SEARCH · Search NASA

Results for “native state simulation”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3

All sources NASA NTRS DOE OSTI

DOE OSTI2024

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↗

DOE OSTI2015

DIRECT DETECTION OF COMPLEX ORGANIC PRODUCTS IN ULTRAVIOLET (Lyα) AND ELECTRON-IRRADIATED ASTROPHYSICAL AND COMETARY ICE ANALOGS USING TWO-STEP LASER ABLATION AND IONIZATION MASS SPECTROMETRY

As discovery of complex molecules and ions in our solar system and the interstellar medium has proliferated, several groups have turned to laboratory experiments in an effort to simulate and understand these chemical processes. So far only infrared (IR) and ultraviolet (UV) spectroscopy has been able to directly probe these reactions in ices in their native, low-temperature states. Here we report for the first time results using a complementary technique that harnesses two-step two-color laser ablation and ionization to measure mass spectra of energetically processed astrophysical and cometary ice analogs directly without warming the ices—a method for hands-off in situ ice analysis. Electron bombardment and UV irradiation of H{sub 2}O, CH{sub 3}OH, and NH{sub 3} ices at 5 K and 70 K led to complex irradiation products, including HCO, CH{sub 3}CO, formamide, acetamide, methyl formate, and HCN. Many of these species, whose assignment was also strengthened by isotope labeling studies and correlate with IR-based spectroscopic studies of similar irradiated ices, are important ingredients for the building blocks of life. Some of them have been detected previously via astronomical observations in the interstellar medium and in cometary comae. Other species such as CH{sub 3}CO (acetyl) are yet to be detected in astrophysical ices or interstellar medium. Our studies suggest that electron and UV photon processing of astrophysical ice analogs leads to extensive chemistry even in the coldest reaches of space, and lend support to the theory of comet-impact-induced delivery of complex organics to the inner solar system.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

A strategy based on thermal flexibility to design triosephosphate isomerase proteins with increased or decreased kinetic stability

Kinetic stability of proteins determines their susceptibility to irreversibly unfold in a time-dependent process, and therefore its half-life. A residue displacement analysis of temperature-induced unfolding molecular dynamics simulations was recently employed to define the thermal flexibility of proteins. This property was found to be correlated with the activation energy barrier (E{sub act}) separating the native from the transition state in the denaturation process. The E{sub act} was determined from the application of a two-state irreversible model to temperature unfolding experiments using differential scanning calorimetry (DSC). The contribution of each residue to the thermal flexibility of proteins is used here to propose multiple mutations in triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) and Trypanosoma cruzi (TcTIM), two parasites closely related by evolution. These two enzymes, taken as model systems, have practically identical structure but large differences in their kinetic stability. We constructed two functional TIM variants with more than twice and less than half the activation energy of their respective wild-type reference structures. The results show that the proposed strategy is able to identify the crucial residues for the kinetic stability in these enzymes. As it occurs with other protein properties reflecting their complex behavior, kinetic stability appears to be the consequence of an extensive network of inter-residue interactions, acting in a concerted manner. The proposed strategy to design variants can be used with other proteins, to increase or decrease their functional half-life.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2011

Investigation of energy levels of Er-impurity centers in Si by the method of ballistic electron emission spectroscopy

The method of ballistic electron emission spectroscopy is used for the first time to study the energy spectrum of Er-impurity complexes in Si. The features are observed in the ballistic electron spectra of mesa diodes based on p{sup +}-n{sup +} Si structures with a thin ({approx}30 nm) p{sup +}-Si:Er surface layer in the region of ballistic-electron energies eV{sub t} lower than the conduction-band-edge energy E{sub c} in this layer. They are associated with the tunnel injection of ballistic electrons from the probe of the scanning tunnel microscope to the deep donor levels of the Er-impurity complexes in the p{sup +}-Si:Er layer with subsequent thermal excitation into the conduction band and the diffusion to the p{sup +}-n{sup +} junction and the direct tunneling in it. To verify this assumption, the ballistic-electron transport was simulated in the system of the Pt probe, native-oxide layer SiO{sub 2}-p{sup +}-Si:Er-n{sup +}, and Si substrate. By approximating the experimental ballistic-electron spectra with the modeling spectra, the ground-state energy of the Er complex in Si was determined: E{sub d} Almost-Equal-To E{sub c} - 0.27 eV. The indicated value is consistent with the data published previously and obtained from the measurements of the temperature dependence of the free-carrier concentration in Si:Er layers.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Characterization of deep level defects and thermally stimulated depolarization phenomena in La-doped TlInS{sub 2} layered semiconductor

Lanthanum-doped high quality TlInS{sub 2} (TlInS{sub 2}:La) ferroelectric-semiconductor was characterized by photo-induced current transient spectroscopy (PICTS). Different impurity centers are resolved and identified. Analyses of the experimental data were performed in order to determine the characteristic parameters of the extrinsic and intrinsic defects. The energies and capturing cross section of deep traps were obtained by using the heating rate method. The observed changes in the Thermally Stimulated Depolarization Currents (TSDC) near the phase transition points in TlInS{sub 2}:La ferroelectric-semiconductor are interpreted as a result of self-polarization of the crystal due to the internal electric field caused by charged defects. The TSDC spectra show the depolarization peaks, which are attributed to defects of dipolar origin. These peaks provide important information on the defect structure and localized energy states in TlInS{sub 2}:La. Thermal treatments of TlInS{sub 2}:La under an external electric field, which was applied at different temperatures, allowed us to identify a peak in TSDC which was originated from La-dopant. It was established that deep energy level trap BTE43, which are active at low temperature (T ≤ 156 K) and have activation energy 0.29 eV and the capture cross section 2.2 × 10{sup −14} cm{sup 2}, corresponds to the La dopant. According to the PICTS results, the deep level trap center B5 is activated in the temperature region of incommensurate (IC) phases of TlInS{sub 2}:La, having the giant static dielectric constant due to the structural disorders. From the PICTS simulation results for B5, native deep level trap having an activation energy of 0.3 eV and the capture cross section of 1.8 × 10{sup −16} cm{sup 2} were established. A substantial amount of residual space charges is trapped by the deep level localized energy states of B5 in IC-phase. While the external electric field is applied, permanent dipoles, which are originated from the charged B5 deep level defects, are aligned in the direction of the applied electric field and the equilibrium polarization can be reached in a relatively short time. When the polarization field is maintained, while cooling the temperature of sample to a sufficiently low degrees, the relaxation times of the aligned dipoles drastically increases. Practically, frozen internal electric field or electrets states remain inside the TlInS{sub 2}:La when the applied bias field is switched off. The influence of deep level defects on TSDC spectra of TlInS{sub 2}:La has been revealed for the first time.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

Dynamics of Organophosphate‐Induced Structural Changes in Acetylcholinesterase Revealed by Time‐Resolved Small‐Angle X‐Ray Scattering and Inelastic Neutron Scattering

Organophosphates (OPs), the active compounds in nerve agents and insecticides such as paraoxon (POX), exert their toxic effects by irreversibly inhibiting acetylcholinesterase (AChE). Currently available antidotes for OP toxicity can reactivate AChE, but reactivation rates are slow which can lead to irreversible nervous system damage or death. We hypothesize that better antidotes with accelerated reactivation rates can be developed by understanding the structural dynamics of OP‐AChE conjugates. Previous steady‐state small‐angle X‐ray scattering (SAXS) experiments showed that POX and certain other OPs induce quaternary structural changes in human AChE (hAChE) that were reversible by oxime antidotes. To characterize the dynamics of these OP‐induced structural changes we have used time‐resolved SAXS (TR‐SAXS) and inelastic neutron scattering (INS). Stopped‐flow TR‐SAXS experiments were performed at BL‐4 at the Stanford Synchrotron Radiation Lightsource by mixing a molar excess of POX (500 μM) with hAChE (50 μM). Scattering data were collected every 20 msec during the first 1000 msec after mixing. Changes in the solution structure of hAChE during this period occurred with k obs = 0.13(±0.01) s −1 . This rate of structural change is comparable to the rate of hAChE inactivation observed using biochemical assays. INS data were collected at the Cold Neutron Chopper Spectrometer at the Spallation Neutron Source at Oakridge National Laboratory using 100 mg samples of hAChE and POX‐hAChE that were lyophilized and rehydrated in D 2 O. INS data collected at 120 K (to prevent translational motions) were used to compare the vibrational density states of native and POX‐conjugated hAChE. The POX‐conjugated hAChE exhibited an increased number of vibrational states, particularly those associated with regional motions such as loop dynamics, whereas global collective motions remained unchanged. Molecular dynamics simulations were used to simulate the vibrational spectra and identify the region(s) in hAChE that contributed to the differences in the INS experimental data. In aggregate, these studies provide experimental evidence for OP conjugate‐induced changes in hAChE dynamics that has to be considered in the design of antidotes for OP poisoning that have improved efficacy and patient outcomes. Support or Funding Information This work was supported by the CounterACT Program, National Institutes of Health Office of the Director, Grant 1U01NS083451 from NINDS, and by grants to SSRL and ORNL from the U.S. Department of Energy, and the National Institutes of Health. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Blumenthal, Donald K.↗

DOE OSTI2025

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↗

DOE OSTI2021

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↗

DOE OSTI2026

Digital quantum magnetism on a trapped-ion quantum computer

Digital quantum matter—realized when discrete quantum gates approximate continuous time evolution—is susceptible to heating into chaotic, structureless states. If digitization errors are adequately suppressed, a long-lived transient regime of approximately energy-conserving dynamics can be observed on gate-based quantum computers. Conservation of energy, in turn, enables the exploration of a wide variety of complex behaviours observed in equilibrium systems, ranging from the non-trivial microscopic origins of thermalization itself to the stabilization of effective models hosting exotic emergent properties. Here we use Quantinuum’s H2 quantum computer to simulate digitized dynamics of the quantum Ising model, suppressing digitization errors well enough to observe thermalization on timescales that severely challenge classical simulation methods. Relaxation of an inhomogeneous state reveals an emergent hydrodynamics owing to approximate energy conservation and we compute the associated diffusion constant. By reprogramming our simulations to take place on a triangular lattice with periodic boundary conditions, we observe thermalization consistent with emergent gauge and topological constraints resulting from lattice frustration. Furthermore, our results were enabled by continued advances in two-qubit gate quality (native partial entangler fidelities of 99.94(1)%) and establish digital quantum computers as powerful tools for studying (effectively) continuous-time dynamics.

Information theory and computation↗

DOE OSTI2026

Modeling supercritical CO 2 flow and mineralization in reactive host rocks with PFLOTRAN v7.0

Understanding the flow and reactivity of CO 2 injected into geological reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO 2 injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO 2 migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping. Recently, CO 2 -reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO 2 in situ to simultaneously dissolve host rock minerals and mineralize CO 2 as carbonates. Engineering rapid CO 2 mineralization in the subsurface is attractive because of the increased density of stored CO 2 , the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO 2 -brine flow and reactive transport for a wide range of injection and production applications involving reactive CO 2 -brine systems. These developments are based on the well established and trusted CO 2 flow capabilities in the STOMP-CO 2 simulator. New capabilities added to PFLOTRAN include new CO 2 -brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN's well-established reactive transport libraries. A series of benchmarks between PFLOTRAN and STOMP-CO 2 verify the newly developed CO 2 -brine flow capabilities. Demonstrations of coupled CO 2 -brine flow modeling and reactive transport show how CO 2 mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO 2 and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature and/or pH dependence of geochemical reactions for specific systems of interest.

Critical Minerals↗

DOE OSTI2016

A high-fidelity method to analyze perturbation evolution in turbulent flows

Small perturbation propagation in fluid flows is usually examined by linearizing the governing equations about a steady basic state. It is often useful, however, to study perturbation evolution in the unsteady evolving turbulent environment. Such analyses can elucidate the role of perturbations in the generation of coherent structures or the production of noise from jet turbulence. The appropriate equations are still the linearized Navier–Stokes equations, except that the linearization must be performed about the instantaneous evolving turbulent state, which forms the coefficients of the linearized equations. This is a far more difficult problem since in addition to the turbulent state, its rate of change and the perturbation field are all required at each instant. In this paper, we develop and use a novel technique for this problem by using a pair (denoted “baseline” and “twin”) of simultaneous synchronized Large-Eddy Simulations (LES). At each time-step, small disturbances whose propagation characteristics are to be studied, are introduced into the twin through a forcing term. At subsequent time steps, the difference between the two simulations is shown to be equivalent to solving the forced Navier–Stokes equations, linearized about the instantaneous turbulent state. The technique does not put constraints on the forcing, which could be arbitrary, e.g., white noise or other stochastic variants. We consider, however, “native” forcing having properties of disturbances that exist naturally in the turbulent environment. The method then isolates the effect of turbulence in a particular region on the rest of the field, which is useful in the study of noise source localization. The synchronized technique is relatively simple to implement into existing codes. In addition to minimizing the storage and retrieval of large time-varying datasets, it avoids the need to explicitly linearize the governing equations, which can be a very complicated task for viscous terms or turbulence closures. The method is illustrated by application to a well-validated Mach 1.3 jet. Specifically, the effects of turbulence on the jet lipline and core collapse regions on the near-acoustic field are isolated. The properties of the method, including linearity and effect of initial transients, are discussed. The results provide insight into how turbulence from different parts of the jet contribute to the observed dominance of low and high frequency content at shallow and sideline angles, respectively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

High-Energy Collision of Quarks and Mesons in the Schwinger Model: From Tensor Networks to Circuit QED

With the aim of studying nonperturbative out-of-equilibrium dynamics of high-energy particle collisions on quantum simulators, we investigate the scattering dynamics of lattice quantum electrodynamics in 1 + 1 dimensions. Working in the bosonized formulation of the model and in the thermodynamic limit, we use uniform-matrix-product-state tensor networks to construct multiparticle wave-packet states, evolve them in time, and detect outgoing particles post collision. This facilitates the numerical simulation of scattering experiments in both confined and deconfined regimes of the model at different energies, giving rise to rich phenomenology, including inelastic production of quark and meson states, meson disintegration, and dynamical string formation and breaking. We obtain elastic and inelastic scattering cross sections, together with time-resolved momentum and position distributions of the outgoing particles. Furthermore, we propose an analog circuit-QED implementation of the scattering process that is native to the platform, requires minimal ingredients and approximations, and enables practical schemes for particle wave-packet preparation and evolution. Furthermore, this study highlights the role of classical and quantum simulation in enhancing our understanding of scattering processes in quantum field theories in real time.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2000

Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.

Darve, Eric↗

DOE OSTI2018

GQLink: an implementation of Quantized State Systems (QSS) methods in Geant4

Simulations in high energy physics (HEP) often require the numerical solution of ordinary differential equations (ODE) to determine the trajectories of charged particles in a magnetic field when particles move throughout detector volumes. Each crossing of a volume interrupts the underlying numerical method that solves the equations of motion, triggering iterative algorithms to estimate the intersection point within a given accuracy. The computational cost of this procedure can grow significantly depending on the application at hand. Quantized State System (QSS) is a recent family of discrete-event driven numerical methods exhibiting attractive features for this type of problems, such as native dense output (sequences of polynomial segments updated only by accuracy-driven events) and lightweight detection and handling of volume crossings. In this work we present GQLink, a proof-of-concept integration of QSS with the Geant4 simulation toolkit which stands as an interface for co-simulation that orchestrates robustly and transparently the interaction between the QSS simulation engine and aspects such as geometry definition and physics processes controlled by Geant4. In conclusion, we validate the accuracy and study the performance of the method in simple geometries (subject to intense volume crossing activity) and then in a realistic HEP application using a full CMS detector configuration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS2001

Better, Cheaper, Faster Molecular Dynamics

Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

Pohorille, Andrew↗

DOE OSTI2016

Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities: Comparison of Native and Non-Native Ubiquitin Oligomers

Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Numerically Testing Conceptual Models of the Utah FORGE Reservoir Using July 2023 Circulation Test Data

Over the past several years, many new data sets have become available regarding the characterization of the Utah FORGE reservoir. These include, but are not limited to, the stimulation of Well 16A, the drilling and completion of Well 16B, and interwell circulation confirmatory testing. As part of the characterization efforts, conceptual models of the reservoir are re-examined as new data become available. As part of the planning for FORGE activities, numerical models are often used to predict the reservoir response to the planned testing. Stochastic methods are often employed to bound uncertainty and allow for evaluation of comprehensive ranges of key reservoir parameters. For the most recent interwell circulation confirmatory testing (July 2023), a priori numerical model predictions did bound the observed behavior (Xinj et al., 2023), but key deviations from expected behavior prompted the FORGE team to reevaluate our conceptual model of the reservoir. In early October 2023, key members of the development, testing, and monitoring teams met for 2 days to review newly collected data and discuss ‘interesting’ or ‘key’ observations. From these discussions, 15 Key Observations were documented, with several significant ones being that the discrete fracture network developed from the 16A stimulation data may not be appropriate and that the early time pressure data obtained during the summer 2023 reservoir testing were best described using radial solutions. In July 2023, two campaigns of interwell confirmatory testing were conducted, the first set of tests occurred on July 4-5 and the second set on July 18-19. The second set of circulation tests conducted at the Utah FORGE site between the injection well 16A(78)-32 and production well 16B(78)-32 on July 18 and 19, 2023 are used to calibrate material properties in a thermal-hydraulic-mechanical (THM) simulation of the discrete fracture network connecting the wells. The spatially and temporally varying reservoir properties are calibrated to match the time dependent pressure and production profiles from the circulation tests. In future work, this calibrated model will be coupled to the native state THM model of the FORGE reservoir to predict surface deformation and strains resulting from pumping schedules.

58 GEOSCIENCES↗

DOE OSTI2024

Numerically Testing Conceptual Models of the Utah FORGE Reservoir Using July 2024 Circulation Test Data

15 GEOTHERMAL ENERGY↗