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At least 307 records · Page 17

Heat transport in liquid water from first-principles and deep neural network simulations

In this work, we compute the thermal conductivity of water within linear response theory from equilibrium molecular dynamics simulations, by adopting two different approaches. In one, the potential energy surface (PES) is derived on the fly from the electronic ground state of density functional theory (DFT) and the corresponding analytical expression is used for the energy flux. In the other, the PES is represented by a deep neural network (DNN) trained on DFT data, whereby the PES has an explicit local decomposition and the energy flux takes a particularly simple expression. By virtue of a gauge invariance principle, established by Marcolongo, Umari, and Baroni, the two approaches should be equivalent if the PES were reproduced accurately by the DNN model. We test this hypothesis by calculating the thermal conductivity, at the GGA (PBE) level of theory, using the direct formulation and its DNN proxy, finding that both approaches yield the same conductivity, in excess of the experimental value by approximately 60%. Besides being numerically much more efficient than its direct DFT counterpart, the DNN scheme has the advantage of being easily applicable to more sophisticated DFT approximations, such as meta-GGA and hybrid functionals, for which it would be hard to derive analytically the expression of the energy flux. We find in this way that a DNN model, trained on meta-GGA (SCAN) data, reduces the deviation from experiment of the predicted thermal conductivity by about 50%, leaving the question open as to whether the residual error is due to deficiencies of the functional, to a neglect of nuclear quantum effects in the atomic dynamics, or, likely, to a combination of the two.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations

Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.

Deprotonation↗

Entanglement and many-body effects in collective neutrino oscillations

Collective neutrino oscillations play a crucial role in transporting lepton flavor in astrophysical settings, such as supernovae, where the neutrino density is large. In this regime, neutrino-neutrino interactions are important and simulations in the mean-field approximation show evidence for collective oscillations occurring at timescales much shorter than those associated with vacuum oscillations. In this work, we study the out-of-equilibrium dynamics of a corresponding spin model using matrix product states and show how collective bipolar oscillations can be triggered by many-body correlations if appropriate initial conditions are present. We find entanglement entropies scaling at most logarithmically in the system size suggesting that classical tensor network methods could be efficient in describing collective neutrino dynamics more generally. These observation provide a clear path forward, not only to increase the accuracy of current simulations, but also to elucidate the mechanism behind collective flavor oscillations without resorting to the mean-field approximation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The influence of V-defects, leakage, and random alloy fluctuations on the carrier transport in red InGaN MQW LEDs

Red InGaN-based light-emitting diodes (LEDs) exhibit lower internal quantum efficiencies than violet, blue, and green InGaN LEDs due to a reduction in radiative recombination rates relative to non-radiative recombination rates as the Indium composition increases. Additionally, the larger polarization and band offset barriers between high indium content InGaN quantum wells and GaN quantum barriers increase the forward voltage. In blue and green LEDs, random alloy fluctuations and V-defects play a key role in reducing the forward voltage. When V-defects are present, either naturally or intentionally introduced, they create an alternative path for carrier injection into the MQWs through the V-defect sidewalls. This injection mechanism explains the turn-on voltages of green LEDs. However, in InGaN red LEDs, these two phenomena do not reduce the forward voltage as effectively as in blue and green LEDs, and consequently, the computed forward voltage remains significantly higher than the measured one. Furthermore, currents are observed at low voltages before the turn-on voltage (V<ℏω/e=2.0 V) of red LEDs. To address this, we introduce dislocation-induced tail states in the modeling, suggesting that leakage current through these states may play a significant role both below and at turn-on voltages. The simulation also indicates that leakage carriers below turn-on accumulate, partially diffuse in the QWs, screen the polarization-induced barrier in the low injection regime, and further reduce the forward voltage. Despite these beneficial effects, a drawback of dislocation-induced tail states is the enhanced nonradiative recombination in the dislocation line region. This study provides a detailed analysis of device injection physics in InGaN QW red LEDs and outlines potential optimization strategies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Runaway electron deconfinement in SPARC and DIII-D by a passive 3D coil

The operation of a 3D coil—passively driven by the current quench (CQ) loop voltage—for the deconfinement of runaway electrons (REs) is modeled for disruption scenarios in the SPARC and DIII-D tokamaks. Nonlinear magnetohydrodynamic (MHD) modeling is carried out with the NIMROD code including time-dependent magnetic field boundary conditions to simulate the effect of the coil. Further modeling in some cases uses the ASCOT5 code to calculate advection and diffusion coefficients for REs based on the NIMROD-calculated fields, and the DREAM code to compute the runaway evolution in the presence of these transport coefficients. Compared with similar modeling in Tinguely et al (2021 Nucl. Fusion 61 124003), considerably more conservative assumptions are made with the ASCOT5 results, zeroing low levels of transport, particularly in regions in which closed flux surfaces have reformed. Of three coil geometries considered in SPARC, only the n = 1 coil is found to have sufficient resonant components to suppress the runaway current growth. Without the new conservative transport assumptions, full suppression of the RE current is maintained when the thermal quench MHD is included in the simulation or when the RE current is limited to 250kA, but when transport in closed flux regions is fully suppressed, these scenarios allow RE beams on the order of 1–2 MA to appear. Additional modeling is performed to consider the effects of the close ideal wall. In DIII-D, the CQ is modeled for both limited and diverted equilibrium shapes. In the limited shape, the onset of stochasticity is found to be insensitive to the coil current amplitude and governed largely by the evolution of the safety-factor profile. In both devices, prediction of the q-profile evolution is seen to be critical to predicting the later time effects of the coil.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Development and assessment of models for turbulent Rayleigh-Taylor mixing using the macroscopic forcing method

Reynolds-Averaged Navier Stokes (RANS) simulations are a popular method for designing ICF experiments, and accurate mixing models are crucial for these simulations to give good predictions. To this end, the present work seeks to demonstrate the Macroscopic Forcing Method (MFM) as a tool for both improving existing RANS models as well as assessing RANS model forms. First, MFM analysis from Lavacot et al. (Phys. Rev. Fluids, 2025) is used to develop the k–L–F model, an extension of the k–L model of Dimonte and Tipton (Phys. Fluids, 2006) that incorporates nonlocality through addition of a turbulent species flux transport equation. MFM is then applied to the k–L–F model along with the k–L and BHR–4 models to assess their forms and compare the model-implied eddy diffusivity moments to those measured from high-fidelity simulations. Furthermore, the analysis reveals that models incorporating nonlocality (k–L–F and BHR–4) match the high-fidelity simulation data better than purely local models (k–L), both in terms of mean fields and eddy diffusivity moments. However, all of the considered RANS models struggle to match temporal moments at high Atwood numbers, highlighting the importance of temporal nonlocality in these regimes and the need for additional improvement even among models incorporating nonlocality.

general physics↗

An efficient protocol for excited states of large biochromophores

Efficient energy transport in photosynthetic antenna is a long-standing source of inspiration for artificial light harvesting materials. However, characterizing the excited states of the constituent chromophores poses a considerable challenge to mainstream quantum chemical and semiempirical excited state methods due to their size and complexity and the accuracy required to describe small but functionally important changes in their properties. In this paper, we explore an alternative approach to calculating the excited states of large biochromophores, exemplified by a specific method for calculating the Q y transition of bacteriochlorophyll a, which we name Chl-xTB. Using a diagonally dominant approximation to the Casida equation and a bespoke parameterization scheme, Chl-xTB can match time-dependent density functional theory’s accuracy and semiempirical speed for calculating the potential energy surfaces and absorption spectra of chlorophylls. We demonstrate that Chl-xTB (and other prospective realizations of our protocol) can be integrated into multiscale models, including concurrent excitonic and point-charge embedding frameworks, enabling the analysis of biochromophore networks in a native environment. We exploit this capability to probe the low-frequency spectral densities of excitonic energies and interchromophore interactions in the light harvesting antenna protein LH2 (light harvesting complex 2). The impact of low-frequency protein motion on interchromophore coupling and exciton transport has routinely been ignored due to the prohibitive costs of including it in simulations. Our results provide a more rigorous basis for continued use of this approximation by demonstrating that exciton transition energies are unaffected by low-frequency vibrational coupling to exciton interaction energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formation of Amorphous Carbon Multi‐Walled Nanotubes from Random Initial Configurations

Amorphous carbon nanotubes (a‐CNT) with up to four walls and sizes ranging from 200 to 3200 atoms have been simulated, starting from initial random configurations and using the Gaussian Approximation Potential. The important variables (like density, height, and diameter) required to successfully simulate a‐CNTs were predicted with the machine learning random forest technique. The width of the a‐CNT models ranged between 0.55–2 nm with an average inter‐wall spacing of 0.31 nm. The topological defects in a‐CNTs were analyzed and new defect configurations were observed. The electronic density of states and localization in these phases were discussed and delocalized electrons in the π subspace were identified as an important factor for inter‐layer cohesion. Spatial projection of the electronic conductivity favors axial transport along connecting hexagons, while non‐hexagonal parts of the network either hinder or bifurcate the electronic transport. A vibrational density of states was calculated and is potentially an experimentally comparable fingerprint of the material. The appearance of a low‐frequency radial breathing mode was discussed and the thermal conductivity at 300 K was estimated using the Green‐Kubo formula.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Role of Cation Coordination in the Electrical and Optical Properties of Amorphous Transparent Conducting Oxides

Amorphous oxide semiconductor materials have demonstrated numerous advantages without compromise of electrical properties as compared to their crystalline counterparts, yet understanding of the fundamental principles allowing this has remained elusive. To study the origins of enhanced optoelectronic properties, we apply high-throughput, combinatorial sputtering, structural and spectral mapping, and computationally intensive ab initio molecular dynamics simulations with density functional theory to a ternary, post-transition metal oxide system, namely, zinc tin oxide. The deposited thin films exhibit a high figure of merit, achieving carrier densities in the range of 1019 to 1020 cm–3 and carrier mobilities up to 35 cm2/Vs. These results highlight the role of local distortions and cation coordination in determining the microscopic origins of carrier generation and transport. In particular, we identify the strong likelihood of Sn undercoordination in both Zn-poor and Zn-rich phases leading to the high carrier concentrations observed. This not only diverges from the still widespread historical indictment of oxygen vacancies controlling carrier population in crystalline oxides but also provides a comprehensive framework to describe the unique structure–property relationships using specific structural and electronic descriptors in disordered phase materials.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,M↗

A level-set immersed boundary method for reactive transport in complex topologies with moving interfaces

A simulation framework based on the level-set and the immersed boundary methods (LS-IBM) has been developed for reactive transport problems in porous media involving a moving solid-fluid interface. The interface movement due to surface reactions is tracked by the level-set method, while the immersed boundary method captures the momentum and mass transport at the interface. The proposed method is capable of accurately modeling transport near evolving boundaries in Cartesian grids. The framework formulation guarantees second order accuracy in space. Since the interface velocity is only defined at the moving boundary, an interface velocity propagation method is also proposed. The method can be applied to other moving interface problems of the “Stefan” type. Here, we validate the proposed LS-IBM both for flow and transport close to an immersed object with reactive boundaries as well as for crystal growth. Lastly, the proposed method provides a powerful tool to model more realistic problems involving moving reactive interfaces in complex domains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Effect of K + Force Fields on Ionic Conductivity and Charge Dynamics of KOH in Ethylene Glycol

Predicting ionic conductivity is crucial for developing efficient electrolytes for energy storage and conversion and other electrochemical applications. An accurate estimate of ionic conductivity requires understanding complex ion–ion and ion–solvent interactions governing the charge transport at the molecular level. Molecular simulations can provide key insights into the spatial and temporal behavior of electrolyte constituents. However, such insights depend on the ability of force fields to describe the underlying phenomena. In this work, molecular dynamics simulations were leveraged to delineate the impact of force field parameters on ionic conductivity predictions of potassium hydroxide (KOH) in ethylene glycol (EG). Four different force fields were used to represent the K + ion. Diffusion-based Nernst–Einstein and correlation-based Einstein approaches were implemented to estimate the ionic conductivity, and the predicted values were compared with experimental measurements. The physical aspects, including ion-aggregation, charge distribution, cluster correlation, and cluster dynamics, were also examined. A force field was identified that provides reasonably accurate Einstein conductivity values and a physically coherent representation of the electrolyte at the molecular level.

25 ENERGY STORAGE↗

Two self-similar Reynolds-stress transport models with anisotropic eddy viscosity

Two Reynolds-averaged Navier-Stokes models with full Reynolds-stress transport (RST) and tensor eddy viscosity are presented. These new models represent RST extensions of the $k−2L−a−\mathscr{C}$ and $k−ϕ−L−a−\mathscr{C}$ models by Morgan. Self-similarity analysis is used to derive constraints on model coefficients required to reproduce expected growth parameters for a variety of canonical flows, including Rayleigh-Taylor (RT) and Kelvin-Helmholtz (KH) mixing layers. Both models are then applied in one-dimensional simulation of RT and KH mixing layers, and the expected self-similar growth rates and anisotropy are obtained. Next, models are applied in two-dimensional simulation of the so-called “tilted rocket rig” inclined RT experiment and in simulation of a shock-accelerated localized patch of turbulence. Here it is found that RST is required to capture the qualitative growth of the shock-accelerated patch, and an anisotropic eddy viscosity provides substantial improvement over a Boussinesq treatment for the tilted rocket rig problem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Machine Phase Fullerene Nanotechnology: 1996

NASA has used exotic materials for spacecraft and experimental aircraft to good effect for many decades. In spite of many advances, transportation to space still costs about $10,000 per pound. Drexler has proposed a hypothetical nanotechnology based on diamond and investigated the properties of such molecular systems. These studies and others suggest enormous potential for aerospace systems. Unfortunately, methods to realize diamonoid nanotechnology are at best highly speculative. Recent computational efforts at NASA Ames Research Center and computation and experiment elsewhere suggest that a nanotechnology of machine phase functionalized fullerenes may be synthetically relatively accessible and of great aerospace interest. Machine phase materials are (hypothetical) materials consisting entirely or in large part of microscopic machines. In a sense, most living matter fits this definition. To begin investigation of fullerene nanotechnology, we used molecular dynamics to study the properties of carbon nanotube based gears and gear/shaft configurations. Experiments on C60 and quantum calculations suggest that benzyne may react with carbon nanotubes to form gear teeth. Han has computationally demonstrated that molecular gears fashioned from (14,0) single-walled carbon nanotubes and benzyne teeth should operate well at 50-100 gigahertz. Results suggest that rotation can be converted to rotating or linear motion, and linear motion may be converted into rotation. Preliminary results suggest that these mechanical systems can be cooled by a helium atmosphere. Furthermore, Deepak has successfully simulated using helical electric fields generated by a laser to power fullerene gears once a positive and negative charge have been added to form a dipole. Even with mechanical motion, cooling, and power; creating a viable nanotechnology requires support structures, computer control, a system architecture, a variety of components, and some approach to manufacture. Additional information is contained within the original extended abstract.

Globus, Al↗

Learning a General Model of Single Phase Flow in Complex 3D Porous Media

Modeling effective transport properties of 3D porous media, such as permeability, at multiple scales is challenging as a result of the combined complexity of the pore structures and fluid physics—in particular, confinement effects which vary across the nanoscale to the microscale. While numerical simulation is possible, the computational cost is prohibitive for realistic domains, which are large and complex. Although machine learning (ML) models have been proposed to circumvent simulation, none so far has simultaneously accounted for heterogeneous 3D structures, fluid confinement effects, and multiple simulation resolutions. By utilizing numerous computer science techniques to improve the scalability of training, we have for the first time developed a general flow model that accounts for the pore-structure and corresponding physical phenomena at scales from Angstrom to the micrometer. Using synthetic computational domains for training, our ML model exhibits strong performance (R 2 = 0.9) when tested on extremely diverse real domains at multiple scales.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Using Computationally-Determined Properties for Machine Learning Prediction of Self-Diffusion Coefficients in Pure Liquids

The ability to predict transport properties of liquids quickly and accurately will greatly improve our understanding of fluid properties both in bulk and complex mixtures, as well as in confined environments. Such information could then be used in the design of materials and processes for applications ranging from energy production and storage to manufacturing processes. As a first step, we consider the use of machine learning (ML) methods to predict the diffusion properties of pure liquids. Recent results have shown that Artificial Neural Networks (ANNs) can effectively predict the diffusion of pure compounds based on the use of experimental properties as the model inputs. In the current study, a similar ANN approach is applied to modeling diffusion of pure liquids using fluid properties obtained exclusively from molecular simulations. A diverse set of 102 pure liquids is considered, ranging from small polar molecules (e.g., water) to large nonpolar molecules (e.g., octane). Self-diffusion coefficients were obtained from classical molecular dynamics (MD) simulations. Since nearly all the molecules are organic compounds, a general set of force field parameters for organic molecules was used. The MD methods are validated by comparing physical and thermodynamic properties with experiment. Computational input features for the ANN include physical properties obtained from the MD simulations as well as molecular properties from quantum calculations of individual molecules. Furthermore, fluid properties describing the local liquid structure were obtained from center of mass radial distribution functions (COM-RDFs). Feature sensitivity analysis revealed that isothermal compressibility, heat of vaporization, and the thermal expansion coefficient were the most impactful properties used as input for the ANN model to predict the MD simulated self-diffusion coefficients. The MD-based ANN successfully predicts the MD self-diffusion coefficients with only a subset (2 to 3) of the available computationally determined input features required. A separate ANN model was developed using literature experimental self-diffusion coefficients as model targets. Although this second ML model was not as successful due to a limited number of data points, a good correlation is still observed between experimental and ML predicted self-diffusion coefficients.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization of uncertainties in electron-argon collision cross sections

Abstract The predictive capability of a plasma discharge model depends on accurate representations of electron-impact collision cross sections, which determine the corresponding reaction rates and electron transport properties. The values of cross sections can be known only approximately either through experiments or simulations and are thus subject to uncertainties. Quantifying the uncertainties in plasma simulations allows us to assess the reliability of simulations and to provide a basis for interpreting discrepancies between simulations and experiments. For such uncertainty quantification of plasma simulations, it is essential to quantify the uncertainties of the underlying cross sections. Although much effort has been committed to calibrate the cross section values, their uncertainties are not well investigated. We characterize uncertainties in electron-argon atom collision cross sections using a Bayesian framework. Six collision processes—elastic momentum transfer, ionization, and four excitations—are characterized with semi-empirical models, which effectively capture the features important to the macroscopic properties of the plasma. A probability model for the uncertain parameters of these semi-empirical models is developed. Specifically, a Gaussian-process likelihood model is proposed to capture discrepancies among data sets, as well as the model-form inadequacies of the semi-empirical models. Two other likelihood models are compared with the proposed Gaussian-process model, to illustrate the importance of the choice of the likelihood model. The cross section models are calibrated using the electron-beam experiments and ab-inito quantum simulations. The resulting calibrated uncertainties capture well the scattering among the data sets. The calibrated cross section models are further validated against swarm-parameter experiments and zero-dimensional Boltzmann equation simulations of widely used cross section datasets.

Chung, Seung Whan (ORCID:0000000302501549)↗

Capturing thin structures in VOF simulations with two-plane reconstruction

A novel interface reconstruction strategy for volume of fluid (VOF) methods is introduced that represents the liquid-gas interface as two planes that co-exist within a single computational cell. In comparison to the piecewise linear interface calculation (PLIC), this new algorithm greatly improves the accuracy of the reconstruction, in particular when dealing with thin structures such as films. The placement of the two planes requires the solution of a non-linear optimization problem in six dimensions, which has the potential to be overly expensive. Further, an efficient solution to this optimization problem is presented here that exploits two key ideas: an algorithm for extracting multiple plane orientations from transported surface data, and an efficient and mass-conserving distance-finding algorithm that accounts for two planes with arbitrary orientation. Additionally, a simple and robust strategy is presented to accurately represent the surface tension forces produced at the interface of subgrid-thickness films. The performance of this new VOF reconstruction is demonstrated on several test cases that illustrate the capability to handle arbitrarily thin films.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Sample shape and boundary dependence of measured transverse thermal properties

In spite of increased interest in thermal Hall measurements for the analysis of insulating quantum materials, there remains large uncertainty in such measurements due to contact misalignment. In this paper, we propose that sample geometry and uncertain boundary conditions provide an additional source of uncertainty in the measurement of $D_{xy}$ or $κ_{xy}$. By running simple simulations in an open source finite-element solver, we demonstrate that measured $D_{xy}$ can be changed by a non-negligible fraction in samples with similar width and length. This geometric corrective factor depends on the distinction between a uniform heat flow and constant temperature boundary couplings to a bath. Sample geometry and boundary conditions can be accounted for through simulation or by using rectangular samples to make thermal Hall measurements more reliable and reproducible. Finally, we detail a contactless optical method for measuring $D_{xy}$ based on an existing photothermal microscope technique. This method is insensitive to the longitudinal diffusivity pollution caused by contact misalignment.

36 MATERIALS SCIENCE↗