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DOE OSTI2022

Path integral Monte Carlo approach to the structural properties and collective excitations of liquid $$^3{\text {He}}$$ without fixed nodes

Abstract Due to its nature as a strongly correlated quantum liquid, ultracold helium is characterized by the nontrivial interplay of different physical effects. Bosonic $$^4{\text {He}}$$ 4 He exhibits superfluidity and Bose-Einstein condensation. Its physical properties have been accurately determined on the basis of ab initio path integral Monte Carlo (PIMC) simulations. In contrast, the corresponding theoretical description of fermionic $$^3{\text {He}}$$ 3 He is severely hampered by the notorious fermion sign problem, and previous PIMC results have been derived by introducing the uncontrolled fixed-node approximation. In this work, we present extensive new PIMC simulations of normal liquid $$^3{\text {He}}$$ 3 He without any nodal constraints. This allows us to to unambiguously quantify the impact of Fermi statistics and to study the effects of temperature on different physical properties like the static structure factor $$S({\mathbf {q}})$$ S ( q ) , the momentum distribution $$n({\mathbf {q}})$$ n ( q ) , and the static density response function $$\chi ({\mathbf {q}})$$ χ ( q ) . In addition, the dynamic structure factor $$S({\mathbf {q}},\omega )$$ S ( q , ω ) is rigorously reconstructed from imaginary-time PIMC data. From simulations of $$^3{\text {He}}$$ 3 He , we derived the familiar phonon–maxon–roton dispersion function that is well-known for $$^4{\text {He}}$$ 4 He and has been reported previously for two-dimensional $$^3{\text {He}}$$ 3 He films (Nature 483:576–579 (2012)). The comparison of our new results for both $$S({\mathbf {q}})$$ S ( q ) and $$S({\mathbf {q}},\omega )$$ S ( q , ω ) with neutron scattering measurements reveals an excellent agreement between theory and experiment.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Dissipative ground state preparation in ab initio electronic structure theory

Dissipative engineering is a powerful tool for quantum state preparation, and has drawn significant attention in quantum algorithms and quantum many-body physics in recent years. In this work, we introduce a novel approach using the Lindblad dynamics to efficiently prepare the ground state for general ab initio electronic structure problems on quantum computers, without variational parameters. These problems often involve Hamiltonians that lack geometric locality or sparsity structures, which we address by proposing two generic types of jump operators for the Lindblad dynamics. Type-I jump operators break the particle number symmetry and should be simulated in the Fock space. Type-II jump operators preserves the particle number symmetry and can be simulated more efficiently in the full configuration interaction space. For both types of jump operators, we prove that in a simplified Hartree-Fock framework, the spectral gap of our Lindbladian is lower bounded by a universal constant. For physical observables such as energy and reduced density matrices, the convergence rate of our Lindblad dynamics with Type-I jump operators remains universal, while the convergence rate with Type-II jump operators only depends on coarse grained information such as the number of orbitals and the number of electrons. To validate our approach, we employ a Monte Carlo trajectory-based algorithm for simulating the Lindblad dynamics for full ab initio Hamiltonians, demonstrating its effectiveness on molecular systems amenable to exact wavefunction treatment.

Quantum chemistry↗

DOE OSTI2025

A spline-based method to obtain spatially dependent viscosity in confined flows

Coupling chemical physics to continuum theories is a critical step to understanding multi-scale phenomena. This paper will connect non-equilibrium molecular dynamics simulations to a continuum-based Navier-Stokes equation that has relaxed the assumption of spatial uniformity in viscosity. Using a form for viscosity based on spline interpolation, viscosity as a function of position is obtained from the least squares fit of the velocity profile measured from molecular simulations of flow in a nanochannel. Viscosity can vary widely, particularly near the channel boundaries, indicating that uniform viscosity is no longer appropriate. Variations of the viscosity near the channel surfaces imply that considering solution and surface chemistry could be necessary to rigorously understand molecular-scale flows in nanochannels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Modeling gas–shell mixing in ICF with separated reactants

Mixing between fuel and shell materials in ICF implosions can affect implosion dynamics and even prevent ignition. We use data from a series of separated reactant experiments on the National Ignition Facility to calibrate and test the predictive power of gas–shell mix models. Two models are used to estimate fuel–shell mix: a Reynolds-averaged turbulence model and molecular diffusion. Minor uncertainties in capsule manufacture, experimental conditions, and values for mix model parameters produce significant variation in simulation results. Using input/output pairs from 1D simulations, we train Gaussian process surrogate models to predict experimental quantities of interest. The surrogates are used to construct posteriors for mix model parameters by marginalizing over uncertainties in capsule manufacture and experimental conditions. Mix models are calibrated with a subset of experimental data (neutron yields, ion temperature, and bang time) and tested using the remaining data. In general, both the diffusion and turbulence model correctly predict experimental DT and TT neutron yields. Despite having more free parameters, the turbulence model underpredicts ion temperature at high convergence ratio. Furthermore, the simpler diffusion model correctly predicts these temperatures, suggesting nonhydrodynamic gas–shell mix. The computational model consistently overpredicts DD neutron yield, indicating possible shortcomings outside of the mix model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Gaussian approximation potential for amorphous Si : H

Hydrogenation of amorphous silicon (a–Si : H) is critical for reducing defect densities, passivating midgap states and surfaces, and improving photoconductivity in silicon-based electro-optical devices. Modeling the atomic-scale structure of this material is critical to understanding these processes, which in turn is needed to describe c–Si/a–Si : H heterojunctions that are at the heart of modern solar cells with world-record efficiency. Density functional theory (DFT) studies achieve the required high accuracy but are limited to moderate system sizes of 100 atoms or so by their high computational cost. Simulations of amorphous materials have been hindered by this high cost because large structural models are required to capture the medium-range order that is characteristic of such materials. Empirical potential models are much faster, but their accuracy is not sufficient to correctly describe the frustrated local structure. Data-driven, machine-learned interatomic potentials have broken this impasse and have been highly successful in describing a variety of amorphous materials in their elemental phase. Here, we extend the Gaussian approximation potential (GAP) for silicon by incorporating the interaction with hydrogen, thereby significantly improving the degree of realism with which amorphous silicon can be modeled. We show that our Si : H GAP enables the simulation of hydrogenated silicon with an accuracy very close to DFT but with computational expense and run times reduced by several orders of magnitude for large structures. Here, we demonstrate the capabilities of the Si : H GAP by creating models of hydrogenated liquid and amorphous silicon and showing that their energies, forces, and stresses are in excellent agreement with DFT results, and their structure as captured by bond and angle distributions are in agreement with both DFT and experiments.

36 MATERIALS SCIENCE↗

NASA NTRS1999

A Design Tool for Liquid Rocket Engine Injectors

A practical design tool for the analysis of flowfields near the injector face has been developed and used to analyze the Fastrac engine. The objective was to produce a computational design tool which was detailed enough to predict the interactive effects of injector element impingement angles and points and the momenta of the individual orifice flows. To obtain a model which could be used to simulate a significant number of individual orifices, a homogeneous computational fluid dynamics model was developed. To describe liquid and vapor sub- and super-critical flows, the model included thermal and caloric equations of state which were valid over a wide range of pressures and temperatures. A homogeneous model was constructed such that the local state of the flow was determined directly, i.e. the quality of the flow was calculated. Such a model does not identify drops or their distribution, but it does allow the flow along the injector face and into the acoustic cavity to be predicted. It also allows the film coolant flow to be accurately described. The initial evaluation of the injector code was made by simulating cold flow from an unlike injector element and from a like-on-like overlapping fan (LOL) injector element. The predicted mass flux distributions of these injector elements compared well to cold flow test results. These are the same cold flow tests which serve as the data base for the JANNAF performance prediction codes. The flux distributions 1 inch downstream of the injector face are very similar; the differences were somewhat larger at further distances from the faceplate. Since the cold flow testing did not achieve good mass balances when integrations across the entire fan were made, the CFD simulation appears to be reasonable alternative to future cold flow testing. To simulate the Fastrac, an RP-1/LOX combustion model must be chosen. This submodel must be relatively simple to accomplish three-dimensional, multiphase flow simulations. Single RP-1 pyrolysis and partial oxidation steps were chosen and the combustion was completed with the wet CO mechanism. Soot was also formed with a single global reaction. To validate the combustion submodel, global data from gas generator tests and from subscale motor test were used to predict qualitatively correct mean molecular weights, temperature, and soot levels. Because such tests do not provide general kinetics rates, the methodology is not necessarily appropriate for other than rocket type flows conditions. Soot predictions were made so that radiation heating to the motor walls can be made. These initial studies of the Fastrac were for a small region close to the injector face and chamber wall which included a segment of the acoustic cavity. The region analyzed includes 11 individual orifice holes to represent the LOL elements and the H2 film coolant holes. Typical results of this simulation are shown in Figure 1. At this point the only available test data to verify the predictions are temperatures measured in the acoustic cavity. These temperatures are in reasonable agreement at about 2000R (1111 K). Future work is expected to include improving the computational efficiency or the CFD model and/or using more computer capacity than the single Pentium PC with which these simulations were made.

Farmer, Richard C.↗

DOE OSTI2025

Electric Field’s Dueling Effects through Dehydration and Ion Separation in Driving NaCl Nucleation at Charged Nanoconfined Interfaces

Investigating nucleation in charged nanoconfined environments under electric fields is crucial for many scientific and engineering applications. Here we study the nucleation of NaCl from aqueous solution near charged surfaces using machine-learning-augmented enhanced sampling molecular dynamics simulations. Our simulations successfully drive phase transitions between the liquid and solid phases of NaCl. The solid phase is stabilized under electric fields, particularly at an intermediate surface charge density. We examine which physical characteristics drive the nucleation of NaCl from aqueous solutions and find that the removal of solvent water from Cl– at the solid precursor surface plays a more critical role than the accumulation of ions. Our simulations reveal the competing effects of electric fields on nucleation processes: they facilitate the removal of water, promoting nucleation, but also promote the separation of ion pairs, thereby hindering nucleation. Here, this work provides a framework for studying nucleation processes in nanoconfined environments under electric fields and provides physical insights for the design of electrochemistry materials.

Electric fields↗

DOE OSTI2026

The CP-PAW Code Package for First-Principles Calculations from a User’s Perspective

CP-PAW is a combined electronic structure and ab initio molecular dynamics code to perform mixed quantum and classical simulations of atomistic condensed phase systems, such as solids, liquids, and molecular systems. As the name suggests, the CP-PAW code unifies the all-electron projector augmented-wave (PAW) method with the Car–Parrinello (CP) approach to determine not only the electronic and nuclear ground states of condensed matter but also to study their properties and dynamics. In addition to briefly outlining the underlying theory, the focus will be on the unique aspects of CP-PAW and how to correctly employ them as a user. How to install CP-PAW using the new build system will also be briefly mentioned.

Blöchl, Peter E [Institute for Theoretical Physic↗

NASA NTRS1997

The rate of the reaction between CN and C2H2 at interstellar temperatures

The rate coefficient for the important interstellar reaction between CN and C2H2 has been calculated as a function of temperature between 10 and 300 K. The potential surface for this reaction has been determined through ab initio quantum chemical techniques; the potential exhibits no barrier in the entrance channel but does show a small exit channel barrier, which lies below the energy of reactants. Phase-space calculations for the reaction dynamics, which take the exit channel barrier into account, show the same unusual temperature dependence as determined by experiment, in which the rate coefficient at first increases as the temperature is reduced below room temperature and then starts to decrease as the temperature drops below 50-100 K. The agreement between theory and experiment provides strong confirmation that the reaction occurs appreciably at cool interstellar temperatures.

NASA Discipline Exobiology↗

DOE OSTI2022

Accurate Fe–He machine learning potential for studying He effects in BCC-Fe

Nanostructured Ferritic Alloys (NFAs) containing oxide nanoparticles are prospective advanced structural materials in future fusion reactors. Lacking fusion neutron sources with an adequate flux, modeling is critical to understand radiation damage in the NFAs, including helium effects. Machine learning interatomic potentials (MLPs) have been demonstrated to be capable of describing atomic interactions in chemically complex systems with comparable accuracy to density functional theory (DFT) but with much less computational costs. Hence, MLPs are chosen to study He bubble accumulation in chemically complex NFAs. As a preliminary step, we develop a Fe–He potential, based on ~10,000 atomic configurations. The developed MLP accurately predicts the bulk properties of BCC-Fe compared to DFT, including the lattice constant (2.832 Å), elastic constants (c 11 = 271 GPa, c 12 = 141, c 44 = 93), and phonon frequencies (maximum error < 3.5%). The MLP predicts He binding energies in He n V bubbles and He n clusters with a mean absolute error (MAE) of only ~70 meV, which is ~3 to ~5 times smaller than the MAE of binding energies estimated using empirical potentials. The MLP also accurately predicts the migration barrier of interstitial He (64 meV). Furthermore, the MLP correctly predicts the maximum number of He atoms (critical size) at which a He n V bubble (He n cluster) can kick-out a self-interstitial atom (SIA), forming a bigger He n V 2 bubble (He n V bubble). Subsequently, we use the MLP to perform molecular dynamics simulations to investigate the effect of temperature on the critical size of He n V bubbles and He n clusters. We find that the critical size decreases with increasing temperature — indicating that smaller bubbles and clusters can kick-out an SIA at higher temperatures, thereby escalating the He bubble growth. We report the current Fe–He MLP can be further developed to include all chemical interactions in NFAs.

36 MATERIALS SCIENCE↗

NASA NTRS2021

Recent Advancements in Modeling and Simulation of Entry Systems at NASA

This paper describes recent development of modeling and simulation technologies for entry systems in support of NASA’s exploration missions. Mission-tailored research and development in modeling of entry systems occurs across the Agency (e.g., within the Orion and Mars 2020 Programs), however the aim of this paper is to discuss the broad, cross-mission research conducted by NASA’s Entry Systems Modeling (ESM) Project, which serves as the Agency’s only concerted effort toward advancing entry systems across a range of technical disciplines. Technology development in ESM is organized and prioritized from a system-level perspective, resulting in four broad technical areas of investment: (1) Predictive material modeling, (2) Shock layer kinetics and radiation, (3) Computational and experimental aerosciences, and (4) Guidance, navigation, and control. Investments in thermal protection material modeling are geared toward high-fidelity, predictive models capable of handling complex structures, with an eye toward optimizing design performance and quantifying thermal protection system reliability. New computational tools have been developed to characterize material properties and behavior at the microstructural level, and experimental techniques (molecular beam scattering, micro-computed tomography, among others) have been developed to measure material kinetics, morphology, and other parameters needed to inform and validate detailed simulations. Advancements have also been made in macrostructural simulation capability to enable 3-D system-scale calculations of material response with complex topological features, including differential recession of tile gaps. Research and development in the area of shock layer kinetics has focused on air and CO2-based atmospheres. Capacity and capability of the NASA Ames Electric Arc Shock Tube (EAST) have been expanded in recent years and analysis of resulting data has led to several improvements in kinetic models, while simultaneously reducing uncertainties associated with radiative heat transfer predictions. First-principles calculations of fundamental kinetic, thermodynamic, and transport data, along with state-specificmodels for non-equilibrium flow regimes, have also yielded new insights and have the potential to vastly improve model fidelity. Aerosciences is a very broad area of interest in entry systems, yet a number of important challenges are being addressed: Coupled fluid-structure simulations of parachute inflation and dynamics; Experimental and computational studies of vehicle dynamics; Multi-phase flow with dust particles to simulate entry environments at Mars during dust storms; Studies of roughness-induced heating augmentation relevant to tiled and woven thermal protection systems; and Advanced numerical methods to optimize computational analyses for desired accuracy versus cost. Guidance and control in the context of entry systems has focused on development of methods for multi-axis control (i.e. pitch and yaw, rather than bank angle alone) of spacecraft during entry and descent. With precision landing requirements driven by Mars human exploration goals, recent efforts have yielded 6-DOF models of multi-axis control with propulsive descent of both inflatable and rigid ellipsled-like architectures. Results for both configurations have demonstrated the ability to land within the 50-meter precision requirement demanded by Mars human exploration missions, while also reducing propellant requirements by enabling more efficient control through entry and descent. Ongoing research in GN&C is developing mechanical specifications for the systems and establishing engineering feasibility.

aerothermodynamics↗

DOE OSTI2021

Computational studies reveal Fluorine based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly

World is witnessing one of the worst pandemics of this century caused by SARS-CoV-2 virus which has affected millions of individuals. Despite rapid efforts to develop vaccines and drugs for COVID-19, the disease is still not under control. Chloroquine (CQ) and Hydroxychloroquine (HCQ) are two very promising inhibitors which have shown positive effect in combating the disease in preliminary experimental studies, but their use was reduced due to severe side-effects. Here, we performed a theoretical investigation of the same by studying the binding of the molecules with SARS-COV-2 Spike protein, the complex formed by Spike and ACE2 human receptor and a human serine protease TMPRSS2 which aids in cleavage of the Spike protein to initiate the viral activation in the body. Both the molecules had shown very good docking energies in the range of -6kcal/mol. Subsequently, we did a high throughput screening for other potential quinoline candidates which could be used as inhibitors. From the large pool of ligand candidates, we shortlisted the top three ligands (binding energy -8kcal/mol). We tested the stability of the docked complexes by running Molecular Dynamics (MD) simulations where we observed the stability of the quinoline analogues with the Spike-ACE2 and TMPRSS2 nevertheless the quinolines were not stable with the Spike protein alone. Thus, although the inhibitors bond very well with the protein molecules their intrinsic binding affinity depends on the protein dynamics. Moreover, the quinolines were stable when bound to electronegative pockets of Spike-ACE2 or TMPRSS2 but not with Viral Spike protein. We also observed that a Fluoride based compound: 3-[3-(Trifluoromethyl)phenyl]quinoline helps the inhibitor to bind with both Spike-ACE2 and TMPRSS2 with equal probability. The molecular details presented in this study would be very useful for developing quinoline based drugs for COVID-19 treatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2019

Recent Advancements in Modeling and Simulation of Entry Systems at NASA

This paper describes recent development of modeling and simulation technologies for entry systems in support of NASA's exploration missions. Mission-tailored research and development in modeling of entry systems occurs across the Agency (e.g., within the Orion and Mars 2020 Programs), however the aim of this paper is to discuss the broad, cross-mission research conducted by NASA's Entry Systems Modeling (ESM) Project, which serves as the Agency's only concerted effort toward advancing entry systems across a range of technical disciplines. Technology development in ESM is organized and prioritized from a system-level perspective, resulting in four broad technical areas of investment: (1) Predictive material modeling, (2) Shock layer kinetics and radiation, (3) Computational and experimental aerosciences, and (4) Guidance, navigation, and control. Investments in thermal protection material modeling are geared toward high-fidelity, predictive models capable of handling complex structures, with an eye toward optimizing design performance and quantifying thermal protection system reliability. New computational tools have been developed to characterize material properties and behavior at the microstructural level, and experimental techniques (molecular beam scattering, micro-computed tomography, among others) have been developed to measure material kinetics, morphology, and other parameters needed to inform and validate detailed simulations. Advancements have also been made in macrostructural simulation capability to enable 3-D system-scale calculations of material response with complex topological features, including differential recession of tile gaps. Research and development in the area of shock layer kinetics has focused on air and CO2-based atmospheres. Capacity and capability of the NASA Ames Electric Arc Shock Tube (EAST) have been expanded in recent years and analysis of resulting data has led to several improvements in kinetic models, while simultaneously reducing uncertainties associated with radiative heat transfer predictions. First-principles calculations of fundamental kinetic, thermodynamic, and transport data, along with state-specific models for non-equilibrium flow regimes, have also yielded new insights and have the potential to vastly improve model fidelity. Aerosciences is a very broad area of interest in entry systems, yet a number of important challenges are being addressed: Coupled fluid-structure simulations of parachute inflation and dynamics; Experimental and computational studies of vehicle dynamics; Multi-phase flow with dust particles to simulate entry environments at Mars during dust storms; Studies of roughness-induced heating augmentation relevant to tiled and woven thermal protection systems; and Advanced numerical methods to optimize computational analyses for desired accuracy versus cost. Guidance and control in the context of entry systems has focused on development of methods for multi-axis control (i.e. pitch and yaw, rather than bank angle alone) of spacecraft during entry and descent. With precision landing requirements driven by Mars human exploration goals, recent efforts have yielded 6-DOF models of multi-axis control with propulsive descent of both inflatable and rigid ellipsled-like architectures.

Barnhardt, Michael D.↗

DOE OSTI2026

Direct Ab Initio Simulation of the Synthesis of BaZrO 3 and the Microstructure Impacts on Proton Transport

Controlling and predicting the processing-structure-performance relationship in functional materials is a grand challenge in materials science, with important implications for a wide range of emerging applications; a high fidelity understanding of the performance impact of microstructures formed under synthesis conditions is required to develop advanced materials, such as solid-state fuel cells and electrolyzers. Using the ceramic BaZrO 3 as a case study, we directly simulate the synthesis and investigate how proton transport is dictated by microstructures. We develop a framework that couples density functional theory (DFT), machine-learning interatomic potential (MLIP) driven molecular dynamics, and grand canonical Monte Carlo to perform large-scale, microstructure-resolved, atomistic simulations of proton transport in experimentally representative polycrystalline structures. Our fully ab initio approach, using a MLIP as a proxy for DFT, allows us to quantify the competition between two distinct diffusion mechanisms: one associated with grain-boundary regions and another within grains. When the impacts of grain boundaries are taken into account, proton transport exhibits substantial deviation from the bulk oxide limit. This addresses long-standing discrepancies between theory and experiments. Our integrated approach provides atomistic insight into microstructure-dependent proton pathways in BaZrO 3 and establishes a general protocol for predicting processing-structure-performance relationships.

organic↗

DOE OSTI2023

Quantum Computation of Dynamical Quantum Phase Transitions and Entanglement Tomography in a Lattice Gauge Theory

Strongly coupled gauge theories far from equilibrium may exhibit unique features that could illuminate the physics of the early universe and of hadron and ion colliders. Studying real-time phenomena has proven challenging with classical-simulation methods but is a natural application of quantum simulation. To demonstrate this prospect, we quantum compute nonequal-time correlation functions and perform entanglement tomography of nonequilibrium states of a simple lattice gauge theory, the Schwinger model, using a trapped-ion quantum computer by IonQ Inc. As an ideal target for near-term devices, a recently predicted dynamical quantum phase transition in this model is studied by preparing, quenching, and tracking the subsequent nonequilibrium dynamics in three ways: (i) overlap echos signaling dynamical transitions, (ii) nonequal-time correlation functions with an underlying topological nature, and (iii) the entanglement structure of nonequilibrium states, including entanglement Hamiltonians. These results constitute the first observation of a dynamical quantum phase transition in a lattice gauge theory on a quantum computer and are a first step toward investigating topological phenomena in nuclear and high-energy physics using quantum technologies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1997

Roto-Translational Collision-Induced Absorption of CO2 for the Atmosphere of Venus at Frequencies from 0 to 250 cm(exp -1), at Temperatures from 200 to 800 K

The collision-induced absorption (CIA)of gaseous CO2 is the primary source of far-infrared opacity of the atmosphere of Venus. At the temperatures and densities of the venusian atmosphere, the absorption is due mainly to binary collisions of CO2 molecules. Using a realistic anisotropic intermolecular potential and assuming the absorbing dipole to be due to the electrostatic induction and a quantum overlap, a series of molecular dynamics simulations were performed for the temperature range 200 to 800 K, and the roto-translational (RT) collision-induced absorption spectra at frequencies from 0 to 250 cm(exp -1) were derived. The absorption coefficient in the submillimeter region, used in constituency retrieval studies, decreases more than 10 times in the temperature range 200 to 800 K. On the other hand, the absorption coefficient at 800 K and at the frequency range above 150 cm(exp -1) was found to be almost 10 times higher than at 200 K. Earlier works relied on experimental RT CIA data at a fixed temperature of 300 K. The new, temperature-dependent absorption bands may, when included in the analysis of the atmospheric radiative transfer of the planet, help explain the observed high far-infrared opacity of the lower layers of the atmosphere. To make the results of the simulations readily available for atmospheric abundance and radiative transfer analysis, an analytic model of the roto-translational collision-induced absorption spectral profile, applicable from 200 to 800 K, is being proposed here. The FORTRAN computer code of this newly developed model is available from the authors on request.

Gruszka, Marcin↗

DOE OSTI2026

Image Distinguishability Analysis Testing Through Principal Components and Its Application to Hot Spot Scale Invariance

Hot spots are spatial regions of intense energy localization that govern initiation of secondary high explosives. Studies that characterize or compare simulated hot spots are frequently either qualitatively descriptive or resort to quantitative distribution functions that neglect stochastic variations and spatial correlations—effects that are also neglected in common comparison tests like the Kolmogorov–Smirnov test. To this end, we develop an image distinguishability analysis (IDA) test based on principal component (PC) analysis that makes pixel-by-pixel comparisons between small, for example, O(<10), image data sets. The IDA test makes comparisons through a generalized distance metric in the PC space and a test statistic that is derived to calculate mathematical equation-values. Here, we derive a statistical distribution and criticality criterion to determine whether images are distinguishable from established baselines. We apply the IDA test on images generated from molecular dynamics simulations of hot spots from pore collapse in TATB to assess scale invariance in the complex patterns of hot spots that form in a representative high explosive crystal. The IDA test shows that TATB hot spot spatial temperature fields and their derived temperature histograms exhibit scale-invariant features over specific intervals of shock orientation, strength, and initial pore diameter. However, the IDA test also shows that qualitatively different conclusions regarding invariance can be reached depending on whether the hot spot is treated as a spatially correlated field as opposed to a distribution function that lacks spatial information.

organic↗

DOE OSTI2026

Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control

In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux between anabolic and catabolic pathways. Although redox-sensitive cysteines in OpcA are known to regulate G6PDH, the mechanisms by which redox post-translational modifications (PTMs) on OpcA control G6PDH structure and activity remain unclear. Here, we combine computational modeling with experimental redox proteomics in Synechococcus elongatus PCC 7942 to dissect this mechanism. Experimentally, redox proteome analysis revealed differential redox PTM patterns, particularly on cysteines within the G6PDH-binding site of OpcA. These environmentally sensitive PTM changes at the interface suggest that thiol modifications in this region form a key regulatory node. More broadly, redox proteomics identified site-specific cysteine modifications under light/dark transitions and circadian cycling, linking distinct redox regimes to discrete PTM states. We employed PTM-Psi simulations to show that thiol PTMs near the OpcA–G6PDH interface are critical for allosteric regulation of G6PDH. The thiol PTMs on OpcA affect a putative gate region in G6PDH for substrate ingress and product egress as well as key hydrogen-bond networks within the active site. We infer that PTMs on OpcA tune the conformational landscapes of individual G6PDH subunits toward functionally relevant configurations according to environmental gradients, biasing the enzyme toward catalytically favorable states. Together, our results reveal a molecular mechanism in which thiol PTMs on OpcA modulate G6PDH structure and function through PTM-induced reorganization of conformational dynamics and allosteric communication. These findings demonstrate that PTM-level regulation provides a critical control layer from genotypes to phenotypes that enables cyanobacteria to rapidly adapt to environmental fluctuations through precise metabolic fine-tuning.

Allosteric regulation↗