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At least 19 records

Utah FORGE: Earth Model Native State Simulation Results

Utah FORGE phase 2C Native State Simulation zip contains the data used for the boundary conditions and subsequent native state simulation results obtained using the simulation code FALCON. Data are from the nodes of the simulation domain, with used a uniform 50m spacing over a 2500 X 2500 X 2750m domain approximately centered on the FORGE footprint. There is also a read me text file, that is included, containing metadata. The Reservoir Porosity and Upscale DFN Permeability zip contains the data used for the spatial distribution of the anisotropic permeability and porosity used in the native state simulation of the Utah FORGE site. Please contact Robert Podgorney at the Idaho National Laboratory with questions, robert.podgorney@inl.gov. There is also a read me text file included containing metadata.

15 GEOTHERMAL ENERGY↗

Biomechanical Analysis of Multilevel Posterior Cervical Spinal Fusion Constructs

Study Design: Controlled Laboratory Study Objective: To compare multilevel posterior cervical fusion (PCF) constructs stopping at C7, T1, and T2 under cyclic load to determine the range of motion (ROM) between the lowest instrumented level and lowest instrumented-adjacent level (LIV-1). Summary of Background Data: PCF is a mainstay of treatment for various cervical spine conditions. The transition between the flexible cervical spine and rigid thoracic spine can lead to construct failure at the cervicothoracic junction. There is little evidence to determine the most appropriate level at which to stop a multilevel PCF. Methods: Fifteen human cadaveric cervicothoracic spines were randomly assigned to 1 of 3 treatment groups: PCF stopping at C7, T1, or T2. Specimens were tested in their native state, following a simulated PCF, and after cyclic loading. Specimens were loaded in flexion-extension), lateral bending, and axial rotation. Three-dimensional kinematics were recorded to evaluate ROM. Results: The C7 group had greater flexion-extension motion than the T1 and T2 groups following instrumentation (10.17±0.83 degree vs. 2.77±1.66 degree and 1.06±0.55 degree, P <0.001), and after cyclic loading (10.42±2.30 degree vs. 2.47±0.64 degree and 1.99±1.23 degree, P <0.001). There was no significant difference between the T1 and T2 groups. The C7 group had greater lateral bending ROM than both thoracic groups after instrumentation (8.81±3.44 degree vs. 3.51±2.52 degree, P =0.013 and 1.99±1.99 degree, P =0.003) and after cyclic loading. The C7 group had greater axial rotation motion than the thoracic groups (4.46±2.27 degree vs. 1.26±0.69 degree, P =0.010; and 0.73±0.74 degree, P =0.003) following cyclic loading. Conclusion: Motion at the cervicothoracic junction is significantly greater when a multilevel PCF stops at C7 rather than T1 or T2. This is likely attributable to the transition from a flexible cervical spine to a rigid thoracic spine. Although this does not account for in vivo fusion, surgeons should consider extending multilevel PCF constructs to T1 when feasible. Level of Evidence: Not applicable.

Neurosciences & Neurology↗

Utah FORGE Phase Native State FALCON Model Files

The submission includes FALCON input file and mesh for the an initial pressure-temperature simulation, and a second set for pressure-temperature-displacement simulation. All simulations are steady state. Data and input for the FORGE Phase 2 native state model were compiled from historic and FORGE specific characterization efforts. The simulations look to find the in-situ pressure, temperature, and stress distributions in the vicinity of the Utah FORGE site. The purpose of the native state model was to establish a baseline for all other modeling analyses—so that the whole modeling team can start from a consistent set of conditions which makes for comparison of results more straightforward and meaningful. Requires the FALCON simulator which can be found in the "FALCON Simulator" link in the submission. Instructions for compiling and running FALCON can be found on the FORGE branch of the FALCON git repository in the README.

15 GEOTHERMAL ENERGY↗

The denatured state of HIV ‐1 protease under native conditions

Abstract The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.

60 APPLIED LIFE SCIENCES↗

Subsurface Characterization and Machine Learning Predictions at Brady Hot Springs Results

Geothermal power plants typically show decreasing heat and power production rates over time. Mitigation strategies include optimizing the management of existing wells - increasing or decreasing the fluid flow rates across the wells - and drilling new wells at appropriate locations. The latter is expensive, time-consuming, and subject to many engineering constraints, but the former is a viable mechanism for periodic adjustment of the available fluid allocations. Data and supporting literature from a study describing a new approach combining reservoir modeling and machine learning to produce models that enable strategies for the mitigation of decreased heat and power production rates over time for geothermal power plants. The computational approach used enables translation of sets of potential flow rates for the active wells into reservoir-wide estimates of produced energy and discovery of optimal flow allocations among the studied sets. In our computational experiments, we utilize collections of simulations for a specific reservoir (which capture subsurface characterization and realize history matching) along with machine learning models that predict temperature and pressure timeseries for production wells. We evaluate this approach using an "open-source" reservoir we have constructed that captures many of the characteristics of Brady Hot Springs, a commercially operational geothermal field in Nevada, USA. Selected results from a reservoir model of Brady Hot Springs itself are presented to show successful application to an existing system. In both cases, energy predictions prove to be highly accurate: all observed prediction errors do not exceed 3.68% for temperatures and 4.75% for pressures. In a cumulative energy estimation, we observe prediction errors that are less than 4.04%. A typical reservoir simulation for Brady Hot Springs completes in approximately 4 hours, whereas our machine learning models yield accurate 20-year predictions for temperatures, pressures, and produced energy in 0.9 seconds. This paper aims to demonstrate how the models and techniques from our study can be applied to achieve rapid exploration of controlled parameters and optimization of other geothermal reservoirs. Includes a synthetic, yet realistic, model of a geothermal reservoir, referred to as open-source reservoir (OSR). OSR is a 10-well (4 injection wells and 6 production wells) system that resembles Brady Hot Springs (a commercially operational geothermal field in Nevada, USA) at a high level but has a number of sufficiently modified characteristics (which renders any possible similarity between specific characteristics like temperatures and pressures as purely random). We study OSR through CMG simulations with a wide range of flow allocation scenarios. Includes a dataset with 101 simulated scenarios that cover the period of time between 2020 and 2040 and a link to the published paper about this project, where we focus on the Machine Learning work for predicting OSR's energy production based on the simulation data, as well as a link to the GitHub repository where we have published the code we have developed (please refer to the repository's readme file to see instructions on how to run the code). Additional links are included to associated work led by the USGS to identify geologic factors associated with well productivity in geothermal fields. Below are the high-level steps for applying the same modeling + ML process to other geothermal reservoirs: 1. Develop a geologic model of the geothermal field. The location of faults, upflow zones, aquifers, etc. need to be accounted for as accurately as possible 2. The geologic model needs to be converted to a reservoir model that can be used in a reservoir simulator, such as, for instance, CMG STARS, TETRAD, or FALCON 3. Using native state modeling, the initial temperature and pressure distributions are evaluated, and they become the initial conditions for dynamic reservoir simulations 4....

15 GEOTHERMAL ENERGY↗

Spin-optomechanical cavity interfaces by deep subwavelength phonon-photon confinement

A central goal of quantum information science is transferring qubits between space, time, and modality. Spin-based systems in solids are promising quantum memories, but high-fidelity transfer of their quantum states to telecom optical fields remains challenging. Here, we introduce a phonon-mediated interface between spins in a diamond nanobeam optomechanical crystal and telecom optical fields by a simultaneous deep-subwavelength confinement of optical and acoustic fields with mode volumes $V_{\textrm{mech}}$$/Λ^3_\textrm{p} ~ 10^{-5}$ and $V_{\textrm{opt}}$$/λ^3 ~ 10^{−3}$, respectively. This confinement boosts the spin-mechanical coupling rate of Group-IV silicon vacancy (SiV − ) centers by an order of magnitude to ~ 32 MHz while retaining high acousto-optical couplings. The optical cavity couples to the spin irrespective of the emitter’s native excited states, avoiding spectral diffusion. Using Quantum Monte Carlo simulations, we estimate heralded entanglement fidelities exceeding 0.96 between two such interfaces. We anticipate broad utility beyond diamond emitter-telecom systems to most solid-state quantum memories.

Raniwala, Hamza [Massachusetts Inst. of Technology↗

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↗

Prospects for simulating a qudit-based model of (1+1)D scalar QED

We present a gauge invariant digitization of (1+1)d scalar quantum electrodynamics for an arbitrary spin truncation for qudit-based quantum computers. We provide a construction of the Trotter operator in terms of a universal qudit-gate set. Here, the cost savings of using a qutrit based spin-1 encoding versus a qubit encoding are illustrated. We show that a simple initial state could be simulated on current qutrit based hardware using noisy simulations for two different native gate set.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗

Evaluation of native Earth system model output with ESMValTool v2.6.0

Earth system models (ESMs) are state-of-the-art climate models that allow numerical simulations of the past, present-day, and future climate. To extend our understanding of the Earth system and improve climate change projections, the complexity of ESMs heavily increased over the last decades. As a consequence, the amount and volume of data provided by ESMs has increased considerably. Innovative tools for a comprehensive model evaluation and analysis are required to assess the performance of these increasingly complex ESMs against observations or reanalyses. One of these tools is the Earth System Model Evaluation Tool (ESMValTool), a community diagnostic and performance metrics tool for the evaluation of ESMs. Input data for ESMValTool needs to be formatted according to the CMOR (Climate Model Output Rewriter) standard, a process that is usually referred to as “CMORization”. While this is a quasi-standard for large model intercomparison projects like the Coupled Model Intercomparison Project (CMIP), this complicates the application of ESMValTool to non-CMOR-compliant climate model output. In this paper, we describe an extension of ESMValTool introduced in v2.6.0 that allows seamless reading and processing of “native” climate model output, i.e., operational output produced by running the climate model through the standard workflow of the corresponding modeling institute. This is achieved by an extension of ESMValTool's preprocessing pipeline that performs a CMOR-like reformatting of the native model output during runtime. Thus, the rich collection of diagnostics provided by ESMValTool is now fully available for these models. For models that use unstructured grids, a further preprocessing step required to apply many common diagnostics is regridding to a regular latitude–longitude grid. Extensions to ESMValTool's regridding functions described here allow for more flexible interpolation schemes that can be used on unstructured grids. Currently, ESMValTool supports nearest-neighbor, bilinear, and first-order conservative regridding from unstructured grids to regular grids. Example applications of this new native model support are the evaluation of new model setups against predecessor versions, assessing of the performance of different simulations against observations, CMORization of native model data for contributions to model intercomparison projects, and monitoring of running climate model simulations. For the latter, new general-purpose diagnostics have been added to ESMValTool that are able to plot a wide range of variable types. Currently, five climate models are supported: CESM2 (experimental; at the moment, only surface variables are available), EC-Earth3, EMAC, ICON, and IPSL-CM6. As the framework for the CMOR-like reformatting of native model output described here is implemented in a general way, support for other climate models can be easily added.

58 GEOSCIENCES↗

Utah FORGE Phase 3 Native State Model: 2022 Update

This is the Phase 3 native state model update. The Phase 3 numerical model represents a significant subsurface volume below the FORGE site footprint. The model domain of 4.0 km x 4.0 km x 4.2 km is located approximately between depths of 4000 to 4200 meters below land surface. This data archive consists of 10 files, 4 of which are simulation input files and the remaining 6 are simulation output files. There is an included readme.txt file that contains details on each of the data files. The input files include meshes, FALCON code inputs, tabulated data of water properties, temperature values, and model boundaries. The output files include simulation outfiles and point data of modeled material properties.

15 GEOTHERMAL ENERGY↗

Hybrid Oscillator-Qubit Quantum Processors: Instruction Set Architectures, Abstract Machine Models, and Applications

This tutorial offers a pedagogical guide to hybrid quantum processors that integrate discrete-variable (DV) qubits and continuous-variable (CV) oscillators. Aimed at computer scientists, engineers, and physicists, it provides an overview of the experimental, algorithmic, and architectural aspects of this novel and rapidly developing hardware model. Experimental realizations of this model include superconducting, trapped-ion, and neutral-atom platforms. By combining DV and CV components, hybrid oscillator-qubit processors enable a powerful new paradigm that offers complementary strengths for quantum control, error correction, computation, and simulation. Working toward the goal of a full-stack system connecting applications to CV-DV hardware, we define and formulate abstract machine models and instruction set architectures. These essential abstractions enable codesign of hardware and software, and resource estimation for exploring the potential of current and future hardware for computational and simulation tasks. Using these abstractions, we present both new and existing examples that illustrate the benefits of hybrid CV-DV processors relative to traditional DV-only hardware in computation as well as quantum simulation of physical models. Examples include algorithms for transferring states between DV and CV systems, performing the quantum Fourier transform, and simulation of lattice gauge theories. Relative to qubit-only hardware, the bosonic degrees of freedom natively available in hybrid architectures can substantially reduce the circuit complexity of simulations for physical models containing bosons. A key technique is the extension of quantum signal processing ideas to CV-DV systems. This work is intended to serve as a timely and comprehensive guide to this relatively unexplored yet promising approach to quantum computation and to provide a road map to guide future development.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Pulse control of superconducting cavity-based qudits with a Fock-state basis

Fock-basis-encoding qudits allow quantum gates to operate on multiple qudit levels simultaneously. This capability is advantageous for applications involving complex local gate operations, such as the digital quantum simulation of non-Abelian gauge theories. However, compiling unitary operations to native qudit gates remains a challenging task, often requiring substantial computational resources. In this work, we theoretically investigate the direct pulse control of a superconducting radio-frequency cavity coupled to an ancilla transmon for gate synthesis. We will discuss the improvements and limitations applicable to high Fock states. This work paves the way toward more efficient and robust qudit-gate synthesis.

Li, Andy C.Y. [Fermilab] (ORCID:0000000345423739)↗

Pulse control of superconducting cavity-based qudits with a Fock-state basis

Fock-basis-encoding qudits allow quantum gates to operate on multiple qudit levels simultaneously. This capability is advantageous for applications involving complex local gate operations, such as the digital quantum simulation of non-Abelian gauge theories. However, compiling unitary operations to native qudit gates remains a challenging task, often requiring substantial computational resources. In this work, we theoretically investigate the direct pulse control of a superconducting radio-frequency cavity coupled to an ancilla transmon for gate synthesis. We will discuss the improvements and limitations applicable to high Fock states. This work paves the way toward more efficient and robust qudit-gate synthesis.

Li, Andy C.Y. [Fermilab] (ORCID:0000000345423739)↗

The dynamic conformational landscape of the protein methyltransferase SETD8

Elucidating the conformational heterogeneity of proteins is essential for understanding protein function and developing exogenous ligands. With the rapid development of experimental and computational methods, it is of great interest to integrate these approaches to illuminate the conformational landscapes of target proteins. SETD8 is a protein lysine methyltransferase (PKMT), which functions in vivo via the methylation of histone and nonhistone targets. Utilizing covalent inhibitors and depleting native ligands to trap hidden conformational states, we obtained diverse X-ray structures of SETD8. These structures were used to seed distributed atomistic molecular dynamics simulations that generated a total of six milliseconds of trajectory data. Markov state models, built via an automated machine learning approach and corroborated experimentally, reveal how slow conformational motions and conformational states are relevant to catalysis. These findings provide molecular insight on enzymatic catalysis and allosteric mechanisms of a PKMT via its detailed conformational landscape.

59 BASIC BIOLOGICAL SCIENCES↗

Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles

The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.

Chemistry↗

Simulating Meson Scattering on Spin Quantum Simulators

Studying high-energy collisions of composite particles, such as hadrons and nuclei, is an outstanding goal for quantum simulators. However, preparation of hadronic wave packets has posed a significant challenge, due to the complexity of hadrons and the precise structure of wave packets. This has limited demonstrations of hadron scattering on quantum simulators to date. Observations of confinement and composite excitations in quantum spin systems have opened up the possibility to explore scattering dynamics in spin models. In this article, we develop two methods to create entangled spin states corresponding to wave packets of composite particles in analog quantum simulators of Ising spin Hamiltonians. One wave-packet preparation method uses the blockade effect enabled by beyond-nearest-neighbor Ising spin interactions. The other method utilizes a quantum-bus-mediated exchange, such as the native spin-phonon coupling in trapped-ion arrays. With a focus on trapped-ion simulators, we numerically benchmark both methods and show that high-fidelity wave packets can be achieved in near-term experiments. We numerically study scattering of wave packets for experimentally realizable parameters in the Ising model and find inelastic-scattering regimes, corresponding to particle production in the scattering event, with prominent and distinct experimental signals. Our proposal, therefore, demonstrates the potential of observing inelastic scattering in near-term quantum simulators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simulating non-native cubic interactions on noisy quantum machines

As a milestone for general-purpose computing machines, we demonstrate that quantum processors can be programed to efficiently simulate dynamics that are not native to the hardware. Moreover, on noisy devices without error correction, we show that simulation results are significantly improved when the quantum program is compiled using modular gates instead of a restricted set of standard gates. We demonstrate the general methodology by solving a cubic interaction problem, which appears in nonlinear optics, gauge theories, as well as plasma and fluid dynamics. To encode the non-native Hamiltonian evolution, we decompose the Hilbert space into a direct sum of invariant subspaces in which the nonlinear problem is mapped to a finite-dimensional Hamiltonian simulation problem. Furthermore, in a three-states example, the resultant unitary evolution is realized by a product of approximately 20 standard gates, using which approximately ten simulation steps can be carried out on state-of-the-art quantum hardware before results are corrupted by decoherence. In comparison, the simulation depth is improved by more than an order of magnitude when the unitary evolution is realized as a single cubic gate, which is compiled directly using optimal control. Alternatively, parametric gates may also be compiled by interpolating control pulses. Modular gates thus obtained provide high-fidelity building blocks for quantum Hamiltonian simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗