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At least 397 records · Page 22

Regularization via f -Divergence: An Application to Multi-Oxide Spectroscopic Analysis

In this paper, we explore the application of convolutional neural networks (CNNs) for predicting the chemical composition of complex geologic samples in a simulated Martian atmospheric environment. Specifically, we aim to characterize oxide weight percentages (wt.%) of rock samples analyzed by remote Laser-Induced Breakdown Spectroscopy (LIBS), framing the problem as a multi-target regression task . Neural networks trained on LIBS spectra are prone to overfitting due to high spectral complexity, limited labeled data, and measurement noise. While regularization is critical for improving generalization, common methods (e.g., ℓ 2 regularization) impose constraints not directly tied to data distribution properties. We propose a novel regularization method based on a specific ƒ-divergence induced by a graph-based estimator, designed to constrain the distributional discrepancy between predictions and targets. This regularizer serves a dual purpose: (a) mitigating overfitting by enforcing a constraint on the distributional difference between predictions and noisy targets, and (b) acting as an auxiliary loss that penalizes large divergences. To enable backpropagation, we develop a differentiable approximation of this particular ƒ-divergence, making the method feasible for neural networks. Experiments on ChemCam and SuperCam LIBS calibration spectra show that mathematical equation-divergence regularization outperforms or matches standard regularization methods (ℓ 1 , ℓ 2 , dropout) and the classical baseline, partial least squares (PLS). Combining ƒ-divergence regularization with standard regularization yields further performance gains, indicating that distributional regularization is useful in this context giving a promising direction for robust model training in planetary science applications. Source code is publicly available at Klein and Li (2025), https://doi.org/10.11578/dc.20250530.7.

58 GEOSCIENCES↗

Quantum effects on dislocation motion from ring-polymer molecular dynamics

Quantum motion of atoms known as zero-point vibration was recently proposed to explain a long-standing discrepancy between theoretically computed and experimentally measured low-temperature plastic strength of iron and possibly other metals with high atomic masses. This finding challenges the traditional notion that quantum motion of atoms is relatively unimportant in solids comprised of heavy atoms. Here we report quantum dynamic simulations of quantum effects on dislocation motion within the exact formalism of Ring-Polymer Molecular Dynamics (RPMD). To extend the reach of quantum atomistic simulations to length and time scales relevant for extended defects in materials, we implemented RPMD in the open-source code LAMMPS thus making the RPMD method widely available to the community. We use our RPMD/LAMMPS approach for direct calculations of dislocation mobility and its effects on the yield strength of α-iron. Our simulation results establish that quantum effects are noticeable at temperatures below 50 K but account for only a modest (≈13% at T = 0 K) overall reduction in the Peierls barrier, at variance with the factor of two reduction predicted earlier based on the more approximate framework of harmonic transition state theory. Our results confirm that zero-point vibrations provide ample additional agitation for atomic motion that increases with decreasing temperature, however its enhancing effect on dislocation mobility is largely offset by an increase in the effective atom size, an effect known as quantum dispersion that has not been accounted for in the previous calculations.

36 MATERIALS SCIENCE↗

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

A method to generate small-scale, high-resolution sedimentary bedform architecture models representing realistic geologic facies

Small-scale (mm to m) sedimentary structures (e.g. ripple lamination, cross-bedding) have received a great deal of attention in sedimentary geology. The influence of depositional heterogeneity on subsurface fluid flow is now widely recognized, but incorporating these features in physically-rational bedform models at various scales remains problematic. The current investigation expands the capability of an existing set of open-source codes, allowing generation of high-resolution 3D bedform architecture models. The implemented modifications enable the generation of 3D digital models consisting of laminae and matrix (binary field) with characteristic depositional architecture. The binary model is then populated with petrophysical properties using a textural approach for additional analysis such as statistical characterization, property upscaling, and single and multiphase fluid flow simulation. One example binary model with corresponding threshold capillary pressure field and the scripts used to generate them are provided, but the approach can be used to generate dozens of previously documented common facies models and a variety of property assignments. An application using the example model is presented simulating buoyant fluid (CO 2 ) migration and resulting saturation distribution.

58 GEOSCIENCES↗

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system—MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. The template-based modeling uses sequence alignment tools with deep multiple sequence alignments to search for structural templates, which are much faster and more accurate than MULTICOM1. The template-free (ab initio or de novo) modeling uses the inter-residue distances predicted by DeepDist to reconstruct tertiary structure models without using any known structure as template. In the blind CASP14 experiment, the average TM-score of the models predicted by our server predictor based on the MULTICOM2 system is 0.720 for 58 TBM (regular) domains and 0.514 for 38 FM and FM/TBM (hard) domains, indicating that MULTICOM2 is capable of predicting good tertiary structures across the board. It can predict the correct fold for 76 CASP14 domains (95% regular domains and 55% hard domains) if only one prediction is made for a domain. The success rate is increased to 3% for both regular and hard domains if five predictions are made per domain. Moreover, the prediction accuracy of the pure template-free structure modeling method on both TBM and FM targets is very close to the combination of template-based and template-free modeling methods. This demonstrates that the distance-based template-free modeling method powered by deep learning can largely replace the traditional template-based modeling method even on TBM targets that TBM methods used to dominate and therefore provides a uniform structure modeling approach to any protein. Finally, on the 38 CASP14 FM and FM/TBM hard domains, MULTICOM2 server predictors (MULTICOM-HYBRID, MULTICOM-DEEP, MULTICOM-DIST) were ranked among the top 20 automated server predictors in the CASP14 experiment. After combining multiple predictors from the same research group as one entry, MULTICOM-HYBRID was ranked no. 5. The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

97 MATHEMATICS AND COMPUTING↗

Accurate real space iterative reconstruction (RESIRE) algorithm for tomography

Tomography has made a revolutionary impact on the physical, biological and medical sciences. The mathematical foundation of tomography is to reconstruct a three-dimensional (3D) object from a set of two-dimensional (2D) projections. As the number of projections that can be measured from a sample is usually limited by the tolerable radiation dose and/or the geometric constraint on the tilt range, a main challenge in tomography is to achieve the best possible 3D reconstruction from a limited number of projections with noise. Over the years, a number of tomographic reconstruction methods have been developed including direct inversion, real-space, and Fourier-based iterative algorithms. Here, we report the development of a real-space iterative reconstruction (RESIRE) algorithm for accurate tomographic reconstruction. RESIRE iterates between the update of a reconstructed 3D object and the measured projections using a forward and back projection step. The forward projection step is implemented by the Fourier slice theorem or the Radon transform, and the back projection step by a linear transformation. Our numerical and experimental results demonstrate that RESIRE performs more accurate 3D reconstructions than other existing tomographic algorithms, when there are a limited number of projections with noise. Furthermore, RESIRE can be used to reconstruct the 3D structure of extended objects as demonstrated by the determination of the 3D atomic structure of an amorphous Ta thin film. We expect that RESIRE can be widely employed in the tomography applications in different fields. Finally, to make the method accessible to the general user community, the MATLAB source code of RESIRE and all the simulated and experimental data are available at https://zenodo.org/record/7273314.

97 MATHEMATICS AND COMPUTING↗

Real space iterative reconstruction for vector tomography (RESIRE-V)

Tomography has had an important impact on the physical, biological, and medical sciences. To date, most tomographic applications have been focused on 3D scalar reconstructions. However, in some crucial applications, vector tomography is required to reconstruct 3D vector fields such as the electric and magnetic fields. Over the years, several vector tomography methods have been developed. Here, we present the mathematical foundation and algorithmic implementation of REal Space Iterative REconstruction for Vector tomography, termed RESIRE-V. RESIRE-V uses multiple tilt series of projections and iterates between the projections and a 3D reconstruction. Each iteration consists of a forward step using the Radon transform and a backward step using its transpose, then updates the object via gradient descent. Incorporating with a 3D support constraint, the algorithm iteratively minimizes an error metric, defined as the difference between the measured and calculated projections. The algorithm can also be used to refine the tilt angles and further improve the 3D reconstruction. To validate RESIRE-V, we first apply it to a simulated data set of the 3D magnetization vector field, consisting of two orthogonal tilt series, each with a missing wedge. Our quantitative analysis shows that the three components of the reconstructed magnetization vector field agree well with the ground-truth counterparts. We then use RESIRE-V to reconstruct the 3D magnetization vector field of a ferromagnetic meta-lattice consisting of three tilt series. Our 3D vector reconstruction reveals the existence of topological magnetic defects with positive and negative charges. We expect that RESIRE-V can be incorporated into different imaging modalities as a general vector tomography method. To make the algorithm accessible to a broad user community, we have made our RESIRE-V MATLAB source codes and the data freely available at https://github.com/minhpham0309/RESIRE-V.

47 OTHER INSTRUMENTATION↗

Application and assessment of deep learning for the generation of potential NMDA receptor antagonists

Uncompetitive antagonists of the N-methyl D-aspartate receptor (NMDAR) have demonstrated therapeutic benefit in the treatment of neurological diseases such as Parkinson's and Alzheimer's, but some also cause dissociative effects that have led to the synthesis of illicit drugs. The ability to generate NMDAR antagonists in silico is therefore desirable for both new medication development and preempting and identifying new designer drugs. Recently, generative deep learning models have been applied to de novo drug design as a means to expand the amount of chemical space that can be explored for potential drug-like compounds. In this study, we assess the application of a generative model to the NMDAR to achieve two primary objectives: (i) the creation and release of a comprehensive library of experimentally validated NMDAR phencyclidine (PCP) site antagonists to assist the drug discovery community and (ii) an analysis of both the advantages conferred by applying such generative artificial intelligence models to drug design and the current limitations of the approach. We apply, and provide source code for, a variety of ligand- and structure-based assessment techniques used in standard drug discovery analyses to the deep learning-generated compounds. Overall, we present twelve candidate antagonists that are not available in existing chemical databases to provide an example of what this type of workflow can achieve, though synthesis and experimental validation of these compounds are still required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of MOF linker rotation and functionalization on methane uptake and diffusion

The flexible degrees of freedom in metal–organic frameworks (MOFs) can have significant effects on guest molecule behavior. However, in the majority of studies applying molecular simulations to MOFs, the framework is assumed to be rigid in order to minimize computational cost. Here, in this work, we assess the significance of this assumption on a representative example of methane uptake and diffusion in UiO-66. We introduce an open-source code to modify MOFs through functionalization and linker rotation and we perform Grand Canonical Monte Carlo and molecular dynamics simulations of methane in each of the functionalized and linker-rotated derivatives of UiO-66. We find that linker rotation moderately influences methane uptake and significantly influences methane diffusion. Our assessment provides ranges of property values that serve as measures of uncertainty of these two properties associated with linker rotation. We further determine that void volume fraction and minimum pore size are the features that govern methane uptake and diffusion, respectively. These findings illustrate the impact of linker rotation on MOFs and provide design principles to guide future investigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Knowledge management: Role of the the Radiation Safety Information Computational Center (RSICC)

The Radiation Safety Information Computational Center (RSICC) at Oak Ridge National Laboratory (ORNL) is an information analysis center that collects, archives, evaluates, synthesizes and distributes information, data and codes that are used in various nuclear technology applications. RSICC retains more than 2,000 software packages that have been provided by code developers from various federal and international agencies. RSICC’s customers (scientists, engineers, and students from around the world) obtain access to such computing codes (source and/or executable versions) and processed nuclear data files to promote on-going research, to ensure nuclear and radiological safety, and to advance nuclear technology. The role of such information analysis centers is critical for supporting and sustaining nuclear education and training programs both domestically and internationally, as the majority of RSICC’s customers are students attending U.S. universities. Additionally, RSICC operates a secure CLOUD computing system to provide access to sensitive export-controlled modeling and simulation (M&S) tools that support both domestic and international activities. This presentation will provide a general review of RSICC’s activities, services, and systems that support knowledge management and education and training in the nuclear field.

Valentine, Timothy↗

Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations

In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-“coupled”- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz–Kalos–Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB source code.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A nucleotide-level coarse-grained model of RNA

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self-consistent continuum solvation for optical absorption of complex molecular systems in solution

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem and a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the QUANTUM ESPRESSO distribution of open-source codes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On implementation of EM-type algorithms in the stochastic models for a matrix computing on GPU

The paper discusses the main ideas of an implementation of EM-type algorithms for computing on the graphics processors and the application for the probabilistic models based on the Cox processes. An example of the GPU’s adapted MATLAB source code for the finite normal mixtures with the expectation-maximization matrix formulas is given. The testing of computational efficiency for GPU vs CPU is illustrated for the different sample sizes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Real-time and imaginary-time quantum hierarchal Fokker-Planck equations

We consider a quantum mechanical system represented in phase space (referred to hereafter as “Wigner space”), coupled to a harmonic oscillator bath. We derive quantum hierarchal Fokker-Planck (QHFP) equations not only in real time but also in imaginary time, which represents an inverse temperature. This is an extension of a previous work, in which we studied a spin-boson system, to a Brownian system. It is shown that the QHFP in real time obtained from a correlated thermal equilibrium state of the total system possesses the same form as those obtained from a factorized initial state. A modified terminator for the hierarchal equations of motion is introduced to treat the non-Markovian case more efficiently. Using the imaginary-time QHFP, numerous thermodynamic quantities, including the free energy, entropy, internal energy, heat capacity, and susceptibility, can be evaluated for any potential. These equations allow us to treat non-Markovian, non-perturbative system-bath interactions at finite temperature. Through numerical integration of the real-time QHFP for a harmonic system, we obtain the equilibrium distributions, the auto-correlation function, and the first- and second-order response functions. These results are compared with analytically exact results for the same quantities. This provides a critical test of the formalism for a non-factorized thermal state and elucidates the roles of fluctuation, dissipation, non-Markovian effects, and system-bath coherence. Employing numerical solutions of the imaginary-time QHFP, we demonstrate the capability of this method to obtain thermodynamic quantities for any potential surface. It is shown that both types of QHFP equations can produce numerical results of any desired accuracy. The FORTRAN source codes that we developed, which allow for the treatment of Wigner space dynamics with any potential form (TanimuranFP15 and ImTanimuranFP15), are provided as the supplementary material.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

wavepy - Python package for x-ray grating interferometry with applications in imaging and wavefront characterization

X-ray grating interferometry has been employed for a wide range of imaging applications by using the Talbot self-images of a grating. At synchrotron facilities, it has also been exploited to characterize the coherence and wavefront of the x-ray beam. The method is relatively straightforward, easy to implement, and provides accurate quantitative data. However, to exploit its full potential, it requires highly specialized, robust data analysis. It this work, we have set the framework for the development and dissemination of a robust open-source code that is tailored to the data analysis for imaging and beam characterization using grating interferometry.

Grizolli, Walan↗

Effects of surface diffusion in electrocatalytic CO 2 reduction on Cu revealed by kinetic Monte Carlo simulations

We report Kinetic Monte Carlo (KMC) methods are frequently used for mechanistic studies of thermally driven heterogeneous catalysis systems but are underused for electrocatalysis. Here, we develop a lattice KMC approach for electrocatalytic CO 2 reduction. The work is motivated by a prior experimental report that performed electroreduction of a mixed feed of 12 CO 2 and 13 CO on Cu; differences in the 13 C content of C2 products ethylene and ethanol (Δ 13 C) were interpreted as evidence of site selectivity. The lattice KMC model considers the effect of surface diffusion on this system. In the limit of infinitely fast diffusion (mean-field approximation), the key intermediates 12 CO* and 13 CO* would be well mixed on the surface and no evidence of site selectivity could have been observed. Using a simple two-site model and adapting a previously reported microkinetic model, we assess the effects of diffusion on the relative isotope fractions in the products using the estimated surface diffusion rate of CO* from literature reports. We find that the size of the active sites and the total surface adsorbate coverage can have a large influence on the values of Δ 13 C that can be observed. Δ 13 C is less sensitive to the CO* diffusion rate as long as it is within the estimated range. We further offer possible methods to estimate surface distribution of intermediates and to predict intrinsic selectivity of active sites based on experimental observations. This work illustrates the importance of considering surface diffusion in the study of electrochemical CO 2 reduction to multi-carbon products. Our approach is entirely based on a freely available open-source code, so will be readily adaptable to other electrocatalytic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗