Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Results for “physical modification”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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The Accelerator Neutrino Neutron InteractionExperiment: Design, Construction and Preparationfor First Physics
This thesis covers work performed for the Accelerator Neutrino Neutron Interaction Experiment (ANNIE) between 2015 and 2020. ANNIE is a beamline neutrino experiment located at the Fermi National Accelerator Laboratory in Chicago. Its primary physics goals are the measurement of neutrino interaction cross-sections on oxygen, and a measurement of the multiplicity of final state neutrons from these interactions, both as functions of final state kinematics. In order to achieve these goals ANNIE will be pioneering the use of Large Area Picosecond Photodetectors and the use of gadolinium doping to enhance neutron visibility in a water Cherenkov detector. Over the time period of this thesis the ANNIE detector was constructed, an initial 'Phase I' background run was completed, the detector was decommissioned and then substantially upgraded in preparation for the main 'Phase II' physics run. At the time of writing ANNIE is being re-commissioned, with Phase II data taking anticipated to begin in 2021. During this time I spent 21/2 years on-site contributing to almost all aspects of hardware work, while performing software development for the simulation and analysis frameworks. As my first software task I developed Monte Carlo simulations of the detector response, based on the WCSim framework. While thismore » framework provided a starting point for the tank simulation significant modifications were required to implement the complete ANNIE detector system. This included a rewrite of the geometry, along with modifications to the photosensor definitions, hit collections, digitization, triggering, input and output interfaces, etc. To take advantage of improved modelling of neutrons in Geant4.10 the physics lists were also reimplemented in the new version format. As part of this work I determined performance metrics based on the output files, calculating kinematic acceptance, detector efficiency and expected event rates. My contributions on reconstruction focused primarily on the MRD, for which I implemented two track reconstruction algorithms, specialised for high and low energy muons. The high energy algorithm achieves >90% efficiency for tracks with at least 8 hits, and is robust against dead paddles and unrelated hits. The low energy algorithm performs a search in combination with tank information to provide sensitivity down to a single MRD hit. Early data handling work for the Phase I background run included writing the code for handling TDC hits and performing studies on neutron detection without the requirement of multi-hit coincidence. As the collaboration moved to a new framework for the Phase II analysis I performed a substantial amount of work to develop the codebase, implementing tools to perform tasks such as file IO, data parsing, waveform processing, event building, timestamp alignment, time clustering, hit residual calculation, event visualisation etc. I helped develop the python API for integrating multi-language tools, and ported the framework into a Singularity container to provide a self-contained environment that…« less
43 PARTICLE ACCELERATORS↗
Modification of b hadronization in small systems at LHCb
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Atomic, Nuclear and Particle Physics↗
Explainable machine learning of the underlying physics of high-energy particle collisions
We present an implementation of an explainable and physics-aware machine learning model capable of inferring the underlying physics of high-energy particle collisions using the information encoded in the energy-momentum four-vectors of the final state particles. We demonstrate the proof-of-concept of our White Box AI approach using a Generative Adversarial Network (GAN) which learns from a DGLAP-based parton shower Monte Carlo event generator. The constrained generator network architecture mimics the structure of a parton shower exhibiting similarities with Recurrent Neural Networks (RNNs). We show, for the first time, that our approach leads to a network that is able to learn not only the final distribution of particles, but also the underlying parton branching mechanism, i.e. the Altarelli-Parisi splitting function, the ordering variable of the shower, and the scaling behavior. While the current work is focused on perturbative physics of the parton shower, we foresee a broad range of applications of our framework to areas that are currently difficult to address from first principles in QCD. Examples include nonperturbative and collective effects, factorization breaking and the modification of the parton shower in heavy-ion, and electron-nucleus collisions.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Systematic study of nuclear effects in p + Al , p + Au , d + Au , and He 3 + Au collisions at s N N = 200 GeV using π 0 production
The PHENIX Collaboration presents a systematic study of inclusive π 0 production from p + p , p + Al , p + Au , d + Au , and He 3 + Au collisions at s N N = 200 GeV . Measurements were performed with different centrality selections as well as the total inelastic, 0–100%, selection for all collision systems. For 0–100% collisions, the nuclear-modification factors, R x A , are consistent with unity for p T above 8 GeV / c , but exhibit an enhancement in peripheral collisions and a suppression in central collisions. The enhancement and suppression characteristics are similar for all systems for the same centrality class. It is shown that for high- p T - π 0 production, the nucleons in the d and He 3 interact mostly independently with the Au nucleus and that the counterintuitive centrality dependence is likely due to a physical correlation between multiplicity and the presence of a hard scattering process. These observations disfavor models where parton energy loss has a significant contribution to nuclear modifications in small systems. Nuclear modifications at lower p T resemble the Cronin effect—an increase followed by a peak in central or inelastic collisions and a plateau in peripheral collisions. The peak height has a characteristic ordering by system size as p + Au > d + Au > He 3 + Au > p + Al . For collisions with Au ions, current calculations based on initial-state cold nuclear matter effects result in the opposite order, suggesting the presence of other contributions to nuclear modifications, in particular at lower p T .
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Do atoms age?
Time evolution generically entangles a quantum state with environmental degrees of freedom. The resulting increase in entropy changes the properties of that quantum system leading to “aging”. It is interesting to ask if this familiar property also applies to simple, single particle quantum systems such as the decay of a radioactive particle. We propose a test of such aging in an ion clock setup where we probe for temporal changes to the energies of the electronic state of an ion containing a radioactive nucleus. Such effects are absent in standard quantum mechanics and this test is thus a potent null test for violations of quantum mechanics. As a proof of principle, we show that these effects exist in causal non-linear modifications of quantum mechanics.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Coupling TRACE with nodal neutronics code Ants using the Exterior Communications Interface and VTT's multi-physics driver Cerberus
In this paper a recently developed coupling between system code TRACE and nodal neutronics code Ants is presented. The TRAC/RELAP Advanced Computational Engine (TRACE) is a reactor system code developed by U.S. Nuclear Regulatory Commission (NRC). The code has been designed to analyse loss-of-coolant accidents (LOCAs), operational transients and other accident scenarios in light water reactors. Ants is the reduced order nodal neutronics code of the Kraken framework. The diffusion solution method in Ants is based on the Analytic Function Expansion Nodal method (AFEN) and Flux Expansion Nodal Method (FENM). Rectangular, hexagonal and triangular geometries are supported. Both steady state and burnup problems including micro-depletion can be simulated. The coupling is implemented using VTT's multi-physics driver Cerberus and the Exterior Communications Interface (ECI) which is supplied with TRACE and enables the coupling of TRACE without source code modifications. The main focus in the paper is on describing the TRACE-Ants coupling in detail in order to share to other code developers what we have learned from the ECI based coupling process. The coupled code system is briefly tested by simulating a simple transient in a SMR core initiated by control rod movement. The results of the test calculation look reasonable and more complicated test cases will be modelled in the near future.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Sculpting the Plasmonic Responses of Nanoparticles by Directed Electron Beam Irradiation
Spatial confinement of matter in functional nanostructures has propelled these systems to the forefront of nanoscience, both as a playground for exotic physics and quantum phenomena and in multiple applications including plasmonics, optoelectronics, and sensing. In parallel, the emergence of monochromated electron energy loss spectroscopy (EELS) has enabled exploration of local nanoplasmonic functionalities within single nanoparticles and the collective response of nanoparticle assemblies, providing deep insight into associated mechanisms. However, modern synthesis processes for plasmonic nanostructures are often limited in the types of accessible geometry, and materials and are limited to spatial precisions on the order of tens of nm, precluding the direct exploration of critical aspects of the structure-property relationships. Here, the atomic-sized probe of the scanning transmission electron microscope is used to perform precise sculpting and design nanoparticle configurations. Using low-loss EELS, dynamic analyses of the evolution of the plasmonic response are provided. It is shown that within self-assembled systems of nanoparticles, individual nanoparticles can be selectively removed, reshaped, or patterned with nanometer-level resolution, effectively modifying the plasmonic response in both space and energy. This process significantly increases the scope for design possibilities and presents opportunities for unique structure development, which are ultimately the key for nanophotonic design.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Enhancing Interpretability in Generative Modeling: Statistically Disentangled Latent Spaces Guided by Generative Factors in Scientific Datasets
This study addresses the challenge of statistically extracting generative factors from complex, high-dimensional datasets in unsupervised or semi-supervised settings. We investigate encoder-decoder-based generative models for nonlinear dimensionality reduction, focusing on disentangling low-dimensional latent variables corresponding to independent physical factors. Introducing Aux-VAE, a novel architecture within the classical Variational Autoencoder framework, we achieve disentanglement with minimal modifications to the standard VAE loss function by leveraging prior statistical knowledge through auxiliary variables. These variables guide the shaping of the latent space by aligning latent factors with learned auxiliary variables. We validate the efficacy of Aux-VAE through comparative assessments on multiple datasets, including astronomical simulations.
97 MATHEMATICS AND COMPUTING↗
Quantification of [MTBD][beti] loading and its effects on Pt/HSC electrode performance in hydrogen fuel cells
High surface area carbon-supported platinum catalysts (Pt/HSC) are widely used in polymer electrolyte membrane fuel cells but often suffer from limited proton and oxygen transport within porous domains. To address these challenges, we integrate the ionic liquid [MTBD][beti] into Pt/HSC catalyst layers using two deposition methods-one-pot and sequential deposition-to tune IL distribution within micropores and mesopores. A combination of ex situ and in operando techniques were employed to elucidate electrode structure-performance relationships across a range of IL loadings. Sequential deposition achieved more efficient pore filling and higher IL retention at lower IL:C ratios, enabling enhanced proton conductivity and protection of active sites. Compared to the IL-free Pt/HSC, IL-modified electrodes demonstrated up to 28% improvement in mass activity and enhanced high-current-density performance under low relative humidity, while maintaining comparable performance under humidified conditions. Electrochemical impedance spectroscopy and CO displacement experiments reveal that improvements are linked to reduced ionic resistance and lower sulfonate adsorption on Pt sites, rather than changes in electrochemical surface area. However, excessive IL loading leads to mass transport losses. These results highlight the importance of selective pore filling and efficient IL distribution in achieving kinetic gains without compromising ionic and gas transport.
08 HYDROGEN↗
Supported Electrophilic Organoruthenium Catalyst for the Hydrosilylation of Olefins
A series of supported electrophilic organoruthenium complexes has been synthesized via surface organometallic chemistry (SOMC) techniques and applied to the selective hydrosilylation of olefins. The air-sensitive 16e - complex Cp*RuMes(PCy 3 ) (1) (Cp* = pentamethylcyclopentadienyl, Mes = mesityl) was synthesized by the treatment of Cp*RuCl(PCy 3 ) with mesityl Grignard MesMgBr. This species was chemisorbed onto sulfated zirconia SO 4 /ZrO 2 , but the resulting material was inactive toward cyclohexene hydrosilylation with phenylsilane. Instead, Cp*RuMes(PCy 3 ) was treated with phenylsilane (PhSiH 3 ) to provide a ruthenium disilyl hydride complex Cp*RuH(SiH 2 Ph) 2 (PCy 3 ) (3), which was fully characterized by NMR spectroscopy and single-crystal X-ray diffraction. Grafting this species onto SO 4 /ZrO 2 resulted in the formation of phenylsilane along with the surface electrophilic species [Cp*RuH(R)(X-SiHPh)(PCy 3 )] (R = H, O 3 S-O or O 3 Zr-O; 4a, 4b, X = O 3 S-O, and O 3 Zr-O, respectively) as the major species. Material 4 was characterized via a combination of spectroscopic techniques including dynamic nuclear polarization (DNP)-enhanced solid-state NMR spectroscopy, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray absorption spectroscopy (XAS), and density function theory (DFT) calculations. Further, capping the remaining acid sites on 4 with Me 3 Si-SiMe 3 provides 5, which significantly reduces side reactions, such as olefin isomerization and silane redistribution. Catalyst 5 is a highly robust and selective hydrosilylation catalyst and can be recycled up to 5 times without significant diminishment of activity. Exclusive anti-Markovnikov regiochemistry, cis-addition selectivity, and the inactivity of secondary and tertiary silanes provide support for the proposed Glaser-Tilley mechanism involving cationic ruthenium silylene species analogous to homogeneous systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Revisiting Theoretical Tools and Approaches for the Valorization of Recalcitrant Lignocellulosic Biomass to Value-Added Chemicals
Biorefinery processes for converting lignocellulosic biomass to fuels and chemicals proceed via an integrated series of steps. Biomass is first pretreated and deconstructed using chemical catalysts and/or enzymes to liberate sugar monomers and lignin fragments. Deconstruction is followed by a conversion step in which engineered host organisms assimilate the released sugar monomers and lignin fragments, and produce value-added fuels and chemicals. Over the past couple of decades, a significant amount of work has been done to develop innovative biomass deconstruction and conversion processes that efficiently solubilize biomass, separate lignin from the biomass, maximize yields of bioavailable sugars and lignin fragments and convert the majority of these carbon sources into fuels, commodity chemicals, and materials. Herein, we advocate that advanced in silico approaches provide a theoretical framework for developing efficient processes for lignocellulosic biomass valorization and maximizing yields of sugars and lignin fragments during deconstruction and fuel and chemical titers during conversion. This manuscript surveys the latest developments in lignocellulosic biomass valorization with special attention given to highlighting computational approaches used in process optimization for lignocellulose pretreatment; enzyme engineering for enhanced saccharification and delignification; and prediction of the genome modification necessary for desired pathway fine-tuning to upgrade products from biomass deconstruction into value-added products. Physics-based modeling approaches such as density functional theory calculations and molecular dynamics simulations have been most impactful in studies aimed at exploring the molecular level details of solvent-biomass interactions, reaction mechanisms occurring in biomass-solvent systems, and the catalytic mechanisms and engineering of enzymes involved in biomass degradation. More recently, with ever increasing amounts of data from, for example, advanced mutli-omics experiments, machine learning approaches have begun to make important contributions in synthetic biology and optimization of metabolic pathways for production of biofuels and chemicals.
09 BIOMASS FUELS↗
Novel alkali intercalated and acid-exfoliated biochars with enhanced surface areas for contaminant adsorption applications
Cost-effective and eco-friendly adsorbents are essential in environmental engineering and biochar is a promising material from the perspective. A novel and efficient surface modification approach involving alkali intercalation and acid exfoliation was designed in this study to enhance the physicochemical properties of biochar. Here, the alkali intercalation process utilizes potassium hydroxide (KOH), while acid exfoliation involves varying HNO 3 , H 2 SO 4 , and H 3 PO 4 concentrations. A simple two-stage pyrolysis process was employed to facilitate the intercalation-exfoliation modification. The modified biochars were characterized using BET, SEM, XRD, etc., to understand physicochemical properties. To quantify the effectiveness of the modifications, adsorption of malachite green dye as a model moiety was investigated. Dye removal sorption rates exceeding 99 % were recorded in the case of the biochars modified through a two-step process using KOH and 0.1MH 3 PO 4 . Specifically, the highest contaminant removal of 99.9 % was recorded when 60 mg of the KOH-0.1MH 3 PO 4 biochar was employed, which is significantly higher than unmodified biochar’s 45.41 % removal at a higher dosage of 100 mg. Moreover, the adsorption kinetics revealed that all the modified biochars attained the maximum removal concentrations (~99 % removal) in a mere 300 min, indicating a tenfold improvement in adsorption rate from unmodified biochar's requirement of over 5000 min. The results achieved through this study provide a cost-effective, fast, and environment-friendly technology for enhancing the adsorption characteristics and performance of biochars toward contaminant removal.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Modifications to the JET Shattered Pellet Injector to Optimize Disruption Mitigation Experiments for Supporting ITER’s DMS Design
Shattered pellet injection (SPI) experiments on Joint European Torus (JET) are an important element in determining the physics basis for mitigating disruptions in ITER. Here, the initial design of the JET SPI system included three barrels to produce pellets with diameters of 4.5, 8.1, and 12.5 mm. The variability of the pellet speed by operating with and without a mechanical punch was limited and led to poor pellet integrity, so the mechanical punch was removed. Fragment size distribution is a function of pellet speed and the desire to change the resulting fragment size distribution was not originally a requirement. After the first set of SPI experiments on JET, different pellet sizes were considered to enable dual injection experiments with identical pellet diameters. It was also determined that speed control is necessary to improve experimental repeatability and to determine how the fragment size distribution impacts mitigation performance. Two barrels were fabricated to form pellets of 10 mm diameter and a third to form an 8.1 mm diameter pellet. New propellant valves were also fabricated and characterized to improve repeatability and overall performance. To have fine control of pellet speed, inserts to reduce the breech volume were fabricated and installed. Laboratory testing was conducted to ensure pellet release and provide a comparison of propellant gas delivered versus pellet speeds for a range of pellet types and mixtures. This article will also discuss how lessons learned from the JET SPI modifications can be applied to other SPI systems, such as the ITER SPI system, as controlling pellet release with the least amount of propellant gas is essential for optimal SPI effectiveness.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Visualizing the NIOSH Pocket Guide: Open-source web application for accessing and exploring the NIOSH Pocket Guide to Chemical Hazards
The NIOSH Pocket Guide to Chemical Hazards is a trusted resource that displays key information for a collection of chemicals commonly encountered in the workplace. Entries contain chemical structures—occupational exposure limit information ranging from limits based on full-shift time-weighted averages to acute limits such as short-term exposure limits and immediately dangerous to life or health values, as well as a variety of other data such as chemical-physical properties and symptoms of exposure. The NIOSH Pocket Guide (NPG) is available as a printed, hardcopy book, a PDF version, an electronic database, and a downloadable application for mobile phones. All formats of the NIOSH Pocket Guide allow users to access the data for each chemical separately, however, the guide does not support data analytics or visualization across chemicals. This project reformatted existing data in the NPG to make it searchable and compatible with exploration and analysis using a web application. The resulting application allows users to investigate the relationships between occupational exposure limits, the range and distribution of occupational exposure limits, and the specialized sorting of chemicals by health endpoint or to summarize information of particular interest. These tasks would have previously required manual extraction of the data and analysis. The usability of this application was evaluated among industrial hygienists and researchers and while the existing application seems most relevant to researchers, the open-source code and data are amenable to modification by users to increase customization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Lattice Disorder and Oxygen Migration Pathways in Pyrochlore and Defect-Fluorite Oxides
Atomic-scale disorder plays an important role in the chemical and physical properties of oxide materials. The structural flexibility of pyrochlore-type oxides allows for crystal-chemical engineering of these properties. Compositional modification can push pyrochlore oxides toward a disordered defect-fluorite structure with anion Frenkel pair defects that facilitate oxygen migration. The local structure of the long-range average cubic defect-fluorite was recently claimed to consist of randomly arranged orthorhombic weberite-type domains. Here, we show, using low-temperature neutron total-scattering experiments, that this is not the case for Zr-rich defect-fluorites. By analyzing data from the pyrochlore/defect-fluorite Y 2 Sn 2–x Zr x O 7 series using a combination of neutron pair distribution function and big-box modelling, we have differentiated and quantified the relationship between anion sub-lattice disorder and Frenkel defects. These details directly influence the energy landscape for oxygen migration and are crucial for simulations and design of new materials with improved properties.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Toward efficient elastocaloric systems: Predicting material thermal properties with high fidelity
A critical need to accurately model thermal behaviors of materials that exhibit strong elastocaloric effects, including predicting the effects themselves at varying stresses and temperatures, has been addressed using a simple and versatile physics-based approach. The key factor leading to the high precision is approximating the underlying elastic phase transition as a smooth modification of lattice entropy between coexisting phases. Once the phase transformation entropy is modeled to match experimentally measured strain as a function of temperature and applied stress, estimating the heat capacity, entropy, and isothermal entropy and adiabatic temperature changes in temperature-stress coordinates becomes straightforward. This approach provides insight into how thermal properties of elastocaloric materials vary through the transition based on strain measurements that are simple to perform and interpret. In addition to aiding in the rapid evaluation of new and existing elastocaloric materials, this advance is expected to prove invaluable for accurate heat transfer modeling aimed at designing efficient regenerative elastocaloric cooling devices.
36 MATERIALS SCIENCE↗