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DOE OSTI2014

Lipid-Based Nanodiscs as Models for Studying Mesoscale Coalescence A Transport Limited Case

Lipid-based nanodiscs (bicelles) are able to form in mixtures of long- and short-chain lipids. Initially, they are of uniform size but grow upon dilution. Previously, nanodisc growth kinetics have been studied using time-resolved small angle neutron scattering (SANS), a technique which is not well suited for probing their change in size immediately after dilution. To address this, we have used dynamic light scattering (DLS), a technique which permits the collection of useful data in a short span of time after dilution of the system. The DLS data indicate that the negatively charged lipids in nanodiscs play a significant role in disc stability and growth. Specifically, the charged lipids are most likely drawn out from the nanodiscs into solution, thereby reducing interparticle repulsion and enabling the discs to grow. We describe a population balance model, which takes into account Coulombic interactions and adequately predicts the initial growth of nanodiscs with a single parameter i.e., surface potential. The results presented here strongly support the notion that the disc coalescence rate strongly depends on nanoparticle charge density. The present system containing low-polydispersity lipid nanodiscs serves as a good model for understanding how charged discoidal micelles coalesce.

Hu, Andrew↗

DOE OSTI2020

Solvation Energy of Ions in a Stockmayer Fluid

We calculate the solvation energy of monovalent and divalent ions in various liquids with coarse-grained molecular dynamics simulations. Our theory treats the solvent as a Stockmayer fluid, which accounts for the intrinsic dipole moment of molecules and the rotational dynamics of the dipoles. Despite the simplicity of the model, we obtain qualitative agreement between the simulations and experimental data for the free energy and enthalpy of ion solvation, which indicates that the primary contribution to the solvation energy arises mainly from the first and possibly second solvation shells near the ions. Our results suggest that a Stockmayer fluid can serve as a reference model that enables direct comparison between theory and experiment and may be invoked to scale up electrostatic interactions from the atomic to the molecular length scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A collective trigger for widespread planetesimal formation revealed by accretion ages

The formation of planetesimals was an integral part of the cascading series of processes that built the terrestrial planets. To illuminate planetesimal formation, here we develop a refined thermal evolution model to calculate the formation ages of meteorite parent planetesimals. This model includes chemical reactions and phase changes during heating, as well as natural variations in the proportions of the constituent phases of these planetesimals. We find that the parent bodies of non-carbonaceous (NC) and carbonaceous (CC) iron meteorites start forming at very similar times ( ∼ 0.95 Myr after calcium-aluminium-rich inclusion [CAI] formation) and occupy overlapping time windows. NC and CC chondrite parent bodies formed later during non-overlapping periods. We combine these ages with proportions of isotopic end-members we recover from mixing models to construct records of motion throughout the protoplanetary disk. These records argue that NC and CC material traversed the barrier in the disk after ∼ 0.95 Myr after CAI formation. The onset of this motion coincided with planetesimal formation, indicating that the phenomenon that drove motion also triggered planetesimal formation. We argue that this feature also served as the semi-permeable barrier in the disk. Although its identity is uncertain, the effects this phenomenon had on the timing of planetesimal formation and motion through the disk can now serve as constraints on models of disk evolution. Models that reproduce these effects would elucidate the nature and implications of this phenomenon, which is key to unlocking a holistic model of terrestrial planet building.

Astronomy and AstroPhysics↗

DOE OSTI2025

High-resolution lidar observations of sedimentation-induced size sorting of droplets near a laboratory cloud top

Cloud optical properties and precipitation, which are crucial to weather and climate, are strongly influenced by cloud microphysical properties that are still poorly understood. Here, we develop a high-resolution time-correlated single-photon-counting lidar and apply it to observe cloud microphysical properties at one-centimeter range resolution in a convection chamber under well-controlled conditions. Together with concurrent in-situ measurements and theoretical analysis, our lidar observations indicate that although turbulent mixing tends to homogenize the cloud in the bulk region, entrainment and sedimentation cause inhomogeneities in droplet concentrations near the cloud top. Specifically, the topmost region is directly affected by entrainment, and lidar profiles show clear evidence of entrained air and detrained cloud filament. The transition region below exhibits vertical size sorting of cloud droplets caused by sedimentation. Our results suggest that using a single sedimentation velocity for all cloud droplets, as is done in many atmospheric models, overlooks key physics relevant to the microphysical structure near the cloud top. In conclusion, our conceptual model used to describe these measurements can serve as a step toward improving the current modeling of processes in the cloud top region.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Open-Source Data for MAC-POSTS: Mobility Data Analytics Center - Prediction, Optimization, and Simulation Toolkit for Transportation Systems

MAC-POSTS (Mobility Data Analytics Center - Prediction, Optimization, and Simulation toolkit for Transportation Systems) is a toolkit for dynamic transportation network modeling. Developed by the Mobility Data Analytics Center (MAC) at Carnegie Mellon University, this package implements many classic dynamic transportation network models, as well as new models proposed by MAC members. It has served as one building block for many other models and research projects. As such, this package used to be treated as an internal research project of the MAC lab, and admittedly, the code base is messy, and the interface is hard to use. However, we are working hard to make it a generally usable and useful toolkit for dynamic transportation network modeling. We would really appreciate any feedback, comments, suggestions, or criticisms.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Stand-Alone and Hybrid Electric Thermal Energy Storage in the System Advisor Model

This project developed stand-alone electric-thermal energy storage (ETES), stand-alone pumped thermal energy storage (PTES), and hybrid molten-salt power tower (MSPT)-ETES performance and dispatch optimization techno-economic models. The models are available to the public through the System Advisor Model (SAM) software, scripting, and as open-source code. We compared results of the dispatch model to PLEXOS dispatch of a similar generator using the same initial grid pricing signal and found our dispatch model performed well, but closer agreement between the models was limited by the inherent differences between price-taker and unit commitment models. Nevertheless, the price-taker models developed in this project are useful to analyze proposed ETES and PTES technologies because they provide more detailed system and component models, solve several orders of magnitude faster, and are available as free open-source software. The model results represent the most optimistic returns considering grid arbitrage from the input electricity pricing, so the financial results can be applied as a feasibility stage-gate. We also submitted a journal draft paper that describes the ETES dispatch model methodology and demonstrates model functionality. An accepted journal article will serve as peer-reviewed documentation for the models, along with the open-source code, SAM help-menu content, and eventually this final project report.

14 SOLAR ENERGY↗

DOE OSTI2014

Gamma ray irradiated silicon nanowires: An effective model to investigate defects at the interface of Si/SiOx

The effect of gamma ray irradiation on silicon nanowires was investigated. Here, an additional defect emerged in the gamma-ray-irradiated silicon nanowires and was confirmed with electron spin resonance spectra. {sup 29}Si nuclear magnetic resonance spectroscopy showed that irradiation doses had influence on the Q{sup 4} unit structure. This phenomenon indicated that the unique core/shell structure of silicon nanowires might contribute to induce metastable defects under gamma ray irradiation, which served as a satisfactory model to investigate defects at the interface of Si/SiOx.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2011

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in wild Drosophila populations, while the most abundant associates of natural Drosophila populations are rare in the lab.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Integration of a grey-box refrigerated case model in EnergyPlus via Python plugin

Commercial buildings, in particular grocery stores (due mainly to their large refrigeration load), provide opportunities for energy cost reductions. Grocery stores could offer substantial load flexibility to the power grid through participation in demand response programs because of their usage patterns and relatively high energy intensity. This load flexibility could come from modifying the control of heating, ventilation, and air conditioning (HVAC) systems, refrigeration systems, or both. Although estimation of the HVAC system’s load flexibility potential is relatively targeted in the literature, estimating load flexibility of refrigeration systems is nascent and has been a challenge, in part because of the lack of proper simulation tools that capture the dynamics in the refrigeration cases. The existing refrigerated case model within EnergyPlus, a whole building energy simulation program, assumes a constant case temperature throughout the simulation period and does not explicitly model the cycling of the compressor serving the refrigerated case. In addition, it does not encompass modeling of temperatures of the product inside the refrigerated case. This difference between modeled and actual operation can be a barrier to the development of demand control algorithm and accurate analysis of load flexibility potential. In this paper, we present a grey-box model for modeling refrigerated cases in grocery stores, which include medium temperature and low temperature. Four cases are modeled; two are low-temperature closed cases and two are medium-temperature cases with one closed and one open. Data from an experimental facility are used to train and test the models. Results demonstrate the efficacy of the grey-box models in predicting the temperatures. This model is integrated into EnergyPlus to capture the dynamic effects of case temperature on the environment and enhance the calculation of sensible and latent heat exchange with the environment (case credits). These enhancements can be leveraged more broadly to model advanced refrigeration controls such as defrost, develop and test unique algorithms that could affect refrigeration interactions with HVAC, and refine store design for any commercial building with refrigeration.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

Fission Product Transport in TRISO Particles and Pebbles

This document demonstrates completion of the goals described in the technical narrative of the FOA project titled: ”Modeling and Simulation Development Pathways to Accelerating KP-FHR Licensing” regarding fission product transport in the Kairos-proposed fuel pebble by INL and Kairos Power. Showcased in this report are code developments and simulations in BISON that extend the state of the art in computation and understanding of fission product transport in a TRISO fuel particle and pebble. These enhancements lay the foundation for making predictions of fission product transport that can be used as input in the fuel licensing process. This was achieved by installing existing fuel material models originally used in PARFUME, developing a new failure probability method that is efficient and multi-dimensional, employing material homogenization, and expanding verification and validation simulations to demonstrate the efficacy of the work. All this work is leveraged to spotlight the main deliverable; a three-dimensional model and corresponding demonstration simulation of a pebble, which will serve as the starting point for models used to predict fission product release.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Fission Product Transport in TRISO Particles and Pebbles

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Providing Experimental Infrastructure for Accelerating Advanced Reactor Demonstrations through the National Reactor Innovation Center

A suite of experimental infrastructure projects has been developed by the National Reactor Innovation Center to accelerate advanced reactor demonstrations and facilitate their development, addressing crucial gaps in data, materials characterization, and modeling. First, the Molten Salt Thermophysical Examination Capability (MSTEC) provides a specialized platform for post-irradiation characterization of molten salt reactor fuel, coolant salts, and structural materials, essential for supporting the design and operation of advanced reactors and future commercial molten salt reactor development and licensing. The Virtual Test Bed (VTB) complements these efforts by leveraging advanced modeling and simulation tools to evaluate reactor performance and safety. Serving as a library of reference models, the VTB offers a database of multiphysics reactor models, facilitating rapid safety evaluations and includes continuous software quality assurance, crucial for accelerating deployment while maintaining reliability. Additionally, the Helium Component Test Facility (HeCTF) addresses the need for high-temperature helium-cooled reactor component testing. As the first-of-its-kind facility in the United States, HeCTF emulates high-temperature gas reactor conditions, reducing time and cost associated with component validation, thereby accelerating reactor development. Finally, In-cell Thermal Creep Frames provide a unique solution for obtaining thermal creep data from irradiated materials, critical for materials qualification and licensing. Developed by the National Reactor Innovation Center, these compact frames enable the examination of previously irradiated materials, overcoming traditional limitations and enhancing the understanding of mechanical properties crucial for reactor development. Collectively, these experimental infrastructure projects form a comprehensive framework aimed at expediting advanced reactor demonstrations, fostering innovation, and ensuring the viability of next-generation nuclear energy solutions.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Fragmentation analysis of a bar with the Lip-field approach

The Lip-field approach was introduced in Moës and Chevaugeon (2021) as a new way to regularize softening material models. It was tested in 1D quasistatic in Moës and Chevaugeon (2021) and 2D quasistatic in Chevaugeon and Moës (2021): this paper extends it to 1D dynamics, on the challenging problem of dynamic fragmentation. The Lip-field approach formulates the mechanical problem to be solved as an optimization problem, where the incremental potential to be minimized is the non-regularized one. Spurious localization is prevented by imposing a Lipschitz constraint on the damage field. Here, the displacement and damage field at each time step are obtained by a staggered algorithm, that is the displacement field is computed for a fixed damage field, then the damage field is computed for a fixed displacement field. Indeed, these two problems are convex, which is not the case of the global problem where the displacement and damage fields are sought at the same time. The incremental potential is obtained by equivalence with a cohesive zone model, which makes material parameters calibration simple. A non-regularized local damage equivalent to a cohesive zone model is also proposed. It is used as a reference for the Lip-field approach, without the need to implement displacement jumps. These approaches are applied to the brittle fragmentation of a 1D bar with randomly perturbed material properties to accelerate spatial convergence. Both explicit and implicit dynamic implementations are compared. Favorable comparison to several analytical, numerical and experimental references serves to validate the modeling approach.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Optimising the use of gene expression data to predict plant metabolic pathway memberships

Not provided.

Plant Sciences↗

DOE OSTI2018

Characterizing the Relative Importance Assigned to Physical Variables by Climate Scientists when Assessing Atmospheric Climate Model Fidelity

Evaluating a climate model’s fidelity (ability to simulate observed climate) is a critical step in establishing confidence in the model’s suitability for future climate projections, and in tuning climate model parameters. Model developers use their judgement in determining which trade-offs between different aspects of model fidelity are acceptable. However, little is known about the degree of consensus in these evaluations, and whether experts use the same criteria when different scientific objectives are defined. Here, we report on results from a broad community survey studying expert assessments of the relative importance of different output variables when evaluating a global atmospheric model’s mean climate. We find that experts adjust their ratings of variable importance in response to the scientific objective, for instance, scientists rate surface wind stress as significantly more important for Southern Ocean climate than for the water cycle in the Asian watershed. There is greater consensus on the importance of certain variables (e.g., shortwave cloud forcing) than others (e.g., aerosol optical depth). We find few differences in expert consensus between respondents with greater or less climate modeling experience, and no statistically significant differences between the responses of climate model developers and users. In conclusion, the concise variable lists and community ratings reported here provide baseline descriptive data on current expert understanding of certain aspects of model evaluation, and can serve as a starting point for further investigation, as well as developing more sophisticated evaluation and scoring criteria with respect to specific scientific objectives.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

PSY (PowerSystems.jl) [SWR-23-105]

PowerSystems.jl is a package to organize and manipulate data for the study of energy systems with diverse modeling requirements. This software serves two main purposes: to reduce the burden of large power system data set development, and to promote reproducible research and simulation. PowerSystems.jl implements an abstract hierarchy to represent and customize power systems data and includes data containers for quasi-static and dynamic simulation applications. Key features include efficient management of large quantities of time series data, optimized serialization, and comprehensive validation capabilities. For further information regarding the Sienna modeling framework at NREL, see: https://www.nrel.gov/analysis/sienna.html

Lara Aguilar, Jose Daniel↗

DOE OSTI2017

Systems Level Regulation of Rhythmic Growth Rate and Biomass Accumulation in Grasses

Objectives: Several breakthroughs have been recently made in our understanding of plant growth and biomass accumulation. It was found that plant growth is rhythmically controlled throughout the day by the circadian clock through a complex interplay of light and phytohormone signaling pathways. While plants such as the C4 energy crop sorghum (Sorghum bicolor (L.) Moench) and possibly the C3 grass Brachypodium distachyon also exhibit daily rhythms in growth rate, the molecular details of its regulation remain to be explored. A better understanding of diurnally regulated growth behavior in grasses may lead to species-specific mechanisms highly relevant to future strategies to optimize energy crop biomass yield. Here we propose to devise a systems approach to identify, in parallel, regulatory hubs associated with rhythmic growth in C3 and C4 plants. We propose to use rhythmicity in daily growth patterns to drive the discovery of regulatory network modules controlling biomass accumulation. Description: The project is divided in three main parts: 1) Performing time-lapse imaging and growth measurement in B. distachyon and S. bicolor to determine growth rate dynamic during the day/night cycle. Identifying growth-associated genes whose expression patterns follow the observed growth dynamics using deep sequencing technology, 2) identifying regulators of these genes by screening for DNA-binding proteins interacting with the growth-associated gene promoters identified in Aim 1. Screens will be performed using a validated yeast-one hybrid strategy paired with a specifically designed B. distachyon and S. bicolor transcription factor libraries (1000 clones each), and 3) Selecting 50 potential growth regulators from the screen for downstream characterization. The selection will be made by using a sytems biology approach by calculating the connectivity between growth rate, rhythmic gene expression profiles and TF expression profile and determine which TF is likely part of a hub and a potential regulator of plant growth. We will confirme the 50 DNA-protein interactions using transient transcriptional assays in B. distachyon and S. bicolor, and perform further testing in vivo by measuring growth parameters in transgenic loss- or gain-of-function lines for the selected transcription factors (25 B. distachyon and 3 S. bicolor lines). In 2016 the Principal Investigator relocated the laboratory to The Scripps Research Institute (TSRI) where the project has continued with an end date of 08/31/17. Accomplishments: We successfully collected large datasets of gene expression form the model grass Brachypodium. We used and developed bioinformatics analysis tools to investigate the structure, dynamics and robustness of circadian regulated gene expression in Brachypodium. Relevant Discoveries: We were able to determine that the endogenous circadian clock appears to play a much more subdued role in growth regulation in Brachypodium, that has been demonstrated in either Arabidopsis, or crop plants like Rice, Corn and Soybean. This led to our conclusion that Brachypodium unfortunately is unlikely to serve as an informative model for understanding how growth regulation in plants is under the control of circadian network circuitry. However, we were able to leverage our datasets in Brachypodium to inform us and reinforce a large collaborative study on gene networks governing cell wall deposition in Arabidopsis. This led to a major and highly cited publication relevant to improving biomass production.

09 BIOMASS FUELS↗

DOE OSTI2019

Decorrelating the errors of the galaxy correlation function with compact transformation matrices

Abstract Covariance matrix estimation is a persistent challenge for cosmology, often requiring a large number of synthetic mock catalogues. The off-diagonal components of the covariance matrix also make it difficult to show representative error bars on the 2-point correlation function (2PCF) since errors computed from the diagonal values of the covariance matrix greatly underestimate the uncertainties. We develop a routine for decorrelating the projected and anisotropic 2PCF with simple and scale-compact transformations on the 2PCF. These transformation matrices are modelled after the Cholesky decomposition and the symmetric square root of the Fisher matrix. Using mock catalogues, we show that the transformed projected and anisotropic 2PCF recover the same structure as the original 2PCF while producing largely decorrelated error bars. Specifically, we propose simple Cholesky-based transformation matrices that suppress the off-diagonal covariances on the projected 2PCF by ${\sim } 95{{\ \rm per\ cent}}$ and that on the anisotropic 2PCF by ${\sim } 87{{\ \rm per\ cent}}$. These transformations also serve as highly regularized models of the Fisher matrix, compressing the degrees of freedom so that one can fit for the Fisher matrix with a much smaller number of mocks.

79 ASTRONOMY AND ASTROPHYSICS↗