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At least 1,153 records · Page 64

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DOE OSTI2020

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism’s fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon β-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in β-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of β-lactamase’s fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Predicting short-range order evolution in WTaCrVHf refractory high-entropy alloys

Short-range order (SRO) in multicomponent concentrated alloys affects their mechanical response. Hence, is paramount to understand how composition modifies the chemical ordering in the system to design materials with optimal properties. Here, in this work, we present a methodology to predict the SRO and thermodynamic properties in chemically complex systems and apply it to the WTaCrVHf quinary alloy. We observe that the addition of Hf significantly modifies the SRO, mainly at intermediate to low temperatures, matching experimental observations.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Experimental signatures of electron cyclotron wave energy condensation in magnetic islands

Here, bifurcation of the electron temperature perturbation (ΔT e ) in magnetic islands due to electron cyclotron current drive (ECCD) is reported for the first time in toroidal plasmas. In this DIIID experiment ΔT e spontaneously increases by 50% in a growing 2,1 island which in turn rapidly shrinks, consistent with improved stabilization by the ECCD due to the temperature bifurcation. This non-linearity of ΔT e maps out a hysteresis in the island evolution cycle, in qualitative agreement with the theoretically predicted radio frequency current condensation effect. Therefore, this observed bifurcation can be critical for the avoidance of disruptions caused by tearing modes in tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Hardness Prediction by Incorporating Heat Transfer and Molten Pool Fluid Flow in a Multi-pass, Multi-layer Weld for Onsite Repair of Grade 91 steel

Introduction: In the current fleet of fossil-fired power plants, creep strength enhanced ferritic steels (CSEF) are used to sustain the harsh service conditions. Enhanced properties of Grade 91 steel result from tempered martensite with a fine distribution of MX and M23C6 carbides. Grade 91 steel is subjected to onsite welding repair to remedy their degradation due to extreme service condition. Knowledge of weld repairability of these steels, such as as-welded hardness distribution, is essential to establishing sound repair procedures. Experimental trial and error tests can consume a lot of time as many welding variables need to be studied. For numerical modelling, most of the multi-pass multi-layer models are based on finite element method, which are limited to solve the heat conduction equation and ignore convective heat transfer due to melt flow. Moreover, the mesh has to be pre-built based on a known or assumed weld cross-section geometry. These finite element based models thus have limited predictive capability as defects are not considered and nugget size are pre-assumed. This research aims at developing a thermal and microstructure evolution model incorporating molten pool dynamics in a multi-pass multi-layer material deposition to predict the as-welded hardness distribution. Technical Approach: All the thermal, physical, and metallurgical properties of Grade 91 as a function of temperature are collected from the literature and inputted into the thermo-fluid model based on Flow-3D, a computational fluid dynamics software. A multi-pass, multi-layer material deposition is simulated where the melting of filler wire into the molten pool is directly considered based on the volume of fluid (VOF) method. The flow behaviour of the molten pool is used to understand the formation of deposition geometry and defects. The temperature profiles during the multi-pass, multi-layer welding are calculated. The results computed using the new model are compared against the experimental data of fusion zone geometry and thermal cycles. Hardness prediction in the heat-affected zone (HAZ) are made using Johnson-Mehl-Avrami (JMA) equation for solid-state phase transformation kinetics. The JMA parameters are extracted from the experimental data available in the literature. For comparison, a standard finite element heat conduction model is also developed to predict the thermal cycles and hardness distribution in the multi-pass, multi-layer weld. Expected Result: Results obtained using the molten pool dynamic simulation versus the finite element heat conduction model are compared. Specifically, the effects of convective heat transfer on the accuracy of the calculated thermal history, bead shape and size, and HAZ hardness distribution are examined.

Modeling, Grade 91 steel, Multi-pass multi-layer d↗

DOE OSTI2022

Continuum Model to Define the Chemistry and Mass Transfer in a Bicarbonate Electrolyzer

Bicarbonate electrolyzers are devices designed to convert CO 2 captured from point sources or the atmosphere into chemicals and fuels without needing to first isolate pure CO 2 gas. In this work, we report here an experimentally validated model that quantifies the reaction chemistry and mass transfer processes within the catalyst layer and cation exchange membrane layer of a bicarbonate electrolyzer. Our results demonstrate that two distinct chemical microenvironments are key to forming CO at high rates: an acidic membrane layer that promotes in situ CO 2 formation and a basic catalyst layer that suppresses the hydrogen evolution reaction. We show that the rate of CO product formation can be increased by modulating the catalyst and membrane layer properties to increase the rate of in situ CO 2 generation and transport to the cathode. These insights serve to inform the design of bicarbonate and BPM-based CO 2 electrolyzers while demonstrating the value of modeling for resolving rate-determining processes in electrochemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Chemical evolution in nitrogen shocked beyond the molecular stability limit

Evolution of nitrogen under shock compression up to 100 GPa is revisited via molecular dynamics simulations using a machine-learned interatomic potential. The model is shown to be capable of recovering the structure, dynamics, speciation, and kinetics in hot compressed liquid nitrogen predicted by first-principles molecular dynamics, as well as the measured principal shock Hugoniot and double shock experimental data, albeit without shock cooling. Our results indicate that a purely molecular dissociation description of nitrogen chemistry under shock compression provides an incomplete picture and that short oligomers form in non-negligible quantities. Finally, this suggests that classical models representing the shock dissociation of nitrogen as a transition to an atomic fluid need to be revised to include reversible polymerization effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Improved single-particle phase-space distributions for viscous fluid dynamic models of relativistic heavy ion collisions

Comparison of hydrodynamic calculations with experimental data inevitably requires a model for converting the fluid to particles. For shear viscous fluids, several different conversion models have been proposed, such as the quadratic Grad corrections, the Strickland-Romatschke (SR) ansatz, self-consistent shear corrections from linearized kinetic theory, or corrections from the relaxation time approach. We show, via comparison to nonlinear 2 → 2 kinetic theory evolution, that even for low specific shear viscosities 0.03 ≲ $\textit{η/s}$ ≲ 0.2 , these four models have varying accuracy and still significant errors in reproducing particle phase space densities from hydrodynamic fields. Moreover, we demonstrate that the overall reconstruction error of additive shear viscous $f = f_{eq} + δf$ models dramatically reduces by up to one order of magnitude, if one ensures through exponentiation that $\textit{f}$ is always positive. Further, we also illustrate how even more accurate viscous $\textit{δf}$ models can be constructed by incorporating the first time derivatives of hydrodynamic fields to account for the past evolution of the system. Such time derivatives are readily available in hydrodynamic simulations, though usually not included in the output. Though our comparisons are limited to a one-component massless system undergoing a (0 + 1)-dimensional (0 + 1D) longitudinal boost-invariant expansion, we expect that the improved models will be useful in 2 + 1D and 3 + 1D hydrodynamic studies as well.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Mass of 101 Sn and Bayesian extrapolations to the proton drip line

The favorable energy configurations of nuclei at magic numbers of 𝑁 neutrons and 𝑍 protons are fundamental for understanding the evolution of nuclear structure. The 𝑍 = 50 (tin) isotopic chain is a frontier for such studies, with particular interest at and around the doubly magic 100 Sn isotope, for which the mass is a topic of debate. Precise mass values for neutron-deficient isotopes provide necessary anchor points for mass models to test extrapolations near the proton drip line, where experimental studies remain out of reach. In this work, we report a Penning trap mass measurement of 101 Sn . The determined mass excess of −59889.89⁢(96) keV for 101 Sn represents a factor-of-300 improvement over the current precision and indicates that 101 Sn is less bound than previously thought. Mass predictions from a recently developed Bayesian model combination framework employing statistical machine learning and nuclear masses computed within seven global models based on nuclear density functional theory agree within 1⁢𝜎 with experimental masses from the 48 ≤ 𝑍 ≤ 52 isotopic chains. The framework's resilience to new mass data gave confidence in the extrapolation of tin masses down to 𝑁 = 46. Our calculations suggest that 96 Sn is a two-proton drip line nucleus and predict a mass excess of −58090⁢(800) keV for 100 Sn , showing a preference within 1⁢𝜎 for the mass of 100 Sn derived from the 𝛽-delayed 𝑄 value measured at GSI.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Dynamics and Structure of Molten Neodymium Titanate

Binary rare earth titanates can be vitrified using levitation melt quenching, and their glasses are promising for optical applications. To better understand their thermophysical properties and dynamics, we have used molecular dynamics (MD) and empirical potential structure refinement (EPSR) to simulate molten neodymium titanate, 83TiO 2 –17Nd 2 O 3 . The models are compared with high-energy synchrotron X-ray diffraction of the melt structure over 1060–1960 K and thermophysical property measurements of electrostatically levitated droplets over 1500–2200 K. As temperature increases, the network periodicity increases and the correlation length decreases, both in monotonic trends that suggest continuous structural evolution through the melt and supercooled liquid regimes. At 1900 K, the mean Ti–O and Nd–O coordination numbers are 5.8(5) and 6.7(5), compared to the glass, 5.72(6) and 7.70(26). The equilibrium melting point is measured as 1860(20) K, over 100 K higher than previous estimates. Viscosity data from MD are in good agreement with experimental measurements. The dynamic propensity of Nd is similar to that of the network-forming Ti, suggesting that Nd does not participate as a conventional modifier. The viscosity of this fragile liquid is likely controlled by the breaking of cation–oxygen bonds and rearrangements of Ti–O polyhedra.

molecular dynamics↗

DOE OSTI2020

Evaporation Sub-model Development for Volume of Fluid (eVOF) Method Applicable to Spray-Wall Interaction Including Film Characteristics with Validation at High Pressure and Temperature Conditions (Final Report)

Internal combustion engines have seen a great evolution over the last several decades through application of high pressure direct injection, multiple injections, and other technologies to reduced fuel consumption, NOx, and PM. Although combustion systems with advanced injection strategies have been studied extensively, there exists a significant fundamental knowledge gap on the fuel-spray interactions with the piston surface and chamber walls. Advanced computational codes validated with experimental techniques have to be developed for accurate representation of the drop impingement, fuel film formation, and vaporization. Current engine CFD spray models utilize a Lagrangian framework for modeling which lacks critical considerations of the physics pertaining to these interactions and thus requiring extensive parameterization, tuning and validation. The team from Michigan Technological University, University of Massachusetts Dartmouth, and Argonne National Laboratory is composed of experts in sprays, combustion, engines and CFD with a wide spectrum of knowledge including specific expertise in the area under consideration. In the proposed work, a VOF modeling approach has been adopted for the spray-wall interaction, film formation and spreading, and vaporization. With the inclusion of a vaporization submodel, a more predictive and accurate simulation of the spray-film was performed without extensive need of parameterization and tuning. Extensive experimentation of the spray-wall interaction under the range of conditions matching the thermodynamic and surface temperatures that occur in diesel and gasoline engines were conducted to validate the SWI submodels and for development of the evaporation sub-model, which has been implemented in the Converge software.

42 ENGINEERING↗

DOE OSTI2020

Evaporation Submodel Development for Volume of Fluid (eVOF) Method Applicable to Spray-Wall Interaction Including Film Characteristics with Validation at High Pressure and Temperature Conditions

Internal combustion engines have seen a great evolution over the last several decades through application of high pressure direct injection, multiple injections, and other technologies to reduced fuel consumption, NOx, and PM. Although combustion systems with advanced injection strategies have been studied extensively, there exists a significant fundamental knowledge gap on the fuel-spray interactions with the piston surface and chamber walls. Advanced computational codes validated with experimental techniques have to be developed for accurate representation of the drop impingement, fuel film formation, and vaporization. Current engine CFD (Computational Fluid Dynamics) spray models utilize a Lagrangian framework for modeling which lacks critical considerations of the physics pertaining to these interactions and thus requiring extensive parameterization, tuning and validation. The team from Michigan Technological University, University of Massachusetts Dartmouth, and Argonne National Laboratory is composed of experts in sprays, combustion, engines and CFD with a wide spectrum of knowledge including specific expertise in the area under consideration. In the proposed work, a VOF (Volume of Fluid) modeling approach has been adopted for the spray-wall interaction, film formation and spreading, and vaporization. With the inclusion of a vaporization submodel, a more predictive and accurate simulation of the spray-film was performed without extensive need of parameterization and tuning. Extensive experimentation of the spray-wall interaction under the range of conditions matching the thermodynamic and surface temperatures that occur in diesel and gasoline engines were conducted to validate the SWI submodels and for development of the evaporation submodel, which has been implemented in the flow solver.

42 ENGINEERING↗

DOE OSTI2024

Assessment of the Effect of Deleting the African Swine Fever Virus Gene R298L on Virus Replication and Virulence of the Georgia2010 Isolate

African swine fever (ASF) is a lethal disease of domestic pigs that is currently challenging swine production in large areas of Eurasia. The causative agent, ASF virus (ASFV), is a large, double-stranded and structurally complex virus. The ASFV genome encodes for more than 160 proteins; however, the functions of most of these proteins are still in the process of being characterized. The ASF gene R298L, which has previously been characterized as able to encode a functional serine protein kinase, is expressed late in the virus infection cycle and may be part of the virus particle. There is no description of the importance of the R298L gene in basic virus functions such as replication or virulence in the natural host. Based on its evolution, it is proposed that there are four different phenotypes of R298L of ASFV in nature, which may have potential implications for R298L functionality. We report here that a recombinant virus lacking the R298L gene in the Georgia 2010 isolate, ASFV-G-∆R298L, does not exhibit significant changes in its replication in primary cultures of swine macrophages. In addition, when experimentally inoculated in pigs, ASFV-G-∆R298L induced a fatal form of the disease similar to that caused by the parental virulent ASFV-G. Therefore, deletion of R298L does not significantly affect virus replication and virulence in domestic pigs of the ASFV Georgia 2010 isolate.

Virology↗

DOE OSTI2026

Time-resolved X-ray imaging of the current filamentation instability in solid-density plasmas

The streaming of energetic charged particles can magnetize astrophysical and laboratory plasmas via the current filamentation instability. Despite its importance, the experimental characterization of this instability has remained a challenge. Here, we report an experiment combining a high-intensity optical laser with a high-brightness X-ray free electron laser that successfully images the instability in solid-density plasmas with 200nm spatial and 50fs temporal resolution. We characterize the development of µm-scale filamentary structures and their evolution over tens of picoseconds through a non-linear merging process. The measured plasma density modulations and long merging time reveal the critical importance of space-charge effects and ion motion on this electron-driven instability. Supporting theoretical analysis and kinetic simulations help distinguish the relative role of space-charge and resistive effects. Our findings indicate that magnetic fields on the order of 10megagauss are produced, with important implications for transport and radiation emission of energetic particles in plasmas.

Schoenwaelder, Christopher↗

DOE OSTI2020

Light meson parton distribution functions from basis light-front quantization and QCD evolution

Here, we investigate the parton distribution functions (PDFs) of the pion and kaon from the eigenstates of a light-front effective Hamiltonian in the constituent quark-antiquark representation suitable for low-momentum scale applications. By taking these scales as the only free parameters, the valence quark distribution functions of the pion, after QCD evolving, are consistent with the E615 experiment at Fermilab. In addition, the ratio of the up quark distribution in the kaon to that in the pion also agrees with the NA3 experimental result at CERN.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Establishing the accuracy of position–specific carbon isotope analysis of propane by GC–pyrolysis–GC–IRMS

Rationale: Position-specific (PS) δ 13 C values of propane have proven their ability to provide valuable information on the evolution history of natural gases. Two major approaches to measure PS δ 13 C values of propane are isotopic 13 C nuclear magnetic resonance (NMR) and gas chromatography-pyrolysis-gas chromatography-isotope ratio mass spectrometry (GC-Py-GC-IRMS). Measurement accuracy of the isotopic 13 C NMR has been verified, but the requirements of large sample size and long experimental time limit its applications. GC-Py-GC-IRMS is a more versatile method with a small sample size, but its accuracy has not been demonstrated. Methods: We measured the PS δ 13 C values of propane from nine natural gases using both 13 C NMR and GC-Py-GC-IRMS, then evaluated the accuracy of the GC-Py-GC-IRMS method. Results: The results show that large carbon isotope fractionations occurred for both terminal and central carbons within propane during pyrolysis. The isotope fractionations during the pyrolysis are reproducible at optimum conditions, but vary between the two GC-Py-GC-IRMS systems tested, affected by experimental conditions (e.g., pyrolysis temperature, flow rate, and reactor conditions). Conclusions: It is necessary to evaluate and calibrate each GC-Py-GC-IRMS system using propane gases with accurately determined PS δ 13 C values. Finally, this study also highlights a need for PS isotope standards for propane and other molecules (e.g., butane and acetic acid).

03 NATURAL GAS↗

DOE OSTI2023

Athermal annealing of pre-existing defects in crystalline silicon

Systematic investigations of electronic energy loss (S e ) effects on pre-existing defects in crystalline silicon (Si) are crucial to provide reliance on the use of ionizing irradiation to anneal pre-existing defects, leading to successful implementation of this technology in the fabrication of Si-based devices. In this regard, the S e effects on nonequilibrium defect evolution in pre-damaged Si single crystals at 300 K has been investigated using intermediate-energy ions (12 MeV O and Si ions) that interact with the pre-damaged surface layers of Si mainly by ionization, except at the end of their range where the nuclear energy loss (S n ) is no longer negligible. Furthermore, under these irradiation conditions, experimental results and molecular dynamics simulations have revealed that pre-existing disorder in Si can be almost fully annealed by subsequent irradiation with intermediate-energy incident ions with S e values as low as 1.5–3.0 keV/nm. Selective annealing of pre-existing defect levels in Si at room temperature can be considered as an effective strategy to mediate the transient enhanced diffusion of dopants in Si. This approach is more desirable than the regular thermal annealing, which is not compatible with the processing requirements that fall below the typical thermal budget.

36 MATERIALS SCIENCE↗

DOE OSTI2022

A reaction–diffusion model for grayscale digital light processing 3D printing

We report that digital light processing (DLP) 3D printing is an additive manufacturing process that utilizes light patterns to photopolymerize a liquid resin into a solid. Due to the accuracy of modern digital micromirror devices (DMD) and recent advances in resin chemistry, it is now possible to create functionally graded structures using different light intensity values, also known as grayscale DLP (g-DLP). Different intensities of light lead to differences in the polymer crosslinking density after curing, which ultimately produces a part with gradients of material properties. However, g-DLP is a complicated process. First, the DLP printing is a highly coupled chemical and physical process that involves light propagation, chemical reactions, species diffusion, heat transfer, volume shrinkage, and changes in mechanical behaviors of the curing resin. Second, in g-DLP, light gradients create strong in plane gradients of chemical species concentrations in the curing liquid resin due to the strong dependence of light intensity on the rate of monomer crosslinking. Furthermore, light gradients through the depth create concentration gradients due to the degree of cure dependent light absorption and the use of photoabsorbers. These complex physical features of the printing process must be understood in order to properly control printing parameters such as light exposure time, printing speed, and grayscale variations to achieve accurate mechanical properties. In this paper, a photopolymerization reaction–diffusion model is developed and used in conjunction with experiments to investigate the coupled effects of light propagation, chemical reaction rates, and species diffusion during g-DLP 3D printing. The model is implemented numerically utilizing the finite difference method and simulation results are compared to experimental findings of simple printed structures. The agreement between experimental and model predictions of simple quantities of interest, such as geometric feature sizes, shows that the model can capture the overcure due to free-radical and other species diffusion during printing when grayscale patterns are employed. This model lays the groundwork for future extensions that can incorporate more complex coupled physics such as heat transfer, volume shrinkage, and material property evolution, which are critically important in utilizing g-DLP 3D printing for the fabrication of high-performance parts which excellent geometric and material property tolerances.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Transverse oscillating bubble enhanced laser-driven betatron X-ray radiation generation

Abstract Ultrafast high-brightness X-ray pulses have proven invaluable for a broad range of research. Such pulses are typically generated via synchrotron emission from relativistic electron bunches using large-scale facilities. Recently, significantly more compact X-ray sources based on laser-wakefield accelerated (LWFA) electron beams have been demonstrated. In particular, laser-driven sources, where the radiation is generated by transverse oscillations of electrons within the plasma accelerator structure (so-called betatron oscillations) can generate highly-brilliant ultrashort X-ray pulses using a comparably simple setup. Here, we experimentally demonstrate a method to markedly enhance the parameters of LWFA-driven betatron X-ray emission in a proof-of-principle experiment. We show a significant increase in the number of generated photons by specifically manipulating the amplitude of the betatron oscillations by using our novel Transverse Oscillating Bubble Enhanced Betatron Radiation scheme. We realize this through an orchestrated evolution of the temporal laser pulse shape and the accelerating plasma structure. This leads to controlled off-axis injection of electrons that perform large-amplitude collective transverse betatron oscillations, resulting in increased radiation emission. Our concept holds the promise for a method to optimize the X-ray parameters for specific applications, such as time-resolved investigations with spatial and temporal atomic resolution or advanced high-resolution imaging modalities, and the generation of X-ray beams with even higher peak and average brightness.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗