Results for “complex simulation” — Page 18

DOE OSTI2025

Cooperative and inhibitory ion transport in functionalized angstrom-scale two-dimensional channels

Significant success has been achieved in fabricating angstrom-scale artificial solid ionic channels aiming to replicate the biological ion channels (BICs). Besides high selectivity, BICs also exhibit sophisticated ion gating and interplay. However, such behavior and functionality are seldomly recreated in the artificial counterparts due to the insufficient understanding of the molecular origin. Here we report cooperative and inhibitory ion transport in angstrom-scale acetate functionalized MoS 2 two-dimensional channels. For cooperative ion transport, the permeability of K + is doubled in the presence of only 1% Pb 2+ (versus K + by molarity), while the permeability of Pb 2+ is independent of K + . Molecular dynamics simulations reveal complex interplay among K + , Pb 2+ , and the anions in governing the cooperativity, such that Pb 2+ ions capture and slow down the anions via long-range interaction, which leads to the synchronization of anions with K + to transport as ion pairs with reduced interaction with the channel surface. For inhibitory ion transport, divalent Co 2+ (or Ba 2+ ) and Pb 2+ can replace each other in the confined channel and compete for the limited transport cross section. Our work reveals ion transport phenomena in extreme confinement and highlights the potential of manipulating ion interplay in confinement for achieving advanced functionalities.

Functionalized Angstrom↗

DOE OSTI2024

Efficient simulations of charge density waves in the transition metal Dichalcogenide TiSe 2

Charge density waves (CDWs) in transition metal dichalcogenides are the subject of growing scientific interest due to their rich interplay with exotic phases of matter and their potential technological applications. Here, using density functional theory with advanced meta-generalized gradient approximations (meta-GGAs) and linear response time-dependent density functional theory (TDDFT) with state-of-the-art exchange-correlation kernels, we investigate the electronic, vibrational, and optical properties in 1T-TiSe 2 with and without CDW. In both bulk and monolayer TiSe 2 , the electronic bands and phonon dispersions in either normal or CDW (semiconducting) phase are described well via meta-GGAs, which separate the valence and conduction bands just as HSE06 does but with significantly more computational feasibility. The experimentally observed humps of electron energy loss spectroscopy are successfully reproduced in TDDFT. Our work opens the door to simulating these complexities in CDW compounds from first principles by revealing meta-GGAs as an accurate low-cost alternative to HSE06.

Electronic properties and materials↗

DOE OSTI2025

Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching

Integrating genome-scale metabolic networks with reactive transport models (RTMs) provides a detailed description of the dynamic changes in microbial growth and metabolism. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated application of linear programming (LP) to obtain flux balance analysis (FBA) solutions in every time step and spatial grid. To address this challenge, we propose a new simulation method where we train and validate artificial neural networks (ANNs) using randomly sampled FBA solutions and incorporate the resulting surrogate FBA model (represented as algebraic equations) into RTMs as source/sink terms. We demonstrate the efficiency of our method via a case study of Shewanella oneidensis MR-1. During aerobic growth on lactate, S. oneidensis produces metabolic byproducts (such as pyruvate and acetate), which are subsequently consumed as alternative carbon sources when the preferred nutrients are depleted. To effectively simulate these complex dynamics, we used a cybernetic approach that models metabolic switches as the outcome of dynamic competition among multiple growth options. In both zero-dimensional batch and one-dimensional column configurations, the ANN-based surrogate models achieved substantial reduction of computational time by several orders of magnitude compared to the original LP-based FBA models. Moreover, the ANN models produced robust solutions without any special measures to prevent numerical instability. These developments significantly promote our ability to utilize genome-scale networks in complex, multi-physics, and multi-dimensional ecosystem modeling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Spectral broadening and vibronic dynamics of the S2 state of canthaxanthin in the orange carotenoid protein

We have performed a series of broadband multidimensional electronic spectroscopy experiments to probe the electronic and vibrational dynamics of the canthaxanthin chromophore of the Orange Carotenoid Protein (OCP) from Synechocystis sp. PCC 6803 in its photoactivated red state, OCPR. Cross-peaks observed below the diagonal of the two-dimensional electronic spectrum indicate that absorption transitions prepare the bright S2 state of the ketocarotenoid canthaxanthin near to a sequence of conical intersections, allowing passage to the dark S1 state via the Sx intermediate in <50 fs. Rapid damping of excited-state coherent wavepacket motions suggests that the branching coordinates of the conical intersections include out-of-plane deformation and C=C stretching coordinates of the π-conjugated isoprenoid backbone. The unusual proximity of the Franck–Condon S2 state structure to the conical intersections with Sx and S1 suggests that the protein surroundings of canthaxanthin prepare it to function as an excitation energy trap in the OCPR–phycobilisome complex. Numerical simulations using the multimode Brownian oscillator model demonstrate that the ground-state absorption spectrum of OCPR overlaps with the fluorescence emission spectrum of allophycocyanin due to spectral broadening derived especially from the intramolecular motions of the canthaxanthin chromophore in its binding site.

Yang, Kunwei↗

DOE OSTI2025

sedacs

O4732 SEDACS Scalable Ecosystem, Driver, and Analyzer for Complex Chemistry Simulations

Stanton, Robert [Los Alamos National Laboratory]↗

DOE OSTI2024

Outcomes of HPC User Support using a Science Gateway AI Assistant

High Performance Computing (HPC) is a vital resource for nuclear energy research, facilitating advanced simulations and complex modeling of the quantification and qualification of advanced reactor technology. However, a common gap in knowledge exists around utilizing HPC systems, particularly for nuclear energy researchers unfamiliar with specific HPC systems. A researcher may be well-versed in using one HPC system and understanding its associated processes. Yet, they might struggle when faced with a different HPC system and its unique processes. HPC support staff play a crucial role in addressing these challenges by providing educational resources and assisting users. However, they also face the challenge of maintaining these systems and ensuring they run efficiently for all users, a responsibility that can be challenging to scale effectively with the increasing demand and expansion of HPC systems. This paper addresses this knowledge gap with an artificial intelligence (AI) assistant that offers on-demand, site-specific HPC support for researchers. Idaho National Laboratory (INL) has deployed an AI assistant that is intended to supplement expert HPC support staff and assist nuclear energy researchers. This paper reports on a four-and-a-half-month study evaluating the integration of an AI assistant within a science gateway, with the goal of enhancing existing HPC support.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

SIERRA Code Coupling Module: Arpeggio User Manual (V.5.20)

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

SIERRA Code Coupling Module: Arpeggio User Manual (V. 5.22)

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

AEOLUS: Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems

The AEOLUS Center is dedicated to developing a unified optimization-under-uncertainty framework for (1) learning predictive models from data and (2) optimizing experiments, processes, and designs governed by these models, all driven by complex, uncertain energy systems. AEOLUS addressed the critical need for principled, rigorous, scalable, and structure-exploiting capabilities for exploring parameter and decision spaces of complex forward simulation models---the so-called outer loop. This report summarizes the work done under DE-SC0021077 on (1) nonlocal models for solidification problems, (2) a multifidelity method for a nonlocal diffusion model, and (3) multifidelity Monte Carlo methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Modeling the Interaction of Laser-Produced Proton Beams with Matter

A major goal of this project is to significantly increase our understanding of isochoric heating of matter using laser produced proton beams, and the associated high energy density (HED) and warm dense matter (WDM) regimes generated. This will benefit research fields such as planetary science, fusion energy, plasma physics, and material science. For example, it will enhance our understanding of WDM properties of iron and silica under conditions encountered in planetary interiors and diagnostic components in fusion devices exposed to high fluxes of energetic plasma ions. The project is motivated by recent experiments that irradiated Si targets with proton beams generated by the 20 TW-laser at the SLAC MEC end-station. The HED/WDM states are probed using the 50 fs hard X-rays available in the 3rd harmonic of the LCLS. As part of this project, results from the phase contrast X-ray imaging, which shows the generation of compression waves that produces rear surface spallation, are compared with results from the 3D multi-physics multi- material code, PISALE, that combines Arbitrary Lagrangian-Eulerian (ALE) hydrodynamics with Adaptive Mesh Refinement (AMR). This comparison required modifications to several physics models in the PISALE (Pacific Island Structured-AMR with ALE) code. An important aspect of this project is the continued training of graduate students in HED physics and in conducting complex multiphysics simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

SIERRA Code Coupling Module: Arpeggio User Manual - Version 5.24

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

CFD Simulation of Aerobic Gas Fermentation to Enable Commercial Conversion of CO 2 into Aquaculture and Animal Feed: Cooperative Research and Development (Final Report)

NovoNutrients’ fermentation technology uses energy from hydrogen to transform industrial CO2 emissions into premium animal feed ingredients and other valuable products. A single NovoNutrients’ commercial manufacturing plant will capture and convert over 200,000 tons/yr of CO2 into over 100,000 tons/yr of high-protein feed. Key to the rapid and widespread deployment of the technology is maximization of its productivity and energy efficiency. Robust, physically based computational models of the technology will significantly increase productivity and efficiency, accelerating NovoNutrients’ technology to manufacturing scale. NREL has unique capabilities for creating and running such computational models. NREL's existing aerobic bioreaction computational fluid dynamics (CFD) models will be adapted to NovoNutrients’ gas fermentation (CO2, H2, O2) technology. The multiphysics CFD simulations require thousands of high-performance computing (HPC) node hours to simulate the complex geometries and contents of NovoNutrients’ industrial bioreactors. The experimentally validated CFD models were used to identify optimally efficient and productive bioreactor designs and operating conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

SIERRA Code Coupling Module: Arpeggio User Manual (V.5.26)

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems (Final Report for AEOLUS)

The AEOLUS Center is dedicated to developing a unified optimization-under-uncertainty framework for: (1) learning predictive models from data; and (2) optimizing experiments, processes, and designs governed by these models, all driven by complex, uncertain energy systems. AEOLUS addresses the critical need for principled, rigorous, scalable, and structure-exploiting capabilities for exploring parameter and decision spaces of complex forward simulation models. This report summarizes the key highlights of our research during the period of performance.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

SIERRA Code Coupling Module: Arpeggio User Manual - Version 5.28

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

SIERRA Code Coupling Module: Arpeggio User Manual - Version 5.30

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Electrochemical testing of metals for petroleum wastewater monitoring

The purpose of this project was to determine the feasibility of ion-selective electrode (ISE) as compared to x-ray fluorescence (XRF) for determining the concentrations of metal ions in petroleum wastewater. ISEs for silver and cadmium were tested in a laboratory under increasingly realistic conditions, then deployed in the sewer wastewater monitoring complex to simulate a petroleum wastewater system. By verifying the ISE calibration after wastewater exposure and comparing its measurements to the XRF systems within the wastewater monitoring system, we determined that the ISE is more sensitive but less feasible for use in live wastewater monitoring due to fouling concerns.

Energy - Petroleum↗

DOE OSTI2026

Best practices in software development for robust and reproducible geoscientific models based on insights from the Global Carbon Budget's dynamic vegetation models

Computational models play an increasingly vital role in scientific research by enabling the numerical simulation of complex processes. Such models are also fundamental in geosciences. For instance, they offer critical insights into the impacts of global change on the Earth system today and in the future. Beyond their value as research tools, models are also software products and should therefore adhere to certain established software engineering standards. However, scientists are rarely trained as software developers, which can lead to potential deficiencies in software quality like unreadable, inefficient, or erroneous code. The complexity of models, coupled with their integration into broader workflows, also often makes it challenging to reproduce results, evaluate processes, and build upon them. In this paper, we review the state and current practices of the development processes of the state-of-the-art land surface models used by the Global Carbon Budget. We combine the experience of modelers from the respective research groups with the expertise of software engineers from tech companies to outline key principles and tools for improving software quality in research. We explore four main areas: (1) model testing and validation, (2) scientific, technical, and user documentation, (3) version control, continuous integration, and code review, and (4) the portability and reproducibility of workflows. Our review reveals that while modeling communities are incorporating many best practices, significant room for improvement remains in areas such as automated testing, automated documentation, and reproducibility. Therefore, we here identify and promote essential software engineering practices, including numerous examples of practices from within the community that can serve as guidelines for other models and could help streamline processes across the entire community. We conclude with an open-source example implementation of these principles, demonstrating portable and reproducible data flows, a continuous integration setup, and web-based visualizations. This example may serve as a practical resource for model developers, users, and all scientists engaged in scientific programming.

Gregor, Konstantin [Technical Univ. of Munich (Ger↗