Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Chl”

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.

53 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Mass removal efficiencies in water and consequences after a river diversion into coastal wetlands: second thoughts

Abstract Salinity control, nutrient additions, and sediment supply were directly or indirectly the rationale for a $220 million coastal wetland restoration project (Davis Pond River Diversion) that began in 2002. We sampled Mississippi River water going in and out of the receiving basin from 1999 to 2018 to understand why wetland loss increased after it began. There was a reduction in inorganic sediments, nitrogen (N), and phosphorus (P) concentrations within the ponding area of 77%, 39% and 34%, respectively, which is similar to that in other wetlands. But the average sediment accumulation of 0.6 mm year −1 inadequately balances the present-day 5.6 mm year −1 sea level rise or the 7.9 ± 0.13 mm year −1 accretion rates in these organic soils. Nutrients added likely reduced live belowground biomass and soil strength, and increased decomposition of the organic matter necessary to sustain elevations. The eutrophication of the downstream aquatic system from the diversion, principally by P additions, increased Chl a concentrations to a category of ‘poor’ water quality. We conclude that this diversion, if continued, will be a negative influence on wetland area and will eutrophy the estuary. It is a case history example for understanding the potential effects arising from proposed river diversions.

Turner, R. Eugene (ORCID:0000000307767506)↗
DOE OSTI2023

Mass spectrometry and spectroscopic characterization of a tetrameric photosystem I supercomplex from Leptolyngbya ohadii , a desiccation-tolerant cyanobacterium

Cyanobacteria inhabiting desert biological soil crusts face the harsh conditions of the desert. They evolved a suite of strategies toward desiccation-hydration cycles mixed with high light irradiations, etc. In this study we purified and characterized the structure and function of Photosystem I (PSI) from Leptolyngbya ohadii, a desiccation-tolerant desert cyanobacterium. We discovered that PSI forms tetrameric (PSI-Tet) aggregate. We investigated it by using sucrose density gradient centrifugation, clear native PAGE, high performance liquid chromatography, mass spectrometry (MS), time-resolved fluorescence (TRF) and time-resolved transient absorption (TA) spectroscopy. MS analysis identified the presence of two PsaB and two PsaL proteins in PSI-Tet and uniquely revealed that PsaLs are N-terminally acetylated in contrast to non-modified PsaL in the trimeric PSI from Synechocystis sp. PCC 6803. Chlorophyll (Chl) a fluorescence decay profiles of the PSI-Tet performed at 77 K revealed two emission bands at ∼690 nm and 725 nm with the former appearing only at early delay time. The main fluorescence emission peak, associated with emission from the low energy Chls a, decays within a few nanoseconds. TA studies demonstrated that the 725 nm emission band is associated with low energy Chls a with absorption band clearly resolved at ∼710 nm at 77 K. As a result, our work suggests that the heterogenous composition of PsaBs and PsaL in PSI-Tet is related with the adaptation mechanisms needed to cope with stressful conditions under which this bacterium naturally grows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Patterns of Initial Relapse from a Phase 3 Study of Response-Based Therapy for High-Risk Hodgkin Lymphoma (AHOD0831): A Report from the Children's Oncology Group

The Children's Oncology Group protocol AHOD0831, for pediatric patients with high-risk classical Hodgkin lymphoma (cHL), used response-adapted radiation fields, rather than larger involved-field radiation therapy (IFRT) that were historically used. This retrospective analysis of patterns of relapse among patients enrolled in the study was conducted to study the potential effect of a reduction in RT exposure.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restrains for non-protein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in Chlorophyll (Chl) proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C 2 symmetry of Photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and Cryogenic electron microscopy (CryoEM) PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restrains play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested, from cyanobacteria to algae. Furthermore, these results highlight both the opportunities and limitations inherent in the structure-based analysis of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

14 SOLAR ENERGY↗
DOE OSTI2024

Controlling Vibronic Coupling in Chlorophyll Proteins: The Effects of Excitonic Delocalization and Vibrational Localization

Vibrational-electronic (vibronic) coupling plays a critical role in excitation energy transfer in molecular aggregates and pigment-protein complexes (PPCs). But the interplay between excitonic delocalization and vibronic interactions is complex, often leaving even qualitative questions as to what conceptual framework (e.g., Redfield versus Forster theory) should be used to interpret experimental results. To shed light on this issue, we report here on the interplay between excitonic delocalization and vibronic coupling in site-directed mutants of the water soluble chlorophyll protein (WSCP), as reflected in 77 K fluorescence spectra. Experimentally, we find that in PPCs where excitonic delocalization is disrupted (either by mutagenesis or heterodimer formation), the relative intensity of the vibrational sideband (VSB) in fluorescence spectra is suppressed by up to 37% compared to the native protein. Furthermore, numerical simulations reveal that this effect results from the localization of high-frequency vibrations in the coupled system; while excitonic delocalization suppresses the purely electronic transition due to H-aggregate-like dipole-dipole interference, high-frequency vibrations are unaffected, leading to a relative enhancement of the VSB. By comparing VSB intensities of PPCs both in the presence and absence of excitonic delocalization, we extract a set of “local” Huang-Rhys (HR) factors for Chl a in WSCP. More generally, our results suggest a significant role for geometric effects in controlling energy-transfer rates (which depend sensitively on absorption/fluorescence line shapes) in molecular aggregates and PPCs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Isolating the Vibrational Spectra of the Red Chlorophylls in Photosystem I with Multispectral Two-Dimensional Spectroscopy

Photosystem I (PSI) uses an antenna of chlorophyll (Chl) molecules to create a charge separated state with high quantum efficiency. Understanding the charge separation mechanism is currently hindered by spectral overlap between the antenna and reaction center (RC) Chls and the fact that energy transfer and electron transfer occur with similar time scales. Here, we characterize the antenna excited states by applying two-dimensional electronic (2DES) and two-dimensional electronic-vibrational (2DEV) spectroscopy to PSI complexes with closed RCs. Comparison of the 2DES and 2DEV spectra, which evolve with the same kinetics, enabled characterization of the vibrational modes of the antenna during energy equilibration between spectrally distinct Chls. Through global analysis, we learn how energy transfer between the Bulk and Red Chls presents in the 2DEV spectra and we definitively identify vibrations of the cationic components of the mixed exciton and intermolecular charge transfer states associated with the Red Chls. This work enables future studies of the initial charge separation mechanism of PSI by 2DEV spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The initial charge separation step in oxygenic photosynthesis

Photosystem II is crucial for life on Earth as it provides oxygen as a result of photoinduced electron transfer and water splitting reactions. The excited state dynamics of the photosystem II-reaction center (PSII-RC) has been a matter of vivid debate because the absorption spectra of the embedded chromophores significantly overlap and hence it is extremely difficult to distinguish transients. Here, we report the two-dimensional electronic-vibrational spectroscopic study of the PSII-RC. The simultaneous resolution along both the visible excitation and infrared detection axis is crucial in allowing for the character of the excitonic states and interplay between them to be clearly distinguished. In particular, this work demonstrates that the mixed exciton-charge transfer state, previously proposed to be responsible for the far-red light operation of photosynthesis, is characterized by the Chl D1 + Phe radical pair and can be directly prepared upon photoexcitation. Further, we find that the initial electron acceptor in the PSII-RC is Phe, rather than P D1 , regardless of excitation wavelength.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Commissioning of a replacement subatmospheric cold box for Jefferson Lab’s Central Helium Liquefier

Jefferson Lab’s Cryogenics Department has designed, fabricated, installed, and commissioned a new subatmospheric cold box to replace one of the two existing units within our Central Helium Liquefier (CHL). The replacement cold box, dubbed SC1R, pumps saturated helium vapor at 0.0385 atm from Jefferson Lab’s continuous electron beam accelerator facility (CEBAF) cryomodules to maintain an operating temperature of nominally 2.1 K. This is accomplished using a five-stage cryogenic centrifugal compressor (cold compressor) system and a brazed aluminum plate-fin heat exchanger operating between 2.1 K and 4.5 K. In this paper we will describe our experience commissioning the SC1R cold box. We will discuss pump-down of the system to 2.1 K and steady-state operation at the cold compressor design flow rates of 170, 200, and 250 g/s. Performance of the heat exchanger and cold compressors has been mapped across a range of flow rates and optimized for CEBAF operations. This commissioning data will be used to monitor future performance and adapt to changing load requirements.

Mastracci, B.↗
DOE OSTI2022

LCLS-II helium cryoplant and cryo distribution system installation

The helium cryoplant and cryo distribution system (CDS) are key elements of the new superconducting Linac Coherent Light Source (LCLS-II) and will provide superfluid helium to the accelerator. The cryoplant consists of two helium refrigerators with an equivalent 4.5 K refrigeration capacity of 18 kW each. The 37 cryomodules of the LINAC will be operated at a temperature of 2.0 K to accelerate a 4 GeV electron beam that will generate extremely bright X-ray laser light. Two five-stage cold compressor cold boxes will be utilized to provide superfluid helium II for the superconducting cavity structures with a total cooling capacity of 8 kW at 2.0 K. This paper describes the installation of the LCLS-II cryoplant and CDS. The LCLS-II cryoplant was designed and contributed by Jefferson Lab. To expedite the project completion the reuse of proven design and technology from the Jefferson Lab CHL-2 cryoplant was the preferred strategy. The CDS consists of ~260 m thermally shielded and vacuum super insulated transfer lines, two distribution boxes and eight feed and end caps, and was designed and contributed by Fermilab. SLAC installed the cryoplant components into a newly erected building and the CDS components into the existing accelerator tunnel and klystron gallery with strong engineering support from both partner labs.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Habitat‐adapted microbial communities mediate Sphagnum peatmoss resilience to warming

Summary Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long‐term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole‐ecosystem warming study to collect field‐grown Sphagnum , mechanically separate the associated microbiome and then transfer onto germ‐free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chl a fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm‐microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Database of low‐temperature absorption and fluorescence spectra of native photosynthetic tetrapyrrole macrocycles

Low-temperature (77 K) absorption and fluorescence spectra of 12 naturally occurring photosynthetic tetrapyrrole macrocycles have been recorded in a frozen glass (2-methyltetrahydrofuran). The compounds encompass distinct chromophore classes: porphyrin, chlorophyll c 2 ; chlorin, chlorophylls a, b, d, f and bacteriochlorophylls c, d, e, f; and bacteriochlorin, bacteriochlorophylls a, b, g. The spectra are compared with those of the same pigment in liquid solution (predominantly 2-methyltetrahydrofuran) at room temperature (293 K). The measured Stokes shifts at 77 K across the 12 macrocycles range from ~30 to 300 cm −1 . The spectral data in digital form are made available as part of the PhotochemCAD databases. Literature searches have revealed extensive published data for Chl a (often in biological matrices) but at best rather limited data for less common macrocycles. The availability of a systematic collection of curated spectral data collected at low temperature should be useful for a variety of assessments, including reconstruction of absorption spectra of (bacterio)chlorophyll-containing protein complexes, vibrational analysis of absorption and fluorescence spectra, and calculations where knowledge of energy levels is important.

Niedzwiedzki, Dariusz M. [Washington University in↗
DOE OSTI2023

Charge separation in the photosystem II reaction center resolved by multispectral two-dimensional electronic spectroscopy

The photosystem II reaction center (PSII RC) performs the primary energy conversion steps of oxygenic photosynthesis. While the PSII RC has been studied extensively, the similar time scales of energy transfer and charge separation and the severely overlapping pigment transitions in the Qy region have led to multiple models of its charge separation mechanism and excitonic structure. Here, we combine two-dimensional electronic spectroscopy (2DES) with a continuum probe and two-dimensional electronic vibrational spectroscopy (2DEV) to study the cyt b559-D1D2 PSII RC at 77 K. This multispectral combination correlates the overlapping Qy excitons with distinct anion and pigment-specific Q x and mid-infrared transitions to resolve the charge separation mechanism and excitonic structure. Through extensive simultaneous analysis of the multispectral 2D data, we find that charge separation proceeds on multiple time scales from a delocalized excited state via a single pathway in which Pheo D1 is the primary electron acceptor, while Chl D1 and P D1 act in concert as the primary electron donor.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2024

RuBisCO activity assays: a simplified biochemical redox approach for in vitro quantification and an RNA sensor approach for in vivo monitoring

Abstract Background Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant soluble protein in nature. Extensive studies have been conducted for improving its activity in photosynthesis through approaches like protein engineering. Concurrently, multiple biochemical and radiolabeling assays have been developed for determining its activity. Although these existing assays yield reliable results, they require addition of multiple external components, rendering them less convenient and expensive. Therefore, in this study, we have developed two relatively cheaper, convenient, and easily reproducible assays for quantitative and qualitative estimation of RuBisCO activity. Results We simplified a contemporary NADH based spectrophotometric RuBisCO assay by using cyanobacterial cell lysate as the source for Calvin cycle enzymes. We analyzed the influence of inorganic carbon substrates, CO 2 and NaHCO 3 , and varying protein concentrations on RuBisCO activity. Ribulose-1,5-bisphosphate (RuBP) consumption rates for the cultures grown under 5% CO 2 were 5–7 times higher than the ones grown with 20 mM NaHCO 3 , at different protein concentrations. The difference could be due to the impaired activity of carbonic anhydrase in the cell lysate, which is required for the conversion of HCO 3 − to CO 2 . The highest RuBisCO activity of 2.13 nmol of NAD + / µg of Chl-a/ min was observed with 50 µg of protein and 5% CO 2 . Additionally, we developed a novel RNA-sensor based fluorescence assay that is based on the principle of tracking the kinetics of ATP hydrolysis to ADP during the conversion of 3-phosphoglycerate (3-PG) to 1,3-bisphosphoglycerate (1,3-BPG) in the Calvin cycle. Under in vitro conditions, the fluorometric assay exhibited ~ 3.4-fold slower reaction rate (0.37 min −1 ) than the biochemical assay when using 5% CO 2 . We also confirmed the in vivo application of this assay, where increase in the fluorescence was observed with the recombinant strain of Synechocystis sp. PCC 6803 (SSL142) expressing the ADP-specific RNA sensor, compared to the WT. In addition, SSL142 exhibited three-fold higher fluorescence when supplemented with 20 mM NaHCO 3 as compared to the cells that were grown without NaHCO 3 supplementation. Conclusions Overall, we have developed a simplified biochemical assay for monitoring RuBisCO activity and demonstrated that it can provide reliable results as compared to the prior literature. Furthermore, the biochemical assay using 5% CO 2 (100% relative activity) provided faster RuBP consumption rate compared to the biochemical assay utilizing 20 mM NaHCO 3 (30.70% relative activity) and the in vitro fluorometric assay using 5% CO 2 (29.64% relative activity). Therefore, the absorbance-based biochemical assay using 5% CO 2 or higher would be suitable for in vitro quantification of the RuBisCO activity. On the other hand, the RNA-sensor based in vivo fluorometric assay can be applied for qualitative analysis and be used for high-throughput screening of RuBisCO variants. As RuBisCO is an enzyme shared amongst all the photoautotrophs, the assays developed in this study can easily be extended for analyzing the RuBisCO activities even in microalgae and higher plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tracking Photochemical and Photophysical Processes for Solar Energy Conversion Via Multidimensional Visible and Vibrational Spectroscopic Methods

This project was motivated by an overarching goal to elucidate the mechanism of energy and electron transfer that governs the efficient charge separation in photosystem I (PSI) complexes. PSI is a natural light harvesting complex that drives oxygenic photosynthesis in plants, algae, and cyanobacteria. It uses ~300 tightly packed chlorophylls (Chls) to absorb photons, transfer the excitation energy to the reaction center (RC), and generate a charge separated state with near unity quantum efficiency (QE). A better understanding of the mechanism of energy transfer and charge separation in PSI is required for understanding the high QE of natural light harvesting complexes, and it could lead to the further development of artificial photosynthetic systems for solar energy conversion. We applied two-dimensional electronic spectroscopy (2DES) to different cyanobacterial photosystem I complexes to map energy transfer pathways to gain insight into the efficient light harvesting of PSI. We interpreted the 2DES spectra through a global analysis procedure, finding two ultrafast equilibration processes involving red-shifted Chl states. The analysis procedure is general and can be readily applied to other natural and artificial light harvesting systems. In addition to investigating PSI complexes, we also performed measurements on model systems to establish general data analysis procedures for interpreting 2D spectra.

14 SOLAR ENERGY↗
DOE OSTI2024

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 (PSI 3 ), PSI 3 mutants, and PSI 3 –IsiA 18 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 PSI 3 and PSI 3 -IsiA 18 supercomplexes allowed us to make inferences about EET from the IsiA 18 ring to the PSI 3 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 IsiA 18 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 IsiA 18 ring to the PSI 3 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.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data Fusion for the Development of a Multimodal Freight Transload Facilities Dataset in the U.S.

To withstand the growing demand of commodity volume and its strain on the transportation infrastructure, it is necessary to identify the flow of commodities by route and mode. However, a national multimodal freight routing model does not exist for the U.S. The development of such model requires multiple building blocks, such as virtual representations of roadway, railway, and waterway networks, transload facilities (TFs), and access/egress links. Most of these blocks have a robust database in the U.S., except for the TFs. Here, this paper presents the fusion of dispersed and heterogeneous representations of multimodal TFs into a single, comprehensive, geospatial freight TF dataset. The TF dataset is derived from several sources, including the U.S. Army Corps of Engineers Master Docks Plus, the National Transportation Atlas Database, the Intermodal Association of North America, industry publications, and other public information. First, individual datasets were queried and reconciled. A geocoding/reverse geocoding process was applied to get the best street address and latitude/longitude location for each terminal. Then, duplicate terminals were identified by a fuzzy match algorithm based on terminal name and location, and removed. Validation was performed by visual inspection of random facilities. The main contributions of this work are: a publicly available version of the TF dataset, including facility location and multimodal transfer capability of 9,003 facilities, and an enterprise-version with the same facilities but including commodity handling capabilities. The main purpose of developing the TF dataset is to inform multimodal routing algorithms. The proposed TF dataset allows for credibly modeling the multimodal transfer of commodities within shipment routes.

Commodity Routing↗
DOE OSTI2026

Arctic Black Carbon Aerosol Deposition Study North Slope of Alaska 2020- ACSM Measurements

Particles are removed from the atmosphere through both wet and dry deposition. These processes are poorly understood, though they constitute important uncertainties in climate and air quality models. This project aims to use observational constraints on particle fluxes to improve model representations of dry deposition. In support of black carbon (SP2) and particles (UHSAS) flux measurements at the meteorological tower, we measured non-refractory chemically-speciated aerosol composition with an Aerosol Chemical Speciation Monitor at the the NSA Central Facility (C1). ACSM measurements were made between 9 Sept and 26 Oct 2021. This site is a coastal tundra location, and received snow during the project.

Chl_ACSM↗