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At least 991 records · Page 55

MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain. The Alphaproteobacterium Novosphingobium aromaticivorans DSM12444 can metabolize several chemically modified aromatics in deconstructed lignin, but not acetovanillone. In this work, adaptive laboratory evolution identified a single amino acid change in the previously uncharacterized gene product Saro_1862 that is necessary and sufficient for N. aromaticivorans growth with acetovanillone as a sole growth substrate, as well as other aromatic monomers not metabolized by wild-type cells. We show that a glutamate (E) to lysine (K) substitution at amino acid residue 16 of Saro_1862 results in a ~1600-fold increase in the rate of ATP-dependent acetovanillone phosphorylation. We also find that recombinant Saro_1862 E16K phosphorylates several other aromatic compounds in vitro , defining the first reported catalytic activity for the widespread UPF0261 protein domain contained in Saro_1862. Thus, we propose naming Saro_1862 MarK, for multiple aromatic kinase. A 1.57 Å crystal structure of MarK E16K predicts that the E16K substitution lies in a potential ATP binding site, suggesting how this amino acid change increased catalytic activity. A search for homologs of MarK and other proteins required for acetovanillone degradation predicts that this pathway for aromatic metabolism exists throughout the bacterial phylogeny.

Novosphingobium↗

Anticancer effect of AZD2461 PARP inhibitor against colon cancer cells carrying wt or dysfunctional p53

Colon cancer is one of the most common cancers, currently treated with traditional chemotherapies or alternative therapies. However, these treatments are still not enough effective and induce several side effects, so that the search of new therapeutic strategies is needed. The use of Poly-(ADP-ribose)-polymerase (PARP) inhibitors, although originally approved against BRCA-1 or BRCA-2 mutated cancers, has been extended, particularly in combination with other treatments, to cure cancers that do not display defects in DNA repair signaling pathways. The role of p53 oncosuppressor in the regulating the outcome of PARP inhibitor treatment remains an open issue. In this study, we addressed this topic by using a well-tolerated PARP 1/2/3 inhibitor, namely AZD2461, against colon cancer cell lines with different p53 status. We found that AZD2461 reduced cell proliferation in wtp53 and p53−/− cancer cells by increasing ROS and DNA damage, while R273H mutant (mut) p53 counteracted these effects. Moreover, AZD2461 improved the reduction of cell proliferation by low dose radiation (IR) in wtp53 cancer cells, in which a down-regulation of BRCA-1 occurred. AZD2461 did not affect cell proliferation of mutp53 colon cancer cells also in combination with low dose radiation, suggesting that only wt p53 or p53 null colon cancer cells could benefit AZD2461 treatment.

60 APPLIED LIFE SCIENCES↗

Identification of Suitable Vacuum Gas Oils as Plasticizers Using HT-GC × GC-HRMS

Vacuum gas oils (VGOs) have long been heralded as effective plasticizers due to their high boiling-points and lubricating properties. One of these VGOs, HyVac Oil 93050, is a paraffinic plasticizer that is currently utilized in polymer–plasticizer explosive formulations, while this oil effectively increases the elasticity and decreases the sensitivity for current formulations. We seek to identify alternative VGOs with similar density, viscosity, molecular composition, and impurities for future formulations. In this study, 18 VGOs, including HyVac Oil 93050, were initially evaluated for their density and viscosity. The oils were then ranked based on physical characteristics and analyzed for molecular composition using high-temperature comprehensive two-dimensional gas chromatography with high-resolution time-of-flight mass spectrometry (HT-GC × GC-HRMS). Further, the HT-GC × GC-HRMS chromatograms of the top 10 most similar VGOs to HyVac Oil 93050, according to density, were compared utilizing the Pearson correlation coefficient. Three of the oils with densities similar to those of HyVac Oil 93050 had a Pearson correlation within the lot-to-lot variation of HyVac Oil 93050. For the top 3 candidates, Pearson correlation was then utilized as a feature selection technique to discover significant chemical differences. Positive chemical ionization (PCI) and negative chemical ionization (NCI) HT-GC × GC-HRMS chromatograms were also evaluated and aided in the discovery and identification of several key compounds including additives that acted as stabilizers for the VGOs. After this further chemical analysis, two of the original 17 potential VGOs were determined to be physically and chemically similar to HyVac Oil 93050.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine-Learning-Based Predictive Modeling of Glass Transition Temperatures: A Case of Polyhydroxyalkanoate Homopolymers and Copolymers

Polyhydroxyalkanoate-based polymers—being ecofriendly, biosynthesizable, and economically viable and possessing a broad range of tunable properties—are currently being actively pursued as promising alternatives for petroleum-based plastics. The vast chemical complexity accessible within this class of polymers gives rise to challenges in the rational discovery of novel polymer chemistries for specific applications. Here, the burgeoning field of polymer informatics addresses this challenge via providing tools and strategies for accelerated property prediction and materials design via surrogate machine-learning models built on reliable past data. In this contribution, we use glass transition temperature T g as an example target property to demonstrate promise of the data-enabled route to accelerated learning of accurate structure–property mappings in PHA-based polymers. Our analysis uses a data set of experimentally measured T g values, polymer molecular weights, and a polydispersity index for PHA-based homo- and copolymers that was carefully assembled from the literature. A fingerprinting scheme that captures key properties based on topology, shape, and charge/polarity of specific chemical units or motifs forming the polymer backbone was devised to numerically represent the polymers. A validated statistical learning model is then developed to allow for a mapping of the polymer fingerprints onto the property space in a physically meaningful and reliable manner. Once developed, the model can not only rapidly predict the property of new PHA polymers but also provide uncertainties underlying the predictions. The model is further combined with an evolutionary-algorithm-based search strategy to efficiently identify multicomponent polymer compositions with a prespecified T g . While the present contribution is focused specifically on T g , the surrogate model development approach put forward here is general and can, in principle, be extended to a range of other properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genomic characterization of rare earth binding by Shewanella oneidensis

Abstract Rare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions, suggesting that genetic engineering could allow it to leapfrog existing technologies. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-1. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We identified 18 gene ontologies and 13 gene operons that make up key systems that affect biosorption. We found, among other things, that disruptions of a key regulatory component of the arc system ( hptA ), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes ( wbpQ , wbnJ , SO_3183 ) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO_4685 , a capsular polysaccharide (CPS) synthesis gene, disruption of which results in an up to 79% increase in biosorption; and nusA, a transcriptional termination/anti-termination protein, disruption of which results in an up to 35% decrease in biosorption. Knockouts of glnA , pyrD , and SO_3183 produce small but significant increases (≈ 1%) in relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Modeling suggests that while these changes to lanthanide biosorption selectivity are small, they could already reduce the length of repeated enrichment process by up to 27%. This broad exploratory study begins to elucidate how genetics affect REE-biosorption by S. oneidensis , suggests new areas of investigation for better mechanistic understanding of the membrane chemistry involved in REE binding, and offer potential targets for improving biosorption and separation of REE by genetic engineering.

Medin, Sean↗

Exploring Future Storage Options for ATLAS at the BNL/SDCC facility

The ATLAS experiment is expected to deliver an unprecedented amount of scientific data in the High Luminosity(HL-LHC) era. As the demand for disk storage capacity in ATLAS continues to rise steadily, the BNL Scientific Data and Computing Center (SDCC) faces challenges in terms of cost implications for maintaining multiple disk copies and adapting to the coming ATLAS storage requirements. To address these challenges, the SDCC Storage team has undertaken a thorough analysis of the ATLAS experiment's requirements, matching them to suitable storage options and strategies, and has explored alternatives to enhance or replace the current storage solution. This paper aims to present the main challenges encountered while supporting big data experiments such as ATLAS. We describe the experiment's specific requirements and priorities, particularly focusing on the critical storage system characteristics of the high-luminosity run and how the key storage components provided by the Storage team work together: the dCache disk storage system; its archival back-end, HPSS; and its OS-level backend Storage. Specifically, we investigate a novel approach to integrate Lustre and XRootD. In this setup, Lustre serves as backend storage and XRootD acts as an access layer frontend, supporting various grid access protocols. Additionally, we also describe the validation and commissioning tests, including the performance comparison between dCache and XRootd. Furthermore, we provide a performance and cost analysis comparing OpenZFS and LINUX MD RAID, evaluate different storage software stacks, and showcase stress tests conducted to validate Third Party Copy (TPC) functionality.

99 GENERAL AND MISCELLANEOUS↗

Fine structure of current noise spectra in nanoelectromechanical resonators

Here, we study the frequency-dependent noise of a suspended carbon nanotube quantum dot nanoelectromechanical resonator induced by electron-vibration coupling. Using a rigorous Keldysh diagrammatic technique, we establish a formal framework connecting the vibrational properties to electrical measurements. We find that the noise power spectrum exhibits a narrow resonant peak at the frequency of the vibrational modes. However, this fine structure tends to disappear due to a coherent cancellation effect when the tunneling barriers are tuned to a symmetric point. Notably, measuring the electrical current noise spectra provides a sensitive alternative method for detecting the damping and dephasing of quantum vibrational modes.

Electric measurements↗

GRB and blazar jets shining through their stripes

Black hole-driven relativistic astrophysical jets, such as blazars and gamma-ray bursts (GRBs), are powerful sources of electromagnetic radiation. Their emission is powered by some energy dissipation and particle acceleration mechanism operating in situ at large distances from the black hole. We propose that the formation of the dissipative structures in the jet is controlled by the time variability of the accretion disc. We argue that the open magnetic field lines through the black hole, which drive a strongly magnetized jet, may have their polarity reversing over time-scales related to the growth of the magnetorotational dynamo in the disc. Consequently, the jet is characterized by an alternating toroidal field polarity along its propagation axis, i.e. it is a ‘striped jet’. Magnetic reconnection in the current sheets that form between the stripes dissipates the alternating field energy and thus powers further jet acceleration. Here, we consider a jet with a broad distribution of stripe widths l > l min , above a dominant scale l min . We find that the bulk acceleration of the jet, driven by the annihilation of the stripes, is very gradual. The dissipation rate peaks at a distance $z_{\rm peak}\sim 10^6 R_\mathrm{ g}\, (\Gamma _\infty /30)^2\, (l_{\rm min}/1000R_\mathrm{ g})$| , where R g is the black hole’s gravitational radius and Γ ∞ the jet’s asymptotic Lorentz factor, and exhibits a very broad plateau extending by ~4–5 orders of magnitude in distance. The prolonged energy dissipation accounts for the flat-to-inverted long-wavelength spectra commonly observed in jets. The model can also account for the broad range of flaring time-scales of blazars and the fact that their bulk acceleration appears to continue out to ~100 pc scales. In GRB jets, the model predicts comparable power for the photopsheric and Thomson-thin emission components.

79 ASTRONOMY AND ASTROPHYSICS↗

Mechanisms of adsorbing hydrogen gas on metal decorated graphene

Hydrogen is a key player in global strategies to reduce greenhouse gas emissions. In order to make hydrogen a widely used fuel, we require more efficient methods of storing it than the current standard of pressurized cylinders. An alternative method is to adsorb H 2 in a material and avoid the use of high pressures. Among many potential materials, layered materials such as graphene present a practical advantage as they are lightweight. However, graphene and other 2D materials typically bind H 2 too weakly to store it at the typical operating conditions of a hydrogen fuel cell, meaning that high pressure would still be required. Modifying the material, for example by decorating graphene with adatoms, can strengthen the adsorption energy of H 2 molecules, but the underlying mechanisms are still not well understood. In this work, we systematically screen alkali and alkaline-earth metal decorated graphene sheets for the static thermodynamic adsorption of hydrogen gas from first principles and focus on the mechanisms of binding. We show that there are three mechanisms of adsorption on metal decorated graphene and each leads to distinctly different hydrogen adsorption structures. The three mechanisms can be described as weak van der Waals physisorption, metal adatom facilitated polarization, and Kubas adsorption. Among these mechanisms, we find that Kubas adsorption is easily perturbed by an external electric field, providing a way to tune H 2 adsorption. In conclusion, this work is foundational and builds our understanding of H 2 adsorption under idealized conditions.

36 MATERIALS SCIENCE↗

Quantum simulations of nuclear resonances with variational methods

Background: The many-body nature of nuclear physics problems poses significant computational challenges. These challenges become even more pronounced when studying the resonance states of nuclear systems, which are governed by the non-Hermitian Hamiltonian. Quantum computing, particularly for quantum many-body systems, offers a promising alternative, especially within the constraints of current noisy intermediate-scale quantum (NISQ) devices. Purpose: This work aims to simulate nuclear resonances using quantum algorithms by developing a variational framework compatible with non-Hermitian Hamiltonians and implementing it fully on a quantum simulator. Methods: We employ the complex scaling technique to extract resonance positions classically and adapt it for quantum simulations using a two-step algorithm. First, we transform the non-Hermitian Hamiltonian into a Hermitian form by using the energy variance as a cost function within a variational framework. Second, we perform 𝜃-trajectory calculations to determine optimal resonance positions in the complex energy plane. To address resource constraints on NISQ devices, we utilize Gray code (GC) encoding to reduce qubit requirements. Results: We first validate our approach using a schematic potential model that mimics a nuclear potential, successfully reproducing known resonance energies with high fidelity. We then extend the method to a more realistic 𝛼−𝛼 nuclear potential and compute the 𝐷- and 𝐺-wave resonance energies with a basis size of 𝑁=16, using only four qubits. The quantum simulation results closely match the classical values, demonstrating the feasibility of our approach. Conclusions: This study demonstrates, for the first time, that the complete 𝜃-trajectory method can be implemented on a quantum computer without relying on any classical input beyond the Hamiltonian. The results establish a scalable and efficient quantum framework for simulating resonance phenomena in nuclear systems. This work represents a significant step toward quantum simulations of open quantum systems and lays the foundation for future investigations into resonance structures in nuclear, atomic, and molecular physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Too Good to Be True? Evaluation of Colonoscopy Sensitivity Assumptions Used in Policy Models

Background: Models can help guide colorectal cancer screening policy. Although models are carefully calibrated and validated, there is less scrutiny of assumptions about test performance. Methods: We examined the validity of the CRC-SPIN model and colonoscopy sensitivity assumptions. Standard sensitivity assumptions, consistent with published decision analyses, assume sensitivity equal to 0.75 for diminutive adenomas (<6 mm), 0.85 for small adenomas (6–10 mm), 0.95 for large adenomas (≥10 mm), and 0.95 for preclinical cancer. We also selected adenoma sensitivity that resulted in more accurate predictions. Targets were drawn from the Wheat Bran Fiber study. In the study, we examined how well the model predicted outcomes measured over a three-year follow-up period, including the number of adenomas detected, the size of the largest adenoma detected, and incident colorectal cancer. Results: Using standard sensitivity assumptions, the model predicted adenoma prevalence that was too low (42.5% versus 48.9% observed, with 95% confidence interval 45.3%–50.7%) and detection of too few large adenomas (5.1% versus 14.% observed, with 95% confidence interval 11.8%–17.4%). Predictions were close to targets when we set sensitivities to 0.20 for diminutive adenomas, 0.60 for small adenomas, 0.80 for 10- to 20-mm adenomas, and 0.98 for adenomas 20 mm and larger. Conclusions: Colonoscopy may be less accurate than currently assumed, especially for diminutive adenomas. Alternatively, the CRC-SPIN model may not accurately simulate onset and progression of adenomas in higher-risk populations. Impact: Misspecification of either colonoscopy sensitivity or disease progression in high-risk populations may affect the predicted effectiveness of colorectal cancer screening. When possible, decision analyses used to inform policy should address these uncertainties.

60 APPLIED LIFE SCIENCES↗

First Results from a Nb3Sn-Coated 1.5-Cell 650 MHz SRF Cavity for Cryogen-Free Industrial Accelerators

First Results from a Nb3Sn-Coated 1.5-Cell 650 MHz SRF Cavity for Cryogen-Free Industrial Accelerators ABSTRACT = Fermilab is advancing the development of a compact, high-power electron beam accelerator using superconducting radio frequency (SRF) technology as a non-radioactive alternative to traditional radiological sources. The current design targets continuous-wave (CW) operation at \SI{1.6}{MeV} and \SI{20}{kW}. To ensure suitability for industrial environments, the system is being designed for cryogen-free operation, driving the adoption of a novel Nb$_3$Sn-coated 1.5-cell SRF cavity operating at \SI{650}{MHz}. This contribution reports on the fabrication, surface preparation, and Nb$_3$Sn coating process of the cavity, as well as first results from vertical test stand (VTS) measurements performed in a liquid helium bath. These initial tests mark a key milestone toward demonstrating the viability of conduction-cooled Nb$_3$Sn SRF cavities for industrial-scale deployment.

Tagdulang, N. [Fermilab]↗

TRP Cutter Head Improvement

The current Target Rod Preparation (TRP) Cutter Head suffers from overheating problems during TPBAR breaching operations. The overheating leads to work stoppage due to the periodic need to allow the TRP Cutter Head motor to cool. This work stoppage and allowance for cooldown of the motor leads to a very inefficient TPBAR breaching process. Due to the increased need for Tritium gas, the system must be improved to increase the efficiency of the TPBAR breaching process. The project would include the following major steps: Determine likely causes of overheating of the TRP cutter head motor. Identify and research methods for cooling currently installed motor. Identify and research alternate motors for TRP cutter head. Procure a new motor for testing. Perform TPBAR breaching mockup testing with new motor. Write report on results and recommendations on potential path forward.

42 ENGINEERING↗

Risk Assessment and Ventilation Modeling for Hydrogen Release in Vehicle Repair Garages

The availability of repair garage infrastructure for hydrogen fuel cell vehicles is becoming increasingly important for future industry growth. Ventilation requirements for hydrogen fuel cell vehicles can affect both retrofitted and purpose-built repair garages and the costs associated with these requirements can be significant. A hazard and operability study (HAZOP) was performed to identify key risk-significant scenarios related to hydrogen vehicles in a repair garage. Detailed simulations and modeling were performed using appropriate computational tools to estimate the location, behavior, and severity of hydrogen release based on key HAZOP scenarios. This work compares current fire code requirements to an alternate ventilation strategy to further reduce potentially hazardous conditions. Overall, the amount of flammable mass of hydrogen at any one time in the simulation is low compared to the total mass of hydrogen released, due to the low flow rate of a low pressure release. It is shown that position, direction, and velocity of ventilation have a significant impact on the amount of instantaneous flammable mass in the domain.

33 ADVANCED PROPULSION SYSTEMS↗

Inertia and the Power Grid: A Guide Without the Spin

This guide provides an overview of inertia’s role in the evolving power system. It describes the sources of inertia in the grid, the intrinsic interplay of inertia and other grid services, the factors that impact the amount of and need for inertia, and the changes that can be made to maintain reliability as it declines. The guide is intended for nontechnical audiences. And it introduces accessible examples to illustrate the concepts of inertia and other grid services that are required to maintain system frequency, which is a key indicator of health in the current grid. The guide also discusses alternatives to traditional inertia and provides several takeaways that may be informative to power system decision makers, planners, operators, analysts, and other stakeholders.

24 POWER TRANSMISSION AND DISTRIBUTION↗

First Results from A $Nb_3Sn$-Coated 1.5-Cell 650MHZ SRF Cavity for Cryogen-Free Industrial Accelerators

Fermilab is advancing the development of a compact, high-power electron beam accelerator using superconducting radio frequency (SRF) technology as a non-radioactive alternative to traditional radiological sources. The current design targets continuous-wave (CW) operation at \SI{1.6}{MeV} and \SI{20}{kW}. To ensure suitability for industrial environments, the system is being designed for cryogen-free operation, driving the adoption of a novel Nb$_3$Sn-coated 1.5-cell SRF cavity operating at \SI{650}{MHz}. This contribution reports on the fabrication, surface preparation, and Nb$_3$Sn coating process of the cavity, as well as first results from vertical test stand (VTS) measurements performed in a liquid helium bath. These initial tests mark a key milestone toward demonstrating the viability of conduction-cooled Nb$_3$Sn SRF cavities for industrial-scale deployment.

Tagdulang, Nikki Diala [Fermilab]↗