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At least 757 records · Page 42

SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory

Multi-reference (MR) electronic structure methods, such as MR configuration interaction or MR perturbation theory, can provide reliable energies and properties for many molecular phenomena like bond breaking, excited states, transition states or magnetic properties of transition metal complexes and clusters. However, owing to their inherent complexity, most MR methods are still too computationally expensive for large systems. Therefore the development of more computationally attractive MR approaches is necessary to enable routine application for large-scale chemical systems. Among the state-of-the-art MR methods, second-order N-electron valence state perturbation theory (NEVPT2) is an efficient, size-consistent, and intruder-state-free method. However, there are still two important bottlenecks in practical applications of NEVPT2 to large systems: (a) the high computational cost of NEVPT2 for large molecules, even with moderate active spaces and (b) the prohibitive cost for treating large active spaces. In this work, we address problem (a) by developing a linear scaling “partially contracted” NEVPT2 method. This development uses the idea of domain-based local pair natural orbitals (DLPNOs) to form a highly efficient algorithm. As shown previously in the framework of single-reference methods, the DLPNO concept leads to an enormous reduction in computational effort while at the same time providing high accuracy (approaching 99.9% of the correlation energy), robustness, and black-box character. In the DLPNO approach, the virtual space is spanned by pair natural orbitals that are expanded in terms of projected atomic orbitals in large orbital domains, while the inactive space is spanned by localized orbitals. The active orbitals are left untouched. Our implementation features a highly efficient “electron pair prescreening” that skips the negligible inactive pairs. The surviving pairs are treated using the partially contracted NEVPT2 formalism. A detailed comparison between the partial and strong contraction schemes is made, with conclusions that discourage the strong contraction scheme as a basis for local correlation methods due to its non-invariance with respect to rotations in the inactive and external subspaces. A minimal set of conservatively chosen truncation thresholds controls the accuracy of the method. With the default thresholds, about 99.9% of the canonical partially contracted NEVPT2 correlation energy is recovered while the crossover of the computational cost with the already very efficient canonical method occurs reasonably early; in linear chain type compounds at a chain length of around 80 atoms. Calculations are reported for systems with more than 300 atoms and 5400 basis functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

UQpy: A general purpose Python package and development environment for uncertainty quantification

In this paper, we present the UQpy software toolbox, an open-source Python package for general uncertainty quantification (UQ) in mathematical and physical systems. The software serves as both a user-ready toolbox that includes many of the latest methods for UQ in computational modeling and a convenient development environment for Python programmers advancing the field of UQ. The paper presents an introduction to the software's architecture and existing capabilities, divided in the code in a set of modules centered around different UQ tasks such as sampling methods, generation of random processes and random fields, probabilistic inverse modeling, reliability analysis, surrogate modeling, and active learning. The paper also highlights the importance of the RunModel module, which is used to drive simulations in the uncertainty analyses performed in UQpy. This module conveniently allows the user to define computational models directly in Python, or to run simulations from a third-party software in serial or in parallel. To illustrate the various capabilities, two examples are tracked throughout the paper and analyzed repeatedly for various UQ tasks. The first is a Python model solving a nonlinear structural dynamics problem, used to illustrate UQpy's capabilities in sampling and forward propagation of high dimensional random vectors (stochastic processes), and probabilistic inference. The second model is a third-party Abaqus finite element model solving the thermomechanical response of a beam structure. This example is used to illustrate UQpy's capabilities in variance reduction sampling techniques, reliability analysis, surrogate modeling and active learning techniques.

97 MATHEMATICS AND COMPUTING↗

Theoretical study of IR and photoelectron spectra of small gallium-arsenide clusters

Relative stabilities of small Ga{sub n}As{sub m} clusters, as well as their structural electronic and vibrational properties, were computed and analysed using a CCSD(T) reference method since experimental data in this area are sparse or unknown. With the aim of investigating larger clusters, we explored several DFT functionals and basis sets able to mimic the reliable CCSD(T) approach. Among them, the PBE0/SBKJC+sp,d appears as the most efficient to describe the structural and vibrational properties since average differences of about 0.042Å and 5.1cm{sup −1} were obtained for bond lengths and fundamental vibrational frequencies, respectively for the first small clusters [1] of the series found from our GSAM method [2]. As further test, this model is used in order to investigate and revisit an experimental IR spectrum of Ga{sub n}As{sub m} mixture previously published by Li et al. [3]. More complicated is the difficulty which arises in the electronic description due to the presence of numerous low lying electronic states nearly degenerated to correctly describe the electronic structure. The case of Ga{sub 2}As will be discussed and the photoelectron spectra of the Ga{sub 2}As anion reanalyzed on the ground of our calculations [4] comparatively to the experimental spectra obtained by Neumark and co-workers [5].

74 ATOMIC AND MOLECULAR PHYSICS↗

PRESAGE: Protecting Structured Address Generation against Soft Errors

Modern computer scaling trends in pursuit of larger component counts and power efficiency have, unfortunately, lead to less reliable hardware and consequently soft errors escaping into application data ("silent data corruptions"). Techniques to enhance system resilience hinge on the availability of efficient error detectors that have high detection rates, low false positive rates, and lower computational overhead. Unfortunately, efficient detectors to detect faults during address generation (to index large arrays) have not been widely researched. We present a novel lightweight compiler-driven technique called PRESAGE for detecting bit-flips affecting structured address computations. A key insight underlying PRESAGE is that any address computation scheme that flows an already incurred error is better than a scheme that corrupts one particular array access but otherwise (falsely) appears to compute perfectly. Enabling the flow of errors allows one to situate detectors at loop exit points, and helps turn silent corruptions into easily detectable error situations. Our experiments using PolyBench benchmark suite indicate that PRESAGE-based error detectors have a high error-detection rate while incurring low overheads.

Sharma, Vishal C.↗

Potential benefit of amorphization in the retention of gaseous species in irradiated pyrochlores

Understanding the structure-property relationship for materials destined for irradiation extremes is a key step in developing materials with reliable, long-term performance. One crucial relationship is the ability of a material to withstand or accommodate amorphization, as this dictates its potential use as a nuclear waste form. Pyrochlores are one such class of materials for consideration as waste forms and there has been significant work examining how both the crystal structure and chemistry impacts amorphization resistance, leading to the important conclusion that the amorphization resistance of pyrochlores (A 2 B 2 O 7 ) is very sensitive to the nature of the B cations. For example, pyrochlores with B=Ti amorphize much more readily than B=Zr compounds. However, there are still questions regarding how these types of materials respond to prolonged or high-dose irradiation conditions. Gd 2 Ti 2 O 7 (GTO) and Gd 2 Zr 2 O 7 (GZO) pyrochlores were implanted with 400 keV Kr++ ions at room temperature to calculated peak damages of 119 and 135 displacements per atom (dpa), respectively. As expected, GTO amorphized completely under irradiation. However, discrete bubbles of Kr coalesced within the amorphous matrix without micro-cracking or spallation. In contrast, GZO transforms to a disordered fluorite structure under irradiation with no indications of localized amorphization. But, the accumulation of Kr within the host material leads to sub-grain structures, extended defects, and the development of micro-cracks. Thus, while GTO readily amorphizes even under low dose irradiations, the resistance of the amorphous GTO matrix to micro cracking and gas release, even in the presence of large bubble formation, suggests an enhanced propensity to retain gaseous species. Finally, consideration of long-term dose accumulation effects in nuclear waste forms would suggest reconsideration of amorphization processes in pyrochlores and related materials as a potential beneficial effect for immobilization and long-term storage of actinide materials.

36 MATERIALS SCIENCE↗

Precision Measurement of the Neutron Magnetic Form Factor via the Ratio Method at Jefferson Lab Hall A

Protons and neutrons, collectively known as nucleons, are composed of quarks and gluons. The Sachs electromagnetic form factors encode information about the spatial distributions of charge and magnetization in the nucleon, particularly at low momentum transfer. In particular, the neutron magnetic form factor (GMn) provides crucial information about the distribution of magnetization inside the neutron and helps constrain theoretical models of nucleon structure. Quasi-elastic electron scattering from deuterium was measured up to Q^2=13.5 GeV^2 using the Super BigBite Spectrometer in Hall A at Jefferson Lab. In this work, the neutron magnetic form factor GMn was extracted at Q^2 = 3.0 GeV^2 and Q^2=4.5 GeV^2 using the Ratio Method. These results represent a subset of the full dataset collected in this experiment, which extended to significantly higher Q^2. The extracted GMn values agree with the existing global fit within approximately two standard deviations at Q^2=3.0 and show excellent agreement at Q^2=4.5. The measurements achieved systematic uncertainties of about 2% and statistical uncertainties below 0.5%, among the most precise determinations of GMn at these kinematics. These results demonstrate the robustness of the experimental technique and provide an important validation point for future extractions at higher Q^2, where data remain scarce. In addition, the GRINCH heavy gas Cherenkov detector—a key component of the experimental apparatus—was commissioned and achieved an electron detection efficiency of approximately 97%, supporting reliable particle identification. Together, the analysis presented here advances both our understanding of nucleon structure and the validation of the experimental methods and instrumentation used to access it.

Satnik, Maria [College of William and Mary, Willia↗

Exploring the Random Phase Approximately for materials chemistry and physics

This proposal focuses on improved accuracy for the delicate energy differences of interest in materials chemistry with the fully nonlocal random phase approximation (RPA) in a density functional context. Could RPA or RPA-like approaches become standard methods of first-principles electronic-structure calculation for atoms, molecules, solids, surfaces, and nano-structures? Direct RPA includes the full exact exchange energy and a nonlocal correlation energy from the occupied and unoccupied Kohn-Sham orbitals and orbital energies, with an approximate but universal description of long-range van der Waals attraction. RPA also improves upon simple pair-wise interaction potentials or vdW density functional theory. This improvement is essential to capture accurate energy differences in metals and different phases of semiconductors. The applications in this proposal are challenges for the simpler approximations of Kohn-Sham density functional theory, which are part of the current “standard model” for quantum chemistry and condensed matter physics. Within this project we already applied RPA on different structural phase transitions on semiconductors, metals and molecules. Although RPA predicts accurate structural parameters, RPA has proven not equally accurate in all kinds of structural phase transitions. Therefore a correction to RPA can be necessary in many cases. We are currently implementing and testing a nonempirical, spatially nonlocal, frequency-dependent model for the exchange-correlation kernel in the adiabatic-connection fluctuation-dissipation context. This kernel predicts a nearly-exact correlation energy for the electron gas of uniform density. If RPA or RPA-like approaches prove to be reliably accurate, then expected increases in computer power may make them standard in the electronic-structure calculations of the future.

74 ATOMIC AND MOLECULAR PHYSICS↗

Three-dimensional phenotyping of peach tree-crown architecture utilizing terrestrial laser scanning

Tree training systems for temperate fruit have been developed throughout history by pomologists to improve light interception, fruit yield, and fruit quality. These training systems direct crown and branch growth to specific configurations. Quantifying crown architecture could aid the selection of trees that require less pruning or that naturally excel in specific growing/training system conditions. Regarding peaches [Prunus persica (L.) Batsch], access tools such as branching indices have been developed to characterize tree-crown architecture. However, the required branching data (BD) to develop these indices are difficult to collect. Traditionally, BD have been collected manually, but this process is tedious, time-consuming, and prone to human error. These barriers can be circumnavigated by utilizing terrestrial laser scanning (TLS) to obtain a digital twin of the real tree. TLS generates three-dimensional (3D) point clouds of the tree crown, wherein every point contains 3D coordinates (x, y, z). To facilitate the use of these tools for peach, we selected 16 young peach trees scanned in 2021 and 2022. These 16 trees were then modeled and quantified using the open-source software TreeQSM. As a result, “in silico” branching and biometric data for the young peach trees were calculated to demonstrate the capabilities of TLS phenotyping of peach tree-crown architecture. The comparison and analysis of field measurements (in situ) and in silico BD, biometric data, and quantitative structural model branch uncertainty data were utilized to determine the reconstructive model’s reliability as a source substitute for field measurements. Mean average deviation when comparing young tree (YT) height was approx. 5.93%, with crown volume was approx. 13.26% across both 2021 and 2022. All point clouds of the YTs in 2022 showed residuals lower than 12 mm to cylinders fitted to all branches, and mean surface coverage greater than 40% for both the trunk and primary branching orders.

09 BIOMASS FUELS↗

Radiation Dose–Dependent Hippocampal Atrophy Detected With Longitudinal Volumetric Magnetic Resonance Imaging

Purpose: After radiation therapy (RT) to the brain, patients often experience memory impairment, which may be partially mediated by damage to the hippocampus. Hippocampal sparing in RT planning is the subject of recent and ongoing clinical trials. Calculating appropriate hippocampal dose constraints would be improved by efficient in vivo measurements of hippocampal damage. In this study we sought to determine whether brain RT was associated with dose-dependent hippocampal atrophy. Methods and Materials: Hippocampal volume was measured with magnetic resonance imaging (MRI) in 52 patients who underwent fractionated, partial brain RT for primary brain tumors. Study patients had high-resolution, 3-dimensional volumetric MRI before and 1 year after RT. Images were processed using software with clearance from the US Food and Drug Administration and Conformité Européene marking for automated measurement of hippocampal volume. Automated results were inspected visually for accuracy. Tumor and surgical changes were censored. Mean hippocampal dose was tested for correlation with hippocampal atrophy 1 year after RT. Average hippocampal volume change was also calculated for hippocampi receiving high (>40 Gy) or low (<10 Gy) mean RT dose. A multivariate analysis was conducted with linear mixed-effects modeling to evaluate other potential predictors of hippocampal volume change, including patient (random effect), age, hemisphere, sex, seizure history, and baseline volume. Statistical significance was evaluated at α = 0.05. Results: Mean hippocampal dose was significantly correlated with hippocampal volume loss (r=−0.24, P=.03). Mean hippocampal volume was significantly reduced 1 year after high-dose RT (mean −6%, P=.009) but not after low-dose RT. In multivariate analysis, both RT dose and patient age were significant predictors of hippocampal atrophy (P<.01). Conclusions: The hippocampus demonstrates radiation dose–dependent atrophy after treatment for brain tumors. Quantitative MRI is a noninvasive imaging technique capable of measuring radiation effects on intracranial structures. This technique could be investigated as a potential biomarker for development of reliable dose constraints for improved cognitive outcomes.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Modelling single atom catalysts for water splitting and fuel cells: A tutorial review

Here, in this tutorial review, we report the state-of-the-art of the modeling approaches of Single Atom Catalysts (SAC) for water splitting and fuel cells reactions. The discussion applies for Hydrogen Evolution Reaction (HER), Oxygen Reduction Reaction (OER), Hydrogen Oxidation Reaction (HOR), and Oxygen Reduction Reaction (ORR). The main scope of this work is to underline the relevant aspects of SACs modelling. On the one hand, the review could help computational chemists aiming to start the study of SACs. On the other hand, experimentalists could find the critical analysis of DFT results of interest to understand better the strengths and weaknesses of simulations, and how to interpret computational results. After an introductory section of SACs, we start by briefly presenting the state-of-the-art methodologies. Then, we analyze the critical aspects for a reliable prediction of the electronic properties, and we discuss the robustness of the structural models and ways to validate them. Furthermore, we discuss the main approaches to predict catalytic activity and selectivity, which is the final goal of the computational catalysis. We conclude this review with a critical analysis of the current challenges in the field, and the main limitations of the modeling approaches that are described.

25 ENERGY STORAGE↗

Effect of 3D-printed surface textures on wear mechanism in 3-body abrasion of soil

This study systematically investigates the enhancement of wear resistance in 3D printed surface textures through both experimental and theoretical approaches. Three distinct surface morphologies (Smooth Surface, Surface with uniformly distributed Pits, and Surface with uniformly distributed Bumps) were fabricated using High-Impact Polystyrene, where the meso-scale textures were precisely controlled through the 3D printing process. Wear behavior was evaluated using a 3-body wear tester in an abrasive particle environment, analyzing the influence of surface textures under various operating conditions. Systematic wear tests revealed that optimally designed surface textures achieved a remarkable 77 % reduction in wear compared to the worst-performing sample. The wear mechanisms were comprehensively characterized through weight loss measurements, Scanning Electron Microscopy (SEM), and Energy Dispersive Spectroscopy (EDS) analyses, elucidating the surface morphology changes and their interaction with wear particles. Notably, the study identified how the geometric characteristics of surface textures influence the movement of wear particles and the distribution of contact stresses. Discrete element method simulations corroborated the experimental findings, providing theoretical validation for the enhanced wear resistance of the optimal structure. The high correlation between simulated wear patterns and experimental results validates the reliability of the proposed design methodology. In conclusion, these results demonstrate that 3D printed surface texturing offers a cost-effective and scalable approach to significantly improve wear resistance in engineering applications, presenting a practical alternative to conventional, high-cost surface engineering methods.

3-body abrasion↗

Ab Initio Reactive Computer Aided Molecular Design

Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge Transport in Solvated Donor–Acceptor Functionalized Peptoids: Molecular Dynamics and Rate Theory

Scalable solar-energy conversion requires photoactive materials that combine the efficiency of natural photosynthetic systems with the stability and processability needed for practical applications. Achieving reliable charge transport in soft, self-assembled organic materials remains challenging, as structural fluctuations and environmental effects strongly influence charge-transfer (CT) rates. Here, we present a broadly applicable computational framework for evaluating CT rates in the condensed phase, combining Fermi’s golden rule rate theory with inputs from all-atom molecular dynamics (MD) simulations and first-principles electronic-structure calculations. The approach does not rely on system-specific parametrization and is applicable to a wide range of soft and disordered materials. We demonstrate the applicability and usefulness of the framework on redox-active peptoids functionalized with iron–porphyrin (Fe–P) complexes, a bioinspired platform with programmable donor–acceptor units and tunable three-dimensional organization. The calculated CT rates exhibit strong sensitivity to molecular conformation, with variations spanning several orders of magnitude. This dependence is shown to arise from the pronounced variation in diabatic electronic coupling with the relative orientations and separations of the Fe–P complexes across the conformational ensemble. The framework provides a consistent route for connecting atomistic structure to CT kinetics in the condensed phase and enables analysis of structure–rate relations in organic semiconducting systems.

Charge transfer↗

Deducing spectroscopic factors from wave-function asymptotics

In a coupled-channel model, we explore the effects of coupling between configurations on the radial behavior of the wave function and, in particular, on the spectroscopic factor (SF) and the asymptotic normalization coefficient (ANC). We evaluate the extraction of a SF from the ratio of the ANC of the coupled-channel model to that of a single-particle approximation of the wave function. We perform this study within a core+n collective model, which includes two states of the core that connect by a rotational coupling. To get additional insights, we also use a simplified model that takes a {delta} function for the coupling potential. Calculations are performed for {sup 11}Be. Fair agreement is obtained between the SF inferred from the single-particle approximation and the one obtained within the coupled-channel models. Significant discrepancies are observed only for large coupling strength and/or large admixture, that is, a small SF. This suggests that reliable SFs can be deduced from the wave-function asymptotics when the structure is dominated by one configuration, that is, for a large SF.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Phononic Helical Nodal Lines with PT Protection in MoB 2

While condensed matter systems host both fermionic and bosonic quasiparticles, reliably predicting and empirically verifying topological states is only mature for Fermionic electronic structures, leaving topological Bosonic excitations sporadically explored. This is unfortunate, as Bosonic systems such as phonons offer the opportunity to assess spinless band structures where nodal lines can be realized without invoking special additional symetries to protect against spin-orbit coupling. Here we combine first-principles calculations and meV-resolution inelastic x-ray scattering to demonstrate the first realization of parity-time reversal symmetry protected helical nodal lines in the phonon spectrum of MoB 2 . This structure is unique to phononic systems as the spin-orbit coupling present in electronic systems tends to lift the degeneracy away from high-symmetry locations. Our study establishes a protocol to accurately identify topological Bosonic excitations, opening a new route to explore exotic topological states in crystalline materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency

A balance between excitatory and inhibitory synaptic currents is thought to be important for several aspects of information processing in cortical neurons in vivo, including gain control, bandwidth and receptive field structure. These factors will affect the firing rate of cortical neurons and their reliability, with consequences for their information coding and energy consumption. Yet how balanced synaptic currents contribute to the coding efficiency and energy efficiency of cortical neurons remains unclear. We used single compartment computational models with stochastic voltage-gated ion channels to determine whether synaptic regimes that produce balanced excitatory and inhibitory currents have specific advantages over other input regimes. Specifically, we compared models with only excitatory synaptic inputs to those with equal excitatory and inhibitory conductances, and stronger inhibitory than excitatory conductances (i.e. approximately balanced synaptic currents). Using these models, we show that balanced synaptic currents evoke fewer spikes per second than excitatory inputs alone or equal excitatory and inhibitory conductances. However, spikes evoked by balanced synaptic inputs are more informative (bits/spike), so that spike trains evoked by all three regimes have similar information rates (bits/s). Consequently, because spikes dominate the energy consumption of our computational models, approximately balanced synaptic currents are also more energy efficient than other synaptic regimes. Thus, by producing fewer, more informative spikes approximately balanced synaptic currents in cortical neurons can promote both coding efficiency and energy efficiency.

59 BASIC BIOLOGICAL SCIENCES↗