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DOE OSTI2016

Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate

Heat-shock protein of 90 kDa (Hsp90) is an essential molecular chaperone that adopts different 3D structures associated with distinct nucleotide states: a wide-open, V-shaped dimer in the apo state and a twisted, N-terminally closed dimer with ATP. Although the N domain is known to mediate ATP binding, how Hsp90 senses the bound nucleotide and facilitates dimer closure remains unclear. In this paper we present atomic structures of human mitochondrial Hsp90 N (TRAP1 N ) and a composite model of intact TRAP1 revealing a previously unobserved coiled-coil dimer conformation that may precede dimer closure and is conserved in intact TRAP1 in solution. Our structure suggests that TRAP1 normally exists in an autoinhibited state with the ATP lid bound to the nucleotide-binding pocket. ATP binding displaces the ATP lid that signals the cis-bound ATP status to the neighboring subunit in a highly cooperative manner compatible with the coiled-coil intermediate state. We propose that TRAP1 is a ligand-activated molecular chaperone, which couples ATP binding to dramatic changes in local structure required for protein folding.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

CO2 response screen in grass Brachypodium reveals the key role of a MAP kinase in CO2-triggered stomatal closure

Abstract Plants respond to increased CO2 concentrations through stomatal closure, which can contribute to increased water use efficiency. Grasses display faster stomatal responses than eudicots due to dumbbell-shaped guard cells flanked by subsidiary cells working in opposition. However, forward genetic screening for stomatal CO2 signal transduction mutants in grasses has yet to be reported. The grass model Brachypodium distachyon is closely related to agronomically important cereal crops, sharing largely collinear genomes. To gain insights into CO2 control mechanisms of stomatal movements in grasses, we developed an unbiased forward genetic screen with an EMS-mutagenized B. distachyon M5 generation population using infrared imaging to identify plants with altered leaf temperatures at elevated CO2. Among isolated mutants, a “chill1” mutant exhibited cooler leaf temperatures than wild-type Bd21-3 parent control plants after exposure to increased CO2. chill1 plants showed strongly impaired high CO2-induced stomatal closure despite retaining a robust abscisic acid-induced stomatal closing response. Through bulked segregant whole-genome sequencing analyses followed by analyses of further backcrossed F4 generation plants and generation and characterization of sodium azide and CRISPR-cas9 mutants, chill1 was mapped to a protein kinase, Mitogen-Activated Protein Kinase 5 (BdMPK5). The chill1 mutation impaired BdMPK5 protein-mediated CO2/HCO3− sensing together with the High Temperature 1 (HT1) Raf-like kinase in vitro. Furthermore, AlphaFold2-directed structural modeling predicted that the identified BdMPK5-D90N chill1 mutant residue is located at the interface of BdMPK5 with the BdHT1 Raf-like kinase. BdMPK5 is a key signaling component that mediates CO2-induced stomatal movements and is proposed to function as a component of the primary CO2 sensor in grasses.

Lopez, Bryn N. K. (ORCID:0009000937288216)↗

DOE OSTI2024

Stomatal closure as a driver of minimum leaf conductance declines at high temperature and vapor pressure deficit in Quercus

Abstract Rising global temperatures and vapor pressure deficits (VPDs) are increasing plant water demand and becoming major drivers of large-scale plant mortality. Controlling transient leaf water loss after stomatal closure (minimum stomatal conductance [gmin]) is recognized as a key trait determining how long plants survive during soil drought. Yet, substantial uncertainty remains regarding how gmin responds to elevated temperatures and VPD and the underlying mechanisms. We measured gmin in 24 Quercus species from temperate and Mediterranean climates to determine whether gmin was sensitive to a coupled temperature and VPD increase. We also explored mechanistic links to phenology, climate, evolutionary history, and leaf anatomy. We found that gmin in all species exhibited a nonlinear negative temperature and VPD dependence. At 25 °C (VPD = 2.2 kPa), gmin varied from 1.19 to 8.09 mmol m−2 s−1 across species but converged to 0.57 ± 0.06 mmol m−2 s−1 at 45 °C (VPD = 6.6 kPa). In a subset of species, the effect of temperature and VPD on gmin was reversible and linked to the degree of stomatal closure, which was greater at 45 °C than at 25 °C. Our results show that gmin is dependent on temperature and VPD, is highly conserved in Quercus species, and is linked to leaf anatomy and stomatal behavior.

Zailaa, Joseph (ORCID:000000019103190X)↗

DOE OSTI2021

Partially averaged Navier-Stokes closure modeling for variable-density turbulent flow

We report this work extends the framework of the partially averaged Navier-Stokes (PANS) equations to variable-density flow, i.e., multimaterial and/or compressible mixing problems with density variations and production of turbulence kinetic energy by both shear and buoyancy mechanisms. The proposed methodology is utilized to derive the PANS BHR-LEVM closure. This includes a priori testing to analyze and develop guidelines toward the efficient selection of the parameters controlling the physical resolution and, consequently, the range of resolved scales of PANS. Two archetypal test-cases involving transient turbulence, hydrodynamic instabilities, and coherent structures are used to illustrate the accuracy and potential of the method: the Taylor-Green vortex at Reynolds number Re = 3000, and the Rayleigh-Taylor flow at Atwood number 0.5 and (Re) max ≈ 500. These representative problems, for which turbulence is generated by shear and buoyancy processes, constitute the initial validation space of the new model, and their results are comprehensively discussed in two subsequent studies. The computations indicate that PANS can accurately predict the selected flow problems, resolving only a fraction of the scales of large-eddy simulation and direct numerical simulation strategies. The results also reiterate that the physical resolution of the PANS model must guarantee that the key instabilities and coherent structures of the flow are resolved. The remaining scales can be modeled through an adequate turbulence scale-dependent closure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Closures for multicomponent reacting flows based on dispersion analysis

This work presents algebraic closure models associated with advective transport and nonlinear reactions in a Reynolds-averaged Navier-Stokes context for a system of species subject to binary reactions and transport by advection and diffusion. Expanding upon analysis originally developed for non-reactive transport in the context of Taylor dispersion of scalars, this work extends the modified gradient diffusion model explicated by Peters [N. Peters, Turbulent Combustion, Cambridge Monographs on Mechanics (Cambridge University Press, Cambridge, 2000)] and based on work by Corrsin [S. Corrsin, The reactant concentration spectrum in turbulent mixing with a first-order reaction, J. Fluid Mech. 11, 407 (1961)] beyond single-component transport phenomena and involving nonlinear reactions. The presented model forms, from this weakly nonlinear extension of the original dispersion theory, lead to an analytic expression for the eddy diffusivity matrix that explicitly captures the influence of the reaction kinetics on the closure operators. Furthermore, we demonstrate that the derived model form directly translates between flow topologies through a priori and a posteriori testing of a binary species system subject to homogeneous isotropic turbulence. Using two- and three-dimensional direct numerical simulations involving laminar and turbulent flows, it is shown that this framework improves prediction of mean quantities compared to previous results. Lastly, the presented model form, collapses to the earlier gradient diffusion and its modified version derived by Corrsin in the limits of nonreactive species and linear reactions, respectively.

42 ENGINEERING↗

DOE OSTI2024

Modeling Microwave-Enhanced Chemical Vapor Infiltration Process for Preventing Premature Pore Closure

The chemical vapor infiltration (CVI) process involves infiltrating a porous preform with reacting gases that undergo chemical transformation at high temperatures to deposit the ceramic phase within the pores, ultimately leading to a dense composite. The conventional CVI process in composite manufacturing needs to follow an isothermal approach to minimize temperature differences between the external and internal surfaces of the preform, ensuring that reactive gases infiltrate internal pores before external surfaces seal. Here, this study addresses the challenge of premature pore closure in CVI processes through microwave heating. A frequency-domain microwave solver is developed in OpenFOAM to investigate volumetric heating mechanisms within the preform. Through numerical studies, we demonstrate the capability of microwave heating of creating an inside-out temperature inversion. This inversion accelerates reactions proximal to the preform center, effectively mitigating the risk of premature external pore closure and ensuring uniform densification. The results reveal a significant enhancement in temperature inversion when high-permittivity reflectors are incorporated to generate resonant waves. This microwave heating strategy is then coupled with high-fidelity direct numerical simulation (DNS) of reacting flow, enabling the analysis of resulting densification processes. The DNS includes detailed chemistry and realistic diffusion coefficients. The numerical results can be used to estimate the impact of microwave-induced temperature inversion on densification in productions.

42 ENGINEERING↗

DOE OSTI2024

Modeling Microwave-Enhanced Chemical Vapor Infiltration Process for Preventing Premature Pore Closure

The chemical vapor infiltration (CVI) process involves infiltrating a porous preform with reacting gases that undergo chemical transformation at high temperatures to deposit the ceramic phase within the pores, ultimately leading to a dense composite. The conventional CVI process in composite manufacturing needs to follow an isothermal approach to minimize temperature differences between the external and internal surfaces of the preform, ensuring that reactive gases infiltrate internal pores before external surfaces seal. This study addresses the challenge of premature pore closure in CVI processes through microwave heating. A frequency-domain microwave solver is developed in Open-FOAM to investigate volumetric heating mechanisms within the preform. Through numerical studies, we demonstrate the capability of microwave heating of creating an inside-out temperature inversion. This inversion accelerates reactions proximal to the preform center, effectively mitigating the risk of premature external pore closure and ensuring uniform densification. The results reveal a significant enhancement in temperature inversion when high-permittivity reflectors are incorporated to generate resonant waves. This microwave heating strategy is then coupled with high-fidelity direct numerical simulation (DNS) of reacting flow, enabling the analysis of resulting densification processes. The DNS simulation includes detailed chemistry and realistic diffusion coefficients. The numerical results can be used to estimate the impact of microwave-induced temperature inversion on densification in productions.

Ge, Wenjun↗

DOE OSTI2013

Shell closures, loosely bound structures, and halos in exotic nuclei

Inspired by the recent experiments indicating doubly magic nuclei that lie near the drip-line and encouraged by the success of our relativistic mean-field (RMF) plus state-dependent BCS approach to the description of the ground-state properties of drip-line nuclei, we develop this approach further, across the entire periodic table, to explore magic nuclei, loosely bound structures, and halo formation in exotic nuclei. In our RMF+BCS approach, the single-particle continuum corresponding to the RMF is replaced by a set of discrete positive-energy states for the calculations of pairing energy. Detailed analysis of the single-particle spectrum, pairing energies, and densities of the nuclei predict the unusual proton shell closures at proton numbers Z = 6, 14, 16, 34, and unusual neutron shell closures at neutron numbers N = 6, 14, 16, 34, 40, 70, 112. Further, in several nuclei like the neutron-rich isotopes of Ca, Zr, Mo, etc., the gradual filling of lowlying single-particle resonant state together with weakly bound single-particle states lying close to the continuum threshold helps accommodate more neutrons but with an extremely small increase in the binding energy. This gives rise to the occurrence of loosely bound systems of neutron-rich nuclei with a large neutron-to-proton ratio. In general, the halo-like formation, irrespective of the existence of any resonant state, is seen to be due to the large spatial extension of the wave functions for the weakly bound single-particle states with low orbital angular momentum having very small or no centrifugal barriers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

Moment Closures on Two-Dimensional Cartesian Grids

Some moment methods for kinetic equations are complicated and take time to develop. Over the course of a couple years, this software was developed to test different closures on standard test problems in the literature. With this software, researchers in the field of moment closures will be able to rapidly test new methods.

Garrett, CharlesK.↗

DOE OSTI2020

Scaling Behavior of a Turbulent Kinetic Energy Closure Scheme for the Stably Stratified Atmosphere: A Steady-State Analysis

Abstract We present a turbulent kinetic energy (TKE) closure scheme for the stably stratified atmosphere in which the mixing lengths for momentum and heat are not parameterized in the same manner. The key difference is that, while the mixing length for heat tends toward the stability independent mixing length for momentum in neutrally stratified conditions, it tends toward one based on the Brunt–Väisälä time scale and square root of the TKE in the limit of large stability. This enables a unique steady-state solution for TKE to be obtained, which we demonstrate would otherwise be impossible if the mixing lengths were the same. Despite the model’s relative simplicity, it is shown to perform reasonably well with observational data from the 1999 Cooperative Atmosphere–Surface Exchange Study (CASES-99) using commonly employed model constants. Analyzing the scaling behavior of the nondimensional velocity and potential temperature gradients, or of the stability (correction) functions, reveals that for large stability the present model scales in the same manner as the first-order operational scheme of Viterbo et al. Alternatively, it appears as a blend of two cases of the TKE closure scheme of Baas et al. Critically, because a unique steady-state TKE can be obtained, the present model avoids the nonphysical behavior identified in one of the cases of Baas et al.

Meteorology & Atmospheric Sciences↗

DOE OSTI2021

The Amazon Water Cycle: Perspectives from Water Budget Closure and Ocean Salinity

Global and regional water cycle includes precipitation, water vapor divergence, and change of column water vapor in the atmosphere, and land surface evapotranspiration, terrestrial water storage change, and river discharge, which is linked to ocean salinity near the river mouth. The water cycle is a crucial component of the Earth system, and numerous studies have addressed its individual components (e.g., precipitation). Here we assess, for the first time, if remote sensing and reanalysis datasets can accurately and self-consistently portray the Amazon water cycle. This is further assisted with satellite ocean salinity measurements near the mouth of the Amazon River. The widely used practice of taking the mean of an ensemble of datasets to represent water cycle components (e.g., precipitation) can produce large biases in water cycle closure. Additionally, closure is achieved with only a small subset of data combinations (e.g., ERA5 precipitation and evapotranspiration plus GRACE satellite terrestrial water storage), which rules out the lower precipitation and higher evapotranspiration estimates, providing valuable constraints on assessments of precipitation, evapotranspiration, and their ratio. The common approach of using the Óbidos stream gauge (located hundreds of kilometers from the river mouth) multiplied by a constant (1.25) to represent the entire Amazon discharge is found to misrepresent the seasonal cycle, and this can affect the apparent influence of Amazon discharge on tropical Atlantic salinity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2013

A comparison of single-suture and double-suture incision closures in seaward-migrating juvenile Chinook salmon implanted with acoustic transmitters: implications for research in river basins containing hydropower structures

Reductions in the size of acoustic transmitters implanted in migrating juvenile salmonids have resulted in the ability to make shorter incisions that may warrant using only a single suture for closure. However, it is not known if one suture will sufficiently hold the incision closed, particularly when outward pressure is placed on the surgical site such as when migrating fish experience pressure changes associated with passage at hydroelectric dams. The objective of this research was to evaluate the effectiveness of single-suture incision closures on juvenile Chinook salmon (Oncorhynchus tshawytscha). Juvenile Chinook salmon were surgically implanted with a 2012 Juvenile Salmon Acoustic Telemetry System (JSATS) transmitter (0.30 g) and a passive integrated transponder tag (0.10 g) and incisions were closed with either one suture or two sutures. Mortality and tag retention were monitored and fish were examined after 7 and 14 days to evaluate tissue responses. In a separate experiment, surgically implanted fish were exposed to simulated turbine passage and then examined for expulsion of transmitters, expulsion of viscera through the incision, and mortal injury. With incisions closed using a single suture, there was no mortality or tag loss and similar or reduced tissue reaction compared to incisions closed with two sutures. Further, surgery time was significantly reduced when one suture was used, which leads to less handling and reduced stress. No tags were expelled during pressure scenarios and expulsion of viscera only occurred in two non-mortally injured fish (5%) with single sutures that were also exposed to very high pressure changes. No viscera expulsion was present in fish exposed to pressure scenarios likely representative of hydroturbine passage at many Columbia River dams (e.g. <2.7 ratio of pressure change; an acclimation pressure of 146.2 absolute kpa and a lowest exposure pressure of ~ 53.3 absolute kpa). Based on these results, we recommend the use of a single suture for surgical implantation of transmitters with incisions that are approximately 5 1/2 mm long after tag insertion.

Brown, Richard S.↗

DOE OSTI2012

Relationship Between Flowability And Tank Closure Grout Quality

After completion of waste removal and chemical cleaning operations, Tanks 5-F and 6-F await final closure. The project will proceed with completing operational closure by stabilizing the tanks with grout. Savannah River Remediation's (SRR) experience with grouting Tanks 18-F and 19-F showed that slump-flow values were correlated with flow/spread inside these tanks. Less mounding was observed when using grouts with higher slump-flow. Therefore, SRNL was requested to evaluate the relationship between flowability and cured properties to determine whether the slump-flow maximum spread of Mix LP#8-16 could be increased from 28 inches to 30 inches without impacting the grout quality. A request was also made to evaluate increasing the drop height from 5 feet to 10 feet with the objective of enhancing the flow inside the tank by imparting more kinetic energy to the placement. Based on a review of the grout property data for Mix LP#8-16 collected from Tank 18-F and 19-F quality control samples, the upper limit for slump-flow measured per ASTM C 1611 can be increased from 28 to 30 inches without affecting grout quality. However, testing should be performed prior to increasing the drop height from 5 to 10 feet or observations should be made during initial filling operations to determine whether segregation occurs as a function of drop heights between 5 and 10 feet. Segregation will negatively impact grout quality. Additionally, increasing the delivery rate of grout into Tanks 5-F and 6-F by using a higher capacity concrete/grout pump will result in better grout spread/flow inside the tanks.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2013

Soil Vapor Extraction System Optimization, Transition, and Closure Guidance

Soil vapor extraction (SVE) is a prevalent remediation approach for volatile contaminants in the vadose zone. A diminishing rate of contaminant extraction over time is typically observed due to 1) diminishing contaminant mass, and/or 2) slow rates of removal for contamination in low-permeability zones. After a SVE system begins to show indications of diminishing contaminant removal rate, SVE performance needs to be evaluated to determine whether the system should be optimized, terminated, or transitioned to another technology to replace or augment SVE. This guidance specifically addresses the elements of this type of performance assessment. While not specifically presented, the approach and analyses in this guidance could also be applied at the onset of remediation selection for a site as a way to evaluate current or future impacts to groundwater from vadose zone contamination. The guidance presented here builds from existing guidance for SVE design, operation, optimization, and closure from the U.S. Environmental Protection Agency, U.S. Army Corps of Engineers, and the Air Force Center for Engineering and the Environment. The purpose of the material herein is to clarify and focus on the specific actions and decisions related to SVE optimization, transition, and/or closure.

guidance↗

DOE OSTI2014

488-4D ASH LANDFILL CLOSURE CAP HELP MODELING

At the request of Area Completion Projects (ACP) in support of the 488-4D Landfill closure, the Savannah River National Laboratory (SRNL) has performed Hydrologic Evaluation of Landfill Performance (HELP) modeling of the planned 488-4D Ash Landfill closure cap to ensure that the South Carolina Department of Health and Environmental Control (SCDHEC) limit of no more than 12 inches of head on top of the barrier layer (saturated hydraulic conductivity of no more than 1.0E-05 cm/s) in association with a 25-year, 24-hour storm event is not projected to be exceeded. Based upon Weber 1998 a 25-year, 24-hour storm event at the Savannah River Site (SRS) is 6.1 inches. The results of the HELP modeling indicate that the greatest peak daily head on top of the barrier layer (i.e. geosynthetic clay liner (GCL) or high density polyethylene (HDPE) geomembrane) for any of the runs made was 0.079 inches associated with a peak daily precipitation of 6.16 inches. This is well below the SCDHEC limit of 12 inches.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2015

Chemical Waste Landfill Annual Post-Closure Care Report Calendar Year 2014

The CWL is a 1.9-acre remediated interim status landfill located in the southeastern corner of SNL/NM Technical Area III (Figures 2-1 and 2-2) undergoing post-closure care in accordance with the PCCP (NMED October 2009 and subsequent revisions). From 1962 until 1981, the CWL was used for the disposal of chemical and solid waste generated by SNL/NM research activities. Additionally, a small amount of radioactive waste was disposed of during the operational years. Disposal of liquid waste in unlined pits and trenches ended in 1981, and after 1982 all liquid waste disposal was terminated. From 1982 through 1985, only solid waste was disposed of at the CWL, and after 1985 all waste disposal ended. The CWL was also used as a hazardous waste drum-storage facility from 1981 to 1989. A summary of the CWL disposal history is presented in the Closure Plan (SNL/NM December 1992) along with a waste inventory based upon available disposal records and information.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2017

488-1D Ash Basin closure cap help modeling- Microdrain® liner option

At the request of Area Completion Engineering and in support of the 488-1D Ash Basin closure, the Savannah River National Laboratory (SRNL) performed hydrologic simulations of the revised 488-1D Ash Basin closure cap design using the Hydrologic Evaluation of Landfill Performance (HELP) model. The revised design substitutes a MicroDrain Liner®—60-mil low-density polyethylene geomembrane structurally integrated with 130-mil drainage layer—for the previously planned drainage/barrier system—300-mil geosynthetic drainage layer (GDL), 300-mil geosynthetic clay liner (GCL), and 6-inch common fill soil layer. For a 25-year, 24-hour storm event, HELP model v3.07 was employed to (1) predict the peak maximum daily hydraulic head for the geomembrane layer, and (2) ensure that South Carolina Department of Health and Environmental Control (SCDHEC) requirements for the barrier layer (i.e., ≤ 12 inches hydraulic head on top of a barrier having a saturated hydraulic conductivity ≤ 1.0E-05 cm/s) will not be exceeded. A 25-year, 24-hour storm event at the Savannah River Site (SRS) is 6.1 inches rainfall (Weber 1998). HELP model v3.07 results based upon the new planned cap design suggest that the peak maximum daily hydraulic head on the geomembrane barrier layer will be 0.15 inches for a minimum slope equal to 3%, which is two orders of magnitude below the SCDHEC upper limit of 12 inches.

58 GEOSCIENCES↗

DOE OSTI2017

488-1D Ash basin closure cap help modeling-Microdrain® liner option

At the request of Area Completion Engineering and in support of the 488-1D Ash Basin closure, the Savannah River National Laboratory (SRNL) performed hydrologic simulations of the revised 488-1D Ash Basin closure cap design using the Hydrologic Evaluation of Landfill Performance (HELP) model. The revised design substitutes a MicroDrain Liner®—50-mil linear low-density polyethylene geomembrane structurally integrated with 130-mil drainage layer—for the previously planned drainage/barrier system—300-mil geosynthetic drainage layer (GDL), 300-mil geosynthetic clay liner (GCL), and 6-inch common fill soil layer. For a 25-year, 24-hour storm event, HELP model v3.07 was employed to (1) predict the peak maximum daily hydraulic head for the geomembrane layer, and (2) ensure that South Carolina Department of Health and Environmental Control (SCDHEC) requirements for the barrier layer (i.e., ≤ 12 inches hydraulic head on top of a barrier having a saturated hydraulic conductivity ≤ 1.0E-05 cm/s) will not be exceeded. A 25-year, 24-hour storm event at the Savannah River Site (SRS) is 6.1 inches rainfall (Weber 1998). HELP model v3.07 results based upon the new planned cap design suggest that the peak maximum daily hydraulic head on the geomembrane barrier layer will be 0.179 inches for a minimum slope equal to 3%, which is approximately two orders of magnitude below the SCDHEC upper limit of 12 inches.

54 ENVIRONMENTAL SCIENCES↗