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DOE OSTI2022

Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria

To reach their final destinations, outer membrane proteins (OMPs) of gram-negative bacteria undertake an eventful journey beginning in the cytosol. Multiple molecular machines, chaperones, proteases, and other enzymes facilitate the translocation and assembly of OMPs. These helpers usually associate, often transiently, forming large protein assemblies. They are not well understood due to experimental challenges in capturing and characterizing protein-protein interactions (PPIs), especially transient ones. Using AF2Complex, we introduce a high-throughput, deep learning pipeline to identify PPIs within the Escherichia coli cell envelope and apply it to several proteins from an OMP biogenesis pathway. Among the top confident hits obtained from screening ~1500 envelope proteins, we find not only expected interactions but also unexpected ones with profound implications. Subsequently, we predict atomic structures for these protein complexes. These structures, typically of high confidence, explain experimental observations and lead to mechanistic hypotheses for how a chaperone assists a nascent, precursor OMP emerging from a translocon, how another chaperone prevents it from aggregating and docks to a β-barrel assembly port, and how a protease performs quality control. This work presents a general strategy for investigating biological pathways by using structural insights gained from deep learning-based predictions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Look Up: Probing the Vertical Profile of New Particle Formation and Growth in the Planetary Boundary Layer With Models and Observations

Abstract The processes of new particle formation (NPF) and growth are important contributors to cloud condensation nuclei (CCN) concentrations, and CCN are important for climate from their impact on planetary radiative forcing. While the general ubiquity and importance of NPF is understood, the vertical extent and governing mechanisms of NPF and growth in the lower troposphere are uncertain. We present an analysis of four NPF events and two non‐NPF events during the HI‐SCALE field campaign at the Southern Great Plains observatory in Oklahoma, USA. First, we analyzed airborne and ground‐based observations of aerosol and gas‐phase properties. Second, we used a column aerosol chemistry and microphysics model to probe factors that influence the vertical profile of NPF. During HI‐SCALE, we found several instances of enhanced NPF occurring several hundred meters above the surface; however, the spatio‐temporal characteristics of the observed NPF made comparisons between airborne‐ and ground‐based observations difficult. The model represented the observed NPF (or lack of NPF) and particle growth at the surface to final diameters within 10 nm. The model predicted enhanced NPF rates in the upper mixed layer, and this enhancement is primarily due to the temperature dependence in the NPF schemes, but this was also dependent on the vertical profile of gas‐phase precursors measured during HI‐SCALE. We found vertical mixing in the model either enhanced or suppressed NPF rates, aerosol number concentrations, and particle growth rates at the surface. Finally, our analysis provides insights for future field campaigns and modeling efforts investigating the vertical profile of NPF.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Estimated timescales for wet deposition of organic compounds as a function of Henry's law constants

Atmospheric organic compounds may deposit to Earth's surfaces via dry deposition, driven by concentration gradients, and wet deposition, driven by the scavenging of compounds by precipitation. Their removal by deposition has downstream impacts on concentrations of secondary organic aerosol by removing potential aerosol precursors that would otherwise oxidize to form particulate matter. The impact of deposition processes can consequently be considered as competition between rates of oxidation and deposition, but timescales for deposition are not well constrained. While timescales for dry deposition have been estimated and experimentally validated in the past, understanding of wet deposition of organics is still very limited. In this work, we estimate the wet deposition timescale for gas-phase organic compounds in the atmosphere as a function of Henry's law constants, H, using real-world precipitation frequency and size distributions at five globally-distributed sites. The wet deposition timescale decreases significantly with the increase of H until reaching a stable minimum for compounds with H > 10 5 M per atm. We estimate that the median wet deposition timescale for highly soluble gases is approximately 5 hours during a continuous rain event for all sites. However, median estimated timescales ranged from 80 to 200 hours, depending on location. Timescales are found to depend primarily on the frequency and duration of precipitation events rather than their intensity or size characteristics. Based on these data, we demonstrate that timescales for wet deposition of gases can be estimated at any given location using only basic precipitation information, without detailed or high-precision measurements.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Direct numerical simulation of a high-pressure hydrogen micromix combustor: Flame structure and stabilisation mechanism

A high-pressure hydrogen micromix combustor has been investigated using direct numerical simulation with detailed chemistry to examine the flame structure and stabilisation mechanism. The configuration of the combustor was based on the design by Schefer et al., using numerical periodicity to mimic a large square array. A precursor simulation of an opposed jet-in-crossflow was first conducted to generate appropriate partially-premixed inflow boundary conditions for the subsequent reacting simulation. The resulting flame can be described as an predominantly-lean inhomogeneously-premixed lifted jet flame. Five main zones were identified: a jet mixing region, a core flame, a peripheral flame, a recirculation zone, and combustion products. The core flame, situated over the jet mixing region, was found to burn as a thin reaction front, responsible for over 85% of the total fuel consumption. The peripheral flame shrouded the core flame, had low mean flow with high turbulence, and burned at very lean conditions (in the distributed burning regime). It was shown that turbulent premixed flame propagation was an order-of-magnitude too slow to stabilise the flame at these conditions. Stabilisation was identified to be due to ignition events resulting from turbulent mixing of fuel from the jet into mean recirculation of very lean hot products. Ignition events were found to correlate with shear-driven Kelvin-Helmholtz vortices, and increased in likelihood with streamwise distance. At the flame base, isolated events were observed, which developed into rapidly burning flame kernels that were blown downstream. Further downstream, near-simultaneous spatially-distributed ignition events were observed, which appeared more like ignition sheets. The paper concludes with a broader discussion that considers generalising from the conditions considered here.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Pressure-stabilized divalent ozonide CaO 3 and its impact on Earth's oxygen cycles

High pressure can drastically alter chemical bonding and produce exotic compounds that defy conventional wisdom. Especially significant are compounds pertaining to oxygen cycles inside Earth, which hold key to understanding major geological events that impact the environment essential to life on Earth. Here we report the discovery of pressure-stabilized divalent ozonide CaO3 crystal that exhibits intriguing bonding and oxidation states with profound geological implications. Our computational study identifies a crystalline phase of CaO 3 by reaction of CaO and O 2 at high pressure and high temperature conditions; ensuing experiments synthesize this rare compound under compression in a diamond anvil cell with laser heating. High-pressure x-ray diffraction data show that CaO 3 crystal forms at 35 GPa and persists down to 20 GPa on decompression. Analysis of charge states reveals a formal oxidation state of -2 for ozone anions in CaO 3 . These findings unravel the ozonide chemistry at high pressure and offer insights for elucidating prominent seismic anomalies and oxygen cycles in Earth’s interior. We further predict multiple reactions producing CaO 3 by geologically abundant mineral precursors at various depths in Earth’s mantle.

58 GEOSCIENCES↗

DOE OSTI2026

Photoenzymatic Csp 3 –Csp 3 bond formation via enzyme-templated radical–radical coupling

Cross-couplings are essential reactions in modern chemical synthesis, enabling the rapid construction of complex molecules from simple precursors. Transition metal catalysts are prized for these transformations because their reactivity and selectivity can be tuned via judicious selection of the metal and ligand. Although enzymes offer analogous opportunities for tuning via protein engineering, their application to cross-coupling remains limited, as nature relies on alternative paradigms for building molecular complexity. Here, we report the cross-coupling of alkyl halides and benzylic carboxylic acids using an engineered flavin-dependent lactate monooxygenase—a photoenzyme. The enzyme achieves this feat by exploiting the redox versatility of the flavin cofactor. Stoichiometric experiments, ultrafast spectroscopy, and computational studies support a mechanism in which photoexcited flavin quinone initiates the reaction via oxidative decarboxylation to generate a benzylic radical. The resulting flavin semiquinone can reduce the alkyl halide to form a second organic radical within the protein active site, which rapidly engages in C(sp 3 )–C(sp 3 ) bond formation. A variant was engineered to control the stereochemical outcome of this radical–radical coupling event, highlighting the ability of the protein to alter the energetic barrier for a mechanistic step that is traditionally understood to be near barrierless. This work demonstrates that the scope for nonnative reaction mechanisms in biocatalysis far exceeds previously established bounds and has potential to solve a variety of reactivity challenges in cross-coupling chemistry.

biocatalysis↗

DOE OSTI2022

Influence of Thermal Treatment on Preceramic Polymer Grafted Nanoparticle Network Formation: Implications for Thermal Protection Systems and Aerospace Propulsion Components

Preceramic polymer grafted nanoparticles (PCP GNPs) offer potential advantages in the production of polymer-derived ceramic composites compared to neat preceramic polymers (PCPs), such as reduced thermal shrinkage and increased char yield. In comparison to traditional composites (particles + free polymer), PCPs avoid issues of compatibility, agglomeration, and phase separation during processing and provide routes to control nanoparticle arrangement. Prior literature has established that the conversion efficiency of PCPs and PCP GNPs to ceramics and ceramic composites is linked to the thermal pretreatment of these precursor polymers (e.g., curing). In this paper, we investigate the material transformations that occur when exposing PCP GNPs to a low-temperature thermal treatment (≤250 °C) prior to pyrolysis. The PCP GNPs explored in this study possessed silica nanoparticle cores but were distinct in their PCP coronas, having poly(1,1-dimethylpropylsilane) (allyl-GNP)- or poly(1,1-dimethylbenzylethylsilane) (styryl-GNP)-grafted polymers. After undergoing low-temperature thermal treatment, these PCP GNPs exhibited increased char yield at 800 °C; however, unlike commercial PCPs (e.g., allylhydridopolycarbosilane (SMP-10)), obvious cross-linkable sites are not present in the PCP corona structure. Differential scanning calorimetry, oscillatory rheology, and X-ray photon correlation spectroscopy were utilized to elucidate the thermally induced material changes in the allyl- and styryl-GNPs. Thermally induced changes to the structure and behavior of the PCP GNPs were determined to be linked to the chemical structure of the grafted polycarbosilane chains. Styryl-GNPs experienced a curing event between 180 and 250 °C, effecting the formation of a network, which contributed to char yield improvement (at 800 °C). The nanoscale dynamics of this material also shows a transition from diffuse behavior to ballistic behavior because of the cross-linking event. Conversely, the allyl-GNPs did not exhibit a curing event under heat treatment but did show an increase in thermally induced physical cross-linking. The allyl-GNP physical network is stronger after the first cycle of thermal treatment, and it is considered that this contributed to the improvement in char yield post thermal treatment. The advancements in the understanding of the cross-linking behavior of these hybrid materials are expected to advance the application of these materials to turbine engine, advanced friction, and heat-shielding components.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Sulfuric Acid New Particle Formation Field Campaign Report

This campaign aimed to measure gaseous sulfuric acid concentrations at the surface level using a newly developed sulfuric acid dimethylamine-reactive condensation particle counter (SAD-RCPC). Sulfuric acid is a key nucleation precursor and is the likely driving compound for new particle formation at the Atmospheric Radiation Measurement (ARM) user facility’s Southern Great Plains (SGP) observatory. The SAD-RCPC will be deployed in the future at ARM SGP (AFC010010: "Vertically Resolved Nucleation Precursors at SGP") scheduled for 2024. The campaign was in conjunction with Eleanor Browne's campaign (AFC010075: Boundary-layer gradients in new particle formation) and took place from 05/7/23 to 5/21/23. The measured sulfuric acid concentrations by the SAD-RCPC will be compared to concentrations measured by Browne's chemical ionization mass spectrometer (CIMS). The SAD-RCPC consisted of a glass flow reactor coupled to a 1-nm diethylene glycol condensation particle counter (DEG CPC). Sampled air was mixed with a high concentration of dimethylamine vapor (~1 ppbv). Sulfuric acid within the sampled gas nucleated with dimethylamine to form detectable 1-nm particles. The measured particle concentration was converted to sulfuric acid concentration using nucleation reaction kinetics. The pulse height distribution of particles detected by the DEG CPC was observed using a multi-channel analyzer. Large pre-existing particles were separated from the freshly formed particles in the SAD-RCPC from the pulse height distribution (PHD). During the short campaign, seven new particle formation events were observed. The SAD-RCPC detected an increase in sulfuric acid concentration, but this also coincided with an increase in pre-existing <3 nm particle concentrations. In addition, Browne's CIMS detect sulfuric acid concentrations in the range of 10 5 -10 6 cm -3 .

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Catalytic Upgrading of Renewable Feedstock (Final Technical Report)

The goal of this DOE-funded project was to investigate the fundamental science related to the development of homogeneous (de)hydrogenation catalysts in order to enable energy-relevant transformations of bio-relevant chemical feedstocks including ethanol. The primary focus was to improve the activity of ethanol upgrading catalysts, specifically informed through mechanistic studies, in order to enable rational design optimization strategies. Following in depth mechanistic studies, targeted reaction optimization approaches included ligand redesign to improve catalyst stability, developing new carbon-carbon bond forming reactions using ethanol as a precursor, and examining photochemically-mediated reactions, ultimately to integrate within other reactor designs such as continuous flow reactors. The high modularity of the catalyst components (ligands) has enabled the preparation and analyses of multiple catalyst precursors. These studies uncovered an unexpectedly beneficial substitution pattern of the ligand structure that led to the development of new catalysts that are the best in class for upgrading ethanol to butanol with a turnover number of 155,890 and a turnover frequency of 12,690 h –1 . In addition to upgrading ethanol to butanol, cascade reaction sequences were developed to form new C-C bonds using ethanol as a bio-relevant feedstock, providing access to platform chemicals from renewable sources. As part of the reaction discovery process, new mechanistic details were uncovered that provided insights into: a) catalyst speciation, b) decomposition pathways, c) carbon monoxide releasing pathways, and d) carbon-carbon and carbon hydrogen bond breaking pathways. Most of these outcomes were previously not known; however, they provide important directions for new catalyst design strategies. Finally, use of high throughput and in situ photochemical reaction analyses enabled detailed studies into changes to the catalyst structure upon irradiation. Irradiation was found to improve hydrogen transfer catalysis, by promoting a ligand dissociation event.

09 BIOMASS FUELS↗

DOE OSTI2022

VisMetHack2022: Visualizing winds and surface variables from the ECMWF IFS 1-km nature run

This data collection was contributed to the Visualisation Hackathon 2022 (#VisMetHack2022), in conjunction with the Using ECMWF's Forecasts (UEF2022) workshop. The European Center for Medium-Range Weather Forecasts (ECMWF) and the Oak Ridge National Laboratory (ORNL) are pleased to announce access to the data collection from global 1-km nature run (NR) simulations using the Integrated Forecast System (IFS) with explicit convection. We invite you to join us in exploring this precursor to a digital twin of the earth! The NR simulations reveal unprecedented detail of the earth’s atmosphere, and the then outgoing Editor-in-Chief of AGU JAMES commended the project as one of “stunning ambitions,” enabled by computational capacity at scale. The project also won the 2020 HPCwire Readers Choice Award for Best Use of HPC in Physical Sciences. A set of two NR seasonal simulations have been completed, one corresponding to the northern hemispheric winter months (NDJF) and the other for the North Atlantic tropical cyclone season (ASO). The project used the Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). The simulations were facilitated with an INCITE award from the US Department of Energy Office of Science. For the first seasonal run of four months (NDJF), the hydrostatic IFS model was initialized at 00Z on 1 November 2018. The NR for the TC season (AS) was initialized at 00Z on 1 August 2019. The NR simulations were constrained only by sea surface temperatures (SST) at the lower boundary. The IFS output was saved every 3 hours. After feedback and interest from the scientific community, the simulations were rerun for four specific extreme events, with output every 15 minutes. The special cases include a tropical cycle and three severe storm events over the continental USA.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

NRC Multiphysics Analysis Capability Deployment FY21: Part 3

This report details the progress and activities of Idaho National Laboratory (INL) on the Nuclear Regulatory Commission (NRC) project “Development and Modeling Support for Advanced Non-Light Water Reactors.” The deliverables completed for this report are: Deliverable 1c: the capability to model gas mixtures was added to Pronghorn. A test problem mimicking the conditions achieved in a depressurized loss of forced cooling (DLOFC) event was solved with both RELAP-5 and Pronghorn. Pronghorn employed a finite vol ume method with the Kurganov-Tadmor discretization. The comparison between the mass fraction spatial profiles computed with RELAP-5 and Pronghorn clearly shows the presence of numerical artifacts (i.e., overly diffusive behavior at low Mach numbers). We confirmed that the problem disappears at higher Mach numbers. We recommend future work on the implementation of a low Mach finite volume formulation to better treat low Mach number problems. Deliverable 2a: we demonstrated two approaches to model the radiation/conduction/natural convection heat transfer across a stagnant gas for the PBMR-400 design using Pronghorn. The first approach is based on the net radiation method, which relies on the computation of view factors with the Multiphysics Object-Oriented Simulation Environment (MOOSE) ray tracing capability. The second method is a traditional thermal resistance approach. The test problems include both 2D and 3D geometries. In all cases, the results show very good agreement during a DLOFC transient. This confirms that the faster thermal resistance method produces solutions that are equivalent to the net radiation method for this geometry. Deliverable 3d: we demonstrated the use of the advection kernel for the delayed neutron precursor equation in Griffin with a 2D MSFR model. The results appear physical but further verification is recommended. We also recommend the addition of conjugate heat transfer to compute the temperatures and model the thermomechanic behavior of the reflectors and other structures. Significant memory and performance issues were encountered in the 3D axisymmetric model. Future work is recommended in this area. Task 8g: this task allows multidimensional MOOSE applications to be coupled to system codes (RELAP-7 and SAM). We implemented a faster multiphysics iteration coupling algorithm, which provides an overall 6× acceleration of the 3D-1D coupling of the core multidi- mensional fluid flow solver and the 1D primary and secondary loop model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae

Microbial metabolism is a fundamental cellular process that involves many biochemical events and is distinguished by its emergent properties. While the molecular details of individual reactions have been increasingly elucidated, it is not well understood how these reactions are quantitatively orchestrated to produce collective cellular behaviors. Here we developed a coarse-grained, systems, and dynamic mathematical framework, which integrates metabolic reactions with signal transduction and gene regulation to dissect the emergent metabolic traits of Saccharomyces cerevisiae. Our framework mechanistically captures a set of characteristic cellular behaviors, including the Crabtree effect, diauxic shift, diauxic lag time, and differential growth under nutrient-altered environments. It also allows modular expansion for zooming in on specific pathways for detailed metabolic profiles. Furthermore, this study provides a systems mathematical framework for yeast metabolic behaviors, providing insights into yeast physiology and metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Metal–bicarbonate ion pairing in alkaline aqueous solutions from multilevel embedded correlated wavefunction theory and molecular dynamics

In this work, we examine ion-pairing mechanisms of bicarbonates in alkaline aqueous solutions with the divalent metal ions most abundantly present in seawater, namely, Ca 2+ and Mg 2+ . We employ a rare-event enhanced sampling approach within first-principles molecular dynamics to explore regions of phase space spanning solvent-shared to contact ion pairs. Second-order Møller–Plesset perturbation theory (MP2) corrections are subsequently applied in an embedding framework (EMB) to refine the electronic structure of stationary states and associated reaction barriers along the free-energy profiles while retaining the extended solvent effects at the density functional theory (DFT) level. Ca 2+ –HCO 3 − was previously hypothesized to exist in a solvent-shared ion pair (SSHIP) by DFT studies with an endergonic contact ion pair (CIP) formation; however, our EMB-MP2 refinement of the DFT ion-pairing pathways reveals that Ca 2+ and HCO 3 − form a virtually barrier-free CIP in alkaline solutions, with even more energetic ease than the widely studied Ca–CO 3 ion pair. We find qualitative agreement between DFT and EMB-MP2 for Mg 2+ —unlike Ca 2+ , Mg 2+ refuses to shed its strong hydration shell, thereby preferring a SSHIP state with a significant activation barrier to crossover to the CIP forms—a trait reminiscent of ion pairing in Mg–CO 3 and closely related to the kinetic limitations underlying the famous subject of the dolomite problem. Our study highlights the importance of improved electronic structure descriptions of liquids, modeled as a condensed phase of matter lacking in long-range crystalline order. It also strongly suggests that Ca 2+ –HCO 3 − CIPs are likely precursors involved in prenucleation of CaCO 3 mineral formation in seawater.

Sharma, Vidushi [Princeton Plasma Physics Laborato↗