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At least 235 records · Page 13

Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics

Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent K C modulus for bilayer bending. Our results show a strong correlation with K C values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.

59 BASIC BIOLOGICAL SCIENCES↗

Dependence of predicted bulk properties of hexagonal hydroxyapatite on exchange-correlation functional

Hydroxyapatite (HA) is the main component of human bones and teeth. HA has also been widely applied in various technological fields due to its unique properties. Reliable computational simulations for this critical material often require input parameters obtained from the first-principles density functional theory (DFT) calculations with appropriate exchange–correlation functionals. Previous DFT calculations are insufficient to verify the reliabilities of various functionals, particularly as they fail to assess predictions for multiple properties of the material. In this paper, we first select 18 different functionals to calculate geometric, elastic, electronic, and thermodynamic properties of hexagonal HA bulk crystal. We find that the results from optB86b-vdW and optB88-vdW functionals with dispersion corrections have the overall best agreement with available experimental data. Then, we choose optB88-vdW functional, as well as PBE functional without dispersion corrections as a comparison, to perform extensive first-principles DFT phonon calculations under the quasiharmonic approximation. Various thermodynamic properties (including phonon contributions to internal energy, entropy, and Helmholtz free energy) and thermal parameters (including thermal expansions of volume, thermal expansion coefficients, heat capacities, isothermal bulk moduli, etc.) versus temperature are consequently obtained. By comparing these quantities, we report that the results from optB88-vdW functional have significantly better agreement with available experimental data than those from PBE functional although the latter has been widely used in previous DFT calculations for HA-based material systems.

36 MATERIALS SCIENCE↗

Development and assessment of a reactor system prognosis model with physics-guided machine learning

Autonomous control systems provide recommendations to help operators in decision-making during plant operations ranging from normal operation to accident management. An important step of autonomous control is prognosis. In nuclear engineering domain, prognosis is the process of predicting future conditions of a system or equipment based on present signs and symptoms of a fault. The prognosis model allows predicting future reactor states for possible candidate control strategies so that the outcomes can be evaluated to determine the best control strategy. The prognosis model requires representing direct relationships between the symptoms and the predictions. In nuclear engineering, computational simulations are approximate representations of the operation of the real system. However, prognosis with computational simulations requires high computation power and time due to possible large number of scenarios. Necessary computation resources can be reduced with machine learning (ML) approach for fast predictions by building a surrogate function using the simulation data. A critical issue is, ML models are ignorant of physical knowledge, and these models approximate statistical relationships between the system variables. This ignorance can produce results that are inconsistent with physical laws, even if an optimal result is achieved from a mathematical point of view. Physics-guided machine learning (PGML) is an approach to tackle this issue. Here, this work formulates and illustrates a framework to guide development and assessment of the ML-based prognosis model for autonomous control systems. The development of the prognosis model considers the training of a ML model which consists of optimizing many aspects of the ML approach. The assessment of the prognosis model considers training data limitations and uncertainties of the ML approach. Prognosis models with standalone ML and PGML are developed and assessed on the loss-of-flow scenario of Experimental Breeder Reactor II. The results indicate that PGML based prognosis model has the best performance compared to other prognosis models.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Assembled peptoid crystalline nanomaterials as carbonic anhydrase mimics for promoted hydration and sequestration of CO 2

Carbonic anhydrase (CA) mimics have received significant attention due to their promising applications in the enhanced hydration and sequestration of CO 2 . Herein, we report the assembly of sequence-defined peptoids into crystalline nanomaterials with controlled microenvironment of active sites as CA mimics for promoted hydration and sequestration of CO 2 . By incorporating specific ligands into self-assembling peptoids and coordinating these ligands with metal cations, we synthesize a variety of crystalline nanosheets and nanotubes as efficient CA mimics comparable to natural bovine CA. Molecular dynamics simulations reveal the critical roles of peptoid-Zn 2+ binding energy and the active site local microenvironment on the catalytic performance of these CA mimics. CO 2 precipitation results show that these CA mimics promote the hydration and sequestration of CO 2 while retaining high thermal and chemical stabilities. This study offers essential guidance for the future design of high-performance CA-mimics suitable for applications in CO 2 capture and sequestration.

Chakma, Progyateg [Pacific Northwest National Labo↗

Light control of surface–bulk coupling by terahertz vibrational coherence in a topological insulator

The demand for disorder-tolerant quantum logic and spin electronics can be met by generating and controlling dissipationless spin currents protected by topology. Dirac fermions with helical spin-locking surface transport offer a way of achieving such a goal. Yet, surface-bulk coupling can lead to strong Dirac electron scattering with bulk carriers and phonons as well as impurities, assisted by such dissipative channel, which results in “topological breakdown”. Here, we demonstrate that coherent lattice vibrations periodically driven by a single-cycle terahertz (THz) pulse can significantly suppress such dissipative channel in topological insulators. This is achieved by reducing the phase space in the bulk available for Dirac fermion scattering into during coherent lattice oscillations in Bi 2 Se 3 . This light-induced suppression manifests as a remarkable transition exclusively in surface transport, absent for bulk, above the THz electric fields for driving coherent phonons, which prolongs the surface transport lifetime. These results, together with simulations, identify the critical role of spin–orbit coupling for the “phase space contraction” mechanism that suppresses the surface-bulk coupling. Imposing vibrational quantum coherence into topological states of matter may become a universal light control principle for reinforcing the symmetry-protected helical transport.

36 MATERIALS SCIENCE↗

Reactive burn model calibration using high-throughput initiation experiments at sub-millimeter length scales

We report a first-of-its-kind model calibration was performed using Sandia National Laboratories’ high-throughput initiation (HTI) experiment for two types of vapor-deposited explosive films consisting of hexanitrostilbene (HNS) or pentaerythritol tetranitrate (PETN). These films exhibit prompt initiation, and they reach steady detonation at sub-millimeter length scales. Following prior work on HNS, we test the hypothesis of approximating these explosive films as fine-grained homogeneous solids with simple Arrhenius kinetics burn models. The model calibration process is described herein using a single-step as well as a two-step Arrhenius rate law, and it consists of systematic parameter sampling leading to a reduction in the model degrees of freedom. Multiple local minima are observed; results are given for seven different optimized parameter sets. Each model set is further evaluated in a two-dimensional simulation of the critical failure thickness for a sustained detonation. Overall, the two-step Arrhenius kinetics model captures the observed behavior for HNS; however, neither model produces a good fit to the PETN data. We hypothesize that the HTI results for PETN correspond to a heterogeneous response, owing to the smaller reaction zone of PETN compared to HNS (i.e., it does not homogenize the fine-grained hot spots as well). Future work should consider using the ignition and growth model for PETN, as well as other reactive burn models such as xHVRB, AWSD, PiSURF, and CREST.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Instrument design for an inertial confinement fusion ion temperature imager

A mix of contaminant mass is a known, performance-limiting factor for laser-driven inertial confinement fusion (ICF). It has also recently been shown that the contaminant mass is not necessarily in thermal equilibrium with the deuterium–tritium plasma. Contaminant mass temperature is one of the dominant uncertainties in contaminant mass estimates. The MixIT diagnostic is a new and potentially transformative diagnostic, capable of spatially resolving ion temperature. The approach combines principles of neutron time-of-flight and neutron imaging diagnostics. The information from the MixIT diagnostic can be used to optimize ICF target and laser drive designs as well as provide key constraints on ICF radiation-hydrodynamic simulations that are critical to contaminant mass estimates. This work details the design and optimization of the major components of the MixIT diagnostic: the neutron aperture, the neutron detector (scintillator), and the recording system.

47 OTHER INSTRUMENTATION↗

Thermally frustrated phase transition at high pressure in B 2-ordered FeV

X-ray diffraction measurements of equiatomic B2-ordered FeV were performed in a diamond-anvil cell at room temperature at several pressure points up to 80 GPa that showed the cubic phase to be stable with no indication of structural phase transitions. Density functional theory at 0 K predicts Fermi surface nesting, an electronic topological transition, and a phonon dynamical instability within the experimentally investigated pressure range. Nevertheless, the instability is absent in phonon dispersion curves extracted from ab initio molecular dynamics simulations below the critical volume at temperatures as low as 10 K, indicating that thermal atomic displacements can frustrate the phase transition by renormalizing the phonon dispersion curves. Ferrimagnetism is critical for the stability of the cubic phase at low temperature, but thermal atomic displacements are enough to support the structure at and above the Néel temperature.

36 MATERIALS SCIENCE↗

Collective neural network behavior in a dynamically driven disordered system of superconducting loops

Collective properties of complex systems composed of many interacting components such as neurons in our brain can be modeled by artificial networks based on disordered systems. We show that a disordered neural network of superconducting loops with Josephson junctions can exhibit computational properties like categorization and associative memory in the time evolution of its state in response to information from external excitations. Superconducting loops can trap multiples of fluxons in many discrete memory configurations defined by the local free energy minima in the configuration space of all possible states. A memory state can be updated by exciting the Josephson junctions to fire or allow the movement of fluxons through the network as the current through them surpasses their critical current thresholds. Simulations performed with a lumped element circuit model of a 4-loop network show that information written through excitations is translated into stable states of trapped flux and their time evolution. Experimental implementation on a high-Tc superconductor YBCO-based 4-loop network shows dynamically stable flux flow in each pathway characterized by the correlations between junction firing statistics. Neural network behavior is observed as energy barriers separating state categories in simulations in response to multiple excitations, and experimentally as junction responses characterizing different flux flow patterns in the network. The state categories that produce these patterns have different temporal stabilities relative to each other and the excitations. This provides strong evidence for time-dependent (short-to-long-term) memories, that are dependent on the geometrical and junction parameters of the loops, as described with a network model.

Josephson junctions↗

Diffusion Synthetic Acceleration for Heterogeneous Domains, Compatible with Voids

A standard approach to solving the S N transport equations is to use source iteration with diffusion synthetic acceleration (DSA). Although this approach is widely used and effective on many problems, there remain some practical issues with DSA preconditioning, particularly on highly heterogeneous domains. For large-scale parallel simulation, it is critical that both (a) preconditioned source iteration converges rapidly and (b) the action of the DSA preconditioner can be applied using fast, scalable solvers, such as algebraic multigrid (AMG). For heterogeneous domains, these two interests can be at odds. In particular, there exist DSA diffusion discretizations that can be solved rapidly using AMG, but they do not always yield robust/fast convergence of the larger source iteration. Conversely, there exist robust DSA discretizations where source iteration converges rapidly on difficult heterogeneous problems, but fast parallel solvers like AMG tend to struggle applying the action of such operators. Moreover, very few current methods for the solution of deterministic transport are compatible with voids. This paper develops a new heterogeneous DSA preconditioner based on only preconditioning the optically thick subdomains. The resulting method proves robust on a variety of heterogeneous transport problems, including a linearized hohlraum mesh related to inertial confinement fusion. Moreover, the action of the preconditioner is easily computed using O(1) AMG iterations, convergence of the transport iteration typically requires 2 to 5× fewer iterations than current state-of-the-art “full” DSA, and the proposed method is trivially compatible with voids. On the hohlraum problem, rapid convergence is obtained by preconditioning less than 3% of the mesh elements with five to ten AMG iterations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

On FIRE mode in KSTAR

We report on the status of Fast Ion Regulated Enhancement (FIRE) mode experiments in the Korea Superconducting Tokamak Advanced Research. This regime is being developed for high-performance, steady-state operation which features a stationary ion internal transport barrier, enabling a central ion temperature approaching 10 keV to be sustained for up to 50 s, without the need for delicate profile control and with no significant impurity accumulation. As its key novelty lies in the significant contribution of fast ions that stabilize core turbulence, the regime has been named FIRE mode. To achieve this regime, neutral beam injection is applied at moderate power levels near the L–H power threshold, while maintaining low plasma density to avoid the L–H transition. The scenario is typically established in diverted magnetic configurations. The core features of FIRE mode were investigated through power balance analysis and fluctuation measurements, revealing a clear transport bifurcation in the ion channel. At the plasma edge, FIRE mode occasionally exhibits I-mode characteristics, particularly in unfavorable magnetic null configurations with q 95 ∼ 4, including the presence of weakly coherent modes. In terms of MHD activity, sawtooth oscillations are observed but appear to be stabilized during the high-performance phase. Fast ion-driven Alfvénic eigenmodes (AEs), indicated by strong frequency chirping near 200 kHz, are also observed. Additionally, lower-frequency MHD activities, distinct from the fast ion-driven AEs, are present and have some influence on plasma performance. The enhancement of core confinement is primarily attributed to fast ion effects, which were evaluated with respect to dilution, alpha stabilization, and resonant interactions with turbulence using gyrokinetic analyses. Among these, the dilution effect was found to be the most dominant. The characteristics of FIRE mode were compared with those of other hot ion plasma scenarios, such as supershot and hot ion mode. While they share many similarities, FIRE mode is distinguished by the accessibility to conditions with T i ≈ T e , presence of I-mode edge features, and its long-duration sustainment. Predictive simulations of FIRE mode were performed using integrated transport modeling with TRIASSIC, employing the TGLF anomalous transport model. These simulations confirmed the critical role of fast ions in achieving this regime. The future prospect of FIRE mode for application in fusion reactors is discussed, with an emphasis on possibly extending the regime to higher density operation.

FIRE mode↗

Quantum state preparation and nonunitary evolution with diagonal operators

Realizing nonunitary transformations on unitary-gate-based quantum devices is critically important for simulating a variety of physical problems, including open quantum systems and subnormalized quantum states. Here, we present a dilation-based algorithm to simulate nonunitary operations using probabilistic quantum computing with only one ancilla qubit. We utilize the singular-value decomposition (SVD) to decompose any general quantum operator into a product of two unitary operators and a diagonal nonunitary operator, which we show can be implemented by a diagonal unitary operator in a one-qubit dilated space. While dilation techniques increase the number of qubits in the calculation, and thus the gate complexity, our algorithm limits the operations required in the dilated space to a diagonal unitary operator, which has known circuit decompositions. We use this algorithm to prepare random subnormalized two-level states on a quantum device with high fidelity. Furthermore, we present the accurate nonunitary dynamics of two-level open quantum systems in a dephasing channel and an amplitude-damping channel computed on a quantum device. The algorithm presented will be most useful for implementing general nonunitary operations when the SVD can be readily computed, which is the case for most operators in the noisy intermediate-scale quantum computing era.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Spin-orbit coupling induced demagnetization in Ni: Ab initio nonadiabatic molecular dynamics perspective

Spin-orbit coupling (SOC), which can induce spin flip during the relaxation of photoexcited charge carrier, plays a crucial role in spin dynamics. Here in this work, we have used time-domain ab initio nonadiabatic molecular dynamics (NAMD) method to study the SOC induced ultrafast demagnetization in Ni at 300K. The spin-diabatic representation using spin-polarized Kohn-Sham (KS) basis sets and spin-adiabatic representation using spinor basis sets have been applied, and both of them achieve demagnetization in Ni with a timescale around 100fs. The spin-diabatic representation suggests a picture that the electron-phonon coupling (EPC) provides direct energy relaxation channel among the same-spin states, while the SOC can induce spin flip. After photoexcitation, it is found the spin-minority electrons relax to the same-spin states rather than the opposite-spin states, since EPC is larger than SOC by one order of magnitude. By contrast, for the spin-majority electrons, spin flip occurs since there are no empty same-spin states as electron acceptor above the Fermi level. The different relaxation pathways for spin-majority and spin-minority electrons induce the demagnetization. The spin-adiabatic representation provides an Elliott-Yafet spin-phonon scattering picture. The SOC induced reduction of magnetic moment in Ni may induce magnon to drive further demagnetization. The ab initio NAMD simulation provides a critical angle to understand how the SOC and EPC affect demagnetization process in Ni.

36 MATERIALS SCIENCE↗

X-ray heating and electron temperature of laboratory photoionized plasmas

We discuss experimental and modeling results for the x-ray heating and temperature of laboratory photoionized plasmas. A method is used to extract electron temperature based on the analysis of transmission spectroscopy data that is independent of atomic kinetics modeling. Boltzmann kinetic and radiation-hydrodynamics simulations emphasized the critical interplay between atomic physics and heating in photoionized plasmas. They also demonstrated the dramatic impact of photoexcitation on excited state populations, line emissivity, and radiation cooling. Temperature calculations performed with astrophysical codes significantly overestimated the measurement.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Lower bounds on entanglement entropy without twin copy

We discuss the possibility of estimating experimentally the von Neumann entanglement entropy S A v N of a symmetric bipartite quantum system A B by using the basic measurement counts (bitstrings) for a single copy of a prepared state. Using exact diagonalization and analog simulations performed with the publicly available QuEra facilities for chains and ladders of Rydberg atoms, we calculate the Shannon entropy S A B X associated with the bitstrings of adiabatically prepared ground states and the reduced entropies S A X and S B X obtained from the marginal probabilities in A and B . We then calculate the classical mutual information I A B X = S A X + S B X − S A B X , which is a lower bound on S A v N . We show that for a broad range of lattice spacing and detuning, I A B X is typically 20% below S A v N in regions where S A v N is large and a less close bound in regions where S A v N is low. We argue that this use of the easily available bitstrings provides a robust and efficient way to explore empirically the phase diagram of qubit-based quantum simulators and identify critical regions. Published by the American Physical Society 2025

Meurice, Yannick (ORCID:0000000209959694)↗

Modeling batch melting: Roles of heat transfer and reaction kinetics

Development of mathematical models of heat and mass transfer in glass-melting furnaces began in the 1970s and progressed rapidly with advances in sophisticated experimental/numerical techniques and increasing computational power. Today, practically all newly built or rebuilt furnaces are optimized with these models to meet stringent quality requirements, reduce the unit costs of manufacturing, or control emissions. One remaining hurdle is to model the batch-to-glass conversion accurately enough to reliably assess the glass production rate. This article summarizes two key aspects of the batch-conversion modeling—the heat transfer and the kinetics of conversion—and reviews the current state-of-the-art approaches to simulating them. We critically examine the advantages of the commonly used heat transfer approach, but also explain that its predictive capabilities are significantly restricted by the dependence of batch thermal properties on the time-temperature history. We argue that kinetic approaches to the batch-conversion modeling would offer a significant improvement when coupled with the heat transfer approach. Finally, we summarize key areas requiring further research on the way toward a realistic model of the batch blanket.

Pokorny, Richard↗

Role of Inlet Boundary Conditions on Fuel-Air Mixing at Supercritical Conditions

Advanced engine design and alternative fuels present the possibility of fuel injection at purely supercritical conditions in diesel engines and gas turbines. The complex interactions that govern this phenomenon still need significant research, particularly the boundary conditions for fuel injection are critical for accurate simulation. However, the flow inside the injector itself is often omitted to reduce the computational efforts, and thus, velocity, mass flux, or total pressure is specified at the injector exit (or domain inlet), often with simplified velocity profiles and turbulence levels. This simplified inlet boundary treatment has minimal effects on results for conventional fuel injection conditions, however, the validity of this approach at supercritical conditions has not been assessed. Comprehensive real-gas and binary fluid mixing models have been implemented for computational fluid dynamics (CFD) analysis of fuel-air mixing at supercritical conditions. The model is verified using prior CFD results from the literature. The model is used to investigate the effects of the shape of axial velocity and mass fraction profiles at the inlet boundary with the goal to improve the comparison of predictions to experimental data. Results show that the boundary conditions have a significant effect on the predictions, and none of the cases match precisely with experimental data. Furthermore, the study reveals that the physical location of the inlet boundary might be difficult to infer correctly from the experiments and highlights the need for high-quality, repeatable measurements at supercritical conditions to support the development of relevant high-fidelity models for fuel-air mixing.

02 PETROLEUM↗

Simulation of Methane Oxycombustion in Supercritical Carbon Dioxide

The Allam-Fetvedt Cycle (AFC) offers the potential for electricity generation with minimal or even negative carbon emissions by using oxycombustion in supercritical carbon dioxide (sCO2). Because of the extreme high temperatures and pressures encountered in these systems, simulation of oxycombustion requires use of a complex equation of state such as the modified Soave-Redlich-Kwong (SRK) equation, coupled with equally complex correlations for transport properties. The current work simulates a model combustor using both an ideal gas equation of state and the SRK equation of state. The model combustor features a jet of CH4 mixing with and reacting with O2 in the sCO2 ambient. Two jet configurations are considered: one of pure CH4, and one of CH4 mixed with sCO2. Comparison of results shows that key output properties such as combustor temperature and flow distribution are impacted by the choice of equations of state. Inspection of simulation results shows that mixing and reaction rates, as well as the uniformity of the flow, are impacted by the choice of equation of state. These results show that even though use of a complex equation of state greatly increases the computational costs of these simulations, it is critical to accurately capturing the physics of these systems.

computational fluid dynamics↗