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At least 181 records · Page 10

Accelerating Hamiltonian Monte Carlo for Bayesian inference in neural networks and neural operators

Hamiltonian Monte Carlo (HMC) is a powerful and accurate method to sample from the posterior distribution in Bayesian inference. However, HMC techniques are computationally demanding for Bayesian neural networks due to the high dimensionality of the network’s parameter space and the non-convexity of their posterior distributions. Therefore, various approximation techniques, such as variational inference (VI) or stochastic gradient MCMC, are often employed to infer the posterior distribution of the network parameters. Such approximations introduce inaccuracies in the inferred distributions, resulting in unreliable uncertainty estimates. In this work, we propose a hybrid approach that combines inexpensive VI and accurate HMC methods to efficiently and accurately quantify uncertainties in neural networks and neural operators. The proposed approach leverages an initial VI training on the full network. We examine the influence of individual parameters on the prediction uncertainty, which shows that a large proportion of the parameters do not contribute substantially to uncertainty in the network predictions. This information is then used to significantly reduce the dimension of the parameter space, and HMC is performed only for the subset of network parameters that strongly influence prediction uncertainties. This yields a framework for accelerating the full batch HMC for posterior inference in neural networks. We demonstrate the efficiency and accuracy of the proposed framework on deep neural networks and operator networks, showing that inference can be performed for large networks with tens to hundreds of thousands of parameters. Finally, we show that this method can effectively learn surrogates for complex physical systems by modeling the operator that maps from upstream conditions to wall-pressure data on a cone in hypersonic flow.

Bayesian inference↗

High-Order Hybrid RANS-LES Study of NACA0012 Wing Sections

We develop hybrid RANS-LES strategies within Nek5000 for application to airfoil sections at small flight configurations. We present a validation and verification study of $k \space – \space \tau$ SST applied to a NACA 0012 wing section in a pure RANS and in a hybrid RANS-LES setup. The study shows good corroboration with existing experimental and numerical datasets. We also analyze some of the observed discrepancies with the experiments by evaluating the side wall “blocking” effect. We demonstrate that for the hybrid turbulence modeling approach a high-order spectral- element discretization converges faster (i.e., with less resolution) than a representative low-order finite-volume-based approach.

42 ENGINEERING↗

Reduced order modeling of a fluidized bed particle receiver for concentrating solar power with thermal energy storage

Oxide particles can serve as both the heat transfer and thermal energy storage (TES) media for next-generation concentrating solar power (CSP) plants where high-temperature TES enables dispatchable electricity from efficient power cycles with firing temperatures above 600 °C. Transferring heat to flowing particles at such high temperatures in a MW-scale central tower receiver remains a challenge for the CSP community. For indirect receivers with external walls to contain the particles, maintaining wall temperatures below the limits of structural metal alloys requires high heat transfer coefficients between the wall and the moving particle stream. Bubbling fluidization of downward-flowing particles can sustain high bed-wall heat transfer coefficients (> 1000 W m -2 K -1 ). Using experimentally calibrated correlations for bed-wall heat transfer and vertical particle dispersion, this study implements an axially discretized zonal model of a counterflow fluidized bed receiver to explore how bubbling fluidization may enable indirect cavity particle receivers. High bed-wall heat transfer coefficients support solar fluxes on angled cavity walls > 200 kW m -2 at peak aperture fluxes of 980 kW m -2 while maintaining external wall temperatures < 950 °C. Lateral particle dispersion enables hotter particles near the receiver leading edge to mix with cooler particles further from the leading edge to lower maximum external wall temperatures. Parametric studies identify how mass fluxes, particle dispersion, and solar concentrations impact indirect receiver thermal efficiency and uniformity for a CSP plant. These studies provide a basis for the design of indirect fluidized-bed cavity receivers that can maintain particle outlet temperatures for TES above 750 °C.

14 SOLAR ENERGY↗

A brief review on strain engineering of ferroelectric K x Na 1- x NbO 3 epitaxial thin films: Insights from phase-field simulations

Strains play a pivotal role in determining the phase equilibrium, domain configuration, and functional properties of the low-dimensional ferroelectrics. There is growing interest in the strain engineering of ferroelectric K x Na 1- x NbO 3 (KNN) epitaxial thin films, which exhibit excellent physical properties and promise as eco-friendly alternatives to lead-based ferroelectrics for microdevice applications. Further, advances have been made in understanding the phase equilibria and transitions, domains and domain walls, and their relations to the physical properties of KNN epitaxial thin films using a combination of experiments and theoretical modeling, particularly phase-field simulations. Here, we review recent progress in these aspects and showcase the phase-field method for establishing strain phase diagrams, elucidating the domain and domain wall structures at equilibrium, and predicting the structure–property relationships in ferroelectric KNN thin films. We also discuss challenges and opportunities to further advance our understanding of KNN thin films and potentially unlock new functionalities by leveraging phase-field simulations.

36 MATERIALS SCIENCE↗

A Review of Modeling Approaches for Predicting Frost Growth and Defrosting on Tube-Fin Heat Exchangers: Preprint

Frost formation and growth on the evaporator surface is a common process that deteriorates the air-refrigerant heat transfer and restricts airflow. This degrades the performance of the vapor compression system by increasing temperature lift and air-side pressure drop. To accurately predict these effects during coil frosting, as well as the energy use and duration of the defrost process, there is a need to estimate the heat and mass transfer, momentum transport, and solid-liquid and liquid-vapor phase change. Therefore, in the past few decades, continuous effort has been made to model frosting and defrosting processes using approaches ranging from empirical correlations to computational fluid dynamic models. To provide a clearer overview for researchers, engineers, and manufacturers in this field, this paper provides a comprehensive literature review for frosting and defrosting models. The paper begins with theoretical background of frost formation and defrost processes, and then reviews the common modeling approaches in literature and their underlying assumptions when trying to account for various physical phenomenon. Based on the literature review, the most critical modeling effort for frost formation is the determination of frost densification rate and frost growth rate. Various methods to predict these two parameters are reviewed. Empirical correlations commonly used for frost density and thermal conductivity are presented and compared. For the defrost process, various multi-stage models have been proposed with different assumptions. Some assume the presence of air gap between the tube wall and the frost, while others consider the melted frost flow due to gravity. We also review physics-based and empirical approaches to integrate defrost models into heat pump models. We conclude by identifying research gaps and providing recommendations.

defrost↗

FY25 Theory and Simulation Performance Target: Development of an integrated modeling framework for fusion reactor design and assessment (Final Report)

This report documents the FY25 Theory and Simulation Performance Target (TSPT) of developing an integrated modeling framework for fusion reactor design and assessment (FREDA). Over Q1-Q4, new capabilities were developed across both plasma and engineering domains and demonstrated on an example representation of a Compact Advanced Tokamak with a Dual Cooled Lead Lithium blanket. This represents a first-of-a-kind demonstration of coupled core-to-wall-to-engineering for a reactor. Self-consistent CESOL workflows were applied to provide core, pedestal, and SOL prediction; new modules were developed for energetic particle stability (FAR3D) and transport (TGLF-EP) analysis; and boundary plasma modeling (SOLPS-ITER, BOUT++/Hermes-3) was expanded to evaluate wall and divertor heat fluxes and interface with engineering thermal analysis. A parameterized CAD tool, TRACER, was expanded to generate medium-fidelity divertor, blanket, and coil geometries; OpenFOAM and Diablo workflows were applied for first-wall and divertor thermal analyses with helium cooling; and reduced-order models were created for high-mass-flux divertor cooling. Magnet multiphysics capabilities were verified between Elmer, Diablo, and a new MFEM-based solver, and workflows enable stress, thermal, and neutron-fluence analysis of TF coils with neutronics-driven heating. Nuclear and blanket analysis workflows were demonstrated, including tritium breeding, transport, and CFD-informed thermo-mechanical assessment. Preliminary multi-fidelity uncertainty quantification workflows were applied to boundary modeling codes and shown to achieve variance reductions with fewer high-fidelity boundary simulations. Key findings highlight the challenges of resolving the ITEP gap to find suitable balance between wall and divertor loads, neutron heating, and practical limits of PFC cooling. Next step priorities are to develop automated workflows to check boundary code convergence and detachment, implement tighter physics-engineering CAD provenance tracking, and inclusion of plasma-material interface models for SLAG and tungsten cracking behavior. Collectively, these developments establish sophisticated capabilities for predictive, multi-fidelity, whole-device modeling that integrates plasma physics, materials, magnets, and nuclear engineering to guide pathways to viable Fusion Pilot Plant design points.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Verification of a Fluid-Based Plasma-Edge Model Within the Multiphysics Object-Oriented Simulation Environment (MOOSE) Framework

As the goal of achieving fusion power on the grid comes closer to fruition, fully coupled multiphysics models of fusion devices will be crucial. These models must incorporate the interconnected phenomena of these devices, including plasma physics, neutronics, first wall interactions, and tritium transport. Currently, there are two main approaches to developing these platforms: (1) loosely coupled, where one couples existing codes and solvers together through input and output parameters and data, and (2) tightly coupled, where one develops the necessary models within a singular, integrated framework. This work focuses on the latter approach for magnetically confined fusion devices by developing a fluid-based plasma-edge model within the Multiphysics Object Oriented Simulation Environment (MOOSE) Framework. This effort is coordinated with other efforts to develop, test, demonstrate, and deploy fusion relevant multiphysics capabilities including electromagnetics, particle-in-cell plasma, tritium transport, and fusion blanket design. This new model is an expansion of the MOOSE-based plasma application, Zapdos, which was originally formulated to model low-temperature, non-magnetized plasma processes. Verification studies have been conducted using newly developed magnetic plasma capabilities. These involved convergence analyses utilizing the method of manufactured solutions to verify new operators and case studies. A modular approach was taken here to demonstrate increasingly complicated simulation scenarios, which included a singular fluid with uniform magnetic field case, a singular fluid with spatially varying magnetic field case, and a coupled multifluid case.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Inverter Model Validation and Calibration Using Phasor Measurement Unit Data

As the penetration of inverter-based renewable energy resources increases in the power grid, especially at the distribution and microgrid levels, the need to accurately represent them in planning studies increases as well. However, due to the lack of well-established standard procedures, and vendor reluctance towards the detailed sharing of proprietary models, automated dynamic model validation and parameter calibration tools for inverter based resources (IBRs) remain scarce. This work presents a model validation and parameter calibration platform for representing IBRs with generic phasor-domain models. Phasor measurements of power system events are used for continuous validation using the data playback method, and model parameters are re-calibrated if a significant mismatch between measurements and model response is observed. Unique features of the proposed platform include- (a) an iterative Bayesian optimization approach towards parameter calibration to address a possible mismatch between the structures of generic models implemented in simulation softwares and actual commercial inverters, (b) error metrics designed to account for a possible mismatch between the time resolution of simulation and measurements, and (c) analysis of the measurement-simulation mismatch to provide guidance to engineering personnel regarding model shortcomings. The performance of the platform has been illustrated using both simulated data and field measurements to validate/calibrate inverter models in GridLAB-D.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

High y + Shear-Stress Turbulence Implementation for High Flux Isotope Reactor Narrow Channel Flows

The research objective of this work was to improve the engineering predictions of the turbulence characteristics of flows in curved narrow channels. Such channel flows are commonly encountered in nuclear research and test reactors, with one of them being the high-flux isotope reactor (HFIR). Research reactors bear high heat fluxes, and the proper computing of turbulence is paramount for safe and reliable reactor operation. The study builds on the results of a previous direct numerical simulation of turbulence to inform a well-known Reynolds-averaged Navier–Stokes shear-stress turbulence model and improves its accuracy in simulating parallel channel flows. A new formulation of the loss term in the dissipation conservation equation is suggested. Combined with high wall distance computational grids, the new implementation provides a fast-running flow solution, suitable for engineering purposes. Model generalization for parallel channel flows, in a broader range of frictional Reynolds numbers, is suggested by introducing a new form of the model constants.

CFD↗

Gram-positive bacterial cell wall components inhibit herpes simplex virus infection

The role of the mucosal microbiome in viral infections remains unclear. Genital herpes, caused by herpes simplex virus 1 and 2 (HSV-1 and HSV-2), is among the most prevalent sexually transmitted infections worldwide. Despite evidence linking vaginal Lactobacillus to protection against sexually transmitted viruses, the specific microbial components and mechanisms that mediate this defense are not well understood. Here, we show that multiple cell wall components from diverse gram-positive bacteria, including lactobacilli, inhibit HSV-1 and HSV-2 infection in cells and in a mouse model of genital herpes infection. Peptidoglycan (PG) and lipoteichoic acid (LTA), both major components of the gram-positive bacterial cell wall, significantly reduced HSV infectivity in vitro and improved survival and disease outcomes in mice. We further showed that Lactobacillus crispatus surface layer proteins SlpA and SlpB bind HSV-1 and inhibit infection. Antiviral effects of cell wall components were dose-dependent, relied on intact PG structure, and, in the case of PG and LTA, were independent of TLR2-mediated host signaling. Collectively, our findings identify a species-independent antiviral function for gram-positive bacterial cell wall components against HSV and suggest that the composition of the mucosal microbiome may play an underappreciated role in suppressing mucosal herpes infection in humans.

Adams↗

Leveraging structure-informed machine learning for fast steric zipper propensity prediction across whole proteomes

Predicting the amyloid fold and the propensity of peptide segments to adopt amyloid-like structures remain a challenge. However, recent progress has facilitated structure-based prediction of steric zipper propensity and the use of machine learning to accelerate the calculation of predictive models across many scientific areas. Leveraging these advances, we have developed a new approach for rapid proteome-wide assessment of zipper profiles that is informed by four million steric zipper predictions collected over ten years. This collection is used to build a machine learning model capable of rapidly predicting steric zipper propensity, and allowing for the assessment of zippers at both the protein and proteome level. Our predictions show enrichment for zipper forming segments in proteins involved in cell wall reorganization in yeast, highlighting a potential category of interest for experimental characterization. Overall, our predictive model allows for the exploration of amyloid formation across the tree of life and provides a tool for assessment of both novel and designed sequences for zipper density.

Biochemistry & Molecular Biology↗

Toroidal phase of post-disruption runaway electron loss to wall in presence of applied 3-D fields in DIII-D

The toroidal distribution of runaway electrons (REs) striking the centre post in DIII-D post-disruption RE final loss events is simulated utilizing the MARS-F code combined with the REORBIT module, by tracing the guiding-centre drift orbits of test REs in the presence of external (applied) plus internal (intrinsic instability) 3-D fields. To better recover the experimental results, three different equilibria with different safety factor profiles are adopted. Dominant resistive magnetohydrodynamic instabilities are found to be m/n=2/1, 3/2 and 1/1 modes (where m and n are the poloidal and toroidal mode numbers). Externally applied n=1 resonant magnetic perturbations (RMPs), with both even and odd parity configuration, are considered in each equilibrium. Locking of MHD instability to the applied RMPs is simulated by minimizing the total perturbed magnetic energy in the plasma. Here, the simulated toroidal locations, where most REs strike in the presence of an edge m/n= 2/1 instability and the n=1 RMPs in even parity, are found to agree well with experiments. Modeling also captures the measured n = 2 RE loss pattern on the wall for experiments where an edge m/n=3/2 instability is dominant instead of the m/n=2/1 mode. The key overall findings include (a) the measured global RE toroidal impact pattern in experiments can be explained by a locked resistive kink instability, (b) the toroidal phase of the locked mode is well predicted by minimizing the total perturbed magnetic energy, and (c) this edge locked mode determines the toroidal phase of the peak RE wall impact.

Bai, Xue [University of California San Diego, La J↗

Opportunities and challenges to study solar neutrinos with a Q-Pix pixel readout

The study of solar neutrinos presents significant opportunities in astrophysics, nuclear physics, and particle physics. However, the low-energy nature of these neutrinos introduces considerable challenges to isolate them from background events, requiring detectors with low-energy threshold, high spatial and energy resolutions, and low data rate. We present the study of solar neutrinos with a kiloton-scale liquid argon detector located underground, instrumented with a pixel readout using the Q-Pix technology. We explore the potential of using volume fiducialization, directional topological information, light signal coincidence, and pulse-shape discrimination to enhance solar neutrino sensitivity. We find that discriminating neutrino signals below 5 MeV is very difficult. However, we show that these methods are useful for the detection of solar neutrinos when external backgrounds are sufficiently understood and when the detector is built using low-background techniques. When building a workable background model for this study, we identify 𝛾 background from the cavern walls and from capture of 𝛼 particles in radon decay chains as both critical to solar neutrino sensitivity and significantly underconstrained by existing measurements. Finally, we highlight that the main advantage of the use of Q-Pix for solar neutrino studies lies in its ability to enable the continuous readout of all low-energy events with minimal data rates and manageable storage for further off-line analyses.

multi-purpose particle detectors↗

Assessing the Heat Transfer Modeling Capabilities of CFD Software for Involute-Shaped Plate Research Reactors

The ongoing efforts to convert High-Performance Research Reactors (HPRRs) using Highly Enriched Uranium (HEU) to Low-Enriched Uranium (LEU) fuel require reliable thermal–hydraulic assessments of modified core designs. The involute-shaped fuel plates used in several major HPRRs present unique modeling challenges due to their compact core geometries and high heat flux conditions. This study evaluates the capability of three commercial CFD tools, STAR-CCM+, COMSOL, and ANSYS CFX, to predict cladding-to-coolant heat transfer using Reynolds-Averaged Navier–Stokes (RANS) methods within the thermal–hydraulic regimes of involute-shaped plate reactors. Broad sensitivity analysis was conducted across a range of reactor-relevant parameters using two turbulence models (k−ϵ and k−ω SST) and different near-wall treatment strategies. The results were benchmarked against the Sieder–Tate correlation and experimental data from historic studies. The codes produced consistent results, showing good agreement with the empirical correlation of Sieder–Tate and the experimental measurements. The findings support the use of these commercial CFD codes as effective tools for assessing the thermal–hydraulic performance of involute-shaped plate HPRRs and guide future LEU core development.

CFD↗

Cathodic Protection Modeling for Hanford Underground Double-Shell Tank Farms

Hanford stores millions of gallons of radioactive and chemically hazardous waste from the production of weapon materials in tank farms consisting of underground carbon-steel storage tanks surrounded by reinforced concrete. Six of these Hanford tank farms use double-shell storage tanks (DSTs). The DST farms were constructed from 1968 to 1986 with a planned 40–50 year design life, so some are already operating beyond their initial life expectancy. Ultrasonic testing (UT) has indicated significant thinning on the bottom of the secondary (outer) liner of these tanks, believed to arise from groundwater intrusion driving concrete side corrosion. There is no direct access to the steel/concrete interface between the tank and the concrete pad, making it difficult to apply a chemical-based mitigation strategy or to conduct repairs, but cathodic protection (CP) is a possible method to inhibit further concrete-side corrosion. Hanford already uses CP to protect below grade steel piping within the tank farms and connected to the tanks, but this system was not designed to protect the tank bottoms. CP design must account for the structures surrounding the DSTs, including the steel reinforcing bars (rebar) within the concrete pad and vault, various process lines, and the existing CP system. In this study, finite element analysis (FEA) modeling was carried out to simulate CP protection of 1) a single tank and CP anode to develop options for modeling the rebar and to compare to a simpler circuit model and 2) the entire Hanford AN tank farm as a representative example consisting of seven tanks, associated piping, and both existing and new CP anodes. Both circuit and FEA models predict that significant protective current could be delivered to the bottoms of the tanks with the addition of tank-protection anodes below the depth of the tanks. Simulations with only the existing pipe-protection anodes active confirmed that only a very small current to the tank bottoms is predicted under present conditions. Multiple simplified representations of the dome and wall rebar were tested to reduce the computational complexity of the tank-farm simulations, resulting in modeling the rebar as edge elements with a prescribed effective circumference that matches the real rebar surface area. The geometry of the rebar is also simplified into horizontal hoops around the tank walls and radial rebar over the dome with increased effective circumference to retain the target surface area. This simplification was found to greatly reduce the complexity and solution time of the models without large changes in current distributions, especially to the tank bottom. A range of values were tested for model parameters such as soil and concrete resistivities and polarization resistance to investigate their impact on the current and electric potential distributions. Depending on the parameters used, FEA simulations predict some risk of overprotection, particularly on the piping system; since overprotection can also lead to surface damage associated with hydrogen gas generation at the interface (e.g. hydrogen embrittlement or damage to coatings), this needs to be considered when refining the design of the new CP system. Comparison between the FEA models and the circuit model representation demonstrated that the circuit model could not match the predicted FEA current distribution, even when using the exact same surface areas. This discrepancy appeared to be at least partly attributable to the impact of the relative positions of the tank components and anodes to each other and to the ground surface. The FEA model accounts for the relative positions since it solves the governing equations in three dimensions, but the circuit model cannot account for the positioning. In particular, the circuit model underpredicts the current to the tank bottom and overpredicts the current to the dome compared to FEA for the baseline geometry. The FEA models omitted the electrically isolated rebar in the bottom concrete slab. However, a circuit based stray current model estimated that only 2.1% of the total current through the slab would stray into the rebar, corresponding to ~0.21 A for a target current density of 2 mA/ft2 to the tank bottom. The estimated corrosion driven by this amount of stray current is predicted to yield a lifetime of >400 years for the minimum rebar diameter, assuming an acceptable cross-section area loss of 10%.

d'Entremont, Anna [Savannah River National Laborat↗

Bim-to-fea Conversion Program

The purpose of this program is to enable interoperability between BIM-based architectural design software (i.e., Revit, ArchiCAD, AVEVA E3D) to structural analysis software (i.e., SAP2000). The program takes in BIM building model data via the IFC file format, automatically transforms the architectural coordination entities (structural beams, columns, slabs, walls) to structural analysis entities (i.e., finite element space frames and shells), automatically adjusts the connectivity of the structural analysis entities, and finally exports the structural analysis entities as a structural analysis model contained within a new IFC file. For example, a 3D building in Revit can be exported to an IFC file, run through this BIM-to-FEA program, then the exported IFC can be inputted into SAP2000.

Crowder, Nicholas [Idaho National Laboratory (INL)↗

End-Use Savings Shapes Upgrade Package Documentation: Wall and Roof Insulation and New Windows

Building on the successfully completed effort to calibrate and validate the U.S. Department of Energy's ResStock and ComStock models over the past 3 years, the objective of this work is to produce national data sets that empower analysts working for federal, state, utility, city, and manufacturer stakeholders to answer a broad range of analysis questions. The goal of this work is to develop energy efficiency, electrification, and demand flexibility end-use load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) upgrade measures, or upgrades. "Measures" refers to energy efficiency variables that can be applied to buildings during modeling. An end-use savings shape is the difference in energy consumption between a baseline building and a building with an energy efficiency, electrification, or demand flexibility upgrade applied. It results in a time-series profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step. ComStock is a highly granular, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual subhourly energy consumption of the commercial building stock across the United States. The baseline model intends to represent the U.S. commercial building stock as it existed in 2018. The methodology and results of the baseline model are discussed in the final technical report of the End-Use Load Profiles project. This documentation focuses on an upgrade package of three end-use savings shapes upgrades - Window Replacement, Exterior Wall Insulation, and Roof Insulation, which we will refer to collectively as the "High Efficiency Envelope" package. More details on the individual upgrades can be found on the ComStock Measures Documentation page. An upgrade package applies two or more EUSS upgrades to a single building model simulation. Since ComStock is a bottom-up physics-based model, an upgrade package will go beyond aggregating or summing the individual upgrade results and produce novel results by simulating interactions between the upgrades. For example, pairing an envelope upgrade with an electrification upgrade would likely result in higher savings results than the sum of these upgrades individually, and the size of the heating, ventilating, and air conditioning (HVAC) equipment may be reduced if the envelope upgrade reduces the loads significantly.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation

ABSTRACT Mycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis (TB), the leading cause of infectious disease-related deaths worldwide. TB infections present on a spectrum from active to latent disease. In the human host,Mtbfaces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions,Mtbcan enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. DormantMtbposes a major challenge to curing infections and eradicating TB globally. We subjectedMtbmc 2 6020 (ΔlysAand ΔpanCD), a double auxotrophic strain, to carbon starvation (CS), a culture condition that induces growth stasis and mimics environmental conditions associated with dormancyin vivo. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or more abundant in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically distinct state of stasis compared to hypoxia inMtb. IMPORTANCE Tuberculosis is a devastating human disease that kills over 1.2 million people a year. This disease is caused by the bacterial pathogenMycobacterium tuberculosis(Mtb).Mtbexcels at surviving in the human host by entering a non-replicating, dormant state. The current work investigated the proteomic changes thatMtbundergoes in response to carbon starvation, a culture condition that models dormancy. The authors found broad effects of carbon starvation on the proteome, with the relative abundance of 37% of proteins significantly altered. Protein changes related to cell wall biosynthesis, metabolism, and drug susceptibility are discussed. Proteins associated with a carbon starvation phenotype are identified, and results are compared to other dormancy models, including hypoxia.

Microbiology↗