Structure and dynamics of an α-fucosidase reveal a mechanism for highly efficient IgG transfucosylation
Explore the source record for details and available documents.
99 GENERAL AND MISCELLANEOUS↗
SEARCH · Engineering Papers
Results for “Structural mechanics”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
A focused review on structures and ionic conduction mechanisms in inorganic solid-state proton and hydride anion conductors
This review provides a focused discussion on the structures and ionic conduction mechanisms of inorganic solid-state proton and hydride anion conductors.
Sun, Shichen↗
Multiscale Modeling of Silicon Carbide Cladding for Nuclear Applications: Thermal Performance Modeling
The complex multiscale and anisotropic nature of silicon carbide (SiC) ceramic matrix composite (CMC) makes it difficult to accurately model its performance in nuclear applications. The existing models for nuclear grade composite SiC do not account for the microstructural features and how these features can affect the thermal and structural behavior of the cladding and its anisotropic properties. In addition to the microstructural features, the properties of individual constituents of the composites and fiber tow architecture determine the bulk properties. Models for determining the relationship between the individual constituents’ properties and the bulk properties of SiC composites for nuclear applications are absent, although empirical relationships exist in the literature. Here, a hierarchical multiscale modeling approach was presented to address this challenge. This modular approach addressed this difficulty by dividing the various aspects of the composite material into separate models at different length scales, with the evaluated property from the lower-length-scale model serving as an input to the higher-length-scale model. The multiscale model considered the properties of various individual constituents of the composite material (fiber, matrix, and interphase), the porosity in the matrix, the fiber volume fraction, the composite architecture, the tow thickness, etc. By considering inhomogeneous and anisotropic contributions intrinsically, our bottom-up multiscale modeling strategy is naturally physics-informed, bridging constitutive law from micromechanics to meso-mechanics and structural mechanics. The effects that these various physical attributes and thermo-physical properties have on the composite’s bulk thermal properties were easily evaluated and demonstrated through the various analyses presented herein. Since silicon carbide fiber-reinforced SiC CMCs are also promising thermal–structural materials with a broad range of high-end technology applications beyond nuclear applications, we envision that the multiscale modeling method we present here may prove helpful in future efforts to develop and construct reinforced CMCs and other advanced composite nuclear materials, such as MAX phase materials, that can service under harsh environments of ultrahigh temperatures, oxidation, corrosion, and/or irradiation.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Tailoring Crosslinks through Time─A Paradigm for Tough Hydrogels
The multidisciplinary applications of hydrogels have motivated a thorough exploration of the relationship between their structural and mechanical properties, i.e., spatial structure–function relationships, with particular regard to strength and toughness. While this approach has driven fundamental advancements in the design of robust hydrogel structures, further complementary perspectives are needed to enable holistic, rational design schemes that integrate considerations such as fabrication and advanced functions like response and adaptation. To these ends, this review focuses on the dynamics of temporal-function relationships and their fundamental bases in order to highlight how the dynamic regulation of polymer interactions programs: 1) polymer assembly and material structure; 2) response to deformation and fracture behavior; 3) dynamic modulation of properties and structural remodeling/self-healing. Here, by exploring this intersection of hydrogel formation, function, and remodeling, this review seeks to shed light on the fundamental relationship between molecular structure, material assembly, and performance in order to connect the emerging area of bioinspired materials processing with tough hydrogel design, and further provides a lasting inspiration and impetus for future hydrogel development that enables valuable scientific and technological advancements.
36 MATERIALS SCIENCE↗
Unveiling decaying mechanism through quantitative structure-activity relationship in electrolytes for lithium-ion batteries
Understanding the decaying mechanism in lithium-ion batteries (LIBs) is critical to establishing a stable electrolyte system. Despite the advent of various novel electrolyte solvents designated for high-voltage LIBs, their working principles are not fully understood. Currently, oxidative decomposition of electrolytes is believed to be the major cause of capacity fade, and tremendous effort has been devoted to discovering a new electrolyte with enhanced anodic stability. However, the oxidative decomposition process cannot solely explain the rapid decay of some electrolyte systems with intrinsic high anodic stability when used with a high-nickel layered oxide cathode such as LiNi 0.6 Mn 0.2 Co 0.2 O 2 (NMC622). In this report, a study of the quantitative structure-activity relationship was conducted to deepen the mechanistic understanding of the decay in high-voltage LIBs. Here, the results obtained from the newly introduced molecular pair analysis and linear free-energy relationship (LFER) studies were highly consistent with the solvation-involved decaying mechanism in a high-nickel layered oxide cathode cycling at high voltage (> 4.5 V vs. Li/Li + ). There was no evidence correlating the solvation ability of electrolyte solvents with the decay of a high-nickel layered oxide cathode cycling at a relatively low voltage (< 4.3 V vs. Li/Li + ), nor with the high-voltage spinel cathode LiNi 0.5 Mn 1.5 O 4 (LNMO). Undoubtedly, the unveiled mechanistic insight provides a critical guideline for the development of an appropriate electrolyte system targeting different high-voltage cathode materials.
25 ENERGY STORAGE↗
Dataset of simulated vibrational density of states and X-ray diffraction profiles of mechanically deformed and disordered atomic structures in Gold, Iron, Magnesium, and Silicon
This dataset is comprised of a library of atomistic structure files and corresponding X-ray diffraction (XRD) profiles and vibrational density of states (VDoS) profiles for bulk single crystal silicon (Si), gold (Au), magnesium (Mg), and iron (Fe) with and without disorder introduced into the atomic structure and with and without mechanical loading. Included with the atomistic structure files are descriptor files that measure the stress state, phase fractions, and dislocation content of the microstructures. All data was generated via molecular dynamics or molecular statics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. This dataset can inform the understanding of how local or global changes to a materials microstructure can alter their spectroscopic and diffraction behavior across a variety of initial structure types (cubic diamond, face-centered cubic (FCC), hexagonal close-packed (HCP), and body-centered cubic (BCC) for Si, Au, Mg, and Fe, respectively) and overlapping changes to the microstructure (i.e., both disorder insertion and mechanical loading).
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Constitutive Model of Radiation Aging Effects in Filled Silicone Elastomers under Strain
Filled silicone elastomers, an essential component in many technological applications, are often subjected to controlled or unintended radiation for a variety of reasons. Radiation exposure can lead to permanent mechanical and structural changes in the material, which is manifested as altered mechanical response, and in some cases, a permanent set. For unfilled elastomers, network theories developed and refined over decades can explain these effects in terms of chain-scission and cross-link formation and a hypothesis involving independent networks formed at different strain levels of the material. In this work, we expose a filled silicone rubber to gamma radiation while being under finite elongational strain and show that the observed mechanical and structural changes can be quantitatively modeled within the same theoretical framework developed for unfilled elastomers as long as nuances associated with the Mullins effect are accounted for in a consistent manner. In this work, we employ Ogden’s incompressible hyperelastic model within the framework of Tobolsky’s two-network scheme to describe the observed permanent set and mechanical modulus changes as a function of radiation dosage. In the process, we conclude that gamma radiation induces both direct cross-linking at chain crossings (H-links) and main-chain-scission followed by cross-linking (Y-links). We provide an estimate of the ratio of chain-scission to cross-linking rates, which is in reasonable agreement with previous experimental estimate from Charlesby–Pinner analysis. We use density functional theory (DFT)-based quantum mechanical calculations to explore the stability of –Si and –SiO radicals that form upon a radiation-induced chain-scission event, which sheds light on the relative rates of Y-linking and H-linking processes.
36 MATERIALS SCIENCE↗
Understanding flavin electronic structure and spectra
Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy
59 BASIC BIOLOGICAL SCIENCES↗
Dataset of tensile properties for sub-sized specimens of nuclear structural materials
Mechanical testing with sub-sized specimens plays an important role in the nuclear industry, facilitating tests in confined experimental spaces with lower irradiation levels and accelerating the qualification of new materials. The reduced size of specimens results in different material behavior at the microscale, mesoscale, and macroscale, in comparison to standard-sized specimens, which is referred to as the “specimen size effect.” Although analytical models have been proposed to correlate the properties of sub-sized specimens to standard-sized specimens, these models lack broad applicability across different materials and testing conditions. The objective of this study is to create the first large public dataset of tensile properties for sub-sized specimens used in nuclear structural materials. We performed an extensive literature review of relevant publications and extracted over 1,000 tensile testing records comprising 55 columns including material type and composition, manufacturing information, irradiation conditions, specimen dimensions, and tensile properties. The dataset can serve as a valuable resource to investigate the specimen size effect and develop computational methods to correlate the tensile properties of sub-sized specimens.
36 MATERIALS SCIENCE↗
Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain
Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Here, through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Chemical transformations and transport phenomena at interfaces
Abstract Interfaces, the boundary that separates two or more chemical compositions and/or phases of matter, alters basic chemical and physical properties including the thermodynamics of selectivity, transition states, and pathways of chemical reactions, nucleation events and phase growth, and kinetic barriers and mechanisms for mass transport and heat transport. While progress has been made in advancing more interface‐sensitive experimental approaches, their interpretation requires new theoretical methods and models that in turn can further elaborate on the microscopic physics that make interfacial chemistry so unique compared to the bulk phase. In this review, we describe some of the most recent theoretical efforts in modeling interfaces, and what has been learned about the transport and chemical transformations that occur at the air–liquid and solid–liquid interfaces. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Structure and Mechanism > Computational Materials Science Software > Quantum Chemistry Software > Simulation Methods
Hao, Hongxia↗
Experimental and Numerical Investigations on Dynamic Mechanical Properties of TPMS Structures
Triply Periodic Minimal Surface (TPMS) lattice structures have been of increasing interest due to their light weighting, enhanced mechanical properties, and energy absorption characteristics for automotive and biomedical applications. With the advent of additive manufacturing and geometric modeling software, TPMS lattices with complex geometries can be realized. In this work, TPMS lattice structures were fabricated with PLA using fused filament fabrication (FFF) and their dynamic properties are characterized through drop tower experiments. Although lightweight TPMS lattices are beneficial for their impact absorption capability, most of the existing works are limited to quasi-static compression and dynamic impact tests are rarely performed. The current study investigates the stress-strain and energy absorption characteristics of TPMS lattices through drop tower testing and numerical modeling. Finite element modeling for TPMS lattices is carried out to validate the experimental responses. The mechanical properties, deformation, and failure mechanisms of TPMS lattices under dynamic impact are summarized for potential future applications.
Pokkalla, Deepak↗
Transformational faulting in Mn 2 GeO 4 from olivine to wadsleyite structure: Implications for physical mechanism of deep-focus earthquakes
High-pressure and temperature deformation experiments interfaced with acoustic emission (AE) monitoring have been conducted to study transformational faulting in Mn 2 GeO 4 olivine, which transforms to the β phase, isostructural to wadsleyite. Metastable Mn 2 GeO 4 olivine exhibits a marked embrittlement behavior at temperatures between 800 and 1100 K, emitting numerous AEs. At each temperature, brittle deformation is characterized by a two-stage process: (1) a “preparation” stage with numerous diffusedly located low-magnitude AEs and large b values (>2), and (2) a failure stage where larger-magnitude AEs form a planar distribution with b values about 1. Microstructure analysis reveals extensive kink band development in olivine grains in the recovered samples. Kink band boundaries (KBBs), with a typical thickness of ∼100 nm, are filled with a nanometric β-Mn 2 GeO 4 “gouge”. A dense array of secondary shear localizations is often present within the kink bands, suggesting significant shear deformation therein. The combined observations suggest that faulting in metastable Mn 2 GeO 4 olivine is a self-similar process, from grain-scale to the sample-scale. Both observed embrittlement behavior and the microstructure of metastable Mn 2 GeO 4 olivine are essentially identical to those in Mg 2 GeO 4 olivine we have reported previously, indicating that the physical mechanism of faulting in metastable olivine is insensitive to the specific crystallographic structure of the high-pressure phase. The low b values (about 1) observed in the faulting process in our experiments are similar to those of deep focus earthquakes in cold subduction zones. Our observed mechanism explains deep focus seismicity in cold metastable mantle wedges, provided that the self-similarity assumption holds to geological scales.
58 GEOSCIENCES↗
Mapping 3D grain and precipitate structure during in situ mechanical testing of open-cell metal foam using micro-computed tomography and high-energy X-ray diffraction microscopy
Open-cell metal foams are ultra-low-density cellular metals with complex hierarchical structures that span bulk, cell, ligament, and sub-ligament scales and give rise to desirable properties such as high strength-to-weight ratio and excellent energy absorption. Although literature suggests that intrinsic material structures at sub-ligament length scales (e.g., grains and precipitates) play an important role in mechanical behavior of open-cell metal foams, there are very few experimental measurements of such structures in three dimensions and for meaningful volumes of foam. This study seeks to map and track the three-dimensional (3D) grain and precipitate structures of an intact volume of open-cell aluminum foam by advancing microstructural characterization techniques that leverage X-ray micro-computed tomography (μCT) and far-field high-energy X-ray diffraction microscopy (FF-HEDM). A 6%-relative-density aluminum foam sample was mechanically tested in compression while μCT and FF-HEDM measurements were collected at interrupted loading states at beamline 1-ID of the Advanced Photon Source. Further, a new scanning strategy and reconstruction algorithm were established to enable characterization of a foam volume with diameter approximately four times wider than the nominal width of the X-ray beam. The result is a set of maps that detail both the 3D grain and precipitate structures throughout the foam volume at successive strain steps. A novel grain tracking procedure was developed to track individual grains within the foam volume by accounting for the large rigid-body motions that individual ligaments can undergo during mechanical loading. The ability to track grains and precipitate structures in three dimensions throughout large bulk deformation of ultra-low-density polycrystalline materials enables new possibilities for validating numerical models and investigating local failure mechanisms. Furthermore, the methods and procedures developed in this study could be applied to other ultra-low-density structures, such as additively manufactured lattices.
36 MATERIALS SCIENCE↗
Cryo-EM structures of NPC1L1 reveal mechanisms of cholesterol transport and ezetimibe inhibition
The intestinal absorption of cholesterol is mediated by a multipass membrane protein, Niemann-Pick C1-Like 1 (NPC1L1), the molecular target of a cholesterol lowering therapy ezetimibe. While ezetimibe gained Food and Drug Administration approval in 2002, its mechanism of action has remained unclear. Here, we present two cryo–electron microscopy structures of NPC1L1, one in its apo form and the other complexed with ezetimibe. The apo form represents an open state in which the N-terminal domain (NTD) interacts loosely with the rest of NPC1L1, leaving the NTD central cavity accessible for cholesterol loading. The ezetimibe-bound form signifies a closed state in which the NTD rotates ~60°, creating a continuous tunnel enabling cholesterol movement into the plasma membrane. Ezetimibe blocks cholesterol transport by occluding the tunnel instead of competing with cholesterol binding. These findings provide insight into the molecular mechanisms of NPC1L1-mediated cholesterol transport and ezetimibe inhibition, paving the way for more effective therapeutic development.
59 BASIC BIOLOGICAL SCIENCES↗
Algorithm advances and applications of time‐dependent first‐principles simulations for ultrafast dynamics
Abstract Far from equilibrium phenomenon is a central theme of contemporary material research. Such phenomenon can exhibit itself in atomic structure and dynamics, but very often it also happens as non‐equilibrium phenomenon in the electronic structure. In ab initio material simulation, density functional theory (DFT) has played an essential role in studying electronic ground state problems. For excited states, besides many‐body perturbation theory, another powerful tool is the time dependent DFT (TDDFT) method. In particular, the real‐time TDDFT (rt‐TDDFT) method can be used to simulate many non‐equilibrium phenomena directly. Here we introduce our works on some algorithm advances based on our recently rt‐TDDFT method. This method uses the plane‐wave basis set, and significantly accelerates its efficiency by increasing the time step from 0.1–1 as in traditional methods to 0.2–0.5 fs. The noncollinear magnetic moments and spin–orbit coupling have also been included in our rt‐TDDFT method. Furthermore, a Boltzmann‐TDDFT algorithm has been developed to solve the hot carrier overheating problem in Ehrenfest dynamics, and a natural orbital branching algorithm has been developed to overcome the mean‐field approximation in Ehrenfest dynamics nuclear trajectory, thus allows stochastic multiple paths in chemical reactions. Utilizing these methods, we have studied the photoinduced ultrafast demagnetization, ultrafast phase transition, energy transfer between plasmon and hot carriers, as well as the high‐energy ion implantation and low‐energy atomic diffusion in semiconductors. We believe the tools as the ones introduced here can enable us to study a wide range of phenomena which are of great interest in modern day material research. This article is categorized under: Structure and Mechanism > Computational Materials Science Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Density Functional Theory
Liu, Wen‐Hao↗
Mixed Precision Fermi-Operator Expansion on Tensor Cores from a Machine Learning Perspective
Here we present a second-order recursive Fermi-operator expansion scheme using mixed precision floating point operations to perform electronic structure calculations using tensor core units. A performance of over 100 teraFLOPs is achieved for half-precision floating point operations on Nvidia’s A100 tensor core units. The second-order recursive Fermi-operator scheme is formulated in terms of a generalized, differentiable deep neural network structure, which solves the quantum mechanical electronic structure problem. We demonstrate how this network can be accelerated by optimizing the weight and bias values to substantially reduce the number of layers required for convergence. We also show how this machine learning approach can be used to optimize the coefficients of the recursive Fermi-operator expansion to accurately represent the fractional occupation numbers of the electronic states at finite temperatures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗