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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Pump House in East River Watershed, Colorado 2019-2024

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors near Pump House at Mount Crested Butte in the East River Watershed. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format ER-X-Y, where ER refers to East River, X is the location identifier, and Y is the depth identifier at the same X (shallow Y=1). Specifically, ER-PHS, ER-LMC, ER-LMF, and ER-SMN are associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and ER-RBTn (upslope n=1) are sampling transects during the 2019 Rootball Campaign. The sample and location information can be found in metadata.csv. Sampling and Measurements Each sample falls into one of the three sampling methods – (1) intact cores, (2) repacked samples, or (3) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. Both intact cores and repacked samples were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores and in-situ soil sensors could be prioritized because these sampling methods are less destructive. While the repacked samples were packed to the target bulk density (estimated post-sampling, when sample volume was known), these samples had altered pore structures. Nevertheless, intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method also has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

EARTH SCIENCE > LAND SURFACE > SOILS↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Snodgrass Mountain in East River Watershed, Colorado 2020-2025

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors at Snodgrass Mountain. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format SG-X-Y, where SG refers to Snodgrass Mountain, X is the location identifier, and Y is the depth identifier at the same X (shallow Y=1). Specifically, SG-EHS is associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and SG-ERTn (upslope n=1) are points along the Snodgrass electrical resistivity tomography transect not associated with the existing site names in the directory. The sample and location information can be found in metadata.csv. Sampling and Measurements Each sample falls into one of the three sampling methods – (1) intact cores, (2) repacked samples, or (3) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. Both intact cores and repacked samples were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores and in-situ soil sensors could be prioritized because these sampling methods are less destructive. While the repacked samples were packed to the target bulk density (estimated post-sampling, when sample volume was known), these samples had altered pore structures. Nevertheless, intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method also has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

EARTH SCIENCE > LAND SURFACE > SOILS↗
DOE OSTI2017

High-Resolution Characterization of Comingled Contaminants in the Deep Vadose Zone, Hanford Site, Washington - 17387

The contaminated deep vadose zone in the Central Plateau of the Hanford Site in Washington state presents a unique challenge to remediation. The Comprehensive Environmental Response, Compensation, and Liability Act, commonly known as the CERCLA project responsible for addressing these deep contaminants is designated as the 200-Deep Vadose Zone Operable Unit (DV-1 project). The vadose zone is 55-82 meters (180-270 feet) thick and is contaminated with both radiological and chemical contaminants from multiple historical waste streams. The mobile contaminants from this waste are still present in the deep vadose zone and pose a potential threat to the groundwater. Characterizing the nature and extent of the comingled mobile contaminants is an important step before assessing possible remedial alternatives. One factor controlling the migration and distribution of subsurface contaminants is the lithologic heterogeneity of the vadose zone sediments. A sampling plan for the DV-1 project includes continuous sediment core collection and analysis to identify key lithologic factors (i.e., small-scale bedding and structural features) that act as barriers, preferential pathways or conduits for mobile contaminants migrating through the vadose zone. Over six hundred meters (2,000 feet) of intact sediment core from 26 boreholes were collected in 1.5 meters (5 feet) long, 10 centimeter (4-inch) diameter segments. These intact sediment samples provide significant improvement in the level of detail and understanding of mechanisms and features controlling contaminant distribution that is not possible with traditional homogenized drill cuttings or conventional split-spoon samples. Detailed geological descriptions and photographs of the intact core are correlated to high-resolution geophysical logs which aid in the development of a comprehensive contaminant distribution profile of the borehole. These lithologic interpretations are used to define specific depth intervals for sampling based on changes in moisture, lithology, and elevated gamma radiation. The selected samples are analyzed for contaminants of concern, geochemical parameters, and hydraulic properties. Significant lithologic features observed in the intact cores include sharp contact boundaries to graded bedding, iron-oxide and carbonate cementation, silty laminations, clastic dike intrusions, and soft sediment deformation. Preliminary geologic logs integrated with the sample analysis indicate features that correlate to the variable distribution of contaminants both laterally and vertically. Integration of measured hydraulic parameters to lithologic units in individual borehole profiles provide key inputs for more precise geo-framework and vadose zone flux models supporting the DV-1 project. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Guanidinium-Assisted Surface Matrix Engineering for Highly Efficient Perovskite Quantum Dot Photovoltaics

Metal halide perovskite quantum dots (Pe-QDs) are of great interest in new-generation photovoltaics (PVs). However, it remains challenging in the construction of conductive and intact Pe-QD films to maximize their functionality. Herein, a ligand-assisted surface matrix strategy to engineer the surface and packing states of Pe-QD solids is demonstrated by a mild thermal annealing treatment after ligand exchange processing (referred to as “LE-TA”) triggered by guanidinium thiocyanate. The “LE-TA” method induces the formation of surface matrix on CsPbI 3 QDs, which is dominated by the cationic guanidinium (GA+) rather than the SCN-, maintaining the intact cubic structure and facilitating interparticle electrical interaction of QD solids. Consequently, the GA-matrix-confined CsPbI 3 QDs exhibit remarkably enhanced charge mobility and carrier diffusion length compared to control ones, leading to a champion power conversion efficiency of 15.21% when assembled in PVs, which is one of the highest among all Pe-QD solar cells. Additionally, the “LE-TA” method shows similar effects when applied to other Pe-QD PV systems like CsPbBr 3 and FAPbI 3 (FA = formamidinium), indicating its versatility in regulating the surfaces of various Pe-QDs. This work may afford new guidelines to construct electrically conductive and structurally intact Pe-QD solids for efficient optoelectronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2019

In Vitro Analysis of the Expression of CD11, CD29, CD36, and DC-STAMP Molecules during the Formation of Multinuclear Macrophages in BCG-Infected Mice

Expression of CD11, CD29, CD36, and DC-STAMP molecules by macrophages was analyzed in in vitro experiments. These molecules mediate cell fusion, one of the mechanisms underlying the formation of multinuclear macrophages. Macrophages were obtained from intact and BCG-infected male BALB/c mice. In intact cultures, multinuclear macrophages appeared primarily due to amitotic division of cell nuclei, while in macrophage cultures from infected mice, the process of cell fusion predominated. In intact macrophage cultures, bi- and multinuclear cells expressed primarily CD29 and CD36. In cultures from infected mice, macrophages expressing CD29 and DC-STAMP predominated, but bi- and multinuclear macrophages expressing CD11 and CD36 predominated over mononuclear ones. The study of macrophage fusion mechanism can be useful for understanding of this biological phenomenon as the mechanisms of delivery of M. tuberculosis and lysosomotropic anti-tuberculosis drugs into tuberculous granulomas to suppress M. tuberculosis persisting in macrophages and reduce the destructive potential of granulomas.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Informing the improvement of forest products durability using small angle neutron scattering

A better understanding of how wood nanostructure swells with moisture is needed to accelerate the development of forest products with enhanced moisture durability. Despite its suitability to study nanostructures, small angle neutron scattering (SANS) remains an underutilized tool in forest products research. Nanoscale moisture-induced structural changes in intact and partially cut wood cell walls were investigated using SANS and a custom-built relative humidity (RH) chamber. SANS from intact wood sections cut from each primary wood orientation showed that although wood scattered anisotropically across 1.3–600 nm length scales, measurement of elementary fibril spacing and low-q surface scattering were independent of orientation. Water sorption caused spacing between elementary fibrils to increase with RH, and this swelling accounted for over half the transverse swelling in S2 secondary wood cell walls. Elementary fibril spacing in longitudinally cut wood cells, which were designed to mimic cells near wood-adhesive bondlines, was greater than the spacing in intact cells above 90 % RH. This suggested that some cell wall hoop constraint from the S1 and S3 cell wall layers on the S2 layer was released by cutting the cells. Furthermore, increased spacing between elementary fibrils may also create diffusion channels that are hypothesized to be responsible for the onset of fungal decay in wood. Finally, protocols were established to use SANS in future research to study adhesives and protection treatments to improve moisture durability in forest products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Snapshot transient absorption spectroscopy: toward in vivo investigations of nonphotochemical quenching mechanisms

Although the importance of nonphotochemical quenching (NPQ) on photosynthetic biomass production and crop yields is well established, the in vivo operation of the individual mechanisms contributing to overall NPQ is still a matter of controversy. In order to investigate the timescale and activation dynamics of specific quenching mechanisms, we have developed a technique called snapshot transient absorption (TA) spectroscopy, which can monitor molecular species involved in the quenching response with a time resolution of 30 s. Using intact thylakoid membrane samples, we show in this study how conventional TA kinetic and spectral analyses enable the determination of the appropriate wavelength and time delay for snapshot TA experiments. As an example, we show how the chlorophyll-carotenoid charge transfer and excitation energy transfer mechanisms can be monitored based on signals corresponding to the carotenoid (Car) radical cation and Car S1 excited state absorption, respectively. The use of snapshot TA spectroscopy together with the previously reported fluorescence lifetime snapshot technique provides valuable information such as the concurrent appearance of specific quenching species and overall quenching of excited Chl. Furthermore, we show that the snapshot TA technique can be successfully applied to completely intact photosynthetic organisms such as live cells of Nannochloropsis. This demonstrates that the snapshot TA technique is a valuable method for tracking the dynamics of intact samples that evolve over time, such as the photosynthetic system in response to high-light exposure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Mutation in the β-hairpin of the Bordetella pertussis adenylate cyclase toxin modulates N-lobe conformation in calmodulin

Highlights: • Bordetella pertussis adenylate cyclase toxin modulates bi-lobal structure of CaM. • The structure and stability of the complex rely on intermolecular associations. • A novel mode of CaM-dependent activation of the adenylate cyclase toxin is proposed. - Abstract: Bordetella pertussis, causative agent of whooping cough, produces an adenylate cyclase toxin (CyaA) that is an important virulence factor. In the host cell, the adenylate cyclase domain of CyaA (CyaA-ACD) is activated upon association with calmodulin (CaM), an EF-hand protein comprised of N- and C-lobes (N-CaM and C-CaM, respectively) connected by a flexible tether. Maximal CyaA-ACD activation is achieved through its binding to both lobes of intact CaM, but the structural mechanisms remain unclear. No high-resolution structure of the intact CaM/CyaA-ACD complex is available, but crystal structures of isolated C-CaM bound to CyaA-ACD shed light on the molecular mechanism by which this lobe activates the toxin. Previous studies using molecular modeling, biochemical, and biophysical experiments demonstrate that CyaA-ACD’s β-hairpin participates in site-specific interactions with N-CaM. In this study, we utilize nuclear magnetic resonance (NMR) spectroscopy to probe the molecular association between intact CaM and CyaA-ACD. Our results indicate binding of CyaA-ACD to CaM induces large conformational perturbations mapping to C-CaM, while substantially smaller structural changes are localized primarily to helices I, II, and IV, and the metal-binding sites in N-CaM. Site-specific mutations in CyaA-ACD’s β-hairpin structurally modulate N-CaM, resulting in conformational perturbations in metal binding sites I and II, while no significant structural modifications are observed in C-CaM. Moreover, dynamic light scattering (DLS) analysis reveals that mutation of the β-hairpin results in a decreased hydrodynamic radius (R{sub h}) and reduced thermal stability in the mutant complex. Taken together, our data provide new structural insights into the β-hairpin’s role in stabilizing interactions between CyaA-ACD and N-CaM.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

All arthroscopic remnant-preserving reconstruction of the lateral ligaments of the ankle: A biomechanical study and clinical application

Highlights: • Two surgical techniques of ATFL and CFL reconstruction produce similar the strength and stiffness • The strength and stiffness of reconstructed ATFL and CFL are weaker than the intact, uninjured ATFL and CFL. • All arthroscopic remnant-preserving reconstruction of ATFL and CFL has good short-term clinical effect. Lateral ankle sprains are one of the most common injuries in sports. Recently, arthroscopic lateral ligament reconstruction has been recently advocated, however no biomechanical studies and clinical application of this technique are available. In this biomechanical study, eighteen fresh-frozen cadaveric ankles were randomized into three groups: (1) intact anterior talofibular ligament (ATFL) and calcaneofibular ligament (CFL), (2) arthroscopic anatomic reconstruction of ATFL and CFL, and (3) all arthroscopic remnant-preserving reconstruction of ATFL and CFL. The specimens were then tested for stiffness and load to ultimate failure using a customized jig. In biomechanical test, the all arthroscopic remnant-preserving reconstruction of ATFL and CFL produced a reconstruction that could withstand loads to failure and stiffness similar to the arthroscopic anatomic reconstruction. However, both two reconstruction groups were much weaker than the intact, uninjured ATFL and CFL. Moreover, we used the technique of all arthroscopic remnant-preserving reconstruction of ATFL and CFL on 20 patients from September 2016 to September 2017. American Orthopaedic Foot and Ankle Society (AOFAS) scores and Anterior Talar Translation (ATT) were applied for statistical collection at preoperative and postoperative 12 months to evaluate clinical efficacy. The differences of the preoperative and postoperative 12 months AOFAS scores and ATT of patients were both statistical significant (P < 0.01). We confirmed that all arthroscopic remnant-preserving reconstruction of ATFL and CFL exhibited positive effect, thus promoting the recovery of ankle function and had good short-term clinical effect.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Geochemical-hydromechanical couplings during water-serpentinized harzburgite interactions at 20° C and 30 bars

Interaction of groundwater with the serpentinized harzburgites of the upper mantle plays an important role in the geologic carbon cycle and serpentinization processes. Here, in this study, an intact serpentinized harzburgite with more than 60% lizardite from the Semail ophiolite in Oman was reacted with water at near neutral pH and low PCO 2 to observe its dissolution behavior and reaction path within the CaO-MgO-SiO 2 -CO 2 -H 2 O system at 20 °C and 30 bars. In the experiment, mass (i.e. H 2 O, ions) transfer is by diffusion and the selected temperature and pressure conditions mimic water-rock interactions at the shallow portions of most ultramafic rock hosted aquifers. Equilibrium activity-activity diagrams and thermodynamic data were used to compare the experimentally determined reaction path with the theoretical stability boundaries for minerals involved to investigate the evolution of bulk chemical composition, mineralogy, and water composition. The experiments demonstrated that (i) the water-rock interactions increased the pH of the aqueous phase from 5.9 to 7.5 over a period of 18 weeks; (ii) the dissolution of lizardite, orthopyroxene (enstatite), and clinopyroxene (diopside and augite) increased the concentration of Mg, Ca, and Si in the aqueous phase; (iii) the dissolution was incongruent with respect to Mg and Si, favoring Si release at pH > 6 due to (a) breaking of more reactive cation‑oxygen bonds that is consistent with the stoichiometry of magnesium for proton exchange reaction which favors a surface that is enriched in Mg at basic conditions, and (b) preferential dissolution of clinopyroxene Mg 1.30 Ca 0.52 Fe 0.06 Si 2 O 6 ; (iv) the aqueous phase was undersaturated with respect to carbonate (e.g. calcite, magnesite, and hydromagnesite) and hydrous (e.g. lizardite, chrysotile, brucite, and talc) minerals; (v) the bulk chemical composition and mineralogy of the intact serpentinized harzburgite matrix did not change; (vi) the thermodynamic data can successfully predict water-intact serpentinized harzburgite behavior if the water chemical composition can be constrained; and (vii) no detectable macroscopic form of damage (e.g. microcracks forming as a result of differential stress fields due to changes in volume during chemical reaction) was observed.

Carbonation↗
DOE OSTI2017

The effects of nearby fractures on hydraulically induced fracture propagation and permeability changes

Fracture propagation caused by hydraulic fracturing operations can be significantly influenced by adjacent fractures. In this paper, we present a detailed coupled hydro-mechanical analysis to study the effects of nearby natural fractures on hydraulically induced fracture propagation and changes in fracture permeability. Two rock domains were considered in comparison: FD1, with one fracture, and FD2, with two adjacent parallel or non-parallel fractures. It was assumed that water injection occurred in a borehole that intersected the single fracture in FD1 and one of the two fractures in FD2. Simulations were made for a time period of 3 h with an injection period of 2 h followed by 1 h of shut-in. An elastic-brittle model based on the degradation of material properties was implemented in a 2D finite-difference scheme and used for elements of the intact rock subjected to tension and shear failure. The intact rock was considered to have a low but non-negligible permeability. A verification study against analytical solutions showed that the fracture propagation and stress concentrations due to differential boundary stresses could be accurately represented by our model. Next, a base case was considered, in which the stress ratio (SR) between the magnitudes of the maximum and minimum boundary stresses, the permeability k R of the intact rock and the initial permeability k TF of the tension failure regions were fixed. In FD2, the distance d F between the two natural fractures defined by the closest distance was also fixed. The results showed that in both rock domains, the fracture started to propagate when the pore pressure was approximately 85% of the magnitude of the minimum boundary stress. The propagation of a single fracture was significantly greater than the propagation of a double fracture system because, in the latter case, the pore pressure decreased when the two fractures connected. As a result, changes in permeability in FD2 were smaller than in FD1. At the end of injection, the maximum ratios between the final and initial permeability of the natural fractures were found to be approximately 3 and 2 for rock domains FD1 and FD2, respectively. For non-parallel fractures, the controlling factor for fracture propagation was the separation between the tips of the pressurised fracture and the neighbouring non-pressurised fracture. A sensitivity study was conducted to study the influence of the key parameters d F , SR, k R and k TF on the simulation results. Lastly, fracture propagation showed more sensitivity to dF and SR than to the other parameters.

58 GEOSCIENCES↗
DOE OSTI2016

Comparison of fission product release predictions using PARFUME with results from the AGR-1 safety tests

Safety tests were conducted on fuel compacts from AGR-1, the first irradiation experiment of the Advanced Gas Reactor (AGR) Fuel Development and Qualification program, at temperatures ranging from 1600 to 1800 °C to determine fission product release at temperatures that bound reactor accident conditions. The PARFUME (PARticle FUel ModEl) code was used to predict the release of fission products silver, cesium, strontium, and krypton from fuel compacts containing tristructural isotropic (TRISO) coated particles during 15 of these safety tests. Comparisons between PARFUME predictions and post-irradiation examination results of the safety tests were conducted on two types of AGR-1 compacts: compacts containing only intact particles and compacts containing one or more particles whose SiC layers failed during safety testing. In both cases, PARFUME globally over-predicted the experimental release fractions by several orders of magnitude: more than three (intact) and two (failed SiC) orders of magnitude for silver, more than three and up to two orders of magnitude for strontium, and up to two and more than one orders of magnitude for krypton. The release of cesium from intact particles was also largely over-predicted (by up to five orders of magnitude) but its release from particles with failed SiC was only over-predicted by a factor of about 3. These over-predictions can be largely attributed to an over-estimation of the diffusivities used in the modeling of fission product transport in TRISO-coated particles. The integral release nature of the data makes it difficult to estimate the individual over-estimations in the kernel or each coating layer. Nevertheless, a tentative assessment of correction factors to these diffusivities was performed to enable a better match between the modeling predictions and the safety testing results. The method could only be successfully applied to silver and cesium. In the case of strontium, correction factors could not be assessed because potential release during the safety tests could not be distinguished from matrix content released during irradiation. Furthermore, in the case of krypton, all the coating layers are partly retentive and the available data did not allow the level of retention in individual layers to be determined, hence preventing derivation of any correction factors.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform

Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. That being said, one significant technical gap of top-down proteomics is the inability to analyze low amount of biological samples, which limits its access to isolated rare cells, fine-needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples), into a top-down proteomics workflow. A unique combination of a nonionic detergent dodecyl-ß-D-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing non-specific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ~170 to ~620 proteoforms from ~70 to ~770 HeLa cells containing ~10 to ~115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical researches, particularly where clinical specimens are not available in amounts amenable to standard workflows.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Toward an Understanding of the Excitonic Structure of the CP47 Antenna Protein Complex of Photosystem II Revealed via Circularly Polarized Luminescence

Identification of the lowest energy pigments in the photosynthetic CP47 antenna protein complex of Photosystem II (PSII) is essential for understanding its excitonic structure, as well as excitation energy pathways in the PSII core complex. Unfortunately, there is no consensus concerning the nature of the low-energy state(s) nor chlorophyll (Chl) site energies in this important photosynthetic antenna. Although, we raised concerns regarding the estimations of Chl site energies obtained from modeling studies of various types of CP47 optical spectra [Reinot, T; et al., Anal. Chem. Insights 2016, 11, 35–48] recent new assignments imposed by the shape of the circularly polarized luminescence (CPL) spectrum [Hall, J.; et al., Biochim. Biophys. Acta 2016, 1857, 1580–1593] necessitate our comments. We demonstrate that other combinations of lowenergy Chls provide equally good or improved simultaneous fits of various optical spectra (absorption, emission, CPL, circular dichroism, and nonresonant hole-burned spectra), but more importantly, we expose the heterogeneous nature of the recently studied complexes and argue that the published composite nature of the CPL (contributed to by CPL 685 , CPL 691 , and CPL 695 ) does not represent an intact CP47 protein. A positive CPL 695 is extracted for the intact protein, which when simultaneously fitted with multiple other optical spectra, provides new information on the excitonic structure of intact and destabilized CP47 complexes and their lowest energy state(s).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Thiophene Derivatives on Gold and Molecular Dissociation Processes

Here, we report a systematic study of thiophene derivatives on gold surfaces. These molecules are of interest in molecular electronics, and the characracteristics of the thiophene–electrode interface in devices needs to be understood as it affects electron transport characteristics. Some experiments indicated S–C bond scission in contact with metals resulting in disruption of the $π$-electron system that affects charge transport, which would also be affected by presence of split-off chemisorbed sulfur. We explored this dissociation aspect by photoemission for the case of monocrystalline Au(111) surfaces and Au films grown on mica for a series of polythiophenes molecules ( n T, n = 1–4, 6) as well as for α,ω-diquaterthiophene (DH 4 T) and dihexylsexithiophene (DH6T). The S 2p X-ray photoelectron spectroscopy peaks are found to have complex line shapes corresponding to S atoms with different core level binding energies (CLBE). Density functional theory calculations of adsorption energies and CLBEs were performed for various adsorption configurations of thiophene on a perfect Au(111) plane and for comparison, calculations were also performed for bithiophene, terthiophene, alkenethiol, alkenethiol chain, and a broken thiophene related metallocycle, incorporating an Au adatom and an S atom. On the basis of these results we relate the different contributions to the S 2p peak to intact molecules on different adsorption sites and broken molecules. Calculations in particular show that the CLBEs for intact thiophene (1T) can be the same as for the alkene and alkanethiol cases as opposed to usual assumptions in the literature. The existence of intact thiophenes is confirmed by the presence of clear $π$ resonance peaks in the near edge X-ray fine structure (NEXAFS) spectra. Spontaneous dissociation appears to a variable extent in different samples, and we tentatively relate this to the presence of a more or less large number of steps and defects sites. X-ray induced beam damage was investigated for 1T and 3T using an intense synchrotron beam of 260 eV photons, and showed changes in the S 2p spectra related to S–C bond scission.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

A Thin Film Viscoplastic Theory for Calving Glaciers: Toward a Bound on the Calving Rate of Glaciers

Projections of the growth and demise of ice sheets and glaciers require physical models of the processes governing flow and fracture of ice. The flow of glacier ice has been treated using increasingly sophisticated models. By contrast, fracture, the process ultimately responsible for half of the mass lost from ice sheets through iceberg calving, is often included using ad hoc parameterizations. In this study we seek to bridge this gap by introducing a model where ice obeys a power law rheology appropriate for intact ice below a yield strength. Above the yield strength, we introduce a separate rheology appropriate for the flow of heavily fractured ice, where ice deformation occurs more readily along faults and fractures. We show that, provided the motion of fractured ice is sufficiently rapid compared to that of intact ice, the behavior of glaciers depends solely on the rheology of intact ice and the yield strength of ice and is insensitive to the precise rheology of fractured ice. Moreover, assuming that glacier ice is unyielded allows us to bound the long‐term average rate of terminus advance, providing a first principles estimate of rates of retreat associated with the marine ice cliff instability. We illustrate model behavior using idealized geometries and climate forcing and show that the model not only exhibits realistic patterns of advance and retreat but also has the potential to exhibit hysteresis. This hysteresis could provide an explanation for the sudden onset of rapid retreat observed in marine‐terminating glaciers.

Bassis, J. N.↗