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At least 343 records · Page 19

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Future Changes in Midwest Extreme Precipitation Depend on Storm Type

Midwestern U.S. extreme precipitation is associated with multiple storm types including mesoscale convective systems (MCSs) and/or training thunderstorms, tropical cyclone (TC) remnants, and winter storms. Anthropogenic warming is expected to increase climatological precipitation globally, however, there may be little correspondence with regional storm-based changes. Furthermore, uncertainty remains in precipitation-temperature scaling due to use of convective parameterization in most global models. In this study, we investigated historically impactful extreme precipitation events from multiple types of Midwest storms using the Weather Research and Forecasting model at convection-permitting resolution. We simulated five-member ensembles of historical hindcasts and experiments representing the storms in the future using the pseudo-global warming method. We found that future precipitation changes depend on storm type, with increases near Clausius-Clapeyron (CC) for winter storms, no consensus for MCSs and/or training thunderstorms, and sub-CC increases for TC remnants. This research highlights the importance of considering storm type in future extreme precipitation projections.

54 ENVIRONMENTAL SCIENCES↗

Summer Convective Precipitation Changes Over the Great Lakes Region Under a Warming Scenario

To understand future summer precipitation changes over the Great Lakes Region (GLR), we performed an ensemble of regional climate simulations through the Pseudo-Global Warming (PGW) approach. We found that different types of convective precipitation respond differently to the PGW signal. Isolated deep convection (IDC), usually concentrated in the southern domain, shows an increase in precipitation to the north of the GLR. Mesoscale convective systems (MCSs), usually concentrated upwind of the GLR, shift to the downwind region with increased precipitation. Thermodynamic variables such as convective available potential energy (CAPE) and convective inhibition energy (CIN) are found to increase across almost the entire studied domain, creating a potential environment more favorable for stronger convection systems and less favorable for weaker ones. Meanwhile, changes in the lifting condensation level (LCL) and level of free convection (LFC) show a strong correlation with variations in convective precipitation, highlighting the significance of these thermodynamic factors in controlling precipitation over the domain. Our results indicate that the decrease in LCL and LCF in areas with increased convective precipitation is mainly due to increased atmospheric moisture. In response to the prescribed warming perturbation, MCSs occur more frequently downwind, while localized IDCs exhibit more intense rain rates, longer durations, and larger rainfall area.

54 ENVIRONMENTAL SCIENCES↗

Connecting energetics to dynamics in particle growth by oriented attachment using real-time observations

The interplay between crystal and solvent structure, interparticle forces and ensemble particle response dynamics governs the process of crystallization by oriented attachment (OA), yet a quantitative understanding is lacking. Using as a model system ZnO, we combine in situ TEM observations of single particle and ensemble assembly dynamics with simulations of interparticle forces and responses to relate experimentally derived interparticle potentials to the underlying interactions. We show that OA is driven by forces and torques due to a combination of electrostatic ion-solvent correlations and dipolar interactions that act at separations well beyond 5 nm. Importantly, coalignment is achieved before particles reach separations at which strong attractions drive the final jump to contact. The observed barrier to attachment is negligible, while dissipative factors in the quasi-2D confinement of the TEM fluid cell lead to abnormal diffusivities with timescales for rotation much less than for translation, thus enabling OA to dominate.

36 MATERIALS SCIENCE↗

Local-scale Arctic tundra heterogeneity affects regional-scale carbon dynamics

In northern Alaska nearly 65% of the terrestrial surface is composed of polygonal ground, where geomorphic tundra landforms disproportionately influence carbon and nutrient cycling over fine spatial scales. Process-based biogeochemical models used for local to Pan-Arctic projections of ecological responses to climate change typically operate at coarse-scales (1km 2 –0.5°) at which fine-scale (<1km 2 ) tundra heterogeneity is often aggregated to the dominant land cover unit. Here, we evaluate the importance of tundra heterogeneity for representing soil carbon dynamics at fine to coarse spatial scales. We leveraged the legacy of data collected near Utqiagvik, Alaska between 1973 and 2016 for model initiation, parameterization, and validation. Simulation uncertainty increased with a reduced representation of tundra heterogeneity and coarsening of spatial scale. Hierarchical cluster analysis of an ensemble of 21 st -century simulations reveals that a minimum of two tundra landforms (dry and wet) and a maximum of 4km 2 spatial scale is necessary for minimizing uncertainties (<10%) in regional to Pan-Arctic modeling applications.

54 ENVIRONMENTAL SCIENCES↗

Projected runoff declines from plant physiological effects on precipitation

Abstract The impact of plants on runoff under high atmospheric CO 2 is a major uncertainty for future water resources. Theory and Earth system models (ESMs) suggest that stricter plant stomatal regulation under high CO 2 will reduce transpiration, potentially boosting runoff. Yet, across a 12-member ensemble of idealized ESM simulations that isolate plant responses to CO 2 , we show that lower transpiration robustly enhances runoff over only 5% of modelled global land area. Precipitation changes are five times more important than transpiration changes in driving runoff responses and are a significant signal of CO 2 physiological forcing over 31–57% of land areas across models. Crucially, ESMs largely disagree on where physiologically forced precipitation changes occur but agree that plant responses in most locations are as likely to reduce runoff as increase it. These results imply that large model uncertainties in precipitation responses, rather than transpiration responses, explain why ESMs disagree on plant physiologically driven runoff changes.

Lesk, Corey S. (ORCID:0000000308684040)↗

Calculating adsorption isotherms using the two-phase thermodynamic method and molecular dynamics simulations

We describe the calculation of adsorption isotherms from molecular dynamics simulations based on the two-phase thermodynamic (2PT) model. The 2PT model developed for bulk fluid phases treats the gas-like components as hard spheres (HSs), which correctly recovers the limiting behaviors of unconfined fluids. We showed that this treatment, however, does not always lead to the correct zero-loading behavior in strongly confining systems. For methane adsorption into zeolite MFI, the HS reference state underestimates entropy by up to 20% at low loadings and leads to an order-of-magnitude increase in the adsorption onset pressure. To fix these issues, we propose the use of ideal adsorbed gas (IAG) as the gas reference model, the properties of which can be computed using the Widom insertion method on an empty adsorbent. We further describe three routes to compute adsorption isotherms from the Helmholtz free energy at different loadings. Comparing against established Monte Carlo (MC) methods, we found that the adsorption isotherms obtained using the IAG reference state agrees to within 40%, which corresponds to deviations of <5% in adsorption free energy. The isotherms calculated using the HS reference state underestimate the adsorption uptake at low to medium loadings in strongly confining systems, but its accuracy improves at higher loadings and as the pore size increases relative to the sorbate diameter. The methods described here provide an alternative approach for computing adsorption isotherms when MC simulations in an open ensemble are undesirable and enable a direct comparison of computed adsorption thermodynamics with experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Melting point of iron at high pressure: An assessment of uncertainties and effect of electronic temperature

An accurate calculation of the melting point of iron at various pressures in the Earth's core is important for understanding the core structure, geodynamo, and the Earth's history. Previous studies have assessed the melt line of iron at these extreme conditions using various experimental measurement techniques as well as both ab initio and classic molecular dynamics simulations. However, experimental measurements have uncertainties up to several hundred Kelvin, and inconsistencies remain among simulation results. Here in this work, we propose an iterative framework that couples density functional theory (DFT) calculations and molecular dynamics simulations performed using an ensemble of interatomic potentials to assess the effect of electronic temperature on the melting point. We systematically validate the potentials by comparing lattice constants and phonon dispersion curves at 0 K and enthalpy differences between liquid and HCP, FCC, BCC phases of iron close to the melt line at 300 GPa with DFT. Our results show that HCP iron melts at 6144 K (at 300 GPa), BCC phase is thermodynamically unstable, and FCC is metastable at this temperature. The melting points of FCC and BCC phases at 300 GPa are 5858 and 5647 K, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG 1 antibody

Subcutaneous injection is the preferred route of administration for many antibody therapeutics for reasons that include its speed and convenience. However, the small volume limit (typically ≤2 mL) for subcutaneous delivery often necessitates antibody formulations at high concentrations (commonly ≥100 mg/mL), which may lead to physicochemical problems. For example, antibodies with large hydrophobic or charged patches can be prone to self-interaction giving rise to high viscosity. Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG 1 antibody prone to self-interaction. An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~200 anti-GCGR IgG 1 variants. A negative correlation was found between the viscosity determined at high concentration (180 mg/mL) and the DLS interaction parameter measured at low concentration (2–10 mg/mL). Additionally, anti-GCGR variants were readily identified with reduced viscosity and antigen-binding affinity within a few fold of the parent antibody, with no identified impact on overall developability. The methods described here may be useful in the optimization of other antibodies to facilitate their therapeutic administration at high concentration.

59 BASIC BIOLOGICAL SCIENCES↗

Scalable Risk Assessment of Rare Events in Power Systems With Uncertain Wind Generation and Loads

Risk assessment of rare events has become increasingly important in power system planning and operation with the increasing integration of renewable energy and the presence of system uncertainties. However, quantifying the risk posed by rare events via the traditional method, i.e., Monte Carlo sampling (MCS), incurs substantial computational expense stemming from the vast ensemble of power flow simulations. To accelerate the assessment, this paper proposes a Deep Neural Network (DNN)-kernelized vector-valued Gaussian Process (VVGP) approach with excellent computational efficiency while maintaining high accuracy. Consequently, serving as a surrogate model for the power flow solver, the DNN-kernelized VVGP enables significantly faster but accurate risk assessment compared to the power flow solver. The developed surrogate model evaluates low-order N - k events that contain more than 90% instances by adeptly capturing the topological features while the high-order N - k events are assessed via a power flow solver, thereby striking a balance between computational efficiency and uncertainty quantification accuracy. Moreover, the model incorporates a Support Vector Machine (SVM) classifier to resample concerning low-probability tail events to counteract the biases potentially introduced during the DNN-kernelized VVGP evaluations. Simulations conducted on the modified IEEE 24-bus, 118-bus, and European 1354-bus systems demonstrate that the proposed method maintains the accuracy benchmark set by MCS while significantly reducing computational demands in large-scale power systems as compared to other state-of-the-art methods.

17 WIND ENERGY↗

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.

59 BASIC BIOLOGICAL SCIENCES↗

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

60 APPLIED LIFE SCIENCES↗

ORNL_AISD_NiPt

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for three different sizes of the crystal structure: 256 atoms, 864 atoms, and 2,048 atoms, each of which contains 1900 configurations. For each size of the crystal structure, the data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in three compressed zipped folders: atoms256.zip, atoms864.zip, atoms2048.zip Each zipped folder contains the data that describes crystals of size 256 atoms, 864 atoms, and 2,048 atoms respectively. Each one of the three zipped folders contains the data structured in the following way: -Ni_ground_state.cfg --> atomic configuration for the pure nickel -Pt_ground_state.cfg --> atomic configuration for the pure platinum -Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder. Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms256.zip is 65,046. The total number of atomic configurations contained in atoms864.zip is 63,936. The total number of atomic configurations contained in atoms2048.zip is 61,997. The total number of atomic configurations spanned by the entire dataset is 190,979. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büccchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D

36 MATERIALS SCIENCE↗

ORNL_AISD_NiPt_108atoms

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for crystal structures with 108 atoms with 1,900 configurations. The data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system 'MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001' [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in a compressed zipped folders atoms108.zip. The zipped folder contains the data structured in the following way: - Ni_ground_state.cfg --> atomic configuration for the pure nickel - Pt_ground_state.cfg --> atomic configuration for the pure platinum - Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder - Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms108.zip is 66,132. This dataset is an extension to the dataset ORNL_AISD_NiPt [5] that has been previously released with crystal structures of 256 atoms, 864 atoms, and 2,048 atoms, with the same methodology for data collection. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D [5] M. Karabin, M. Lupo Pasini, and M. Eisenbach. ORNL_AISD_NiPt. United States: N. p., 2023. Web. doi:10.13139/OLCF/1958172.

36 MATERIALS SCIENCE↗

libEnsemble: A complete Python toolkit for dynamic ensembles of calculations

Almost all science and engineering applications eventually stop scaling: their runtime no longer decreases as available computational resources increase. Therefore, many applications will struggle to efficiently use emerging extreme-scale high-performance, parallel, and distributed systems. libEnsemble is a complete Python toolkit and workflow system for intelligently driving ensembles of experiments or simulations at massive scales. It enables and encourages multidisciplinary design, decision, and inference studies portably running on laptops, clusters, and supercomputers.

97 MATHEMATICS AND COMPUTING↗

Exascale Algorithms and Software for Lattice Field Theory in High Energy Physics: Searching Beyond the Standard Model

The Boston University component has focused on the algorithmic development of new Multigrid solver for the critical kernel for the Dirac propagators that dominated the both simulation require for lattice ensemble and the analysis of physical correlation functions. Progress on this has meet the above objects, even exceeding them a bit. The result is the beginning if multiscale lattice QCD applicable to future Exascale hardware and the development of the QUDA software for NVIDIA GPUs to give near optimal performance. As we approach exascale hardware and computation at that scale this provides the infrastructure for further advances.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nucleon valence quark distribution functions from Lattice QCD

We present results on the nucleon valence quark distribution extracted from Lattice QCD simulations, using a gauge ensemble of Nf=2+1 Wilson-Clover fermions with a pion mass of m?=350 MeV and lattice spacing of a=0.091 fm. We obtain reduced Ioffe Time Distributions (rITDs) by computing appropriate matrix elements on the lattice, and elaborate on the extraction of the desired quark distributions from the rITDs following the pseudo-PDF approach. A set of techniques are considered in order to ensure ground state dominance. Theoretical and experimental implications of our calculation are discussed.

Kallidonis, Christos↗

An overview of the Western United States Dynamically Downscaled Dataset (WUS-D3)

Abstract. Predicting future climate change over a region of complex terrain, such as the western United States (US), remains challenging due to the low resolution of global climate models (GCMs). Yet the climate extremes of recent years in this region, such as floods, wildfires, and drought, are likely to intensify further as climate warms, underscoring the need for high-quality and high-resolution predictions. Here, we present an ensemble of dynamically downscaled simulations over the western US from 1980–2100 at 9 km grid spacing, driven by 16 latest-generation GCMs. This dataset is titled the Western US Dynamically Downscaled Dataset (WUS-D3). We describe the challenges of producing WUS-D3, including GCM selection and technical issues, and we evaluate the simulations' realism by comparing historical results to temperature and precipitation observations. The future downscaled climate change signals are shaped in physically credible ways by the regional model's more realistic coastlines and topography. (1) The mean warming signals are heavily influenced by more realistic snowpack. (2) Mean precipitation changes are often consistent with wetting on the windward side of mountain complexes, as warmer, moister air masses are uplifted orographically during precipitation events. (3) There are large fractional precipitation increases on the lee side of mountain complexes, leading to potentially significant changes in water resources and ecology in these arid landscapes. (4) Increases in precipitation extremes are generally larger than in the GCMs, driven by locally intensified atmospheric updrafts tied to sharper, more realistic gradients in topography. (5) Changes in temperature extremes are different from what is expected by a shift in mean temperature and are shaped by local atmospheric dynamics and land surface feedbacks. Because of its high resolution, comprehensiveness, and representation of relevant physical processes, this dataset presents a unique opportunity to evaluate societally relevant future changes in western US climate.

Rahimi, Stefan (ORCID:0000000331884462)↗