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Two bacterial isolates were recovered from wetland sediments from Tims Branch, a heavy metal contaminated wetland located at the Savannah River Site. Draft genomes of the two recovered isolates, Rhodoblastus strain 17X3 and Comamonas strain 17RB, were generated from Illumina MiSeq sequencing data.
Thermal ionization mass spectrometry (TIMS) is often regarded as the preferred technique for trace-level isotopic analysis of actinides owing to its high sensitivity and absence of carry-over effects. However, actinide sample utilization efficiency (SUE) is typically low (<0.05%) without the use of activators or specialized loading approaches which can yield SUEs of >5%. To this effect, we investigate a series of metal–organic framework (MOF)-based nanoporous ion emitters (nano-PIEs) that show enhanced ionization of actinides when used in TIMS loading. We study the impact of physical and chemical properties of MOFs on TIMS SUEs using two families of MOFs that can be synthesized under similar reaction conditions. The structural and chemical properties of these MOFs can be systematically modified one at a time while keeping other features the same. This allows us to strategically investigate their impact on SUEs. The first family of MOFs considered in this study is Zeolitic Imidazole Frameworks (ZIFs) which are made using 2 methyl-imidazole as an organic linker with zinc (ZIF-8) and cobalt (ZIF-67) as metal centers. Additionally, the effect of morphology was also studied using Zn-based ZIF-L with a 2-dimensional structure. The second family of MOFs was synthesized using benzene-1,3,5-tricarboxylate (BTC) with copper (Cu-BTC) and zinc (Zn-BTC) as the metal center. Among the MOFs tested, Cu-BTC showed the highest SUE with an average SUE of 0.27 ± 0.15%, followed closely by Zn-BTC (0.24 ± 0.10%), ZIF-8 (0.17 ± 0.10%), and trailed by the other MOFs. When the MOFs were pyrolyzed in N 2 before loading, an apparent increase in the SUE was observed with ZIF-8 and Cu-BTC showing average SUEs of 0.25 ± 0.08% and 0.34 ± 0.13%, respectively, with the highest measured SUE of 0.53% for pyrolyzed Cu-BTC. In conclusion, this observed increase in SUE by up to an order of magnitude compared to bare filaments demonstrates the efficacy and potential of MOF-derived nano-PIEs for TIMS application.
Kinetic stability of proteins determines their susceptibility to irreversibly unfold in a time-dependent process, and therefore its half-life. A residue displacement analysis of temperature-induced unfolding molecular dynamics simulations was recently employed to define the thermal flexibility of proteins. This property was found to be correlated with the activation energy barrier (E{sub act}) separating the native from the transition state in the denaturation process. The E{sub act} was determined from the application of a two-state irreversible model to temperature unfolding experiments using differential scanning calorimetry (DSC). The contribution of each residue to the thermal flexibility of proteins is used here to propose multiple mutations in triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) and Trypanosoma cruzi (TcTIM), two parasites closely related by evolution. These two enzymes, taken as model systems, have practically identical structure but large differences in their kinetic stability. We constructed two functional TIM variants with more than twice and less than half the activation energy of their respective wild-type reference structures. The results show that the proposed strategy is able to identify the crucial residues for the kinetic stability in these enzymes. As it occurs with other protein properties reflecting their complex behavior, kinetic stability appears to be the consequence of an extensive network of inter-residue interactions, acting in a concerted manner. The proposed strategy to design variants can be used with other proteins, to increase or decrease their functional half-life.
Accurate and stable x-ray beam position monitors (XBPMs) are key elements in obtaining the desired user beam stability in the Advanced Photon Source Upgrade. In the next-generation XBPMs for the canted-undulator front ends, where two undulator beams are separated by 1.0 mrad, the lower beam power (<10 kW) per undulator allows us to explore lower-cost solutions based on Compton scattering from a diamond placed edge-on to the x-ray beam. Because of the high peak power density of the x-ray beams, this diamond experiences high temperatures and has to be clamped to a water-cooled heat spreader using thermal interface materials (TIMs), which play a key role in reducing the temperature of the diamond. To evaluate temperature changes through the interface via thermal simulations, the thermal contact resistance (TCR) of TIMs at an interface between two solid materials under even contact pressure must be known. This paper addresses the TCR measurements of several TIMs, including gold, silver, pyrolytic graphite sheet, and 3D graphene foam. In addition, a prototype of a Compton-scattering XBPM with diamond blades was installed at APS Beamline 24-ID-A in May 2015 and has been tested. This study presents the design of the Compton-scattering XBPM, and compares thermal simulation results obtained for the diamond blade of this XBPM by the finite element method with in situ empirical measurements obtained by using reliable infrared technology.
This 2018 progress report contains a list of Los Alamos National Laboratory's top innovations of the time, including: Inventing - Los Alamos National Laboratory has been inventing for the past 75 years to accomplish the difficult, the unexpected and at times, what seems impossible. The Feynman Center is rethinking roadmaps for patent and software strategies to enable Los Alamos to achieve greater impact of its innovations; Innovating - The US technology advantage in national security is dependent on continual innovation. Los Alamos’ immense contributions in leading edge science and technology research and development are directed into solving complex and forthcoming national security challenges. Check out the Technology Snapshot platform at https://techsnapshot.lanl.gov to explore Los Alamos’s technologies ready to be developed into disruptive applications; Disrupting - Known well for developing the first nuclear weapon, big and small science at Los Alamos is behind many other disruptive innovations. This year we are highlighting Los Alamos’s leadership in small modular nuclear reactor design and development, work on international nuclear safeguards electronics instrumentation, and first demonstrated deployment of non-destructive testing to measure corrosion in nuclear material storage containers; Partnering - Los Alamos science has assisted partners big and small with their toughest challenges, this year Los Alamos scientists assisted two New Mexico farm owners—Tim Seaman with Manzanar Los Silvestres apple orchard in Abiquiu and Christopher Bassett of Freshies of New Mexico in El Guique — protect their crops from frost.
The Tims Branch watershed in Savannah River Site (SRS), South Carolina is a small-scale watershed that has been impacted by contaminated runoff and discharge wastewater from nuclear research facilities located within the watershed over the past century. Innovative remediation technologies, such as tin injection and pump and treat, have been implemented to remove heavy metals and volatile organic compounds (VOCs) from the watershed. Today, the Tims Branch watershed serves as a test-bed for monitoring the performance of remediation activities. This study describes the development of the two-dimensional integrated surface water/groundwater model for Tims Branch watershed to assess the impact of cleanup activities on hydrological processes in this watershed. This model will serve as a tool to simulate the effect of climatic events on overland flow distribution and further on will be used to assess contaminant transport. This paper illustrates the application of the developed model for simulation of overland flow depth and velocity in Tims Branch watershed and streamflow in A-014 outfall tributary. The watershed includes the second order Tims Branch stream, several outfalls, and a network of tributaries. Simulation of non-calibrated overland flow was conducted for the years 2016 using available stream flow data within the watershed. Recent flow data from a newly deployed stage gauge was also used to assess the model results. The results show the model ability to simulate overland flow and stream flow and can be used as a tool to represent the hydrological conditions in the Tims Branch watershed. The results of this model simulation will be further used to develop contaminant transport model. (authors)
Abstract. The Hadean Jack Hills zircons represent the oldest known terrestrial material, providing a unique and truly direct record of Hadean Earth history. This zircon population has been extensively studied via high-spatial-resolution high-throughput in situ isotopic and elemental analysis techniques, such as secondary ionization mass spectrometry (SIMS), but not by comparatively destructive, high-temporal-precision (<0.05 % two-sigma) thermal ionization mass spectrometry (TIMS). In order to better understand the lead loss and alteration history of terrestrial Hadean zircons, we conduct stepwise chemical abrasion–isotope dilution–thermal ionization mass spectrometry with trace element analysis (CA-ID-TIMS-TEA) on manually microfractured Hadean Jack Hills zircon fragments previously dated by SIMS. We conducted three successive HF leaching steps on each individual zircon fragment, followed by column chromatography to isolate U–Pb and trace element fractions. Following isotopic and elemental analysis, the result is an independent age and trace element composition for each leachate of each zircon fragment. We observe ~50 Myr of age heterogeneity in concordant residues from a single zircon grain, along with a protracted history of post-Hadean Pb loss with at least two modes circa ~0 and 2–4 Ga. Meanwhile, stepwise leachate trace element chemistry reveals enrichments of light rare earth elements, uranium, thorium, and radiogenic lead in early leached domains relative to the zircon residue. In addition to confirming the efficacy of the LREE-I alteration index and providing new insight into the mechanism of chemical abrasion, the interpretation and reconciliation of these results suggest that Pb loss is largely driven by low-temperature aqueous recrystallization and that regional thermal events may act to halt – not initiate – Pb loss from metamict domains in the Hadean Jack Hills zircons.
Using contemporary theory for ion mobility spectrometry (IMS), gas-phase ion mobilities within a trapped ion mobility-mass spectrometer (TIMS) are not easily deduced using first principle equations due to non-linear pressure changes and consequently variations in E/N. It is for this reason that prior literature values have traditionally been used for TIMS calibration. Additionally, given that verified mobility standards currently do not exist and the that the exact conditions used to measure reported literature values may not always represent the environment within the TIMS, a direct approach to validating the behavior of the TIMS system is warranted. A calibration procedure is presented where an ambient pressure, ambient temperature, two-gate, printed circuit board drift-tube IMS (PCBIMS) is coupled to the front of a TIMS allowing reduced mobilities to be directly measured on the same instrument as the TIMS. These measured mobilities were used to evaluate the TIMS calibration procedure which correlates reduced mobility and TIMS elution voltages with literature values. When using the measured PCBIMS-reduced mobilities of tetraalkyl ammonium salts and tune mix for TIMS calibration of the alkyltrimethyl ammonium salts, the percent error is less than 1% as compared with using the reported literature K{sub 0} values where the percent error approaches 5%. This method provides a way to obtain accurate reference mobilities for ion mobility techniques that require a calibration step (i.e., TIMS and TWAVE). .
In aqueous systems, including groundwater, nano-colloids (1–100 nm diameter) and small colloids (<450 nm diameter) provide a vast store of surfaces to which organic carbon (OC) can sorb, precluding its normal bioavailability. Because nanomaterials are ubiquitous and abundant throughout Earth systems, it is reasonable that they would play a significant role in biogeochemical cycles. As such, mineral nano-colloids (MNC) and small colloids, formed through mineral weathering and precipitation processes, are both an unaccounted-for reservoir and unquantified vector for transport of OC and nutrients and contaminants within watersheds. Water extractions and leaching experiments were conducted under (1) aerobic (ambient) and (2) anaerobic (environmental chamber) conditions for each of two contrasting riparian sediments from (1) Columbia River, Washington and (2) Tims Branch, South Carolina. Water dispersible colloid-adsorbed OC was as high as 48% of OC for Tims Branch anaerobic batch water extraction and as low as 0% for Columbia River aerobic batch water extractions. Anaerobic leaching from column experiments yielded higher colloid and OC release rates. Transmission electron microscopy with electron dispersive spectroscopy mapping revealed organic carbon associated with aggregations of nano-particulate silicate minerals and Mossbauer identified nano-particulate goethite. This exploratory study demonstrates that mineral facilitated release of OC in riparian sediments is both significant and variable between locations.
Due to the substantial increase in power density, thermal interface resistance that can constitute more than 50% of the total thermal resistance has generally become a bottleneck for thermal management in electronics. However, conventional thermal interface materials (TIMs) such as solder, epoxy, gel, and grease cannot fulfill the requirements of electronics for high-power and long-term operation. Here, we demonstrate a high-performance TIM consisting of a heterogeneous copper-tin nanowire array, which we term 'supersolder' to emulate the role of conventional solders in bonding various surfaces. The supersolder is ultracompliant with a shear modulus 2-3 orders of magnitude lower than traditional solders and can reduce the thermal resistance by two times as compared with the state-of-the-art TIMs. This supersolder also exhibits excellent long-term reliability with >1200 thermal cycles over a wide temperature range. By resolving this critical thermal bottleneck, the supersolder enables electronic systems, ranging from microelectronics and portable electronics to massive data centers, to operate at lower temperatures with higher power density and reliability.
Tryptophan synthase catalyzes the last two steps of tryptophan biosynthesis in plants, fungi and bacteria. It consists of two protein chains, designated α and β, encoded by trpA and trpB genes, that function as an αββα complex. Structural and functional features of tryptophan synthase have been extensively studied, explaining the roles of individual residues in the two active sites in catalysis and allosteric regulation. TrpA serves as a model for protein-folding studies. In 1969, Jackson and Yanofsky observed that the typically monomeric TrpA forms a small population of dimers. Dimerization was postulated to take place through an exchange of structural elements of the monomeric chains, a phenomenon later termed 3D domain swapping. The structural details of the TrpA dimer have remained unknown. Here, the crystal structure of the Streptococcus pneumoniae TrpA homodimer is reported, demonstrating 3D domain swapping in a TIM-barrel fold for the first time. The N-terminal domain comprising the H0–S1–H1–S2 elements is exchanged, while the hinge region corresponds to loop L2 linking strand S2 to helix H2′. The structural elements S2 and L2 carry the catalytic residues Glu52 and Asp63. As the S2 element is part of the swapped domain, the architecture of the catalytic apparatus in the dimer is recreated from two protein chains. The homodimer interface overlaps with the α–β interface of the tryptophan synthase αββα heterotetramer, suggesting that the 3D domain-swapped dimer cannot form a complex with the β subunit. In the crystal, the dimers assemble into a decamer comprising two pentameric rings.
Cellulases from glycoside hydrolase family 5 (GH5) are key endoglucanase enzymes in the degradation of diverse polysaccharide substrates and are used in industrial enzyme cocktails to break down biomass. The GH5 family shares a canonical (βα) 8 -barrel structure, where each (βα) module is essential for the enzyme’s stability and activity. Despite their shared topology, the thermostability of GH5 endoglucanase enzymes can vary significantly, and highly thermostable variants are often sought for industrial applications. Based on the previously characterized thermophilic GH5 endoglucanase Egl5A from Talaromyces emersonii ( Te Egl5A), which has an optimal temperature of 90°C, we created 10 hybrid enzymes with elements of the mesophilic endoglucanase Cel5 from Stegonsporium opalus ( So Cel5) to determine which elements are responsible for enhanced thermostability. Five of the expressed hybrid enzymes exhibit enzyme activity. Two of these hybrids exhibited pronounced increases in the temperature optimum (10 and 20°C), the temperature at which the protein lost 50% of its activity ( T 50 ) (15 and 19°C), and the melting temperature ( T m ) (16.5 and 22.9°C) and extended half-lives ( t 1/2 ) (~240- and 650-fold at 55°C) relative to the values for the mesophilic parent enzyme and demonstrated improved catalytic efficiency on selected substrates. The successful hybridization strategies were validated experimentally in another GH5 endoglucanase, Cel5 from Aspergillus niger ( An Cel5), which demonstrated a similar increase in thermostability. Based on molecular dynamics (MD) simulations of both the So Cel5 and Te Egl5A parent enzymes and their hybrids, we hypothesize that improved hydrophobic packing of the interface between α 2 and α 3 is the primary mechanism by which the hybrid enzymes increase their thermostability relative to that of the mesophilic parent So Cel5.Thermal stability is an essential property of enzymes in many industrial biotechnological applications, as high temperatures improve bioreactor throughput. Many protein engineering approaches, such as rational design and directed evolution, have been employed to improve the thermal properties of mesophilic enzymes. Structure-based recombination has also been used to fuse TIM barrel fragments, and even fragments from unrelated folds, to generate new structures. However, little research has been done on GH5 endoglucanases. In this study, two GH5 endoglucanases exhibiting TIM barrel structure, So Cel5 and Te Egl5A, with different thermal properties, were hybridized to study the roles of different (βα) motifs. This work illustrates the role that structure-guided recombination can play in helping to identify sequence function relationships within GH5 enzymes by supplementing natural diversity with synthetic diversity.
Abstract In this study, thermal interface material (TIM) degradation is driven through highly accelerated life test (HALT) using temperature cycling with a prescribed vibrational acceleration for two commercially available materials having thermal conductivities of 6.0 and 8.5 W/m K. HALT specimens were prepared by applying TIM through a 4-mil stencil over AlSiC baseplates in the shape of those used in Wolfspeed CAS325M12HM2 power electronics modules. Baseplates were mounted onto aluminum carrier blocks with embedded thermocouples to characterize the thermal resistance across the baseplate and TIM layer. Thermal dissipation into the top of the baseplates was provided by a custom heating block, which mimics the size and placement of the die junctions in CAS325 modules, applying power loads of 200, 300, and 400 W. After initial characterization, samples were transferred to the HALT chamber with one set of samples exposed to temperature cycling only (TCO) and the other temperature cycling and vibration (TCV). Both sample sets were cycled between temperature extremes of −40 °C and 180 °C with vibrations applied at a peak acceleration of 3.21 Grms. After hundreds of cycles, samples were reevaluated to assess changes in thermal resistance to provide an accelerated measure of TIM degradation. This allows for reliability prediction of useful lifetime (illustrated in a solar inverter case study herein), as well as to provide a basis for developing an accelerated testing method to related temperature cycling to faster methods of degradation. Such techniques provide a means to develop maintenance schedules for power modules for ensuring sufficient thermal performance over the operating lifetime.
This AI4ESP white paper is the outcome of an open ideation session led by PNNL that numerous institutions participated in. The leadership team included Amy Goldman, Huiying Ren, Tim Scheibe, and James Stegen. The white paper is broken into two sections: (1) A summary of the ideation session, and (2) a short summary of a ‘meta idea’ that emerged from combining multiple ideas spanning the three primary focal area themes articulated in BER’s AI4ESP guidance: A - Data Acquisition and Assimilation, B - Predictive Modeling, and C - Insight from Complex Data. The white paper, therefore, has two goals. The first section is meant to be a resource for innovating around how to pursue open, community-based ideation in virtual environments. The second section is meant as an example of the kinds of ‘meta ideas’ that can emerge from bringing diverse ideas together in a single shared space. We consider the second section to be a submission to BER’s request for white papers around AI4ESP.
The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.
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Determining process–structure–property linkages is one of the key objectives in material science, and uncertainty quantification plays a critical role in understanding both process–structure and structure–property linkages. In this work, we seek to learn a distribution of microstructure parameters that are consistent in the sense that the forward propagation of this distribution through a crystal plasticity finite element model matches a target distribution on materials properties. This stochastic inversion formulation infers a distribution of acceptable/consistent microstructures, as opposed to a deterministic solution, which expands the range of feasible designs in a probabilistic manner. Furthermore, to solve this stochastic inverse problem, we employ a recently developed uncertainty quantification framework based on push-forward probability measures, which combines techniques from measure theory and Bayes’ rule to define a unique and numerically stable solution. This approach requires making an initial prediction using an initial guess for the distribution on model inputs and solving a stochastic forward problem. To reduce the computational burden in solving both stochastic forward and stochastic inverse problems, we combine this approach with a machine learning Bayesian regression model based on Gaussian processes and demonstrate the proposed methodology on two representative case studies in structure–property linkages.
Iodine environmental measurements have consistently been backed up in the literature by standard materials like IAEA-375, Chernobyl Soil. There are not many other sources of a certified reference material for 129I content for mass spectrometry measurements. Some that have been found in the literature include NIST-4354 and NIST-4357. They are still available at the time of this writing. They don’t have certified content or isotopic values. There has been some work in the literature to show that iodine is present, but there hasn’t been enough to establish a consensus value. These materials have been analyzed at INL through two separate mass spectrometry techniques. They involve a combustion method of the starting material in oxygen, followed by TIMS analysis and a leaching preparation analyzed by accelerator mass spectrometry. Combustion/TIMS preparation of NIST SRM-4354 resulted in a 129I/127I ratio of 1.92 x 10-6 which agrees with AMS measurements which measured the 129I/127I ratio to be 1.93 x 10-6.