DOE SBIR Ph I Spatial Excitation Emission Matrix Spectroscopy (SEEMS) Bioimager Instrument Final Scientific Technical Report
Explore the source record for details and available documents.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Engineering Papers
Results for “Fluorescence spectroscopy”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts
Abstract Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial‐microbial holobiont (termed HT‐58‐2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a , complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH 2 Cl 2 /2‐propanol, 1:1) of HT‐58‐2 cultures with NaBH 4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17‐dioxobacteriochlorins) exhibit a bathochromic shift ( λ abs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 13 1 ‐oxochlorin) exhibits a hypsochromic shift ( λ abs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λ em 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non‐axenic cultures at microscale quantities (2 mL, 2 μ m ), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT‐58‐2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.
Nguyen, Kathy‐Uyen↗
SILIA: software implementation of a multi-channel, multi-frequency lock-in amplifier for spectroscopy and imaging applications
In this work, we describe a software implementation of a multi-channel, multi-frequency Lock-in Amplifier (SILIA) to extract modulated signals from noisy data distributed over multiple channels of arbitrary number and size. This software implementation emulates the functionality of a multi-channel, multi-frequency lock-in amplifier in a post-processing step following data acquisition. Unlike most traditional lock-in amplifiers, SILIA can work with any number of input channels and is especially useful to analyze data distributed over many channels. We demonstrate the versatility and performance for extracting weak signals in spectroscopy and fluorescence microscopy. We also discuss more general applications and exhibit a method to automatically estimate error from a lock-in result.
47 OTHER INSTRUMENTATION↗
Immobilization of Cyanines in DNA Produces Systematic Increases in Fluorescence Intensity
Cyanines are useful fluorophores for a myriad of biological labeling applications, but their interactions with biomolecules are unpredictable. Cyanine fluorescence intensity can be highly variable due to complex photoisomerization kinetics, which are exceedingly sensitive to the surrounding environment. This introduces large errors in Förster resonance energy transfer (FRET)-based experiments where fluorescence intensity is the output parameter. However, this environmental sensitivity is a strength from a biological sensing point of view if specific relationships between biomolecular structure and cyanine photophysics can be identified. We describe a set of DNA structures that modulate cyanine fluorescence intensity through the insertion of adenine or thymine bases. These structures simultaneously provide photophysical predictability and tunability. We characterize these structures using steady-state fluorescence measurements, fluorescence correlation spectroscopy (FCS), and time-resolved photoluminescence (TRPL). Here, we find that the photoisomerization rate decreases over an order of magnitude across the adenine series, which is consistent with increasing immobilization of the cyanine moiety by the surrounding DNA structure.
59 BASIC BIOLOGICAL SCIENCES↗
Electronic spectroscopy and ionization potentials for YbOH and YbOCH 3
The polyatomic molecules YbOH and YbOCH 3 have been recognized as being of potential value for spectroscopic experiments that explore charge-parity and time reversal symmetry violation effects. These measurements require very high precision, which, in turn, will necessitate that the molecules be manipulated at ultra-cold temperatures. Both YbOH and YbOCH 3 have electronic transitions that appear suitable for laser cooling ($\tilde{A}$ 2 Π 1/2 -$\tilde{X}$ 2 Σ + and $\tilde{A}$2E 1/2 -$\tilde{X}$ 2 A 1 , respectively) but the currently available spectroscopic data is not sufficient to determine the extent to which population leaks may compromise the optical cooling processes. A further complication is that the quantum states of interest for these measurements will need to be selectively populated. The $\tilde{A}$-$\tilde{X}$ band systems of both YbOH and YbOCH 3 show evidence of vibronic perturbations, such that there are unassigned vibronic features at energies that are just above the origin bands. Here, in the present study we have recorded spectra for the $\tilde{A}$ 2 Π 1/2 -$\tilde{X}$ 2 Σ + transition of jet-cooled YbOD to facilitate the vibronic assignments. In addition, spectra for the $\tilde{B}$ 2 Σ + - $\tilde{X}$ 2 Σ + transition of YbOH were recorded, establishing the origin band at 20473.8 cm -1 . Previously, the reaction of Yb with CH 3 OH has been used to generate gas-phase YbOCH 3 . As this reaction also yields YbOH, there have been complications in spectroscopic studies of YbOCH 3 due to overlap of the $\tilde{A} -\tilde{X}$ band systems. To identify specific regions of overlap, resonantly enhanced two-photon ionization spectra were recorded using mass-resolved detection of the YbOH + and YbOCH 3 + ions. These data confirmed the overlap of vibronic bands near 17640 and 17680 cm -1 . Two-photon ionization spectroscopy also provided accurate ionization energies of IE(YbOH)=45788(10) and IE(YbOCH 3 )=45283(10) cm -1 . The IE for YbOH is relevant to problems encountered in previous attempts to determine the bond dissociation energy of YbOH + .
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Observation of biexciton emission from single semiconductor nanoplatelets
Quasi-two-dimensional semiconductor nanoplatelets (NPLs) are intriguing systems for studying the influence of Auger recombination processes on the multiexciton emission efficiencies in the weak in-plane confinement regime. We investigate CdSe/CdS core/shell NPLs using cryogenic temperature single particle spectroscopy and observe bright biexciton emission at high excitation powers. The average binding energy of the biexcitons is determined to be 16.5 meV. The observed switching between the biexciton and trion states indicates charging-decharging dynamics of the NPLs mediated by the Auger ionization process. These findings are highly relevant for harvesting efficient biexciton emission for energy, lighting, and quantum applications.
36 MATERIALS SCIENCE↗
Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium between excited states
Pyrene fluorescence after a high-energy electronic excitation exhibits a prominent band shoulder not present after excitation at low energies. The standard assignment of this shoulder as a non-Kasha emission from the second-excited state (S 2 ) has been recently questioned. To elucidate this issue, we simulated the fluorescence of pyrene using two different theoretical approaches based on vertical convolution and nonadiabatic dynamics with nuclear ensembles. To conduct the necessary nonadiabatic dynamics simulations with high-lying electronic states and deal with fluorescence timescales of about 100 ns of this large molecule, we developed new computational protocols. The results from both approaches confirm that the band shoulder is, in fact, due to S 2 emission. We show that the non-Kasha behavior is a dynamic-equilibrium effect not caused by a metastable S 2 minimum. However, it requires considerable vibrational energy, which can only be achieved in collisionless regimes after transitions into highly excited states. This strict condition explains why the S 2 emission was not observed in some experiments.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Optical tuning of the diamond Fermi level measured by correlated scanning probe microscopy and quantum defect spectroscopy
Quantum technologies based on quantum point defects in crystals require control over the defect charge state. Here we tune the charge state of shallow nitrogen-vacancy and silicon-vacancy centers by locally oxidizing a hydrogenated surface with moderate optical excitation and simultaneous spectral monitoring. The loss of conductivity and change in work function due to oxidation are measured in atmosphere using conductive atomic force microscopy and Kelvin probe force microscopy (KPFM). We correlate these scanning probe measurements with optical spectroscopy of the nitrogen-vacancy and silicon-vacancy centers created via implantation 15–25 nm beneath the diamond surface and annealing. The observed charge state of the defects as a function of optical exposure demonstrates that laser oxidation provides a way to precisely tune the Fermi level over a range of at least 2.00 eV. We also observe a significantly larger oxidation rate for implanted surfaces compared to unimplanted surfaces under ambient conditions. Here, combined with knowledge of the electron affinity of a surface, these results suggest KPFM is a powerful, high-spatial-resolution technique to advance surface Fermi level engineering for charge stabilization of quantum defects.
36 MATERIALS SCIENCE↗
Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA’s structural heterogeneity.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Calibration of a versatile multi-energy soft x-ray diagnostic for WEST long pulse plasmas
A compact multi-energy soft x-ray diagnostic is being installed on the W Environment in Steady-state Tokamak (WEST), which was designed and built to test ITER-like tungsten plasma facing components in a long pulse (~1000 s) scenario. The diagnostic consists of a pinhole camera fielded with the PILATUS3 photon-counting Si-based detector (≲100 kpixel). The detector has sensitivity in the range 1.6–30 keV and enables energy discrimination, providing a higher energy resolution than conventional systems with metal foils and diodes with adequate space and time resolution (≲1 cm and 2 ms). The lower-absorption cut-off energy is set independently on each one of the ~100 kpixels, providing a unique opportunity to measure simultaneously the plasma emissivity in multiple energy ranges and deduce a variety of plasma parameters (e.g., T e , n Z , and ΔZ eff ). The energy dependence of each pixel is calibrated here over the range 3–22 keV. The detector is exposed to a variety of monochromatic sources—fluorescence emission from metallic targets—and for each pixel, the lower energy threshold is scanned to calibrate the energy dependence. The data are fit to a responsivity curve (“S-curve”) that determines the mapping between the possible detector settings and the energy response for each pixel. Here, the calibration is performed for three energy ranges: low (2.3–6 keV), medium (4.5–13.5 keV), and high (5.4–21 keV). We determine the achievable energy resolutions for the low, medium, and high energy ranges as 330 eV, 640 eV, and 950 eV, respectively. The main limitation for the energy resolution is found to be the finite width of the S-curve.
47 OTHER INSTRUMENTATION↗
Cryogenic Correlative Single-Particle Photoluminescence Spectroscopy and Electron Tomography for Investigation of Nanomaterials
Cryogenic single-particle photoluminescence (PL) spectroscopy has been used with great success to directly observe the heterogeneous photophysical states present in a population of luminescent particles. Cryogenic electron tomography provides complementary nanometer scale structural information to PL spectroscopy, but the two techniques have not been correlated due to technical challenges. Here, we present a method for correlating single-particle information from these two powerful microscopy modalities. We simultaneously observe PL brightness, emission spectrum, and in-plane excitation dipole orientation of CdSSe/ZnS quantum dots suspended in vitreous ice. Stable and fluctuating emitters were observed, as well as a surprising splitting of the PL spectrum into two bands with an average energy separation of 80 meV. In some cases, the onset of the splitting corresponded to changes in the in-plane excitation dipole orientation. These dynamics were assigned to structures of individual quantum dots and the excitation dipoles were visualized in the context of structural features.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Altering the spectroscopy, electronic structure, and bonding of organometallic curium(III) upon coordination of 4,4'–bipyridine
Structural and electronic characterization of (Cp' 3 Cm) 2 (μ–4,4'–bpy) (Cp' = trimethylsilylcyclopentadienyl, 4,4'–bpy = 4,4'–bipyridine) is reported and provides a rare example of curium–carbon bonding. Cp' 3 Cm displays unexpectedly low energy emission that is quenched upon coordination by 4,4'–bipyridine. Electronic structure calculations on Cp' 3 Cm and (Cp' 3 Cm) 2 (μ–4,4'–bpy) rule out significant differences in the emissive state, rendering 4,4'–bipyridine as the primary quenching agent. Comparisons of (Cp' 3 Cm) 2 (μ–4,4'–bpy) with its samarium and gadolinium analogues reveal atypical bonding patterns and electronic features that offer insights into bonding between carbon with f-block metal ions. Here we show the structural characterization of a curium–carbon bond, in addition to the unique electronic properties never before observed in a curium compound.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Spectroscopic and Chemical Properties of Ionic Liquids: Computational Study
A brief account is given of highlights of our computational efforts – often in collaboration with experimental groups – to understand spectroscopic and chemical properties of ionic liquids (ILs). Molecular dynamics, including their inhomogeneous character, responsible for key spectral features observed in dielectric absorption, infra-red (IR) and fluorescence correlation spectroscopy (FCS) measurements are elucidated. Mechanisms of chemical processes involving imidazolium-based ILs are illustrated for CO 2 capture and related reactions, transesterification of cellulose, and Au nanocluster-catalyzed Suzuki cross-coupling reaction with attention paid to differing roles of IL ions. A comparison with experiments is also made.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Getting to the Core of PARAFAC2, A Nonnegative Approach
In this paper, the authors present a novel method of performing PARAFAC2 factorization of three-way data using a compact representation of that data. In the standard PARAFAC2 algorithm, two modes of the data are recovered directly during the decomposition while the third mode is returned as a transformation matrix, which is then used to rotate sets of orthogonal third-mode basis factors into interpretable factors. In our new method, the data are first decomposed into a core matrix and orthogonal factor loading matrices in the first two modes as well as sets of orthogonal factors in the third mode (as in standard PARAFAC2). The core matrix is then decomposed using a the standard PARAFAC2 strategy to produce transformation matrices in all three modes. The algorithm is particularly useful for very large data sets and essentially permits imposition of nonnegativity in all three modes.
97 MATHEMATICS AND COMPUTING↗
Mesoscale interplay among composition heterogeneity, lattice deformation, and redox stratification in single-crystalline layered oxide cathode
Single-crystalline layered oxide materials for lithium-ion batteries are featured by their excellent capacity retention over their polycrystalline counterparts, making them sought-after cathode candidates. Their capacity degradation, however, becomes more severe under high-voltage cycling, hindering many high-energy applications. It has long been speculated that the interplay among composition heterogeneity, lattice deformation, and redox stratification could be a driving force for the performance decay. The underlying mechanism, however, is not well-understood. In this study, we use X-ray microscopy to systematically examine single-crystalline NMC particles at the mesoscale. This technique allows us to capture detailed signals of diffraction, spectroscopy, and fluorescence, offering spatially resolved multimodal insights. Focusing on early high-voltage charging cycles, we uncover heterogeneities in valence states and lattice structures that are inherent rather than caused by electrochemical abuse. These heterogeneities are closely associated with compositional variations within individual particles. Our findings provide useful insights for refining material synthesis and processing for enhanced battery longevity and efficiency.
36 MATERIALS SCIENCE↗
Preparation and characterization of isotopically pure Mo targets for nuclear science measurements
Isotopically pure molybdenum targets are essential in various nuclear science measurements. For studies of cross sections of capture reactions on molybdenum, uniform targets with areal densities of hundreds of g/cm 2 are desired. Mechanical rolling of enriched metal pieces or vacuum sputtering methods used in previous studies to prepare molybdenum targets are challenging and involve labor- and time-intensive processes. Therefore, reliable and straightforward methods to produce molybdenum targets are crucial. We have developed a new double-step method to produce targets meeting these needs. The first step consists of evaporating isotopically enriched MoO 3 onto gold backings. The second step involves the reduction of the oxide layer in a 5% H 2 -Ar environment to obtain molybdenum targets. X-ray fluorescence (XRF) spectroscopy, X-ray Diffraction (XRD), a scanning electron microscope/focused ion beam milling, and energy-dispersive X-ray spectroscopy (EDS) were used to characterize the targets. These methods show that the targets exhibit a uniform coverage of Mo over the gold backings. Furthermore, significant volume shrinkage occurring during the reduction of MoO 3 creates a porous Mo layer where the gold diffuses due to the high processing temperatures, resulting in mixed Mo–Au layers.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Spectroscopic study and lifetime measurement of the 6d7p 3 F 2 o state of radium
We report a method for the precision measurement of the oscillator strengths and the branching fractions of the decay channels of the 6d7p 3 F 2 o state in 226 Ra. Here, this method exploits a set of metastable states present in Ra, allowing a measurement of the oscillator strengths that does not require knowledge of the number of atoms in the atomic beam. We measure the oscillator strengths and the branching fractions for decays from the 6d7p 3 F 2 o state to the 7s6d 3 D 1 , 7s6d 3 D 2 , and 7s6d 1 D 2 states and constrain the branching fraction to the 7s6d 3 D 3 state to be less than 0.4% (68% confidence limit). The lifetime of the 3 F 2 o state is determined to be 15 ± 4 ns.
74 ATOMIC AND MOLECULAR PHYSICS↗
Laser ablation spectrometry for studies of uranium plasmas, reactor monitoring, and spent fuel safety
Nuclear security is one of the defining challenges of our time. Nuclear threats range from deliberate dispersal of radioactive material to contaminate the vital infrastructure to diversion and smuggling of special nuclear material for clandestine nuclear programs and nuclear terrorism, respectively. There is an associated need to develop and sustain the nuclear forensics capabilities, which requires the understanding of complex processes that occur in plasmas of nuclear materials. The area of nuclear safety has seen a resurgence of public interest, and there is a concomitant need to safely store used nuclear fuel and detect structural material failure in nuclear power systems, especially in innovative reactor designs envisioned for future adoption. Laser-produced plasmas are complicated extreme environments that can generate intense and rich, highly specific signatures of nuclear and radiological materials, which can then be explored in a wide range of applications. They include interdiction and rapid detection of nuclear materials, including their isotopic composition, detection over long distances, laboratory simulation of weapons effects, monitoring the condition of structural materials in dry cask storage containers, and novel instrumentation for nuclear power systems. We present a compilation of recent representative examples of the application of laser spectroscopy, and laser-induced breakdown spectroscopy in particular, to nuclear safety and security problems. A case is made that spectroscopic techniques based on laser-produced plasmas offer complementary, and sometimes unique, capabilities that motivate the continued exploration of their efficient production and understanding of the signatures they produce
(020.3260) Isotope shifts, (140.3440) Laser-induce↗