Engineering topics
Xu, Chen
Publications and source records attributed to Xu, Chen.
Hydrological controls of a riparian wetland based on stable isotope data and model simulations
Isotopic evidence of groundwater and stream water is frequently used to investigate water exchanges with groundwater. Monthly sampling of rain, stream water, and groundwater was conducted at Tims Branch watershed in South Carolina for the oxygen and hydrogen stable isotope (δ 2 H and δ 18 O) measurement, as well as pH and oxidation–reduction potential (ORP). Together with a mass balance perspective, it was determined that it takes a few weeks to one month for groundwater in the hyporheic zone to fully exchange with stream water. From hydrodynamic modelling, we show that substantial (up to 70 %) groundwater exchange occurs at gaining and losing sites. Groundwater exfiltration, i.e. inflow into stream water, contributes up to 4 % to stream water, with the remainder from upstream exfiltration. A 2–4 % per day renewal rate of adjacent groundwater would indirectly indicate a groundwater residence time in the order of half a month to a full month (assuming either a well-mixed case or large dispersion rate in pulse flow case), in agreement with a greatly reduced variability of δ 2 H and δ 18 O of groundwater compared to stream water and rain. This reduced variability of stable isotope signal from groundwater confirms our hypothesis that riparian groundwater mixing at Tims Branch is more of a mixed type rather than a pulse flow type. As a result, a monthly time scale is sufficient for groundwater to become anoxic at exit points into stream water resulting in the episodic production of natural organic matter- and iron-rich flocs upon oxidation.
Structures of the Mycobacterium tuberculosis efflux pump EfpA reveal the mechanisms of transport and inhibition
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Presence of aromatic-rich organic matter and its characterization in grout materials: Implications for radionuclide immobilization
Grout materials are commonly used to immobilize low-level radioactive waste. Organic moieties can be unintentionally present in common ingredients used to make these grout waste forms, which may result in the formation of organo-radionuclide species. These species can positively or negatively affect the immobilization efficiency. However, the presence of organic carbon compounds is rarely considered in models or characterized chemically. Here, we quantify the organic pool of grout formulations with and without slag, as well as the individual dry ingredients used to make the grout samples (ordinary Portland cement (OPC), slag and fly ash), including total organic carbon (TOC) and black carbon, followed by aromaticity evaluation and molecular characterization via Electro Spray Ionization Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (ESI-FTICRMS). All dry grout ingredients contained significant amounts of organic carbon, ranging from 550 mg/kg to 6250 mg/kg for the TOC pool, with an averaged abundance of 2933 ± 2537 mg/kg, of which 60 ± 29% was composed of black carbon. The significant abundance of a black carbon pool implies the presence of the aromatic-like compounds, which was further identified by both phosphate buffer-assisted aromaticity evaluation (e.g., >1000 mg-C/kg as aromatic-like carbon in the OPC) and dichloromethane (DCM) extraction with ESIFTICRMS analysis. Besides aromatic-like compounds, other organic moieties were also detected in the OPC, such as carboxyl-containing aliphatic molecules. While the organic compound only consists of minor fractions of the grout materials investigated, our observations of the presence of various radionuclide-binding organic moieties suggests the potential formation of organo-radionuclides, such as radioiodine, which might be present at lower molar concentrations than TOC. Here, evaluating the role of organic carbon complexation in controlling the disposed radionuclides, especially for those radionuclides with strong association with organic carbon, has important implications for the long-term immobilization of radioactive waste in grout systems.
Iodide uptake by forest soils is principally related to the activity of extracellular oxidases
129 I is a nuclear fission decay product of concern because of its long half-life (16 Ma) and propensity to bioaccumulate. Microorganisms impact iodine mobility in soil systems by promoting iodination (covalent binding) of soil organic matter through processes that are not fully understood. Here, we examined iodide uptake by soils collected at two depths (0–10 and 10–20 cm) from 5 deciduous and coniferous forests in Japan and the United States. Autoclaved soils, and soils amended with an enzyme inhibitor (sodium azide) or an antibacterial agent (bronopol), bound significantly less 125 I tracer (93%, 81%, 61% decrease, respectively) than the untreated control soils, confirming a microbial role in soil iodide uptake. Correlation analyses identified the strongest significant correlation between 125 I uptake and three explanatory variables, actinobacteria soil biomass ( p = 6.04E-04, 1.35E-02 for Kendall-Tau and regression analysis, respectively), soil nitrogen content ( p = 4.86E-04, 4.24E-03), and soil oxidase enzyme activity at pH 7.0 using the substrate L-DOPA ( p = 2.83E-03, 4.33E-04) and at pH 5.5 using the ABTS ( p = 5.09E-03, 3.14E-03). Together, the results suggest that extracellular oxidases, primarily of bacterial origin, are the primary catalyst for soil iodination in aerobic, surface soils of deciduous and coniferous forests, and that soil N content may be indicative of the availability of binding sites for reactive iodine species.
Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers
The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.
Large seasonal fluctuations of groundwater radioiodine speciation and concentrations in a riparian wetland in South Carolina
Recent studies evaluating multiple years of groundwater radioiodine ( 129 I) concentration in a riparian wetland located in South Carolina, USA identified strong seasonal concentration fluctuations, such that summer concentrations were much greater than winter concentrations. These fluctuations were observed only in the wetlands but not in the upland portion of the plume and only with 129 I, and not with other contaminants of anthropogenic origin: nitrate/nitrite, strontium-90, technecium-99, tritium, or uranium. This unexplained observation was hypothesized to be the result of strongly coupled processes involving hydrology, water temperature, microbiology, and chemistry. To test this hypothesis, an extensive historical groundwater database was evaluated, and additional measurements of total iodine and iodine speciation were made from recently collected samples. During the summer, the water table decreased by as much as 0.7 m, surface water temperature increased by as much as 15 °C, and total iodine concentrations were consistently greater (up to 680%) than the following winter months. Most of the additional iodine observed in the summer could be attributed to proportional gains in organo-iodine, and not iodide or iodate. Furthermore, 129 I concentrations were observed to be two-orders-of-magnitude greater at the bottom of the upland aquifer than at the top. A coupled hydrological and biogeochemical conceptual model is proposed to tie these observations together. First, as the surface water temperature increased during the summer, microbial activity was enhanced, which in turn stimulated the formation of mobile organo-I. Hydrological processes were also likely involved in the observed iodine seasonal changes: (1) as the water table decreased in summer, the remaining upland water entering the wetland was comprised of a greater proportion of water containing elevated iodine concentrations from the low depths, and (2) water flow paths in summer changed such that the wells intercepted more of the contaminant plume and less of the diluting rainwater (due to evapotranspiration) and streamwater (as the lower levels promote a predominantly recharging system). Furthermore, these results underscore the importance of coupled processes influencing contaminant concentrations, and the need to assess seasonal contaminant variations to optimize long-term monitoring programs of wetlands.
Production of Uranium from Seawater Using a Novel Polymer Adsorbent – Process Development and Cost Analysis (Final Scientific/Technical Report SBIR Phase II)
Research in developing techniques for extracting uranium from seawater is of considerable current interest. One reason which drives scientists to develop techniques of sequestering uranium from ocean is the prediction that the land-based uranium reserves would be depleted by the end of this century based on the current production rate. Uranium exists in seawater at a very low concentration (about 3 ppb) and as highly stable uranyl tris-carbonato complexes, primarily in the form Ca 2 [UO 2 (CO 3 ) 3 ]. Because of the enormous volume of seawater, the total amount of uranium in ocean is estimated to be a thousand times greater than the land-based uranium resources. As early as 1964, the idea of extracting uranium from seawater was discussed by Davies et al. in a Nature paper. In the past decades, many different materials were tested to evaluate their ability for sequestering uranium from seawater. Among them, amidoxime and carboxylate containing polymer fiber adsorbents appear most promising because of their high uranium adsorption capacity and stability in seawater. The carboxylate groups are necessary to make the polymer adsorbent hydrophilic whereas the amidoxime groups provide strong coordination sites for uranyl ions. Moreover, according to theoretical analysis, the adsorbability of uranium may involve synergistic effects of both amidoxime and carboxyl groups in the fiber adsorbent.
Coupled effects of electronic and nuclear energy deposition on damage accumulation in ion-irradiated SiC
Coupling between electronic and nuclear energy dissipation in ion-irradiated, single crystal 4H-SiC has been investigated using Si, Ti, and Ni ions over a range of energies at 300 K, and irradiation damage accumulation is characterized using Rutherford backscattering spectroscopy in channeling geometry. The damage production rate from nuclear energy loss (S n ) is observed to decrease with increasing electronic energy loss (S e ) of the incident ions. A dynamic threshold (S e,th ) in electronic energy loss is determined for each ion species, which defines two regions: i) S e > S e,th , where electronic energy dissipation fully suppresses damage production due to nuclear energy loss along incident ion paths, and ii) S e < S e,th , where simultaneous damage recovery due to Se competes with damage production processes. Here, the electronic energy loss threshold (S e,th ) increases sublinearly with incident ion atomic number. Here, the assessment of S e,th and how it affects damage accumulation is important to advance the understanding of complex processes occurring under ion-solid interactions, as well as in the design of functional materials for opto-electronics and novel structural materials and devices tolerant to harsh thermal and radiation environments.
Studying the effects of thermally diffusing Ce into the surface of YAlO3 for associated particle imaging
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Megahertz single-particle imaging at the European XFEL
The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.
Collaborative Research: Natural Organic Matter and Microbial Controls on Mobilization/Immobilization of I and Pu in Soils and Waters Affected by Radionuclide Releases in USA and Japan
In this project, the relationship between natural organic matter (NOM) and two radioactive elements that are relevant to nuclear waste disposal were studied: Plutonium (Pu) and Iodine. The human and environmental risks associated with Pu stem mainly from the very long half-lives of several of its isotopes ( 238 Pu, 88 yr; 239 Pu, 24,100 yr; 240 Pu, 6560 yr) and its radiotoxicity. Understanding Pu biogeochemical behavior in both near-field (>10-11M) and far-field scales (<10-11M) is imperative to the development of approaches for reprocessing Pu, remediation of Pu contamination and accurate assessment of risks posed by disposal practices for Pu-bearing wastes. The environmental mobility of Pu can be affected by redox potential, pH, adsorption, precipitation, complexation, colloid formation, and microbial activity, of which the first characteristic has the most profound influence. Numerous studies have shown high affinity of Pu towards NOM, as well as to mineral phases. NOM is ubiquitous in the environment, e.g., both fulvic and humic acids are able to reduce Pu(V,VI) to Pu(IV) and the redox potential of NOM is positively related to the abundance of phenolic/acidic OH groups. NOM can either facilitate or limit actinide migration, depending on specific biogeochemical conditions including pH, mineral and organic matter characteristics, etc. The other radionuclide of interest is radioiodine ( 129 I). 129I is a major by-product of nuclear fission and of serious concern to the Department of Energy (DOE) as it is among the top risk drivers at existing and potential radiowaste-contaminated sites. The risk of 129 I stems largely from its high bioconcentration factor (90% of the body’s iodine is accumulated in the thyroid), a high inventory at source terms, a very long-half life (16M years), and rapid mobility in the subsurface environment. As a consequence, 129 I has the lowest drinking water standard (1 pCi/L) among all radionuclides in the Federal Register. With a novel and sensitive gas chromatography-mass spectrometry (GC-MS) method developed in our lab, it is possible to quickly and simultaneously determine the distribution of 129 I and stable 127 I forms in environments, as low as 2 pCi/L for 129 I. This method was subsequently validated using accelerator mass spectroscopy, AMS. IO 3 - and organo-I were determined as major species in the groundwater of SRS and the Hanford Site, contrary to thermodynamic predictions that I- should be the dominant species at these sites. Mobility of 129 I was also demonstrated to depend greatly on the I species and its concentration, sediment pH, and redox state, with times to achieve equilibrium taking up to 12 weeks. Along the groundwater pathway in the F-Area of SRS, 129 I- supplied from the seepage basins was transformed to 129 IO 3 - and organo- 129 I with increasing iodine sediment sorption, causing the lower total 127 I and 129 I concentrations along the gradient transect of the waste plume. By contrast, groundwater 129 I concentrations in the wetlands (as high as 1617.3 pCi/L) were greatly elevated with respect to the source term (159.3 pCi/L). While the NOM promoted the uptake of 129 I to the wetland sediment, it also promoted the formation of soluble organic fraction. A small fraction of NOM that is bound to iodine can behave as a mobile organo-I source. Iodide was enzymatically incorporated into NOM, whereas both iodide and iodate were abiotically bound to NOM, under certain conditions. Iodate removal from the mobile aqueous phase can also occur through incorporation into carbonate (e.g., at the Hanford Site, USA). Thus immobilization and re-mobilization of iodine species were influenced by pH, Eh and the presence of NOM and metal oxides, which adds to the complexity of site remediation action. A ground-breaking result was to elucidate the products (i.e. organo-iodine moieties formed via enzymatic and non-enzymatic processes) at the molecular level by nuclear magnetic resonance (NMR) and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS). We found that iodine-NOM interactions may be influenced by NOM hydrophobic aliphatic moieties. From the perspective of ESI-FTICRMS, organo-iodine formulas were ascribed to the groups of unsaturated hydrocarbons, lignins and proteins. Iodate is likely abiotically reduced to reactive iodine species by lignin- and tannin-like compounds or carboxylic-rich alicyclic molecules (CRAM). We also investigated microbial mechanisms in iodine incorporation into NOM. We established that soil bacteria isolated from F-Area of SRS did not accumulate significant amounts of I- (0.2-2%). Intracellular uptake of I- decreases with increasing pH when pH ranged from 4 to 6. In contrast, 44 out of 84 strains isolated from the F-Area of SRS can transform I- to IO 3 - and organo-iodine. In some cases, oxidation was facilitated in the presence of H 2 O 2 . Microbes can also excrete organic acids that enhance I- oxidation by lowering the ambient pH and reacting with H 2 O 2 to form peroxy carboxylic acids. At lower pH values (≤5), H 2 O 2 hydrolysis was the driving force for iodide-oxidation; whereas, at pH ≥ 6, spontaneous decomposition of peroxy carboxylic acids, originating from H 2 O 2 and organic acids were the primary cause of iodide oxidation. Lastly, it was determined that microbial processes involved in Mn (II) are capable of directly oxidizing I- via enzymatic catalysis (i.e., multicopper oxidases), or indirectly through the formation of reactive oxygen species (ROS) and/or biogenic manganese oxides. ROS-mediated oxidation of I- was found to predominate at pH >5, whereas the enzymatic and Mn oxide pathways were more active at pH < 5. Together, this project has resulted in 9 publications in high-impact journals, and the training of 1 Ph.D and 4 undergraduate students.
Membrane protein megahertz crystallography at the European XFEL
The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.
Molecular Interaction of Aqueous Iodine Species with Humic Acid Studied by I and C K-Edge X-ray Absorption Spectroscopy
Iodine-129 is one of three key risk drivers at several US Department of Energy waste management sites. Natural organic matter (NOM) is thought to play important roles in the immobilization of aqueous iodide (I – ) and iodate (IO 3 – ) in the environment, but molecular interactions between NOM and iodine species are poorly understood. In this work, we investigated iodine and carbon speciation in three humic acid (HA)-I systems using I K-edge XANES and EXAFS and C K-edge XANES spectroscopy: (1) I – in the presence of laccase (an oxidase enzyme) and a mediator, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) in a pH 4 buffer, (2) I– in the presence of lactoperoxidase (LPO) and H 2 O 2 in a pH 7 buffer, and (3) IO 3 – in a pH 3 groundwater. Both oxidase and peroxidase systems could oxidize I – to I 2 or hypoiodide (HOI) leading to organo-I formation. However, the laccase-ABTS mediator was the most effective and enhanced I – uptake by HA up to 13.5 mg/g, compared to 1.9 mg/g for the LPO–H 2 O 2 . IO 3 – was abiotically reduced to I 2 or HOI leading to an organo-I formation. Pathways for HA iodination include covalent modification of aromatic-type rings by I 2 / HOI or iodine incorporation into newly formed benzoquinone species arising from the oxidation of phenolic C species. Our study improves our molecular-level understanding of NOM–iodine interactions and stresses the important role that mediators may play in the enzymatic reactions between iodine and NOM.