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At least 739 records · Page 41

Understanding the structural mechanics of ligated DNA crystals via molecular dynamics simulation

DNA self-assembly is a highly programmable method to construct arbitrary architectures based on sequence complementarity. Among various constructs, DNA crystals are macroscopic crystalline materials formed by assembling motifs via sticky end association. Due to their high structural integrity and size ranging from tens to hundreds of micrometers, DNA crystals offer unique opportunities to study the structural properties and deformation behaviors of DNA assemblies. For example, enzymatic ligation of sticky ends can selectively seal nicks resulting in more robust structures with enhanced mechanical properties. However, the research efforts have been mostly on experiments involving different motif designs, structural optimization, or new synthesis methods, while their mechanics are not yet fully understood. The complex properties of DNA crystals are difficult to study via experiments alone, and numerical simulation can complement and aid the experiments. The coarse-grained molecular dynamics (MD) simulation is a powerful tool that can probe the mechanics of DNA assemblies. Here, we investigate DNA crystals made of four different motif lengths with various ligation patterns (full ligation, major directions, connectors, and in-plane) using oxDNA, an open-source, coarse-grained MD platform. We found that several distinct deformation stages emerge in response to mechanical loading and that the number and the location of ligated nucleotides can significantly modulate structural behaviors. These findings should be useful for predicting crystal properties and thus improving the design.

DNA crystal↗

Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate–dependent nonheme ferrous enzymes

Determining the requirements for efficient oxygen (O 2 ) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)–dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O 2 ) and a sequential mechanism (cofactor binding and reaction with O 2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Interestingly, spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the Fe II ), αKG binding to Fe II -DAOCS results in ~45% five-coordinate sites that selectively react with O 2 relative to the remaining six-coordinate sites. However, this reaction produces an Fe III species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to Fe II -DAOCS produces five-coordinate sites that rapidly react with O 2 to form an Fe IV =O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reaction mechanism for atmospheric pressure plasma treatment of cysteine in solution

Mechanisms for the cold atmospheric plasma (CAP) treatment of cells in solution are needed for more optimum design of plasma devices for wound healing, cancer treatment, and bacterial inactivation. However, the complexity of organic molecules on cell membranes makes understanding mechanisms that result in modifications (i.e. oxidation) of such compounds difficult. As a surrogate to these systems, a reaction mechanism for the oxidation of cysteine in CAP activated water was developed and implemented in a 0-dimensional (plug-flow) global plasma chemistry model with the capability of addressing plasma-liquid interactions. Reaction rate coefficients for organic reactions in water were estimated based on available data in the literature or by analogy to gas-phase reactions. The mechanism was validated by comparison to experimental mass-spectrometry data for COST-jets sustained in He/O 2 , He/H 2 O and He/N 2 /O 2 mixtures treating cysteine in water. Results from the model were used to determine the consequences of changing COST-jet operating parameters, such as distance from the substrate and inlet gas composition, on cysteine oxidation product formation. Results indicate that operating parameters can be adjusted to select for desired cysteine oxidation products, including nitrosylated products.

60 APPLIED LIFE SCIENCES↗

Aging studies on chemical vapor deposition and mechanically exfoliated molybdenum disulfide flakes heated in ambient air

The structural integrity of atomically thin two-dimensional molybdenum disulfide (MoS 2 ) is crucial for high-temperature applications, including nanoelectronics and optoelectronics. This study explores the structural stability and electrical performance, under extended thermal exposure in air, of MoS 2 flakes synthesized via chemical vapor deposition (CVD) and mechanical exfoliation. The MoS 2 flakes, both CVD-grown and mechanically exfoliated, were subjected to heating at 200 °C with a relative humidity of 60(±5)% for a prolonged period and investigated with atomic force microscopy and Raman spectroscopy. This study shows that CVD-grown flakes developed noticeable cracks after prolonged heating, whereas mechanically exfoliated flakes mostly retained their structural integrity. Also, both types of flakes showed a decrease in layer thickness and lateral size over time, with mechanically exfoliated flakes exhibiting a comparatively smaller reduction in substrate coverage area. In addition, MoS 2 -based two-terminal devices were subjected to heating at 150 °C for approximately 1100 h, and their electrical characterization revealed a steady rise in current during constant voltage (5 V) conditions. This study enhances our understanding of MoS 2 stability and provides guidance for improving the reliability of MoS 2 -based devices in high-temperature electronic applications.

2D materials↗

Emergent quantum mechanics at the boundary of a local classical lattice model

We formulate a model in which quantum mechanics emerges from classical mechanics. Given a local Hamiltonian H acting on n qubits, we define a local classical model with an additional spatial dimension whose boundary dynamics is approximately—but to arbitrary precision—described by Schrödinger's equation and H. The bulk consists of a lattice of classical bits that propagate towards the boundary through a circuit of stochastic matrices. The bits reaching the boundary are governed by a probability distribution whose deviation from the uniform distribution can be interpreted as the quantum-mechanical wave function. Bell nonlocality is achieved because information can move through the bulk much faster than the boundary speed of light. Finally, we analytically estimate how much the model deviates from quantum mechanics, and we validate these estimates using computer simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A prediction of the thermodynamic, thermophysical, and mechanical properties of CrTaO 4 from first principles

It is reported that the self-forming CrTaO 4 oxide scale can protect refractory high-entropy alloys from oxidation, superior to Cr 2 O 3 . In this paper, the phase stability, mechanical, and thermal properties of three polymorphous phases of CrTaO 4 are systematically investigated from first-principles density functional theory calculations. The mechanical properties predicted using the strain–energy methods indicated that all three phases are mechanically stable. The temperature dependence of elastic constants and polycrystalline moduli of three phases demonstrated the thermal softening as temperature increase. The Helmholtz-free energies as a function of volume and temperature are derived from phonon dispersions within the quasi-harmonic approximation at six strained volumes. The calculated apparent bulk coefficients of thermal expansion of these three phases are evaluated, the highest value approximately 13.4× 10 –6 K –1 within a temperature range of 500–2000 K for the rutile I4 1 md phase. The lattice thermal conductivity calculated by the Debye–Callaway model suggested that the rutile type I4 1 md phase has the lowest value of approximately 2.1 W/m/K at 1800 K. The other two phases, C2/m and P2/c, exhibit higher values due to relatively lower Grüneisen parameters and larger phonon velocities. The melting point of CrTaO 4 is predicted to be between 1975 and 2449 K using ab initio molecular dynamics simulations. Finally, this work provides a comprehensive theoretical understanding of the thermodynamic, mechanical, and thermal properties for the new material CrTaO 4 and serves as an example of a viable computational design strategy for improved oxidation resistance of refractory alloys at high temperatures.

36 MATERIALS SCIENCE↗

Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo

The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear. Manipulation of the mechanical constraints affecting either the in vivo or in vitro growth of oilseed rape embryos was combined with analytical approaches, including magnetic resonance imaging and computer graphic reconstruction, immunolabelling, flow cytometry, transcriptomic, proteomic, lipidomic and metabolomic profiling. Our data implied that, in vivo, the imposition of mechanical restraints impeded the expansion of testa and endosperm, resulting in the embryo's deformation. An acceleration in embryonic development was implied by the cessation of cell proliferation and the stimulation of lipid and protein storage, characteristic of embryo maturation. The underlying molecular signature included elements of cell cycle control, reactive oxygen species metabolism and transcriptional reprogramming, along with allosteric control of glycolytic flux. Constricting the space allowed for the expansion of in vitro grown embryos induced a similar response. The conclusion is that the imposition of mechanical constraints over the growth of the developing oilseed rape embryo provides an important trigger for its maturation.

59 BASIC BIOLOGICAL SCIENCES↗

A Simple, Scalable Large Deformation Solid Mechanics Implementation in the MOOSE Framework

This article describes a large deformation solid mechanics solver implemented as part of the freely available and open source MOOSE finite element simulation framework. The article documents the choices made in developing the solid mechanics framework and describes novel formulations for the gradient operator and constitutive modeling framework made to simplify implementations of different coordinate systems, stabilized gradient operators, and different constitutive model inputs and outputs. In the process, the article describes a new formulation that casts objective integration of the Cauchy stress as a linear transformation of the small stress rate. Finally, the article presents key implementation details and examines the parallel efficiency of the solid mechanics solver implemented in MOOSE. The implementation retains a good weak scaling efficiency beyond 1,000 parallel processes. The article includes a discussion of the factors limiting the parallel efficiency of implicit, large deformation solid mechanics codes on current high-performance computers, with the main current limitation being the scalability of the algebraic multigrid methods used to solve the linearized equilibrium equations.

Applied computing → Computer-aided design↗

Electrochemical-Mechanical Coupling Strongly Affects the Performance of Nanopore, Thin-Film, and Solid-State Batteries

Here, the present study focuses on the electrochemical-mechanical (ECM) coupling effects of a thin-film, solid-state battery with only stiff, ceramic materials, in contrast to prior investigations that focus on individual active material particles or aggregations of particles. We model the impacts of ECM couplings including stress-transport and stress-equilibrium potential on the full-cell performance and potential mechanical failure modes of a thin-film battery conformally deposited in a nanopore scaffold, which is an experimentally achievable device. Model results indicate electrode volume changes due to lithium insertion or removal, along with mechanical boundary conditions, result in stress gradients that alter the lithium-ion flux, reduce lithium concentration gradients, and improve cell rate capability. However, the high stress levels in the cell can also lead to mechanics-related failure such as the separation of cell layers. For the parameter set in this work, stress-transport coupling has a much greater influence on rate capability than stress-potential coupling. Optimization of thin-film batteries to harness the benefits of ECM coupling effects requires leveraging geometric design and material selection. The current work underscores the need for further theoretical and experimental investigation into ECM coupling effects in thin-film batteries to enhance their understanding and design optimization.

25 ENERGY STORAGE↗

Design and Evaluation of a Ring Tension Test Grip for Remote Mechanical Testing of Irradiated Tubular Specimens

Here, the ring tension test (RTT) is a mechanical testing method for determining bulk mechanical behavior in the circumferential or hoop direction for tubular materials. The test is especially useful for testing materials with anisotropic mechanical properties, such as zirconium alloys, which are commonly used as nuclear fuel cladding. Anisotropy requires direction-specific testing to determine the hoop strength. Historically, several RTT methods and grips have been used, each method has its strengths and weaknesses, and, in all cases, the measured strength is subject to uncertainty due to variations of the testing geometry and experimental tolerances. Recent analysis has shown that grips with a hemicylindrical mandrel configuration are recommended as the most robust configuration. The two strictest aspects to be controlled are the ability to determine gage region orientation and closely matching the size of the mandrels to the test specimen. This last requirement is particularly challenging when the dimensions of the specimen vary because of environmental effects such as dimensional changes due to irradiation. This paper presents a new RTT grip designed to incorporate this mandrel shape, hold the gage at the desired orientation, be suitable for remote operation in a hot-cell environment, and be adaptable for different sizes or variations in the specimen size. The general description and the unique design features of the test specimen and grips are given in detail. The performance of the grips in mechanical testing, including in a remote hot-cell environment, is also provided.

42 ENGINEERING↗

Micro-architected material design for mechanical response

Rapid advances in additive manufacturing (AM) have enabled the creation of micro-architected materials—also known as mechanical metamaterials—with unprecedented control over fine-scale geometries and arrangements of multiple material constituents. These “materials” can achieve unique and extraordinary effective mechanical properties through their complex architectures rather than composition alone. A key challenge is to design for these bespoke effective mechanical responses within the constraints of available AM techniques (i.e., given a set of desired effective properties), identify a (often nonunique) micro-architecture and selection of material constituents that achieves them. Two main strategies have emerged. Gradient-based methods use sensitivity analysis to iteratively refine candidate designs, while data-driven methods learn micro-architecture-constituent relationships from existing examples to propose new designs. This article reviews these design approaches for micro-architected materials with tailored mechanical responses that can be fabricated by AM as well as their applications.

Spadaccini, Christopher M [Lawrence Livermore Nati↗

Putting a spin on metamaterials: Mechanical incompatibility as magnetic frustration

Mechanical metamaterials present a promising platform for seemingly impossible mechanics. They often require incompatibility of their elementary building blocks, yet a comprehensive understanding of its role remains elusive. Relying on an analogy to ferromagnetic and antiferromagnetic binary spin interactions, we present a general approach to identify and analyze topological mechanical defects for arbitrary building blocks. We underline differences between two- and three-dimensional metamaterials, and show how topological defects can steer stresses and strains in a controlled and non-trivial manner and can inspire the design of materials with hitherto unknown complex mechanical response.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Reactor Pressure Vessel Fracture Mechanics Development and Concrete Application Testing for Grizzly

The Grizzly code is being developed to address degradation issues in nuclear reactor structures and components. For light-water reactors, Grizzly currently has capabilities to simulate degradation processes and their effects on structural integrity in two key areas: reactor pressure vessels (RPVs) and reinforced concrete structures. This report documents improvements made to Grizzly’s ability to address both of these structural systems. For RPVs, the reduced-order models (ROMs) used in fracture mechanics calculations have been expanded to allow their application over a broader range of the parameter space than was permitted by the previous models. The ROMs currently used in Grizzly for the evaluation of flaws that are fully embedded within the RPV (as opposed to surface-breaking flaws) are based on a model that is known to be conservative, indicating higher stress intensity factors than would be obtained from direct simulations. A more accurate model that eliminates these excess conservatisms has been recently included in the American Society of Mechanical Engineers Boiler and Pressure Vessel Code but was not applicable for flaws near the RPV surface, which is where the most critical flaws are usually located. That model has recently been extended for increased applicability in this near-surface region. The ROMs for embedded flaws in the Grizzly code have been expanded to include these recent extensions, which permit their use in a much broader set of cases than previously possible. Direct 3D simulations have been used to check these ROMs and have shown good agreement in most cases, although there are still some cases that need further investigation. There are considerable benefits to using these these more accurate and less conservative ROMs for embedded flaws. On a benchmark probabilistic fracture mechanics problem tested here, the conditional probability of fracture initiation computed for a population of flaws in a single plate in an RPV decreased by over a factor of 3. To address aging in reinforced concrete structures, a capability to simulate multiple degradation mechanisms, including alkali-silica reaction and radiation-induced volumetric expansion has been developed in Grizzly over the past several years. This had previously been demonstrated on laboratory-scale specimens but not on full-scale nuclear concrete structures with reinforcement. To demonstrate the applicability of Grizzly to the analysis of large-scale structures of interest, a full 3D model of a representative reinforced concrete structure, including a complex arrangement of reinforcing bars, was developed and demonstrated in Grizzly.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Elucidating the mechanical and thermal response of nanotwinned Ni alloys

Transformative advances in nanoscale materials synthesis, characterization and modeling are enabling the synthesis of materials with unprecedent properties and greater understanding of the nanoscale mechanisms that underpin these properties. Nanotwinned Cu alloys have received considerable attention due to their impressive balance of strength and ductility, but they have limited microstructural stability. Recent instantiation of nanotwins in sputter deposited Ni-Mo-W, and several commercial Ni-based superalloys, point to the potential development of a new class of high temperature materials with a very beneficial suite of mechanical and physical properties. The experimental study described in this report was undertaken to elucidate the nanoscale origins of the thermal and mechanical behavior of nanotwinned Ni alloys. Micropillar compression experiments have shown nanotwinned Ni 85 Mo 15-x W x alloys to possess unusually high strengths above 3.5GPa and enhanced microstructural stability. The strength of these nanotwinned alloys is determined by the abrupt formation of shear bands. This study focused on identifying the nanoscale trigger, or triggers, for shear banding in nanotwinned materials using in situ experiments and atomic-scale postmortem analysis. Contrasting and comparing the mechanical response and postmortem nanostructures of “Mo-rich” and “W-rich” nanotwinned specimens elucidated the importance of the lateral motion of easy glide defects that results in erasure of twins and local coarsening of the nanotwinned microstructure. This twin coarsening was then associated with very localized plasticity, strain softening, and shear band formation. The difference between alloys was further studied by considering the role of various material factors: stacking fault energy, coherent twin boundary spacing and flatness, grain size, and the interactions of solute atoms with twin and grain boundaries. The effect of alloy composition and sputtering power and temperature were also investigated and used to control twin spacing and geometry. Combined with atomic-scale simulations, these experiments insights should allow us to identify strategies for achieving concomitant ultrahigh strength and ductility in nanotwinned Ni alloys. In parallel but synergistic studies, our work was buoyed by collaborative state-of-the-art nanoscale orientation and strain mapping at the DOE National Center for Electron Microscopy (NCEM). For example, novel 4D-STEM techniques were used to acquire nanoscale strain maps. The extremely fine twin spacing limited our measurements of atomic-scale thermal expansion within twins, but recent results from NCEM suggest that it will soon be possible to conduct such measurements and to unravel the origins of the novel thermal expansion characteristics of nanotwinned Ni alloys.

36 MATERIALS SCIENCE↗

Elucidating the Link Between Alkali Metal Ions and Reaction-Transport Mechanisms in Cathode Electrodes for Alkali-ion Batteries

Our long-term goal is to improve the reliability of electrode materials and their ability to transport and store various metal ions for electrochemical energy storage applications. The main objective of this work was to investigate the intrinsic relationship between the role of alkali metal ions and electrochemically driven mechanical stability and kinetic properties of battery materials. The overall question was “What is the role of alkali metal ions on the electrochemical and mechanical behavior of cathode electrodes? Our guiding hypothesis was that intercalation of larger alkali metal ions (Na and K) inevitably alters the coupled transport-reaction processes during battery operation in organic electrolytes, leading to more intensive chemo-mechanical instabilities in cathode electrodes, resulting in rapid capacity fade. To validate the hypothesis, we experimentally characterized the reaction-transport processes and governing forces driving the instability of electrode materials in different alkali metal-ion environments. The project had three main tasks. The first one was to investigate intercalation-induced strains and associated stress generation, and their impact on structural deformations in composite cathode electrodes. The second task focused on identifying potential-dependent dynamic changes in the electrode-electrolyte interface in alkali metal ion batteries. The last task was focused on determining how larger alkali metal ions with slower diffusivity affect the transport-mechanics coupling at faster scan rates, compared to smaller ions with faster diffusivity in electrodes. We shortly provided the outcome of each task in the accomplishment section. This project produced 10 peer-reviewed publications (9 research papers and one review manuscript) and supported two Ph.D. students, who graduated from Oklahoma State University.

25 ENERGY STORAGE↗

Mechanical Solutions Scan Report

Power lines, poles, and towers are the backbone of the United States (U.S.) electric-power grid. These transmission and distribution networks route electricity from generator to loads. The characteristics of these routes are rapidly changing -- trending towards decentralized renewable generation, electric heating, vehicle charging, and large data-center loads. Coupled with aging infrastructure and the increased frequency of extreme weather events, there is concern about the future reliability and transmission capacity of conductors and adjacent components. This scan report seeks to provide an overview of mechanical solutions to challenges caused by extreme weather events associated with components of transmission and distribution infrastructure, including conductor heat sag, ice accumulation, wind, and wildfire. Many options could increase transmission capacity or reliability, and these are at various stages of technological readiness. Some have only been lab tested, while some have been widely deployed in the U.S. or overseas for decades. The solution categories and providers featured in this report are intended to be comprehensive at the time of publication and to serve as a reference for decision-makers concerned about transmission and distribution reliability. There are two other categories of large, complex solutions, which are not covered in this report: replacing existing conductors with advanced conductors and implementing digital grid enhancing technologies. A separate scan report titled “Advanced Conductor Scan Report,” which discusses advanced carbon-core conductors, was published by the Idaho National Laboratory (INL) in 2023. Information on digital technologies, such as dynamic line ratings, power-flow controllers, and other power electronics and communications-based devices, can be found on the Grid- Enhancing Technologies landing page. Mechanical grid-enhancing technologies, or solutions covered in this report, often do not require full equipment replacement and do not rely on digital components. Mechanical technologies are overlooked because they may be older, simpler, or seemingly “more obvious” than digital or carbon-core technologies. However, it is wise to consider mechanical solutions in a thorough evaluation of grid enhancing technology solutions.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

Mechanical Characterization of the NIF Ignition Target TMPSA Bonding Flexure

The Thermo-Mechanical Package Sub-Assembly (TMPSA) provides a critical mechanical, thermal, and electrical interface between a silicon arm and a TMP aluminum can in a NIF ignition target. During assembly, sixteen silicon pads are bonded to the aluminum using a fixture that positions the components and applies a repeatable prescribed displacement through a compliant flexure. The flexure converts fixture interference into displacement and reaction force. Because bondline thickness variation must be maintained within +/-4 µm, consistent flexure behavior is important to the assembly process. With a recent string of TMPSAs exhibiting low bond strength, the flexures were inspected. Despite being manufactured to the same specifications, flexures were found to exhibit variation in measured stiffness. Additionally, the measured stiffness values did not always follow the presumed beam mechanics model. This work addresses two questions: whether the bonding fixture is working as intended, and whether the previously made stiffness measurements are accurate representations of the use case. The flexures are analyzed using Euler-Bernoulli beam theory, measured beam dimensions, finite element analysis, and tolerance stack-up calculations. The analysis shows that the fixed-guided beam mechanics model appropriately represents the flexure during TMPSA bonding, but the chisel-tip stiffness measurement method introduces a deformation to the inner ring of the flexure that is not represented during use. The measured stiffness values should therefore be interpreted as test-condition stiffness values rather than direct measurements of operational flexure stiffness. The discrepancy is therefore attributed primarily to the measurement boundary condition rather than to failure of the fixed-guided beam model. Recommendations are provided for GD&T, dimensional inspection, and a representative stiffness testing method to better control bondline variation.

42 ENGINEERING↗

First-Principles Calculations of the Structural, Electronic, Optical, and Mechanical Properties of 21 Pyrophosphate Crystals

Pyrophosphate crystals have a wide array of applications in industrial and biomedical fields. However, fundamental understanding of their electronic structure, optical, and mechanical properties is still scattered and incomplete. In the present research, we report a comprehensive theoretical investigation of 21 pyrophosphates A 2 M (H 2 P 2 O 7 ) 2 •2H 2 O with either triclinic or orthorhombic crystal structure. The molecule H 2 P 2 O 7 is the dominant molecular unit, whereas A = (K, Rb, NH 4 , Tl), M = (Zn, Cu, Mg, Ni, Co, Mn), and H 2 O stand for the cation elements, transition metals, and the water molecules, respectively. The electronic structure, interatomic bonding, partial charge distribution, optical properties, and mechanical properties are investigated by first-principles calculations based on density functional theory (DFT). Most of these 21 crystals are theoretically investigated for the first time. The calculated results show a complex interplay between A, M, H 2 P 2 O 7 , and H 2 O, resulting in either metallic, half-metallic, or semi-conducting characteristics. The novel concept of total bond order density (TBOD) is used as a single quantum mechanical metric to characterize the internal cohesion of these crystals to correlate with the calculated properties, especially the mechanical properties. This work provides a large database for pyrophosphate crystals and a road map for potential applications of a wider variety of phosphates.

36 MATERIALS SCIENCE↗