248722040)↗

DOE OSTI2020

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus : McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗