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At least 505 records · Page 28

The anaerobic fungus Caecomyces churrovis produces H 2 via a non-bifurcating NADH-dependent enzyme complex

ABSTRACT Hydrogenosomes are mitochondria-derived organelles that produce ATP and H 2 to support energy metabolism in anaerobic eukaryotes. H 2 production allows reoxidation of reduced cofactors generated during fermentative metabolism; however, the metabolic mechanisms for H 2 production in anaerobic eukaryotes remains incompletely understood. In particular, it remains unclear whether anaerobic fungi (AF) hydrogenosomes use a ferredoxin-dependent pathway or a distinct mechanism to regenerate NAD(P) + and link electron transfer to H 2 formation. Here, by combining genomic search, proteomic analysis, and enzymology, we reveal the molecular mechanism for H 2 production in the AF strain Caecomyces churrovis . Our enzyme assays on the organelle fraction of C. churrovis revealed the activity of H 2 :NAD + oxidoreductase but not pyruvate:ferredoxin oxidoreductase, which is usually linked to H 2 formation. We identified genes encoding [FeFe] hydrogenase (Hyd) and NADH dehydrogenase subunits E and F (NuoE, NuoF) in C. churrovis , and confirmed their expression in the isolated hydrogenosomal fractions by proteomic analysis. Combining the individually purified enzymes, we found Hyd and NuoEF proteins formed H 2 directly from NADH independently of ferredoxin, functioning as a non-bifurcating NADH-dependent enzyme rather than an electron-bifurcating enzyme. We identified homologs of hydrogenosomal NuoE, NuoF, and Hyd in many other AF, indicating this pathway is commonly shared among the AF. This work demonstrates the existence of a non-bifurcating NADH-dependent enzyme complex in eukaryotes. Moreover, this complex could potentially be exploited as a target for controlling AF H 2 production and altering fungal metabolism. IMPORTANCE H 2 production is a prominent feature of anaerobic energy metabolism, yet our understanding of eukaryotic mechanisms remains limited. Anaerobic fungi (AF) are key decomposers of lignocellulose and contribute to hydrogen flux in anaerobic environments. Although it has been more than 40 years since the H 2 production from AF was first reported, the molecular mechanism for hydrogenosomal H 2 production and redox balance remains unclear. We demonstrate that AF produce H 2 from NADH utilizing a non-bifurcating NADH-dependent enzyme complex rather than an electron-bifurcating, ferredoxin-dependent variant. We show that this enzyme complex is conserved across multiple AF lineages and thus demonstrate the occurrence of a non-bifurcating NADH-dependent enzyme in eukaryotes. This discovery expands our understanding of eukaryotic hydrogenosomal metabolism, reveals a previously unknown strategy for redox balancing, and highlights potential targets for manipulating H 2 production. These insights have broad implications for microbial energy metabolism, anaerobic ecosystems, and bioengineering of H 2 -producing systems.

Zhang, Bo [Department of Chemical Engineering, Uni↗

Neutrino Flavor Classification in ICARUS Experiment Using Convolutional Visual Networks

In this work, I adapt the Convolutional Visual Network (CVN) approach to the ICARUS detector by incorporating TPC stitching methods inspired by NuGraph. The stitching technique used here is unique to ICARUS, designed specifically to handle its distinct detector segmentation s. I then retrain the network using ICARUS-specific data. This study underscores the flexibility of deep learning models in high-energy physics and the importance of accounting for detector-specific features when transferring machine learning techniques between experiments. This dissertation presents the methods, classification performance, and insights gained from applying CVN to ICARUS data.

Wieler, Felipe Andre [Parana Tech. Fed. U., Toledo↗

Radar Motion Measurements and Synthetic Aperture Radar Image Geolocation Accuracy

Once a Synthetic Aperture Radar (SAR) image is formed, the natural question then is, "Where is this image?" and/or "Where exactly is this feature displayed in the image?" Thus, geolocation is an important exploitation of the SAR image. Since SAR measures relative location to its own position, it is crucial to understand how the radars position and motion imp acts the ability to geolocate a feature in the SAR image. Furthermore, accuracy and precision of navigation aids like GPS directly impact the goodness of the geolocation solution. These relationships are developed and discussed.

58 GEOSCIENCES↗

HIGH-LOW FIDELITY THERMAL HYDRAULIC COUPLING USING AI/MACHINE LEARNING ALGORITHMS

The primary goal of the US Department of Energy (DOE) office of Nuclear Energy Integrated Energy Systems (IES) program is to develop the tools and framework for coupling multi-scale and multi-physical thermal and electrical energy usage and storage systems. High- and low-fidelity (high–low) coupling is a key feature of multi-scale, multi-component systems and has been an important focus of research in the nuclear energy community for the past two decades. An essential feature of demonstrating the capability to couple high-fidelity and low-fidelity systems for real-time applications are surrogate/reduced order models (ROM). For the purposes of this study, surrogate models are essentially Blackbox models, typically developed using supervised Machine learning (ML) algorithms. The surrogate models can be used to mimic the response of high-fidelity models to represent large historical datasets and coupled with more general low-fidelity system models distributed as Functional Mock-up Interface (FMI) or Functional Mock-up Units (FMU) modules. The example is demonstrated with Spallation Neutron Source (SNS) First Target Station flow loop data. The flow loop is a liquid mercury loop with a pump, piping, heat exchange, and internal heat generation in the target window. This work elucidates some of the potential benefits and future needs of developing tools for high–low system coupling of energy systems.

Williams, Wesley↗

Crossover from quantum to classical transport

Understanding the crossover from quantum to classical transport phenomena has become of fundamental importance not only for technological applications due to the creation of sub-10nm transistors – an important building block of our modern life – but also for elucidating the role played by quantum mechanics in the evolutionary fitness of biological complexes. This article provides a basic introduction into the nature of charge and energy transport in the quantum and classical regimes. Here, it will identify the characteristic transport properties in both limits, and demonstrate how they can be connected through the loss of quantum mechanical coherence. I will identify the salient features of the crossover physics, and demonstrate their importance in opening new transport regimes and for understanding efficient and robust energy transport in biological complexes.

charge↗

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model

The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g., sound frequency, reach angle) are reflected in population neural activity is important for understanding how the brain operates. Often, high-dimensional neural population activity is confined to low-dimensional latent spaces. However, many current methods fail to extract latent spaces that are clearly structured by exogenous variables. This has contributed to a debate about whether or not brains should be thought of as dynamical systems or representational systems. Here, we developed a new latent process Bayesian regression framework, the orthogonal stochastic linear mixing model (OSLMM) which introduces an orthogonality constraint amongst time-varying mixture coefficients, and provide Markov chain Monte Carlo inference procedures. We demonstrate superior performance of OSLMM on latent trajectory recovery in synthetic experiments and show superior computational efficiency and prediction performance on several real-world benchmark data sets. We primarily focus on demonstrating the utility of OSLMM in two neural data sets: μ ECoG recordings from rat auditory cortex during presentation of pure tones and multi-single unit recordings form monkey motor cortex during complex arm reaching. We show that OSLMM achieves superior or comparable predictive accuracy of neural data and decoding of external variables (e.g., reach velocity). Most importantly, in both experimental contexts, we demonstrate that OSLMM latent trajectories directly reflect features of the sounds and reaches, demonstrating that neural dynamics are structured by neural representations. Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale biological time-series datasets.

59 BASIC BIOLOGICAL SCIENCES↗

Generic FEPs Catalogue and Salt Knowledge Archive

This report describes the development of a comprehensive catalogue of generic features, events, and processes (FEPs) that are potentially important for the post-closure performance of a repository for high-level radioactive waste (HLW) and spent nuclear fuel (SNF) in salt (halite) host rock. The FEPs and other supporting information have been entered into a “SaltFEP” Database. The generic salt repository FEPs include consideration of relevant FEPs from a number of U.S., Dutch, German, and international FEP lists and should be a suitable starting point for any repository program in salt host rock. The salt FEP catalogue and database employ a FEP classification matrix approach that is based on the concept that a FEP is typically a process or event acting upon or within a feature. The FEP matrix provides a two-dimensional structure consisting of a Features/Components axis that defines the “rows” and a Processes/Events axis that defines the “columns” of the matrix. The design of the FEP classification matrix is consistent with repository performance assessment – the Features/Components axis is organized vertically to generally correspond to the direction of potential radionuclide migration (from the waste to the biosphere) and the Processes/Events axis is designed to represent the common two-way couplings between thermal processes and other processes (such as thermal-mechanical or thermal-hydrologic processes). Related FEPs can be easily identified – related FEPs will typically be grouped in a single matrix cell or aligned along a common row (Feature/Component) or column (Process/Event). The online SaltFEP database can be downloaded from www.saltfep.org. It contains the FEP matrix, the FEPs, and the associated processes for each FEP. It provides a starting point to create and document site-specific individual FEPs. Furthermore, the FEP matrix is connected to the Salt Knowledge Archive (SKA), a database of about 20,000 references and documents representing the historical knowledge on radioactive disposal in salt. This work is the result of an ongoing collaboration between researchers in the U.S., the Netherlands, and Germany, and supports the NEA Salt Club Mandate. It builds upon prior work which is documented.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Characterizing the Influence of Fracture Density on Network Scale Transport

The topology of natural fracture networks is inherently linked to the structure of the fluid velocity field and transport therein. Here we study the impact of network density on flow and transport behaviors. We stochastically generate fracture networks of varying density and simulate flow and transport with a discrete fracture network model, which fully resolves network topology at the fracture scale. We study conservative solute trajectories with Lagrangian particle tracking and find that as fracture density decreases, solute channelization to large local fractures increases, thereby reducing plume spreading. Furthermore, in sparse networks mean particle travel distance increases and local network features, such as velocity zones where flow is counter to the primary pressure gradient, become increasingly important for transport. As the network density increases, network statistics homogenize and such local features have a reduced impact. We quantify local topological influence on transport behavior with an effective tortuosity parameter, which measures the ratio of total advective distance to linear distance at the fracture scale; large tortuosity values are correlated to slow-velocity regions. Additionally, these large tortuosity, slow-velocity regions delay downstream transport and enhance tailing on particle breakthrough curves. Finally, we predict transport with an upscaled, Bernoulli spatial Markov random walk model and parameterize local topological influences with a novel tortuosity parameter. Furthermore, Bernoulli model predictions improve when sampling from a tortuosity distribution, as opposed to a fixed value as has previously been done, suggesting that local network topological features must be carefully considered in upscaled modeling efforts of fracture network systems.

58 GEOSCIENCES↗

Hot Springs and Geysers: Exploring Historical and Modern Impacts of Geothermal Energy Production on Associated Natural Surface Systems and Standardizing Management Practices

Surface thermal features, most notably hot springs and geysers are increasingly being recognized for their importance to ecosystems, indigenous cultures, and in some cases agriculture, recreation, and tourism. Geothermal project development poses a potential risk to these natural features but current regulatory requirements for assessing and managing these risks during exploration, permitting and monitoring are somewhat inconsistent and unpredictable across different geothermal fields. This has resulted in uncertainty and increases in exploration risk for geothermal energy developers that have led to costly project delays, cancellations, or hesitation to commit. Varying regulatory requirements may also influence public perception, fostering confusion, distrust and ultimately opposition to geothermal projects, further contributing to project delays or cancellations. At a time when there is an increasing urgency for reliable baseload clean energy, geothermal is a net-zero, renewable solution that additionally provides access to more equitable and environmentally just clean power. Continued integration of geothermal energy into the national energy roadmap can be facilitated through consistent and predictable permitting, providing regulators the framework they need, developers a clear path forward, and transparency that the public deserves. This project, currently in its beginning phases, seeks to address this important issue by providing a technical basis from which to build a preliminary protocol for assessing and managing potential impacts from new or existing geothermal energy projects to surface thermal features and their associated ecosystems. Development of this preliminary protocol will be informed by (1) a literature review of well-documented case studies in the western U.S. and New Zealand to understand the range of conditions that exemplify geothermal-surface thermal systems; (2) development of generic illustrative conceptual-numerical models to quantify, understand, and predict the first-order controls (e.g., pressure and permeability) on surface flows; and (3) additional independent and scientifically rigorous evaluations of geothermal-surface thermal system case studies from the Basin and Range Province that incorporate publicly available data as well as data provided by industry through data-sharing agreements. Learning from the successes of the process used to develop the Induced Seismicity Management Protocol (ISMP), we ultimately aim to use these initial efforts as a springboard for establishing a surface thermal feature management working group that will work collaboratively to finalize the protocol as well as co-create recommended best practices for implementation. We envision that the working group will primarily be composed of representatives from regulatory entities, government agencies, Tribes, academia, national laboratories, and industry, and will include early and regular engagement with community organizations and environmental groups. This will help ensure broad acceptance and implementation of the protocol, which will facilitate a more consistent, predictable, and standardized regulatory process, and help to ensure that geothermal energy continues to provide a reliable source of clean energy, and a pathway to achieving greater energy equity in the U.S.

Best Practices↗

WinnowML: Stable feature selection for maximizing prediction accuracy of time-based system modeling

Online deep learning (ODL) has become an important methodology for modeling time-based performance of computer systems. An open problem is the intelligent selection of features from raw workload traces of computer systems. The best methods are overly sensitive to noisy data, causing frequent feature changes and re-training. Using all available features inflates training time and introduces model artifacts if some features should have been dropped. We present WinnowML, a method for automatically determining the most relevant feature subset for a predictive time-series model. WinnowML combines existing feature ranking algorithms and a history of each feature's ranking to iteratively rank a feature set to lower prediction error and maximize long term relevance. From this ranked feature set, the most relevant and stable subset is selected to train a model. Experimentally, we show how WinnowML can lower a model's mean absolute relative error up to 42% on average compared to the closest performing approach. Additionally, we lower the fluctuation in feature ranking and selection up to 65%. We also demonstrate how to combine WinnowML and a model search tool to provide improvements in performance of up to 14.5% when compared to using all the feature available.

Bel, Oceane MS↗

Dynamic Features of Cu-Ceria Interface under CO 2 Hydrogenation to Methanol

It is generally accepted that metal–support interaction is very important for the hydrogenation of CO 2 to methanol, but little has been revealed about the feature of interfacial active sites under real reaction conditions since there are only limited techniques that can be applied under high-pressure conditions. Here, in this work, by combining multiple in situ and operando techniques on a model Cu/ceria catalyst, we have tracked Cu and ceria sites for methanol formation. Under the reaction condition, it is found that upon reaching the reaction temperature, oxidized Cu species in the as-synthesized catalyst immediately change into metallic Cu species. Following this, it is the gradual formation of methanol, the changing rate of which coincides with the formation of a unique Ce 3+ species. The combined experimental results and density functional theory (DFT) calculations have determined that the formed Ce 3+ sites driven by the reaction conditions are bound to hydrides, adsorbed carbonate species, and interfacial active Cu sites. The Cu-ceria interaction in this complex moiety is weak and can be easily disturbed with reaction environment variations, leading to dynamic changes at the interface upon the hydrogenation of active carbonate intermediates, which are precursors for the formation of methanol. The formation of this unique Cu–Ce 3+ interface and its dynamicity lead to an increase of methanol selectivity from less than 20% to 60%. These results suggest that reactant-derived species (H – and carbonate in this work) can be essential components of the active center with the functions of manipulating the metal−oxide interaction and directing reaction pathways.

CO2 hydrogenation to methanol↗

Trigger Detection for the sPHENIX Experiment via Bipartite Graph Networks with Set Transformer

Trigger (interesting events) detection is crucial to high-energy and nuclear physics experiments because it improves data acquisition efficiency. It also plays a vital role in facilitating the downstream offline data analysis process. The sPHENIX detector, located at the Relativistic Heavy Ion Collider in Brookhaven National Laboratory, is one of the largest nuclear physics experiments on a world scale and is optimized to detect physics processes involving charm and beauty quarks. Furthermore, these particles are produced in collisions involving two proton beams, two gold nuclei beams, or a combination of the two and give critical insights into the formation of the early universe. This paper presents a model architecture for trigger detection with geometric information from two fast silicon detectors. Transverse momentum is introduced as an intermediate feature from physics heuristics. We also prove its importance through our training experiments. Each event consists of tracks and can be viewed as a graph. A bipartite graph neural network is integrated with the attention mechanism to design a binary classification model. Compared with the state-of-the-art algorithm for trigger detection, our model is parsimonious and increases the accuracy and the AUC score by more than 15%.

97 MATHEMATICS AND COMPUTING↗

Pressure engineering of intertwined phase transitions in lanthanide monopnictide NdSb

Coexistence of non-trivial band topology and intrinsic magnetic order not only leads to emergent phenomena but also allows for the tunability of the exotic properties from different degrees of freedom. By performing transport measurements at synergetic extreme conditions, here we report on pressure engineering of intertwined structural, magnetic, and topological phase transitions in antiferromagnetic Dirac semimetal NdSb. We show that the original antiferromagnetic state is strengthened in the low pressure region while destabilized upon further compression close to the critical pressure when a structural transition from Fm-3m phase to P4/mmm phase takes place at P C ~ 18 GPa, forming a Ger-shaped evolution in response to magnetic field, pressure and temperature. Concomitant with the structural transition, NdSb simultaneously carries on a magnetic transition to the ferromagnetic state. Further, theoretical calculations unravel that the ferromagnetic tetragonal phase presents nontrivial features of Weyl fermions. These findings offer new important insight into the microscopic interplay among lattice, spin, and relativistic fermions in lanthanide monopnictides.

42 ENGINEERING↗

Role of Tensile Stress in DNA Nanoresonators for Epigenetic Studies

The evaluation of epigenetic features such as DNA methylation is becoming increasingly important in many biochemical processes like gene expression and transcription as well as in several diseases like schizophrenia or diabetes. Here, in this work, we report that self-assembled nanomechanical resonators entirely composed of DNA molecules can be used to explore gross changes in DNA methylation levels (0–25–50%), while careful control of tensile stress is needed to reduce the variability of resonance frequency for rigorous quantification. The effect of the tensile stress retained by the suspended DNA nanoresonators on the application of the technique is extensively explored using a combination of laser Doppler vibrometry and atomic force spectroscopy. DNA nanoresonators are real-time, label-free sensors and could avoid chemical functionalization and sample amplification. Therefore, they may represent in the future a key complementary routine tool for global DNA methylation analysis needed to evaluate the consequences of environmental stresses on the human genome.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tunable Multisite Proton-Coupled Electron Transfer Mediators: Distinct Pathways for Substrate Reduction Versus Competing Hydrogen Evolution

Proton-coupled electron transfer (PCET) reagents have emerged as powerful tools for transferring net H atoms to organic substrates from relatively weak X–H bonds. One advantage of employing PCET reagents is the tunability of the X–H bond strength by independently varying their redox potential and/or p K a for selective substrate reductions; however, the rational development of modular catalytic PCET reagents based on these features remains underdeveloped. In this work, we address important mechanistic questions relevant to a dimethylaniline-appended cobaltocene PCET mediator that our lab has previously introduced. Specifically, we examine where protonation occurs within the reactive Co(II, NH) + intermediate of a Brønsted-base modified cobaltocene mediator, whether substrate reduction and hydrogen evolution reaction (HER) proceed by a common or bifurcated mechanistic pathway, and how the redox, acid–base, and structural properties of PCET mediators can dictate their reactivity and selectivity. We show that substrate compatibility can be tuned and, via a model study with N -aryl imine substrates, provide data pointing to a multisite PCET (MS-PCET) pathway. Moreover, we rigorously characterize the site of protonation in the reactive reduced, protonated form of the mediator, and through kinetic analysis establish that the pathway for undesired competing HER is fundamentally different and involves Cp-ring protonation. Our findings point to a high degree of flexibility in the design of reductive PCET mediators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Doping evolution of the charge excitations and electron correlations in electron-doped superconducting La 2-x Ce x CuO 4

Electron correlations play a dominant role in the charge dynamics of the cuprates. We use resonant inelastic X-ray scattering (RIXS) to track the doping dependence of the collective charge excitations in electron doped La 2-x Ce x CuO 4 (LCCO). From the resonant energy dependence and the out-of-plane momentum dependence, the charge excitations are identified as three-dimensional (3D) plasmons, which reflect the nature of the electronic structure and Coulomb repulsion on both short and long lengthscales. With increasing electron doping, the plasmon excitations increase monotonically in energy, a consequence of the electron correlation effect on electron structure near the Fermi surface (FS). Importantly, the plasmon excitations evolve from a broad feature into a well-defined peak with much increased life time, revealing the evolution of the electrons from incoherent states to coherent quasi-particles near the FS. Such evolution marks the reduction of the short-range electronic correlation, and thus the softening of the Mottness of the system with increasing electron doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Code-to-code comparison and validation of the radiation-hydrodynamics capabilities of the FLASH code using a laboratory astrophysical jet

The potential for laser-produced plasmas to yield fundamental insights into high energy density physics (HEDP) and deliver other useful applications can sometimes be frustrated by uncertainties in modeling the properties and behavior of these plasmas using radiation-hydrodynamics codes. In an effort to overcome this and to corroborate the accuracy of the HEDP capabilities in the publicly available FLASH radiation-hydrodynamics code, we present detailed code-to-code comparisons between FLASH and the HYDRA code developed at Lawrence Livermore National Laboratory using previously published HYDRA simulations from Grava et al. [Phys. Rev. E 78, 016403 (2008)]. That study describes a laser experiment that produced a jet-like feature that the authors compare to astrophysical jets. Importantly, the Grava et al. [Phys. Rev. E 78, 016403 (2008)] experiment included detailed x-ray interferometric measurements of electron number densities and a time-integrated measurement of the soft x-ray spectrum. Despite markedly different methods for treating the computational mesh, and different equations of state and opacity models, the FLASH results resemble the results from HYDRA and, most importantly, the experimental measurements of electron density. Having validated the FLASH code in this way, we use the code to further investigate and understand the formation of the jet seen in the Grava et al. [Phys. Rev. E 78, 016403 (2008)] experiment and discuss its relation to the Wan et al. [Phys. Rev. E 55, 6293 (1997)] experiment at the NOVA laser.

Orban, Chris (ORCID:0000000312004538)↗

Multi-beam operation of LANSCE accelerator facility

The Los Alamos Neutron Science Center (LANSCE) accelerator facility has been in operation for 50 years performing important scientific support for national security. The unique feature of the LANSCE accelerator facility is multi-beam operation, delivering beams to five experimental areas. The near-term plans are to replace obsolete and almost end-of-life systems of the LANSCE linear accelerator with a modern 100-MeV Front End with significant improvement in beam quality. This paper summarizes experimental results obtained during the operation of the LANSCE accelerator facility and considers plans to expand the performance of the accelerator for near- and long-term operations.

47 OTHER INSTRUMENTATION↗