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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Impact of Grazing Duration and Environment on Soil Carbon in Reclaimed Uranium Mines Tailings: A Region Specific Study

ABSTRACT Grassland ecosystems, which cover over one‐third of the Earth's land area, store 10%–30% of global soil carbon (C). However, these ecosystems face substantial impacts from human activities, including mining. This study investigates the spatial distribution of soil C and related environmental factors in reclaimed grasslands on former uranium mine sites in Wyoming. We hypothesized that grazing duration and environmental factors would influence soil C levels. Interactions between topography, vegetation diversity, soil properties, and soil C in the context of grazing management in both natural and reclaimed grasslands from a wide range of periods from 1 year to 100 years were analyzed using geographically weighted regression models. Data collected from 2022 to 2023 showed that total carbon was consistently higher in natural grasslands (1.2%–4.9%) than in reclaimed grasslands (0.8%–1.3%). Additionally, soil C was significantly higher in natural grasslands grazed for 1 year compared to those grazed for 100 years. In contrast, reclaimed grasslands had lower soil C in areas grazed for 1 year compared to those grazed for 7 or 14 years. The absolute values of coefficients from environmental covariates indicated that areas grazed for a shorter duration (~1 year) were more influenced by biotic and abiotic factors than areas grazed for longer periods (> 7 years). Our findings show moderate grazing increases the resiliency of grassland ecosystems when grazed 7 years or longer and acknowledge the roles of topographic, soil, and vegetative factors in enhancing soil C concentration and developing sustainable land management practices in rangeland conditions.

Shilpakar, Chandan [Department of Plant Sciences U↗
DOE OSTI2022

Recent Developments in the WEC-Sim Open-Source Design Tool: Preprint

WEC-Sim (Wave Energy Converter SIMulator) is an open-source code for simulating wave energy converters, which has been actively developed and applied to simulate a wide variety of device archetypes and has become a popular tool since its initial release in 2014. WEC-Sim is developed jointly by the National Renewable Energy Laboratory (NREL) and Sandia National Laboratories (SNL) within the MATLAB/SIMULINK environment. Figure 1 illustrates a general wave-to-wire model which begins with a deployment site resource characterization, which is used to complete the hydrodynamic simulation of a single WEC (or array), with the power generation profile imported to a grid simulator to understand the influence on the local electrical network. While modelling the entire wave-to-wire is difficult and encompass multiple time scales and physics, WEC-Sim is focused on the hydrodynamics simulation to predict, analyze and optimize WEC dynamics and power performance. WEC-Sim simulations are performed in the time domain based on the radiation and diffraction method using hydrodynamics coefficients derived from boundary element method (BEM) based-frequency-domain potential flow solvers (e.g., WAMIT, NEMOH, Capytaine, or ANSYS-AQWA). Within this level of modeling fidelity, WEC-Sim can handle floating body hydrodynamics, mechanical and electrical power generation methods, advanced control implementation, mooring systems, and other unique applications such as desalination. Table 1 lists additional WEC-Sim functionalities, which are created using prebuilt Simulink blocks and MATLAB scripts that can simulate a wide range of floating systems and the corresponding auxiliary subsystems.

hydrodynamics modeling↗
DOE OSTI2020

Hydrogen Diffusivity Measurements of YH 1.87 Moderator Material with Incoherent Quasielastic Neutron Scattering

Yttrium hydride is an optimal choice of moderator material for thermal neutron spectrum reactors requiring small core volumes. The Transformation Challenge Reactor (TCR) program at Oak Ridge National Laboratory (ORNL) aims to develop an additively manufactured microreactor core by leveraging recent advances in materials, manufacturing, data analytics, and high-fidelity modeling and simulation. Yttrium hydride was selected as the moderator material for TCR due to its high moderating power, which enables the spatially efficient reactor design and thermal stability that is superior when compared with zirconium hydride. Hydrogen desorption from yttrium hydride is expected at elevated temperatures, posing safety and performance concerns. As a lifetime component in advanced reactors, appropriate strategies to mitigate hydrogen release from yttrium hydride over long-term reactor operation are required. Understanding hydrogen mobility in yttrium hydride provides the scientific basis for developing a hydrogen barrier for hydride moderator and predicting the hydrogen redistribution within the material during various operational conditions. This study investigated the hydrogen motion in YH 1.87 as a function of temperature ranging from 200 to 1,173 K using incoherent quasielastic neutron scattering (IQNS) at the Spallation Neutron Source (SNS). The results are presented and discussed in terms of hydrogen self-diffusion coefficients, activation energy for translational hydrogen motion, and hydrogen jump distances. Based on the IQNS data, YH 1.87 is found to be stable at high temperatures with no translational H motion below 1,023 K within the IQNS detection limits. In the temperature range of 1,073–1,173 K, hydrogen diffusivity in YH 1.87 is $D = 4.57 X 10^{⁻3} [m^2/s] exp (⁻\frac{1.73[eV]}{RT}$). The hydrogen concentration’s dependence on hydrogen diffusivity is also discussed in this report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Hanford Tank Waste Matrix Impact on Ion Exchange Performance Using Crystalline Silicotitanate

The removal of radiocesium from Hanford tank waste supernate is a critical step in preparing feed for low-activity waste immobilization. This study evaluated cesium ion exchange performance using crystalline silicotitanate (CST) media in a series of tests designed to evaluate the influence of waste matrix variability on capacity and kinetics. Tank waste supernate subsampled from five Hanford double-shell tanks encompassed a range of sodium, hydroxide, nitrate, and nitrite concentrations in order to assess the impact of feed variability on the performance of the ion exchange system. Both equilibrium and dynamic ion exchange tests were conducted to quantify cesium distribution coefficients and breakthrough behavior under prototypic operating conditions. Results indicated that effective cesium capacity varied by up to a factor of five across the matrices tested, with higher sodium concentrations significantly reducing uptake. Kinetic behavior was similarly matrix-dependent, with solution viscosity contributing to a twofold variation in mass-transfer rates. These results demonstrate the strong dependence of CST ion exchange performance on waste composition and must be incorporated into predictive models for future treatment system design and optimization.

Westesen, Amy M.↗
DOE OSTI2025

Cartesian equivariant representations for learning and understanding molecular orbitals

Qualitative and quantitative orbital properties such as bonding/antibonding character, localization, and orbital energies are critical to how chemists understand reactivity, catalysis, and excited-state behavior. Despite this, representations of orbitals in deep learning models have been very underdeveloped relative to representations of molecular geometries and Hamiltonians. Here, we apply state-of-the-art equivariant deep learning architectures to the task of assigning global labels to orbitals, namely energies characterizations, given the molecular coefficients from Hartree–Fock or density functional theory. The architecture we have developed, the Cartesian Equivariant Orbital Network (CEONET), shows how molecular orbital coefficients are readily featurized as equivariant node features common to all graph-based machine-learned potentials. We find that CEONET performs well at predicting difficult quantitative labels such as the orbital energy and orbital entropy. Furthermore, we find that the CEONET representation provides an intuitive latent space for differentiating orbital character for the qualitative assignment of e.g. bonding or antibonding character. In addition to providing a useful representation for further integrating deep learning with electronic structure theory, we expect CEONET to be useful for automatizing and interpreting the results of advanced electronic structure methods such as complete active space self-consistent field theory. In particular, the ability of CEONET to infer multireference character via the orbital entropy paves the way toward the machine-learned selection of active spaces.

chemical reactions↗
DOE OSTI2022

Sodium diffusion in heterogeneous porous media: Connecting laboratory experiments and simulations

Sodium has been suggested as a tracer for brine in reservoir formations where a significant amount of sodium ion is found mainly in the aqueous phase. Fortunately, the most abundant sodium isotope, 23 Na, is Nuclear Magnetic Resonance (NMR) active, making it possible to study the structure and dynamical properties of both bulk and pore confined fluid systems. We investigated the diffusion of key dissolved sodium species in bulk solution and porous media as a function of composition, ionic strength, and permeability of the carbonate samples using NMR relaxometry and pulsed-field gradient (PFG) NMR techniques. We use Indiana limestone as an example of natural porous media and water as a freely diffusible tracer and carrier. We demonstrate apparent diffusion measurement of sodium based on changes in spin–spin relaxation time (T 2 ) signal in pore confinement. The diffusion rate of sodium decreases with increasing counter-ion size. This effect is greater at higher ionic strengths and lower chemical potentials in porous media. The reactive transport code, CrunchFlow, was used to complement the NMR experiments to simulate diffusion behavior in porous media. Combining these two methods provides a powerful approach to estimating effective diffusion coefficients in heterogeneous matrices. The modeling considers the influence of physical properties (porosity and tortuosity) and chemical properties (geochemical composition and chemical gradients). The results presented in this work highlight the advantage of measuring apparent diffusivity using NMR T 2 relaxometry in conjunction with numerical simulation to derive effective diffusivity and the corresponding matrix properties (i.e., tortuosity) of the system.

58 GEOSCIENCES↗
DOE OSTI2026

Avoidance of disruptions on KSTAR due to vertical displacement events via novel real-time stability assessment

Disruption avoidance via the DECAF approach has been achieved on KSTAR using a novel real-time vertical stability assessment and a multiactuator feedback control strategy. The development of disruption avoidance strategies with reactor-relevant reliability is an urgent activity, enabling future fusion power plants. The stability metric employed is based on a new formulation of a vertical force gradient balance metric evaluated across the poloidal cross section of the plasma, with parameters tuned using historical data. Evaluation of this metric on a validation set of 400 recent KSTAR shots indicates >82% of Vertical displacement events can be avoided via feedback control. Essential to its calculation is the two-dimensional toroidal current density distribution in the plasma. Measurement of this profile faster than fully-converged equilibrium reconstructions can deliver is found to improve forecaster performance and is achieved with a surrogate model that takes as input magnetic diagnostic measurements and outputs the current profile on a basis comprising the top principal components of historical current profiles (from past equilibrium reconstructions). This method solves the non-uniqueness problem typically faced when reconstructing current profiles directly from diagnostics, while improving computational time and accuracy. On average, profiles produced by this model reach coefficients of determination of >0.99 with respect to those from equilibrium reconstructions. The avoidance actuators employed include poloidal field coils and an electron cyclotron current drive system. The multiactuator approach, as shown in this first demonstration, allows disruption avoidance while minimizing impact to operational performance. This ability, along with its flexibility and speed, makes this new approach an attractive option for avoiding these types of disruptions in reactors.

Tobin, Matthew [Columbia Univ., New York, NY (Unit↗
DOE OSTI2023

Demonstrating non-isothermal vacuum membrane air dehumidification for efficient next-generation air conditioning

Vacuum membrane air dehumidification has gained significant interest in recent years as a highly efficient means of air dehumidification. Prior theoretical modeling work by the authors introduced the Active Membrane Energy Exchanger (AMX) concept, which combines active heat exchange and vacuum membrane dehumidification into one non-isothermal system, and found that it could outperform other air conditioning technologies under many conditions. However, no experimental literature exists on combining active heat exchangers and vacuum membrane dehumidification. Here, the goal of the present study is to evaluate the dehumidification (mass transfer) performance of the AMX concept relative to isothermal membrane dehumidification through three main methodologies: (1) membrane material-level characterization, (2) experimental prototype development and testing, and (3) computational fluid dynamics (CFD) simulations. The dense membranes used in this work showed up to a 40% increase in water vapor permeance at cooler temperatures, and the prototype system showed up to a 6% increase in humidity removal when the air was simultaneously cooled. Furthermore, the membrane module-integrated heat exchange tubes provided additional mixing and turbulence, leading to a 4–8% increase in humidity removal. The upper limit coefficient of performance was equal to approximately 2.2, necessitating advanced system designs to improve efficiency. This study is the first to highlight that combining the cooling and vacuum dehumidification processes can improve dehumidification performance.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2025

Determining hexavalent chromium transport properties in alkaline nuclear waste using nuclear magnetic resonance spectroscopy

This study focuses on the transport properties of hexavalent chromium, specifically the chromate anion, to improve predictive models and environmental remediation strategies for Cr(VI) migration. Using 53 Cr Nuclear Magnetic Resonance (NMR) spectroscopy, the research quantifies chromate in multicomponent electrolytes replicating nuclear waste conditions at the Hanford Site in Washington State. The consistency of the 53 Cr NMR signal integral with chromate concentration, despite varying matrix compositions, establishes it as a reliable concentration indicator. The transport properties of chromate in an alkaline solution were assessed using relaxation-based measurements via saturation recovery and Carr-Purcell-Meiboom-Gill experiments, determining spin-lattice and spin-spin relaxation times. These measurements, combined with the Bloembergen-Purcell-Pound equation, helped estimate the rotational correlation time and the 53 Cr self-diffusion coefficient using Stokes-Einstein-Debye and Stokes-Einstein equations. Direct measurements were obtained through pulsed field gradient stimulated echo 53 Cr NMR spectroscopy. Monte Carlo simulations further estimated uncertainty propagation. The results enhance comprehension of chromate transport and highlight prospects for identifying transport properties of NMR-active nuclei, traditionally considered unreachable.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Computational Imaging for Intelligence in Highly Scattering Aerosols (Final Report)

Natural and man-made degraded visual environments pose major threats to national security. The random scattering and absorption of light by tiny particles suspended in the air reduces situational awareness and causes unacceptable down-time for critical systems and operations. To improve the situation, we have developed several approaches to interpret the information contained within scattered light to enhance sensing and imaging in scattering media. These approaches were tested at the Sandia National Laboratory Fog Chamber facility and with tabletop fog chambers. Computationally efficient light transport models were developed and leveraged for computational sensing. The models are based on a weak angular dependence approximation to the Boltzmann or radiative transfer equation that appears to be applicable in both the moderate and highly scattering regimes. After the new model was experimentally validated, statistical approaches for detection, localization, and imaging of objects hidden in fog were developed and demonstrated. A binary hypothesis test and the Neyman-Pearson lemma provided the highest theoretically possible probability of detection for a specified false alarm rate and signal-to-noise ratio. Maximum likelihood estimation allowed estimation of the fog optical properties as well as the position, size, and reflection coefficient of an object in fog. A computational dehazing approach was implemented to reduce the effects of scatter on images, making object features more readily discernible. We have developed, characterized, and deployed a new Tabletop Fog Chamber capable of repeatably generating multiple unique fog-analogues for optical testing in degraded visual environments. We characterized this chamber using both optical and microphysical techniques. In doing so we have explored the ability of droplet nucleation theory to describe the aerosols generated within the chamber, as well as Mie scattering theory to describe the attenuation of light by said aerosols, and correlated the aerosol microphysics to optical properties such as transmission and meteorological optical range (MOR). This chamber has proved highly valuable and has supported multiple efforts inclusive to and exclusive of this LDRD project to test optics in degraded visual environments. Circularly polarized light has been found to maintain its polarization state better than linearly polarized light when propagating through fog. This was demonstrated experimentally in both the visible and short-wave infrared (SWIR) by imaging targets made of different commercially available retroreflective films. It was found that active circularly polarized imaging can increase contrast and range compared to linearly polarized imaging. We have completed an initial investigation of the capability for machine learning methods to reduce the effects of light scattering when imaging through fog. Previously acquired experimental long-wave images were used to train an autoencoder denoising architecture. Overfitting was found to be a problem because of lack of variability in the object type in this data set. The lessons learned were used to collect a well labeled dataset with much more variability using the Tabletop Fog Chamber that will be available for future studies. We have developed several new sensing methods using speckle intensity correlations. First, the ability to image moving objects in fog was shown, establishing that our unique speckle imaging method can be implemented in dynamic scattering media. Second, the speckle decorrelation over time was found to be sensitive to fog composition, implying extensions to fog characterization. Third, the ability to distinguish macroscopically identical objects on a far-subwavelength scale was demonstrated, suggesting numerous applications ranging from nanoscale defect detection to security. Fourth, we have shown the capability to simultaneously image and localize hidden objects, allowing the speckle imaging method to be effective without prior object positional information. Finally, an interferometric effect was presented that illustrates a new approach for analyzing speckle intensity correlations that may lead to more effective ways to localize and image moving objects. All of these results represent significant developments that challenge the limits of the application of speckle imaging and open important application spaces. A theory was developed and simulations were performed to assess the potential transverse resolution benefit of relative motion in structured illumination for radar systems. Results for a simplified radar system model indicate that significant resolution benefits are possible using data from scanning a structured beam over the target, with the use of appropriate signal processing.

58 GEOSCIENCES↗
DOE OSTI2021

Modernizing the active neutron collar poison rod correction using simulations to enhance PWR fresh fuel verification

The declared inventory of 235 U in fresh, low enriched uranium, nuclear fuel assemblies is routinely verified by nuclear safeguards inspectorates using the UNCL (Uranium Neutron Collar – Light Water Reactor Fuel) nondestructive assay instrument. The trend in modern fuels is towards higher initial enrichment, which in turn requires a larger number of burnable poison pins with higher Gadolinia concentration to hold down the initial reactivity. UNCL assay error for modern fuel assemblies typically exceeds 10%. The traditional algorithm used to correct the response for burnable poison content needs revision to achieve accuracy comparable to the $\sigma_\text{R}$ of 4.5% expected for poison-free assemblies. Here we review the problem and use a large set of 287 Monte Carlo simulations based on an experimentally benchmarked model corresponding to the 16×16 PWR array used in Brazilian Angra type II and III fuel. Simulated relative responses are used to evaluate the functional form of the poison correction and determine parameters optimal for 16×16 PWR assemblies. This update is conducted using between 4–24 Gadolinia pins ranging 2–11 wt% Gd 2 O 3 with assemblies having mean enrichments ranging 2.5%–5%. Experimental validation of the updated coefficients using seven measurements shows bias is reduced by an order of magnitude and $\sigma_\text{R}$R reduced from 10% to less than 2%. Two updated sets of coefficients are provided, the most accurate of which is directly useable in the existing analysis code (INCC) in use by inspectorate at fuel fabrication facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Towards the Development of Molten Salt Reactor Multiphysics Modeling Capabilities: Depletion, Thermochemistry, Reactor Dynamics, and Species Tracking

This report documents the simulation and modeling work performed under the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, utilizing the tools and codes developed under the program. The focus in this Fiscal Year (FY) is on the depletion, thermochemistry, reactor dynamics, and species transport in MSRs. The fission products travelling in the entire primary loop is unique in MSRs. There are many physical/chemical mechanisms that can significantly affect the fission products concentration in the fuel salt, e.g., diffusion into gas bubbles, diffusion in the core moderators, deposition on the surface of structures/pipes, etc. The fission product concentration in the fuel salt can potentially affect the neutronics, system dynamics, chemical potentials, etc., so accurately predicting the fission products distribution in the primary loop is important. Under the main objective, different activities are pursued to assess the NEAMS tools applicability for a variety of areas on species transport, including the depletion analyses using Griffin (fission product source), the redox potential assessment at different depletion points, the assessment of xenon transport effect on the neutronics and reactor dynamics, a survey of correlations for calculating the mass transfer coefficient of different fission products, etc.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Inverse Method for Noninvasive Material Discrimination with Multienergy X-Ray Radiography

Active x-ray inspections have great potential for noninvasive detection of illicit materials. Dual-energy x-ray radiography, in particular, has been used to determine material composition by utilizing the energy-dependence of the x-ray attenuation coefficients. However, current implementations of this method are limited in their ability to determine the material composition of composite objects. Here, in this paper, we present an inverse algorithm that uses multienergy x-ray radiography data to noninvasively reconstruct the contents of a container. A critical feature of the current contribution is that material identification can be performed using conventional detectors and x-ray spectra with different endpoint energies produced by varying nothing more than the tube voltage. Adaptive regularization is used to increase the accuracy of material estimations from multienergy data sets. The utility of these methods is demonstrated with experimentally acquired radiographs obtained using a tunable x-ray source that produces spectra with endpoint energies of 100–450 keV. The object inspected is a scale model of a nuclear materials storage container composed of three-dimensional printed plastic and stainless-steel spheres inside a thin-walled steel container. Reconstructions of the steel sphere thicknesses are within a root-mean-square error of 0.37 cm.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Machine learning–assisted prediction of heat fluxes through thermally anisotropic building envelopes

Thermally anisotropic building envelope (TABE) is a novel active building envelope that can save energy use to maintain thermal comfort in buildings by redirecting heat and coolness from building envelopes to thermal loops. Finite element models (FEMs) can be used to compute the heat fluxes through TABEs, but the high computational cost of finite element simulations has prevented parametric studies and design optimizations. This paper proposes a domain knowledge–informed, finite element–based machine learning framework to reduce the computation cost for the energy management of buildings installed with TABE that uses a ground thermal loop. First, the training heat flux data set was generated by FEM simulations with different thermal loop schedules. Then, both shallow learning models (i.e., multivariate linear regression and eXtreme Gradient Boost, or XGBoost) and a deep learning model (i.e., deep neural network, or DNN) were trained to predict the heat fluxes. Domain knowledge was used for data preprocessing and feature selection. Finally, the suitability of the selected machine learning model was tested under different thermal loop schedules. Herein, the case study results showed that: (1) XGBoost can be as accurate as DNN (coefficient of determination equal to 0.81) with much less training time; (2) the annual energy cost savings for different thermal loop schedules obtained by the XGBoost-predicted and FEM-calculated heat fluxes are consistent, having a difference of only 4%; and (3) XGBoost can reduce the computation time for the annual energy analysis of the case study building with a given thermal loop schedule from around 12 h by using FEM to less than 1 min.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Simulations of saturated MHD activity in the HBT-EP tokamak

The NIMROD code is used to perform simulations of MHD activity in the HBT-EP tokamak, including the effect of a resistive wall. Linear simulations are conducted to scan current and pressure profiles to establish self-consistent baseline equilibria that result in MHD instabilities with low error between experimental diagnostics and synthetic equivalents. A family of such equilibria is found with relatively peaked current and pressure profiles. Nonlinear simulations are performed using the optimal equilibrium, which is linearly unstable to a Resistive Wall Mode—stable in the ideal wall limit and with an Alfvénic growth rate in the no-wall limit. Using resistive wall boundary conditions, nonlinear Hall MHD simulations yield a rotating, saturated n=1 mode similar to the type observed experimentally in HBT-EP discharges. An n=1 mode around the q=2 surface mediates a localized axisymmetric perturbation that flattens the plasma current from a linearly unstable state to a 3D, rotating, stable state. During the saturated period, periodic changes in inter-diagnostic phase lag allow for qualitative estimations of effective, macroscopic transport coefficients used in MHD closure models and could be extended to model post-disruption MHD structure rotation after thermal quenches seen in HBT-EP.

Arnold, David A. (ORCID:0009000059535761)↗
DOE OSTI2022

Building a machine learning surrogate model for wildfire activities within a global Earth system model

Abstract. Wildfire is an important ecosystem process, influencing land biogeophysical and biogeochemical dynamics and atmospheric composition. Fire-driven loss of vegetation cover, for example, directly modifies the surface energy budget as a consequence of changing albedo, surface roughness, and partitioning of sensible and latent heat fluxes. Carbon dioxide and methane emitted by fires contribute to a positive atmospheric forcing, whereas emissions of carbonaceous aerosols may contribute to surface cooling. Process-based modeling of wildfires in Earth system land models is challenging due to limited understanding of human, climate, and ecosystem controls on fire counts, fire size, and burned area. Integration of mechanistic wildfire models within Earth system models requires careful parameter calibration, which is computationally expensive and subject to equifinality. To explore alternative approaches, we present a deep neural network (DNN) scheme that surrogates the process-based wildfire model with the Energy Exascale Earth System Model (E3SM) interface. The DNN wildfire model accurately simulates observed burned area with over 90 % higher accuracy with a large reduction in parameterization time compared with the current process-based wildfire model. The surrogate wildfire model successfully captured the observed monthly regional burned area during validation period 2011 to 2015 (coefficient of determination, R2=0.93). Since the DNN wildfire model has the same input and output requirements as the E3SM process-based wildfire model, our results demonstrate the applicability of machine learning for high accuracy and efficient large-scale land model development and predictions.

58 GEOSCIENCES↗
DOE OSTI2025

Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to model an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large data sets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750 ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores present within BMC shell tiles. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately 3 orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least 10-fold higher than it would be in neat solution and is the real driver for varying permeability estimates we obtained through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs, highlighting how permeable BMC shells can be.

Diffusion↗
DOE OSTI2020

Optomechanical interaction in fibre lasers with micro-optomechanical resonance structures

We report the results of studies of fibre lasers with passive modulators based on light-excited micro-optomechanical resonance structures (micro-oscillators). It is shown that in fibre lasers based on active fibres doped with rare-earth elements (Er, Er/Yb, Yb, Nd), the optomechanical interaction of laser radiation with micro-oscillators of various types (fibre-optic, microvolume) leads to self-oscillations of the characteristics of laser radiation at frequencies of relaxation oscillations and intermode beats synchronised with the frequencies of elastic eigenoscillations of micro-oscillators. It is found that in an ultra-long erbium – ytterbium fibre laser with a nonlinear mirror based on a microcantilever, laser photothermal excitation of the second mode of elastic transverse oscillations of the microcantilever makes it possible to perform passive mode locking exclusively due to Q-switching of the laser cavity. Pulsed lasing with a controlled repetition rate (∼76 kHz), a pulse duration of 2 – 5 μs and an output energy of 0.1 μJ per pulse is implemented. Based on a simplified physical model of the indicated fibre lasers with micro-oscillators, we have developed an approximate mathematical model describing the regimes of passive mode locking of fibre lasers with micro-oscillators that play the role of mirrors with a nonlinear reflection coefficient in the laser cavity. The prospects for the development and application of the considered laser systems are discussed. (control of laser radiation parameters)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗