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At least 469 records · Page 26

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl – into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation–diffusion process upon light-triggered retinal isomerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Roadmap on data-centric materials science

Science is and always has been based on data, but the terms ‘data-centric’ and the ‘4th paradigm’ of materials research indicate a radical change in how information is retrieved, handled and research is performed. It signifies a transformative shift towards managing vast data collections, digital repositories, and innovative data analytics methods. The integration of artificial intelligence and its subset machine learning, has become pivotal in addressing all these challenges. This Roadmap on Data-Centric Materials Science explores fundamental concepts and methodologies, illustrating diverse applications in electronic-structure theory, soft matter theory, microstructure research, and experimental techniques like photoemission, atom probe tomography, and electron microscopy. While the roadmap delves into specific areas within the broad interdisciplinary field of materials science, the provided examples elucidate key concepts applicable to a wider range of topics. The discussed instances offer insights into addressing the multifaceted challenges encountered in contemporary materials research.

36 MATERIALS SCIENCE↗

Application of machine learning in the determination of impact parameter in the 132 Sn+ 124 Sn system

Here, 132 Sn + 124 Sn collisions at a beam energy of 270 MeV/nucleon were performed at the Radioactive Isotope Beam Factory (RIBF) in RIKEN to investigate the nuclear equation of state. Reconstructing the impact parameter is one of the important tasks in the experiment as it relates to many observable. In this work, we employ three commonly used algorithms in machine learning, the artificial neural network (ANN), the convolutional neural network (CNN), and the light gradient boosting machine (LightGBM), to determine the impact parameter by analyzing either the charged particle spectra or several features simulated with events from the ultrarelativistic quantum molecular dynamics (UrQMD) model. To closely imitate experimental data and investigate the generalizability of the trained machine learning algorithms, incompressibility of nuclear equation of state and the in-medium nucleon-nucleon cross sections are varied in the UrQMD model to generate the training data. The mean absolute error Δb between the true and the predicted impact parameter is smaller than 0.45 fm if training and testing sets are sampled from the UrQMD model with the same parameter set. However, if training and testing sets are sampled with different parameter sets, Δb would increase to 0.8 fm. The generalizability of the trained machine learning algorithms suggests that these machine learning algorithms can be used reliably to reconstruct the impact parameter in experiment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Specific conductivity, pH, dissolved oxygen, water temperature, alkalinity and sulfide in-situ data; Slate River floodplain, Crested Butte, CO; May 2020-October 2020

This data package includes a time-series of field measurements from May to October 2020 in groundwater and surface water from the Slate River floodplain in Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The data packade includes 6 data files, one for each measured variable: specific conductivity, pH, dissolved oxygen, water temperature, alkalinity and sulfide. All measurements were recorded in the field immediately after water sampling. Groundwater samples were extracted from a network of installed rhizons (Rhizosphere Research Products, part no. 19.60.21F, 0.6 micrometer mesh size) and piezometer wells within the floodplain. In addition to the data files, there is a terminology file explaining the terms used, a file level metadata file, and a sensor file with metadata about the sensors used.All files are in csv format.

54 ENVIRONMENTAL SCIENCES↗

Specific conductivity, pH, dissolved oxygen, water temperature and alkalinity in-situ data; Slate River floodplain, Crested Butte, CO; March 2021-October 2021

This data package includes a time-series of field measurements from March to October 2021 in groundwater and surface water from the Slate River floodplain in Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The data package includes 5 data files, one for each measured variable: specific conductivity, pH, dissolved oxygen, water temperature and alkalinity. All measurements were recorded in the field immediately after water sampling. Groundwater samples were extracted from a network of installed rhizons (Rhizosphere Research Products, part no. 19.60.21F, 0.6 micrometer mesh size) and piezometer wells within the floodplain. In addition to the data files, there is a terminology file explaining the terms used, a file level metadata file, and a sensor file with metadata about the sensors used.All files are in csv format.

54 ENVIRONMENTAL SCIENCES↗

In-situ electrochemical and water quality data; Slate River and East River floodplains, Crested Butte, CO; May 2022-September 2022

This data package includes a time-series of field measurements from May to September 2022 in groundwater and surface water from the Slate River and East River floodplains in Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The data package includes 5 data files, one for each measured variable: specific conductivity, pH, dissolved oxygen, water temperature and alkalinity. All measurements were recorded in the field immediately after water sampling. Groundwater samples were extracted from a network of installed rhizons (Rhizosphere Research Products, part no. 19.60.21F, 0.6 micrometer mesh size) and piezometer wells within the floodplain. In addition to the data files, there is a terminology file explaining the terms used, a file level metadata file, and a sensor file with metadata about the sensors used.All files are in csv format.

54 ENVIRONMENTAL SCIENCES↗

Groundwater level elevation and temperature data, Oct 2018-Dec 2021, Slate River Floodplain, Crested Butte, CO

This data package includes a time series of water level and temperature measurements from October 2018 to December 2021 in groundwater and surface water from the Slate River floodplain outside Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The data were recorded by pressure transducers were installed in four types of piezometers: 1) a network of gravel bed ("GB") drive-point piezometers with a 6-inch screen interval installed all at ~330 cm below ground surface. 2) a network of piezometers screened across the water table, used to measure evapotranspiration ("ET") using the White method. Each of these piezometers is screened along almost its entire length.3) a suite nested piezometers used the measure the vertical hydraulic gradient ("VHG") across the fines-cobble interface. Each of these piezometers uses a 6-inch screen length.4) a group of piezometers scattered across the boundaries of the floodplain, used to monitor boundary conditions ("BC") flowing into and out of the floodplain. With the exception of "SR-BD-WT", each of these piezometers is screened along its entire length. Within the data package, "FLMD.csv" describes file-level metadata and "dd.csv" defines column headers and universal terms across the dataset. The data package includes 11 "*data.csv" files, one for each piezometer type for each calendar year. Because piezometers have been added over time, not every sensor has data dating back to Oct 2018. Each "*data.csv" file has a corresponding "*_InstallationMethods.csv" file that describes the location, elevation, screen depth, sediment type and sensor metadata for each piezometer and pressure transducer.

54 ENVIRONMENTAL SCIENCES↗

Data Science-Driven Discovery of Multimetallic Oxygen-cycle Electrocatalysts for Enhanced Energy Conversion

The overarching objective of this effort has been to combine state-of-the-art data science techniques, first principles analyses, and molecular-level characterization of electrocatalyst structure and reactivity to identify both in-situ mechanisms for degradation and transformation of electrocatalysts with highly complex catalytic structures and the impact of these transformations on catalytic activity. The primary catalysts of interest have been multielemental alloys, including high entropy alloys (HEA’s), which are characterized by a high degree of disorder and up to 20 different elements within a single nanoparticle. We have applied these strategies primarily to energy-critical oxygen cycle electrocatalytic reactions, including oxygen reduction (ORR), but we have also considered extensions to non-electrochemical chemistries such as ammonia synthesis and decomposition. We have made strong progress in the development of computational methods on both the level of machine learning methods development as well as first principles-based treatments of HEA’s, and we have leveraged these insights to propose promising HEA catalysts for the ORR. On the experimental side, we developed new HEA synthesis and characterization protocols relevant to these reactions and developed a database combining our experimental results with corresponding computational tools.

36 MATERIALS SCIENCE↗

Comparison of scattering ratio profiles retrieved from ALADIN/Aeolus and CALIOP/CALIPSO observations and preliminary estimates of cloud fraction profiles

The space-borne active sounders have been contributing invaluable vertically resolved information of atmospheric optical properties since the launch of Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) in 2006. To build long-term records from space-borne lidars useful for climate studies, one has to understand the differences between successive space lidars operating at different wavelengths, flying on different orbits, and using different viewing geometries, receiving paths, and detectors. In this article, we compare the results of Atmospheric Laser Doppler INstrument (ALADIN) and Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) lidars for the period from 28 June to 31 December 2019. First, we build a dataset of ALADIN–CALIOP collocated profiles (Δdist<1°; Δtime<6 h). Then we convert ALADIN's 355 nm particulate backscatter and extinction profiles into the scattering ratio vertical profiles SR(z) at 532 nm using molecular density profiles from Goddard Earth Observing System Data Assimilation System, version 5 (GEOS-5 DAS). And finally, we build the CALIOP and ALADIN globally gridded cloud fraction profiles CF(z) by applying the same cloud detection threshold to the SR(z) profiles of both lidars at the same spatial resolution. Before comparing the SR(z) and CF(z) profiles retrieved from the two analyzed lidar missions, we performed a numerical experiment to estimate the best achievable cloud detection agreement CDA norm (z) considering the differences between the instruments. We define CDA norm (z) in each latitude–altitude bin as the occurrence frequency of cloud layers detected by both lidars, divided by a cloud fraction value for the same latitude–altitude bin. We simulated the SR(z) and CF(z) profiles that would be observed by these two lidars if they were flying over the same atmosphere predicted by a global model. By analyzing these simulations, we show that the theoretical limit for CDA$_{norm}^{theor}$(z) for a combination of ALADIN and CALIOP instruments is equal to 0.81±0.07 at all altitudes. In other words, 19 % of the clouds cannot be detected simultaneously by two instruments due to said differences. The analyses of the actual observed CALIOP–ALADIN collocated dataset containing ~78 000 pairs of nighttime SR(z) profiles revealed the following points: (a) the values of SR(z) agree well up to ~3 km height. (b) The CF(z) profiles show agreement below ~3 km, where ~80 % of the clouds detected by CALIOP are detected by ALADIN as expected from the numerical experiment. (c) Above this height, the CDA$_{norm}^{obs}$(z) reduces to ~50 %. (d) On average, better sensitivity to lower clouds skews ALADIN's cloud peak height in pairs of ALADIN–CALIOP profiles by ~0.5±0.6 km downwards, but this effect does not alter the heights of polar stratospheric clouds and high tropical clouds thanks to their strong backscatter signals. (e) The temporal evolution of the observed CDA$_{norm}^{obs}$(z) does not reveal any statistically significant change during the considered period. This indicates that the instrument-related issues in ALADIN L0/L1 have been mitigated, at least down to the uncertainties of the following CDA$_{norm}^{obs}$(z) values: 68±12 %, 55±14 %, 34±14 %, 39±13 %, and 42±14 % estimated at 0.75, 2.25, 6.75, 8.75, and 10.25 km, respectively.

54 ENVIRONMENTAL SCIENCES↗

WHONDRS-GUI: a web application for global survey of surface water metabolites

Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811 , which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server ( https://xmlin.shinyapps.io/whondrs/ ).

59 BASIC BIOLOGICAL SCIENCES↗

Differentiating Thermal Conductances at Semiconductor Nanocrystal/Ligand and Ligand/Solvent Interfaces in Colloidal Suspensions

Infrared-pump, electronic-probe (IPEP) spectroscopy is used to measure heat flow into and out of CdSe nanocrystals suspended in an organic solvent, where the surface ligands are initially excited with an infrared pump pulse. Subsequently, the heat is transferred from the excited ligands to the nanocrystals and in parallel to the solvent. Parallel heat transfer in opposite directions uniquely enables us to differentiate the thermal conductances at the nanocrystal/ligand and ligand/solvent interfaces. Using a novel solution to the heat diffusion equation, we fit the IPEP data to find that the nanocrystal/ligand conductances range from 88 to 135 MW m –2 K –1 and are approximately 1 order of magnitude higher than the ligand/solvent conductances, which range from 7 to 26 MW m –2 K –1 . Transient nonequilibrium molecular dynamics (MD) simulations of nanocrystal suspensions agree with IPEP data and show that ligands bound to the nanocrystal by bidentate bonds have more than twice the per-ligand conductance as those bound by monodentate bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of composition and symmetry energy on the temperature of quasiprojectiles simulated with antisymmetrized molecular dynamics

The equation of state describes the emergent physical properties of matter. Experimental data is needed to help constrain the equation of state for nuclear matter. These constraints can help distinguish between an “asy-stiff” and an “asy-soft” equation of state, which has astrophysical implications. One path to help constrain the models is to analyze the nuclear caloric curve; some experiments have shown dependence on neutron excess, and may thus be sensitive to the asymmetry. A difference in the caloric curve based on the asymmetry of the reconstructed quasiprojectile (QP) had been observed using 70 Zn on 70 Zn at 35 MeV/nucleon taken with the NIMROD array. Antisymmetrized molecular dynamics calculations were performed for the same system and deexcited with gemini++. Both Gogny (asy-soft) and Gogny-as (asy-stiff) data sets were generated. The particles were then filtered based on detector geometric acceptance and thresholds. From the accepted particles, the excitation energy and temperature were calculated in the same way as for experimental data. Additionally, filter effects on the observed nuclear caloric curves were investigated. A tendency for the asy-stiff nuclear caloric curves to have higher temperatures than their asy-soft counterparts was observed for a number of probes. In addition, some probes may show sensitivity to the reconstructed composition of the QP, but this is inconclusive due to high statistical fluctuations and a large dependence on the exact method of event selection.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Deciphering the Solvation Structure of Aqueous ZnCl 2 Solutions from X-ray Absorption Spectra Using the Interpretable Graph Neural Network

Machine learning (ML) provides powerful pathways for predicting spectroscopic observables from atomic structures, but its broader impact depends on making model predictions interpretable in terms of physical and chemical principles. Here, we introduce a physics-guided graph neural network (GNN) model that predicts Zn K-edge X-ray spectroscopy (XAS) spectra of aqueous ZnCl 2 solutions. Training data are generated from ab initio XAS calculations on molecular dynamics snapshots obtained using a machine learning interatomic potential. The GNN reproduces experimental spectra across concentrations from dilute (<0.1 m) to highly concentrated (30 m, “water-in-salt”) regimes and scales efficiently to large, disordered liquid systems beyond the reach of conventional ab initio approaches. Gradient-based attribution analysis reveals that the model learns physically meaningful structure-spectrum relationships. Ligand-specific attributions reflect orbital hybridization patterns and the origin of the excitations derived from the density functional theory. Bond-length attributions recover spectral shifts consistent with multiple-scattering theory. Finally, this work bridges data-driven prediction with electronic-structure theory, establishing a general paradigm for interpretable ML that links atomic structure, electronic structure, and spectroscopic observables.

25 ENERGY STORAGE↗

Post Access Report: Initial testing of wave energy powered UV-C LED anti-biofouling system

In the experiment entitled “Initial Testing of Wave Energy Powered UV-C LED Anti-Biofouling System,” a UV-C LED was used to treat platinum-coated titanium coupons emulating CTD electrode material. An additional control set of coupons were exposed to seawater without the LED treatment. The experimental setup was deployed in seawater tanks at PNNL-Sequim’s Marine and Coastal Research Laboratory (MCRL) for the duration of six months. Tank seawater temperature data were collected for the duration of the experimental campaign. At two-month intervals triplicate sets of coupons were removed from both treatment and control test chambers and weighed to characterize biomass accumulation. After weighing, the coupons were photographed in initial condition, with a stain applied to highlight biofouling growth, and after rinsing off excess stain. These photographs were analyzed using PNNL’s Biofouling Growth Index (BGI) software and with a calculation of percentage dark pixels after conversion to grayscale. Additionally, at the final 6-month datapoint triplicate sets of control and test coupons were sent to PNNL-Richland’s Environmental Molecular Sciences Laboratory (EMSL) for scanning electron microscopy. All data organization and collection methods are described in further detail in the document “TEAMER_3newable_Data_Guide.pdf.” Biomass accumulation increased over time on both sets of coupons, and percent area biofouled demonstrated a similar trend. Analysis of the collected data resulted in the findings that treatment method has an impact on biofouling growth, though to a much less significant extent than time does. Additionally, qualitative findings included the presence of advanced life forms such as worms in the control test chamber, but not in the treated test chamber.

16 TIDAL AND WAVE POWER↗

Personal and environmental predictors of polycyclic aromatic hydrocarbon exposure identified through repeated silicone wristband sampling

This study integrates quantitative data on personal exposure to polycyclic aromatic hydrocarbons (PAHs) in 162 silicone wristbands with demographics, behavioral information, and housing characteristics to explore contributions to residential exposure in a superfund-adjacent community over the course of a year. Forty-six residents completed questionnaires and wore silicone wristbands as personal passive samplers for seven consecutive days on up to four separate occasions in alternating months between November 2022 and June 2023. It was hypothesized that individual behaviors and housing characteristics are sources of dependence and correlation between personal PAH exposures. 50 PAHs were detected at least once, 17 of which were alkylated PAHs. Exposure to PAHs of similar molecular weight was often correlated, notably between naphthalenes (2-rings) and higher molecular weight PAHs (3 or more rings). Generalized linear mixed models identified flooring type, participant age, and sampling month as important predictors of increased PAH exposure, and flooring type, and use of wood stoves or heavy machinery as predictors of increased naphthalene exposure relative to higher molecular weight PAHs. Individual chemical models based on concentration data and detection frequencies corroborated these findings across multiple PAHs. We demonstrate that personal exposure is not static and the degree of variability in personal exposure is individual. Hence, identification of influential exposure factors through repeated measures of chemical exposure and characterization of variability in personal exposure as performed in this study, is important in the development of exposure mitigation strategies.

Bonner, Emily↗

Direct structural retrieval from gas-phase ultrafast diffraction data using a genetic algorithm

Ultrafast scattering techniques such as ultrafast electron diffraction and ultrafast x-ray diffraction have been utilized to elucidate the structural dynamics, reaction intermediates, and final products in molecular reactions following photoexcitation. The time-dependent structures are typically not directly retrieved from the experimental data, but they rely on comparison with calculations. The genetic algorithm (GA), a global optimization strategy, can be used to retrieve the molecular structures directly from diffraction patterns without any theoretical input. However, the robustness of the GA with respect to real experimental conditions such as a limited momentum transfer range, noise, and artifacts has not been studied in detail. In this work, we characterize the performance of the GA with simulated data that mimic realistic experimental conditions. We have developed and implemented a variant of the GA specific to diffraction measurements which performs better in the presence of imperfect data compared to the standard implementation of the GA. We demonstrate this method with both synthetic data and experimental ultrafast electron diffraction data on the UV-induced photodissociation of trifluoroiodomethane (C⁢F 3⁡ I) molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

A data-driven multiscale model for reactive wetting simulations

Here, we describe a data-driven, multiscale technique to model reactive wetting of a silver–aluminum alloy on a Kovar™ (Fe-Ni-Co alloy) surface. We employ molecular dynamics simulations to elucidate the dependence of surface tension and wetting angle on the drop’s composition and temperature. A design of computational experiments is used to efficiently generate training data of surface tension and wetting angle from a limited number of molecular dynamics simulations. The simulation results are used to parameterize models of the material’s wetting properties and compute the uncertainty in the models due to limited data. The data-driven models are incorporated into an engineering-scale (continuum) model of a silver–aluminum sessile drop on a Kovar™ substrate. Model predictions of the wetting angle are compared with experiments of pure silver spreading on Kovar™ to quantify the model-form errors introduced by the limited training data versus the simplifications inherent in the molecular dynamics simulations. The paper presents innovations in the determination of “convergence” of noisy MD simulations before they are used to extract the wetting angle and surface tension, and the construction of their models which approximate physio-chemical processes that are left unresolved by the engineering-scale model. Together, these constitute a multiscale approach that integrates molecular-scale information into continuum scale models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗