Computational Optimization of Mechanical Energy Transduction (COMET) Toolkit.
Abstract not provided.
Kohtanen, Eetu↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Computational Optimization of Mechanical Energy Transduction (COMET) Toolkit.
Abstract not provided.
Kohtanen, Eetu↗
Computational study of the effect of core–skin structure on the mechanical properties of carbon nanofibers
The effect of the core–skin structure on the mechanical properties of carbon nanofibers is investigated in large-scale molecular dynamics simulations of tensile deformation of carbon nanofibers with the core–skin and homogeneous structures. Contrary to an established notion of the deleterious effect of the skin layer on the strength of carbon fibers, the presence of a high-quality skin layer is found to increase both the Young’s modulus and tensile strength of the nanofiber. A detailed analysis of the fracture process indicates that the nanofiber strengthening is related to the ability of skin layer to suppress crack nucleation at the core–skin interface. Furthermore, the computational predictions suggest that the design of new approaches to carbon fiber manufacturing and processing leading to the generation of a high-quality skin layer while avoiding the introduction of structural defects at the core–skin interface may yield a significant enhancement of the mechanical properties of carbon fibers.
36 MATERIALS SCIENCE↗
Final Report, 2024 DOE STTR, Phase I, Release II: Improving Waste Repository Simulations with a Fracture-Enhanced Conforming Reproducing Kernel Method
Explore the source record for details and available documents.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Final Report, 2024 DOE SBIR, Phase I, Release I: Leveraging Compadre and MFEM in Geometrically Versatile Numerical Methods
Explore the source record for details and available documents.
97 MATHEMATICS AND COMPUTING↗
OptimiSM v.0.0.1
SAND2021-15062 O OptimiSM is a library for solving solid mechanics problems and for rapid prototyping of computational solid mechanics research ideas. It was originally created to facilitate research and development of algorithms for contact mechanics. It is a realization of a philosophy that problems can be represented with variational least-action principles, even when there is history-dependent material behavior and contact. This opens the door to using powerful methods from non-convex optimization for solutions. The code was successful in its original purpose, but along the way, the authors realized that it could be of general use to the computational solid mechanics research community as an R&D platform. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Talamini, Brandon↗
Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure
The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. Here, to clarify the mechanism, we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ~18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme–substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A combined experimental and computational analysis of failure mechanisms in open-hole cross-ply laminates under flexural loading
In this work, integrated experimental tests and computational modeling are proposed to investigate the failure mechanisms of open-hole cross-ply carbon fiber reinforced polymer (CFRP) laminated composites. In particular, we propose two effective methods, which include width-tapered double cantilever beam (WTDCB) and fixed-ratio mixed-mode end load split (FRMMELS) tests, to obtain the experimental data more reliably. We then calibrate the traction-separation laws of cohesive zone model (CZM) used among laminas of the composites by leveraging these two methods. The experimental results of fracture energy, i.e. G Ic and G Tc , obtained from WTDCB and FRMMELS tests are generally insensitive to the crack length thus requiring no effort to accurately measure the crack tip. Moreover, FRMMELS sample contains a fixed mixed-mode ratio of G IIc /G Tc depending on the width taper ratio. Examining comparisons between experimental results of FRMMELS tests and failure surface of B–K failure criterion predicted from a curve fitting, good agreement between the predictions and experimental data has been found, indicating that FRMMELS tests are an effective method to determine mixed-mode fracture criterion. In addition, a coupled experimental-computational modeling of WTDCB, edge notched flexure, and FRMMELS tests are adopted to calibrate and validate the interfacial strengths. Finally, failure mechanisms of open-hole cross-ply CFRP laminates under flexural loading have been studied systematically using experimental and multi-scale computational analyses based on the developed CZM model. The initiation and propagation of delamination, the failure of laminated layers as well as load-displacement curves predicted from computational analyses are in good agreement with what we have observed experimentally.
36 MATERIALS SCIENCE↗
Hybrid Quantum Mechanical, Molecular Mechanical, and Machine Learning Potential for Computing Aqueous-Phase Adsorption Free Energies on Metal Surfaces
Performing reliable computer simulations of elementary processes occurring at metal–water interfaces is pivotal for novel catalyst design in sustainable energy applications. Computational catalyst design hinges on the ability to reliably and efficiently compute the potential energy surface (PES) of the system. Here, due to the large system sizes needed for studying processes at liquid water–metal interfaces, these systems can currently not be described using density functional theory (DFT). In this work, we used a hybrid quantum mechanical, molecular mechanical, and machine learning potential for studying the adsorption behavior of phenol, atomic hydrogen, 2-butanol, and 2-butanone on the (0001) facet of Ru under reducing conditions when Ru is not oxidized. Specifically, we describe the adsorbate and the surrounding metal atoms at the DFT level of theory. Here, we also considered the electrostatic field effect of the water molecules on adsorbate–metal interactions. Next, for the water–water and water–adsorbate interactions, we used established classical force fields. Finally, for the water–Ru surface interaction, for which no reliable force fields have been published, we used Behler–Parrinello high-dimensional neural network potentials (HDNNPs). Employing this setup, we used our explicit solvation for metal surface (eSMS) approach to compute the aqueous-phase effect on the low-coverage adsorption of selected molecules and atoms on the (0001) facet of Ru. In agreement with previous experimental and computational studies of oxygenated molecules over transition metal facets, we found that liquid water destabilizes the tested adsorbates on Ru(0001). Interestingly, our findings indicate that adsorbates on Ru are less affected by the presence of an aqueous phase than on other transition metals (e.g., Pt), highlighting the necessity of experimental investigations of Ru-based catalytic systems in liquid water.
Adsorption↗
ElasTool v3.0: Efficient computational and visualization toolkit for elastic and mechanical properties of materials
Efficient computation and visualization of elastic and mechanical properties are crucial in the selection of materials and the design of new materials. Here, the ElasTool v3.0 toolkit marks a significant advancement in the computational analysis and visualization of elastic and mechanical properties of materials, essential in material selection and design. This enhanced version extends beyond standard calculations like elastic tensor, Young's modulus, bulk modulus, and Poisson's ratio. It introduces capabilities for computing minimum thermal conductivity, linear compressibility, rendering the Christoffel equation, and elastic energy density. Notably, it integrates advanced visualization tools, including compatibility with Plotly and Elate web platforms for interactive web-based property exploration. A key feature of ElasTool v3.0 is the implementation of second-order elastic constants (SOECs) for tubular 2D-based nanostructures and nanotubes. Leveraging high-efficiency strain-matrix sets (OHESS), the toolkit now facilitates efficient computation of elastic constants and mechanical properties at both zero and finite temperatures for 1D, 2D, and 3D dimensions. ElasTool is openly accessible on GitHub: https://github.com/gmp007/elastool.
1D, 2D, 3D, and tubular 2D nanostructure and nanot↗
Sulfurized Polyacrylonitrile for High-Performance Lithium–Sulfur Batteries: In-Depth Computational Approach Revealing Multiple Sulfur’s Reduction Pathways and Hidden Li + Storage Mechanisms for Extra Discharge Capacity
Like no other sulfur host material, polyacrylonitrile-derived sulfurized carbon (SPAN) promises improved electrochemical performance for lithium–sulfur batteries, based on its compatibility with carbonate solvents and ability to prevent self-discharge and shuttle effect. However, a complete understanding of the SPAN’s lithiation mechanism is still missing because its structural features vary widely with synthesis conditions, and its electrochemical performance deviates from elemental sulfur. This study continues our research on the elucidation of the SPAN’s structural characteristics and lithiation mechanisms via computational approaches. Here, our models reproduce most experimental data regarding carbon’s graphitization level and conjugated ordering, sulfur–carbon covalent bonding, sulfur loading, and elemental composition. Our simulations emulate the discharge voltage observed in experiments for the first discharge, which reveals that sulfur follows multiple reduction pathways based on its interaction with the carbon backbone. Sulfur reduction takes place above 1.0 V vs Li/Li + mostly in the SPAN-like material, with no long-chain lithium polysulfide formation. Below 1.0 V vs Li/Li + , the backbone’s electrochemical activity occurs via multiple C–Li and N–Li interactions, mostly with edge carbon atoms and pyridinic nitrogen. Moreover, we identify Li + binding sites throughout the graphitized backbone that might lead to prohibited energy costs for Li + deintercalation, which may explain the irreversible capacity loss between the first and second discharges. This work improves understanding of lithiation mechanisms in sulfurized carbon, which is useful for rationally designing SPAN synthesis pathways tailored to increase sulfur loading and enhanced electrochemical performance.
25 ENERGY STORAGE↗
Metal Chalcogenides for Neuromorphic Computing: Emerging Materials and Mechanisms
The approaching end of Moore's Law scaling has significantly accelerated multiple fields of research including neuromorphic-, quantum-, and photonic computing, each of which possesses unique benefits unobtained through conventional binary computers. One of the most compelling arguments for neuromorphic computing systems is power consumption, noting that computations made in the human brain are approximately 106 times more efficient than conventional CMOS logic. This review article focuses on the materials science and physical mechanisms found in metal chalcogenides that are currently being explored for use in neuromorphic applications. We begin by reviewing the key biological signal generation and transduction mechanisms within neuronal components of mammalian brains and subsequently compare with observed experimental measurements in chalcogenides. With robustness and energy efficiency in mind, we will focus on short-range mechanisms such as structural phase changes and correlated electron systems that can be driven by low-energy stimuli, such as temperature or electric field. We aim to highlight fundamental materials research and existing gaps that need to be overcome to enable further integration or advancement of metal chalcogenides for neuromorphic systems.
36 MATERIALS SCIENCE↗
Impact of the adhesion-force lever-arm “a” on the Rock ‘n’ Roll resuspension model and how to compute it from contact mechanics
The paper proposes a methodology to fill a gap in the context of mechanistic particle resuspension models related to the adhesion and lift force lever arms ( a ): to date, only one experimental observation exists from a centrifuge experiment with a specific particle/surface pair which found r P / a = 100 and assumed that the contact points were symmetric with respect to the particle center. However, the Reeks and Hall’s (2001) model is highly sensitive to this parameter, which therefore cannot be used as-is for different particle diameters or materials. This paper proposes a methodology to compute the adhesion and lift force lever arms ( a A and a L , respectively) based on Atomic Force Microcopy (AFM) surface roughness measurements and contact mechanics arguments. In practice, a spherical, perfectly smooth particle is brought in contact (computationally) with the measured surface roughness and is then rotated by the point of contact to determine the two or more asperities over which the particle would sit on the surface. A method to compute the asperity radius of curvature is devised to compute the asperity deformation and the correct partitioning of the total deformation between the particle and the asperity is presented. For the glass surface under consideration, the asperity deformation was negligible, i.e., it was below the van der Waals radius, which is the limit of applicability of contact mechanics. The Reeks and Hall’s (2001) model is then extended to account for the joint probability of a A and a L . Significant differences in particle resuspended after a day in common atmospheric conditions are found between the approach that uses the lever-arm distributions or their mean values. Also, important differences are found when comparing the lever-arm distribution and r P / a = 100. Hence, one should be cautious of using r P / a = 100 for surface/particle pairs differing from those in the original study. Finally, limits of applicability of the theories used are presented together with considerations regarding how to extend the method to non-spherical particles and different materials.
42 ENGINEERING↗
A simple solution to the Rietveld refinement recipe problem
Rietveld refinements are widely used for many purposes in the physical sciences. Conducting a Rietveld refinement typically requires expert input because correct results may require that parameters be added to the fit in the proper order. This order will depend on the nature of the data and the initial parameter values. A mechanism for computing the next parameter to add to the refinement is shown. The fitting function is evaluated with the current parameter value set and each parameter incremented and decremented by a small offset. This provides the partial derivatives with respect to each parameter, along with information to discriminate meaningful values from numerical computational errors. The implementation of this mechanism in the open-source GSAS-II program is discussed. This new method is discussed as an important step towards the development of automated Rietveld refinement technology.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Latent Pitfalls in Microstructure-Based Modeling for Thermally Aged 9Cr-1Mo-V Steel (Grade 91)
A case study was conducted on a mechanistic model development that predicted tensile strength deterioration with thermal aging of 9Cr-1Mo-V steel in supporting the 60-year design life expected for advanced nuclear reactors. For property prediction beyond practical testing times, mechanistic modeling is highly desired, as it taps into the physics of structure–property relationships and therefore can generate reliable results for extrapolation. Meanwhile, as mechanistic models are often complicated, reflecting the intricacy of microstructure and strengthening mechanisms, pitfalls that are difficult to detect often exist. Here, this paper discusses latent pitfalls that are common in mechanistic modeling or specific in this 9Cr-1Mo-V case development through using the American Society of Mechanical Engineers verification and validation in computational solid mechanics (ASME V&V 10) standard for evaluating credibility of modeling in materials engineering. Suggestions are also made for enhancing reliability of microstructure-based modeling.
36 MATERIALS SCIENCE↗
Coupled Microbial-Conversion and Computational-Fluid-Dynamics (CFD) Models for Butanediol Production in Micro-Aerated Reactors
Microbial conversion of substrates to macromolecules has been widely used in the synthesis of value-added products in pharmaceutical and biotechnology industries. These bioreactions are also being investigated in the production of low-value commodities such as biofuels [1]. Gas-liquid mass-transfer and transport-reaction coupling are important challenges when designing and scaling up these reactor systems. Experiments in wellmixed small-scale reactors have enabled characterization of microbial reactivity, while their coupling with macroscale transport remains relatively unexplored. In this work, we use a coupled metabolic-CFD model to study the action of a genetically engineered microbe Zymomonas mobilis [2] on sugars to produce 2,3-Butanediol (BDO). BDO is an important hydrocarbon intermediate that can be catalytically upgraded to several fuels and chemicals [3]. An important aspect to this particular microbial conversion is the need for micro-aerated environments as opposed to traditional aerobic fermentation. Slight variations in oxygen concentration can result in competing reaction pathways that disable BDO production. Hence, gas-liquid mass transfer and transport need to be optimized in large-scale reactors to maximize BDO production, for which CFD is a valuable tool. The aerobic-fermentation CFD model previously developed by the authors [5] for simulating bubble-column and airlift reactors at scale was used in this study. The Reynolds-averaged mass, momentum and energy transport equations for interpenetrating gas and liquid phase are solved in this model along with the transport and interphase mass transfer of oxygen. Our previous work used a phenomenological model for microbial oxygen uptake that neglected microbial growth and other reaction pathways. In this work, a detailed metabolic model enabled prediction of product formation and inhibition pathways. In order to manage computational cost, we used a subcycling technique [6] that takes advantage of the clear separation in transport (~ 200 sec) and reaction (~ 2-3 hours) timescales. The CFD model is first solved to steady state, after which the metabolic model is advanced at every cell in the computational domain using the local oxygen concentration. The CFD model is then run to achieve a new steady state that provides a new oxygen distribution for the metabolic model. This process, where reaction and fluid updates are interleaved together, is iterated until reactants are completely exhausted. This work will examine the performance of different reactor designs such as bubble column and airlift reactors at scale (250-500 m3). Oxygen mass-transfer coefficient and distribution are critically analyzed among reactors, and optimization studies pertaining to aeration is presented. Furthermore, it has been observed in experiments that high BDO production may be achieved by manipulating the aerobic environment over the course of reaction, such that oxygen concentration is high during the growth phase, and very low as sugar is depleted. This characteristic will be addressed by our simulations for which a timedependent scheduling strategy for aeration is presented that maximizes BDO production. [1] Humbird, D., Davis, R., and McMillan, J., Aeration costs in stirred-tank and bubble column bioreactors, Biochemical Engineering Journal, 127, 161—166, 2017 [2] Yang, S., Mohagheghi, A., Franden, M. A., Chou, Y.-C., Chen, X., Dowe, N., Himmel, M. E., and Zhang, M., Metabolic engineering of zymomonas mobilis for 2, 3-butanediol production from lignocellulosic biomass sugars. Biotechnology for biofuels, 9(1):189, 2016 [3] Kim, S. J., Sim, H. J., Kim, J. W., Lee, Y. G., Park, Y. C., and Seo, J. H., Enhanced production of 2,3-butanediol from xylose by combinatorial engineering of xylose metabolic pathway and cofactor regeneration in pyruvate decarboxylase-deficient Saccharomyces cerevisiae. Bioresource Technology, 245:1551–1557, 2017 [4] Weller, H., Tabor, G., Jasak, H. and Fureby, C., A tensorial approach to computational continuum mechanics using object-oriented techniques, Computers in physics, 12, 6, 620--631, 1998
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Gas-Liquid Flow Modeling for Renewable Fuels Production
Aerobic/anaerobic and gas fermentation pathways have emerged as promising new technologies for the generation of renewable fuels/chemicals from biomass derived sugars, and mixtures of greenhouse/energy rich gas streams (CO2/CH4/H2/CO) via microbial action. Example pathways include sugars-to-ethanol conversion, biomethanation (CO2/H2 to CH4), biogas upgrading, CO fermentation and wet-waste conversion. Gas and liquid phase transport, mass-transfer, and mixing physics at large length scales can significantly affect microbial conversion rates, particularly when the microbial reaction requires a narrow set of conditions. These phenomena are difficult to study in small-scale bench-top reactors that are typically well-mixed. Predictive computational fluid dynamics (CFD) based simulations can therefore aid in the scale-up, design and optimization of these reactors. This work presents multiphase Euler-Euler CFD simulations of at-scale (~500 m3) bioreactors. Our mathematical model treats the gas and liquid as interpenetrating phases. This approach reduces the computational complexity of tracking individual gas bubbles that are several orders of magnitude smaller than reactor dimensions. We solve the Reynolds averaged Navier-Stokes (RANS) multiphase equations that account for phase and chemical species transport, interphase mass and momentum transfer and uses a phenomenological model for gas uptake by microbes. We use a customized solver derived from open-source CFD toolbox, OpenFOAM [1], to perform these simulations, which has been validated against small-scale reactors in our previous work [2]. There is currently a knowledge-gap regarding bubble-size distributions when using gas mixtures with vastly different properties, which can have a significant impact overall mass-transfer. For example, hydrogen bubbles are more buoyant compared to other relatively heavier gases (CO2/CH4/CO), resulting in a large distribution of residence times and bubble sizes. This work therefore develops a deeper understanding of bubble dynamics and interphase mass transfer in such heterogenous gas mixtures through well-resolved computational models. We use a population balance model (PBM) for bubble-size-distribution modeling that is validated against small-scale experiments in our solver with an uncertainty quantification study for bubble coalescence and break-up model parameters. Results pertaining to multiple simulations of gas-fermentation reactors are presented where gas mixtures with varying compositions of CO2/CH4/CO/H2 are imposed at the sparger boundaries. The spatio-temporal variations in bubble-size distribution and mass transfer coefficient are analyzed for varying superficial velocities and gas-compositions for varying sizes of bubble-column and airlift reactors. This work will also examine the performance of different reactor designs, viz. bubble column reactor, airlift reactor with an internal draft tube, and a stirred-tank reactor with Rushton impellers. Reactor mass-transfer coefficient, gas hold-up, and dissolved gas distribution are critically analyzed among reactors, and sensitivity studies pertaining to gas flow rates and reactor geometry will be presented. [1] Weller, H., Tabor, G., Jasak, H. and Fureby, C., A tensorial approach to computational continuum mechanics using object-oriented techniques, Computers in physics, 12, 6, 620--631, 1998. [2] Rahimi, M., Sitaraman, H., Humbird, D. and Stickel, J., Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas-liquid mass transfer, oxygen uptake, and dynamic oxygen distribution, Chemical Engineering Research and Design, 139: 283-295.
BIOMASS FUELS↗
HOSS: Hybrid Optimization Software Suite
HOSS software, developed at LANL, is a powerful, flexible, and parallelized package that enables the user to predict deformation and failure of materials in a variety of situations. LANL’s HOSS software is an R&D 100 finalist that integrates solid mechanics and computational fluid dynamics into a multi-physics platform able to handle millions of interacting and fracturing solids and/or particle systems. This nextgeneration simulation software integrates solid mechanics and computational fluid dynamics into a multi-physics platform able to provide state-of-the-art simulation solutions for a wide field of applications including oil and gas, construction, mining, defense, material sciences, and biomechanics.
36 MATERIALS SCIENCE↗