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At least 955 records · Page 53

DeePMD-kit v2: A software package for deep potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.

97 MATHEMATICS AND COMPUTING↗

Nanorod length-dependent photodriven H2 production in 1D CdS–Pt heterostructures

Colloidal quantum confined semiconductor-metal heterostructures are promising candidates for solar energy conversion because their light absorbing semiconductor and catalytic components can be independently tuned and optimized. Although the light-to-hydrogen efficiencies of such systems have shown interesting dependences on the morphologies of the semiconductor and metal domains, the mechanisms of such dependences are poorly understood. Here, we use Pt tipped 0D CdS quantum dots (with ∼4.6 nm diameter) and 1D CdS nanorods (of ∼13.8, 27.8, 66.6, and 88.9 nm average rod lengths) as a model system to study the distance-dependence of charge separation and charge recombination times and their impacts on photo-driven H2 production. The H2 generation quantum efficiency increases from 0.2% ± 0.0% in quantum dots to 28.9% ± 0.4% at a rod length of 28 nm and shows negligible changes at longer rod lengths. The half-life time of electron transfer from CdS to Pt increases monotonically with rod length, from 0.7 ± 0.1 in quantum dots to 170.2 ± 29.5 ps in the longest rods, corresponding to a slight decrease in electron transfer quantum efficiency from 92% to 81%. The amplitude-weighted average lifetime of charge recombination of the electron in Pt with the hole in CdS increases from 4.7 ± 0.4 µs in quantum dots to 149 ± 34 µs in 28 nm nanorods, and the lifetime does not increase further in longer rods, resembling the trend in the observed H2 generation quantum efficiency. Our result suggests that the competition of the charge recombination process with the hole removal by the sacrificial electron donor plays a dominant role in the observed nanorod length dependent overall light driven H2 generation quantum efficiency.

Chemistry↗

Enhancing high-fidelity neural network potentials through low-fidelity sampling

The efficacy of neural network potentials (NNPs) critically depends on the quality of the configurational datasets used for training. Prior research using empirical potentials has shown that well-selected liquid–solid transitional configurations of a metallic system can be translated to other metallic systems. This study demonstrates that such validated configurations can be relabeled using density functional theory (DFT) calculations, thereby enhancing the development of high-fidelity NNPs. Training strategies and sampling approaches are efficiently assessed using empirical potentials and subsequently relabeled via DFT in a highly parallelized fashion for high-fidelity NNP training. Our results reveal that relying solely on energy and force for NNP training is inadequate to prevent overfitting, highlighting the necessity of incorporating stress terms into the loss functions. To optimize training involving force and stress terms, we propose employing transfer learning to fine-tune the weights, ensuring that the potential surface is smooth for these quantities composed of energy derivatives. This approach markedly improves the accuracy of elastic constants derived from simulations in both empirical potential-based NNPs and relabeled DFT-based NNPs. Overall, this study offers significant insights into leveraging empirical potentials to expedite the development of reliable and robust NNPs at the DFT level.

97 MATHEMATICS AND COMPUTING↗

Neuromorphic heat transport effects in a molecular junction

Understanding energy transport at the nanoscale is an open and fundamental challenge in the molecular sciences with direct implications for the design of new electronics, computing devices, and materials. While nanoscale energy transport under steady-state conditions has been studied extensively, there is much less known about energy transport under time-dependent driving forces, particularly in the far-from-equilibrium regime. In this work, we use nonequilibrium molecular dynamics simulations and stochastic thermodynamics to investigate energy transport in a well-studied nanoscale system—a molecular junction—subjected to a time-periodic temperature gradient. The primary observation is that molecular junctions can exhibit heat transport hysteresis, a phenomenon in which the heat flux through a system depends not only on the instantaneous value of a time-dependent temperature bias but also on the temporal history of that bias. The presented findings illustrate that molecular junctions can exhibit the specific memory effect—heat transport hysteresis—that is essential for the design of thermal neuromorphic computers. This work elucidates a potential pathway toward the realization of such devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Optimization and active stabilization of a far-infrared laser for NSTX-U high poloidal wavenumber scattering diagnostics

The far-infrared (FIR) laser output beam power and profile are important parameters in the laser-aided diagnostics, directly influencing the spatial resolution and signal-to-noise ratio of measurements. Here, this work focuses on developing a systematic control method to enhance FIR laser beam quality through optimized mirror alignment and real-time feedback-based precision cavity length tuning. A 150 W CO 2 laser, aligned with the waveguide axis using a HeNe reference laser, serves as the pump source. The sensitivity of FIR beam intensity to pump gas pressure and thermal expansion is investigated, revealing that even a 1 µm cavity expansion can significantly degrade output power stability to about two-thirds of its original value. To address this, a feedback control module has been designed and implemented for active cavity length adjustment, stabilizing the output power at ∼30 mW. In addition, maintaining a high formic acid gas pressure ($>$190 mTorr) within the cavity ensures reliable operation. The optimized FIR laser will be deployed on the National Spherical Torus eXperiment-U high poloidal wavenumber scattering system for studying electron-scale turbulence in tokamak plasmas.

Xu, Xinhang [Univ. of California, Davis, CA (Unite↗

Exploring high-intensity laser-driven secondary sources via high-order spectral pulse shaping for high-energy-density experiments

We present here the results of an investigation that aims to explore the impact of spectral pulse shaping on the generation of high-energy electrons (>1 MeV) and x rays (∼5–9 keV) using a high-intensity (I∼10 21 W/cm 2 ) laser system. The study involved a systematic scan of a broad parameter space in group delay dispersion and third-order dispersion, with variations up to 4 × 10 3 fs −2 and 6 × 10 4 fs −3 , respectively, to identify optimal conditions for enhancing secondary source yields. Several spectral phase conditions were found to significantly enhance the generation of hot electrons and x rays by amounts reaching up to 50% relative to the transform-limited pulse. The experiment, conducted at the Scarlet laser facility (800 nm, 5 J, 30 fs) at the Ohio State University, highlights the potential of spectral pulse shaping as a powerful tool for tuning secondary laser-driven sources. These findings are particularly relevant for advancing brighter x-ray and electron probes for high-energy-density science.

Physics - Plasma physics↗

Physical bioenergetics: Energy fluxes, budgets, and constraints in cells

Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. In this work, we review recent advances and discuss open questions and challenges in physical bioenergetics.

59 BASIC BIOLOGICAL SCIENCES↗

Cholesterol-dependent enzyme activity of human TSPO1

The amino acid sequence of the tryptophan-rich sensory proteins (TSPO) is substantially conserved throughout all kingdoms of life. Human mitochondrial TSPO1 (HsTSPO1) binds to porphyrins and steroids, although its interactions with these molecules remains unknown.HsTSPO1 is associated with numerous physiological and pathological disorders, but the underlying molecular mechanisms are unknown. Here, we disclose the finding of human mitochondrial TSPO as a cholesterol-dependent protoporphyrin IX oxygenase. The results of our biochemical characterization are consistent with structural data and evolutionary analysis. The dependence ofHsTSPO1 activity on cholesterol may be the result of the coevolution of this membrane protein with the membrane system. Our study provides a molecular foundation for comprehending the various roles played by mitochondrial TSPO in normal physiological and pathological situations.

Science & Technology - Other Topics↗

Three-dimensional high-content imaging of unstained soft tissue with subcellular resolution using a laboratory-based X-ray microscope

With increasing interest in studying biological systems across spatial scales—from centimeters down to nanometers—histology continues to be the gold standard for tissue imaging at cellular resolution, providing an essential bridge between macroscopic and nanoscopic analysis. However, its inherently destructive and two-dimensional nature limits its ability to capture the full three-dimensional complexity of tissue architecture. Here, we show that phase-contrast X-ray microscopy can enable three-dimensional virtual histology with subcellular resolution. This technique provides direct quantification of electron density without restrictive assumptions, allowing for direct characterization of cellular nuclei in a standard laboratory setting. By combining high spatial resolution and soft tissue contrast, with automated segmentation of cell nuclei, we demonstrated virtual Hematoxylin and Eosin (H&E) staining using machine learning-based style transfer, yielding volumetric datasets compatible with existing histopathological analysis tools. Furthermore, by integrating electron density and the sensitivity to nanometric features of the dark field contrast channel, we achieve stain-free, high-content imaging capable of distinguishing nuclei and extracellular matrix.

3D virtual histology↗

Assessment of RELAP5-3D Code with Molten Salt Heat Transfer Experiments

The accurate thermal-hydraulic assessment of thermal storage systems is crucial for addressing the integrity and performance of the storage system design. This is particularly important for thermal storage systems using molten salts as a heat transport and storage medium, as the chemical corrosion and erosion by the high-temperature molten salts can cause serious damage to the structural components of the storage system. To understand these effects for TerraPower’s Natrium® Demonstration Reactor design, the system thermal-hydraulic analysis code, RELAP5-3D, is utilized to analyze the thermal storage system. This study evaluates two heat transfer correlations implemented in the RELAP5-3D code—the Dittus-Boelter and Gnielinski correlations—using selected benchmark cases from two molten salt heat transfer experiments conducted at Xi’an Jiao Tong University and the German Aerospace Center. The Nusselt numbers calculated using the Gnielinski correlation agree with the experimental data within ±5% of the relative deviations at 300°C and 400°C. With the increasing Reynolds numbers, the Dittus-Boelter correlation underestimates the Nusselt numbers by up to 22% compared to the Gnielinski correlation. Comparison of the RELAP5-3D calculation results with experimental data at a high temperature of 550°C revealed that the thermo-chemical characteristics of solar salt at high temperatures surpassing the decomposition temperatures of nitrate salts reduce the accuracy of heat transfer model of the RELAP5-3D code. Specifically, it has been observed that the temperatures of the wall surface and liquid near the wall can surpass the decomposition temperatures, even though the bulk temperature of molten salts remains significantly lower than these decomposition temperatures. In summary, this study recommends the use of the Gnielinski correlation for the heat transfer analysis of molten salt, rather than the Dittus-Boelter correlation.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

Probing Diffuse Polymer Brush Interfaces Using Resonant Soft X-ray Scattering

The success of a neutron or x-ray scattering experiment relies on sufficient signal from the system being studied. The intensity of scattered radiation depends on instrument resolution, the structure of the scattering elements, and the interaction between the incident radiation and the sample—so-called ‘scattering contrast’. The contrast depends on the square of the difference in the scattering length densities (SLDs) for each component, and each SLD depends on the atoms and radiation involved (eq. 1). For neutrons, the scattering lengths bi are specific to the type of nuclei involved. For conventional x-ray scattering, b i depends on the electron density and thus the atomic number Z.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Topological background discrimination in the PandaX-III neutrinoless double beta decay experiment

The PandaX-III experiment plans to search for neutrinoless double beta decay (0ν ββ ) of 136 Xe in the China JinPing underground Laboratory (CJPL). The experiment will use a high pressure gaseous time projection chamber (TPC) to register both the energy and the electron track topology of an event. This article is devoted to demonstrate our particular detector setup capabilities for the identification of 0ν ββ and the consequent background reduction. As software tool we use REST, a framework developed for the reconstruction and simulation of TPC-based detector systems. We study the potential for background reduction by introducing appropriate parameters based on the properties of 0ν ββ events. We exploit for the first time not only the energy density of the electron track-ends, but also the electron scattering angles produced by an electron near the end of its trajectory. To implement this, we have added new algorithms for detector signal and track processing inside REST. Their assessment shows that background can be reduced by about 7 orders of magnitude while keeping 0ν ββ efficiency above 20% for the PandaX-III baseline readout scheme, a two-dimensional 3 mm pitch stripped readout. More generally, we use the potential of REST to handle 2D/3D data to assess the impact on signal-to-background significance at different detector granularities, and to validate the PandaX-III baseline choice. Finally, we demonstrate the additional potential to discriminate surface background events generated at the readout plane in the absence of to, by making use of event parameters related with the diffusion of electrons.

Majorana↗

The scoping, design, and plasma physics optimization of the Eos neutron source stellarator

On the path to a fusion pilot plant, Thea Energy plans to build Eos, a sub-breakeven, deuterium-deuterium, beam-target fusion, stellarator neutron source facility for producing tritium and other valuable radioisotopes. In this paper, a set of 1D plasma physics models are coupled and used to design the operating point of the facility and predict performance. At this foundational stage of the design, analytic and approximate models are sufficient to capture the leading-order effects, and fast enough to run in the inner loop of an optimizer. Higher-fidelity analyses will follow. Models of 1D profile-dependent neutral beam stopping, ion beam slowing down, beam-target fusion, electron-ion classical heat transfer, energy confinement (ISS04), beam pressure, beam heating of ions and electrons, beam-beam fusion fraction, and neutral beam injection and gyrotron heating electrical efficiencies are included. A numerical optimizer is used to determine the minimum required facility electric power to generate tritium at a given rate. A potentially advantageous regime is described in which modern precisely-quasisymmetric stellarators, new high-temperature superconductors, ITER-derived neutral beam injection, and new high-frequency gyrotrons enable a suitible target plasma with hot electrons, cold ions, peaked density and temperature profiles, and high beam-injected ion density. It appears possible at this time for a facility with a medium-scale and medium-strength stellarator whose required facility electric power is less than 40 MW to produce $2.5\times 10^{17}$ neutrons s -1 for the production of radioisotopes. With the addition of a tritium breeding blanket, such a facility could produce 0.2 grams d -1 or 70 grams yr -1 of tritium.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measurement of Liquid Argon Scintillation Light Properties by means of an Alpha Source placed inside the CERN 10-PMT LAr Detection System

A particle detection system that exploits the scintillation light produced by ionizing particles in liquid argon (LAr) has been assembled at CERN. The system is based on 10 large-area photomultiplier tubes (PMT) immersed in a 1500-liter dewar filled with liquid argon and equipped with an extendible feed-through and mechanical support for an alpha source (241Am). The position of the source can be changed with respect to the PMT plane in vertical and horizontal directions. Arrays of silicon photomultiplier (SiPM) photodetectors, integrated in the source support, are used for the data acquisition trigger and to define the t0 of the light generation. PMT and SiPM signals can be recorded at different distances and different positions allowing the measurement of some of the LAr scintillation light properties. The system was studied and characterized in detail, and physics results on LAr scintillation properties are expected soon.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A poloidal high- k scattering system for NSTX-U

A previous 5-channel tangential high-k scattering system is being replaced by an 8-channel, poloidal high-k scattering system on the National Spherical Torus eXperiment Upgrade (NSTX-U) device located in Princeton, NJ, USA. The 693 GHz poloidal scattering system replaces a 280 GHz tangential scattering system to study high-k electron density fluctuations on NSTX-U, thereby considerably enhancing planned turbulence physics studies by providing a measurement of the k θ -spectrum of both electron temperature gradient (ETG) and ion temperature gradient (ITG) modes. Two approaches to generating the 693 GHz probe beam are under development: an optically-pumped far-infrared (FIR) laser that generates ~50 mW, and a compact gyrotron that can potentially generate in excess of 5 W. Large aperture optics collect radiation scattered from density fluctuations in the plasma core at 8 simultaneous scattering angles ranging from 2 to 15° corresponding to poloidal wavenumbers that extend to >40 cm -1 . Finally, steerable launch optics coupled with receiver optics mounted on a 5-axis receiver carriage allow the scattering volume to be placed radially from r/a = 0.3 out to the pedestal region (r/a ~ 0.99) and translated horizontally as needed to satisfy wavenumber matching.

47 OTHER INSTRUMENTATION↗

Electron spin coherence on a solid neon surface

We report a single electron floating on the surface of a condensed noble-gas liquid or solid can act as a spin qubit with ultralong coherence time, thanks to the extraordinary purity of such systems. Previous studies suggest that the electron spin coherence time on a superfluid helium (He) surface can exceed 100 s. In this paper, we present theoretical studies of the electron spin coherence on a solid neon (Ne) surface, motivated by our recent experimental realization of single-electron charge qubit on solid Ne. The major spin decoherence mechanisms investigated include the fluctuating Ne diamagnetic susceptibility due to thermal phonons, the fluctuating thermal current in normal metal electrodes, and the quasi-statically fluctuating nuclear spins of the 21 Ne ensemble. We find that at a typical experimental temperature about 10 mK in a fully superconducting device, the electron spin decoherence is dominated by the third mechanism via electron–nuclear spin–spin interaction. For natural Ne with 2700 ppm abundance of 21 Ne, the estimated inhomogeneous dephasing time ${T}_{2}^{*}$ is around 0.16 ms, already better than most semiconductor quantum-dot spin qubits. For commercially available, isotopically purified Ne with 1 ppm of 21 Ne, ${T}_{2}^{*}$ can be 0.43 s. Under the application of Hahn echoes, the coherence time T 2 can be improved to 30 ms for natural Ne and 81 s for purified Ne. Therefore, the single-electron spin qubits on solid Ne can serve as promising new spin qubits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Building spatial symmetries into parameterized quantum circuits for faster training

Abstract Practical success of quantum learning models hinges on having a suitable structure for the parameterized quantum circuit. Such structure is defined both by the types of gates employed and by the correlations of their parameters. While much research has been devoted to devising adequate gate-sets, typically respecting some symmetries of the problem, very little is known about how their parameters should be structured. In this work, we show that an ideal parameter structure naturally emerges when carefully considering spatial symmetries (i.e. the symmetries that are permutations of parts of the system under study). Namely, we consider the automorphism group of the problem Hamiltonian, leading us to develop a circuit construction that is equivariant under this symmetry group. The benefits of our novel circuitstructure, called ORB, are numerically probed in several ground-state problems. We find a consistent improvement (in terms of circuit depth, number of parameters required, and gradient magnitudes) compared to literature circuit constructions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Deeply uncertain: comparing methods of uncertainty quantification in deep learning algorithms

We present a comparison of methods for uncertainty quantification (UQ) in deep learning algorithms in the context of a simple physical system. Three of the most common uncertainty quantification methods - Bayesian Neural Networks (BNN), Concrete Dropout (CD), and Deep Ensembles (DE) - are compared to the standard analytic error propagation. We discuss this comparison in terms endemic to both machine learning ("epistemic" and "aleatoric") and the physical sciences ("statistical" and "systematic"). The comparisons are presented in terms of simulated experimental measurements of a single pendulum - a prototypical physical system for studying measurement and analysis techniques. Our results highlight some pitfalls that may occur when using these UQ methods. For example, when the variation of noise in the training set is small, all methods predicted the same relative uncertainty independently of the inputs. This issue is particularly hard to avoid in BNN. On the other hand, when the test set contains samples far from the training distribution, we found that no methods sufficiently increased the uncertainties associated to their predictions. This problem was particularly clear for CD. In light of these results, we make some recommendations for usage and interpretation of UQ methods.

59 BASIC BIOLOGICAL SCIENCES↗