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Results for “Dynamics (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.

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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Performance evaluation of surface riding wave energy converter with linear electric generator

In this work, we devised a new WEC (wave energy converter) called SR-WEC (Surface Riding WEC). The SR-WEC consists of two bodies: the outer cylinder with an armature assembly (body #1) and a magnet assembly (body #2) sliding inside the armature. For the SR-WEC, the relative sliding displacement and velocity are caused by gravity acceleration and the outer cylinder's motions, and they lead to electrical power generation. To evaluate its performance, a numerical simulation tool was developed, which solves the fully-coupled floater-mooring-generator dynamics. During the developing stage, the appropriate hydrodynamics model, sliding mechanics model, mooring dynamics model, and LEG (linear electric generator) electro-magnetic model were independently developed and then fully coupled in time domain to account for the cross-coupling interactions among them. Then, the developed simulation tool was verified component by component against various laboratory tests. Subsequently, systematic parametric studies were conducted with several important design parameters under various wave conditions to enhance power generation. After that, the average output power was evaluated in enlarged operational wave conditions. The present SR-WEC is particularly designed to be efficient at low sea states, which is good since they cover the majority of typical annual sea states.

42 ENGINEERING↗
DOE OSTI2026

PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation

PARP1 detection of DNA strand breaks allosterically leads to PARP1 synthesis of poly(ADP-ribose) modifications that signal DNA damage. HPF1 engages activated PARP1 to control modification site selection. Understanding of the mechanism of DNA break detection and catalytic activation is incomplete, due largely to limited structural information for full-length PARP1. Here, single-particle cryo-EM provides views of the full complement of PARP1 domains engaging a DNA single-strand break in the presence of HPF1 and a fragment of binding partner Timeless. Cryo-EM, single-molecule DNA dynamics, and small-angle X-ray scattering analysis indicate that PARP1 remains dynamic even when the multi-domain structure is organized on a DNA break, with the minimal catalytic region displaying high mobility relative to domains engaging damage. We propose that the organization of PARP1 domains on a DNA break releases a tethered, constitutively active catalytic region to modify molecules in a radius surrounding the DNA break site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Advanced Methodology and Preliminary Measurements of Molecular and Mechanical Properties of Heart Valves under Dynamic Strain

Mammalian heart valves are soft tissue assemblies with multi-scale material properties. This is because they are constructs comprising both muscle and non-contractile extracellular matrix proteins (such as collagens and proteoglycans) and transition regions where one form of tissue structure becomes another, significantly different form. The leaflets of the mitral and tricuspid valves are connected to chordae tendinae which, in turn, bind through papillary muscles to the cardiac wall of the ventricle. The transition regions between these tissue subsets are complex and diffuse. Their material composition and mechanical properties have not been previously described with both micro and nanoscopic data recorded simultaneously, as reported here. Annotating the mechanical characteristics of these tissue transitions will be of great value in developing novel implants, improving the state of the surgical simulators and advancing robot-assisted surgery. We present here developments in multi-scale methodology that produce data that can relate mechanical properties to molecular structure using scanning X-ray diffraction. We correlate these data to corresponding tissue level (macro and microscopic) stress and strain, with particular emphasis on the transition regions and present analyses to indicate points of possible failure in these tissues.

valve failure↗
DOE OSTI2025

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↗
DOE OSTI2021

Dynamic Control of Photocatalytic Proton Reduction through the Mechanical Actuation of a Hydrogel Host Matrix

This paper describes a photocatalytic hydrogen evolution system that is dynamically and reversibly responsive to the pH of the surrounding solution through actuation of a micro-hydrogel (microgel) matrix that hosts the photocatalysts (CdSe/CdS nanorods). Here, the reversible actuation occurs within 0.7 s (swelling) and 1.7 s (contraction). A ΔpH of 0.01 relative to the pK a of the tertiary amine on the microgel polymer (7.27) results in a reversible change in the average diameter of the microgel hosts by a factor of 2.5 and a change in the photocatalytic turnover frequency (TOF) by a factor of five. Kinetic isotope effect and photoluminescence quenching experiments reveal that the scavenging of the photoexcited hole by sulfite ions is the rate-limiting step and leads to the observed response of the TOF to pH through actuation of the microgel. Molecular dynamics simulations quantify a greater local concentration of sulfite hole scavengers for pH < pK a .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Synchrotron based transient x-ray absorption spectroscopy for emerging solid-state energy materials

The rational design of cutting-edge materials for an efficient solar energy conversion process is a challenging task, which demands a fundamental understanding of the mechanisms operative during the photoinduced physical and chemical reactions. In response to these issues, progress in the field has steered attention toward the use of time-resolved spectroscopic techniques to resolve the multiple intermediate species involved in these photoinduced reactions. Thanks to the advent of pump–probe technique, which leads to the development of various time-resolved spectroscopic methods, significant progress has been made in understanding the photophysical and photochemical properties (e.g., excited state dynamics, charge transfer mechanism, charge separation dynamics, etc.) of energy materials. Synchrotron-based x-ray transient absorption (XTA) spectroscopy is one of the most important time-resolved techniques to unravel the direct correlation of the material structure with their photophysical properties owing to its unique capability in directly observing electronic and structural evolution simultaneously. As a result, the aim of this work is to provide a systematic overview of the recent progress in using XTA for capturing the structural dynamics associated with excited state and charge separation dynamics in emerging solid-state energy materials.

14 SOLAR ENERGY↗
DOE OSTI2021

Molecular dynamics and experimental study on the adhesion mechanism of polyvinyl alcohol (PVA) fiber in alkali-activated slag/fly ash

This paper aims to study the adhesion mechanism of polyvinyl alcohol (PVA) fiber within alkali-activated slag/fly ash (AASF) matrix using molecular dynamics (MD) simulation in combination with systematic experimental characterization. The adhesion of PVA to C-(N-)A-S-H gel with different Ca/(Si+Al) and Al/Si ratios was modeled using MD simulation, with the related adsorption enthalpy calculated and the adhesion mechanism explored. The experimentally attained chemical bonding energy of PVA fiber in AASF coincides well with the simulation results. In both cases, the adhesion enhances primarily with increasing Ca/(Si+Al) ratio of C-(N-)A-S-H gel. Additionally, MD simulation indicates preferential element distributions of Ca around PVA molecule, which was confirmed experimentally by the detection of the Ca-rich C-(N-)A-S-H gel in the interfacial transition zone (ITZ). }This study provides further insights into the adhesion mechanism of PVA fiber to C-(N-)A-S-H gel formed in AASF, which is particularly valuable for the future development of PVA-based high-performance alkali-activated composites.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Effect of Topology on Transient Dynamic and Shock Response of Polymeric Lattice Structures

Architected cellular materials, such as lattice structures, offer potential for tunable mechanical properties for dynamic applications of energy absorption and impact mitigation. In this work, the static and dynamic behavior of polymeric lattice structures was investigated through experiments on octet-truss, Kelvin, and cubic topologies with relative densities around 8%. Here, dynamic testing was conducted via direct impact experiments (25–70 m/s) with high-speed imaging coupled with digital image correlation and a polycarbonate Hopkinson pressure bar. Mechanical properties such as elastic wave speed, deformation modes, failure properties, particle velocities, and stress histories were extracted from experimental results. At low impact velocities, a transient dynamic response was observed which was composed of a compaction front initiating at the impact surface and additional deformation bands whose characteristics matched low strain-rate behavior. For higher impact velocities, shock analysis was carried out using compaction wave velocity and Eulerian Rankine–Hugoniot jump conditions with parameters determined from full-field measurements.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Predicting the Mechanical Response of Polyhydroxyalkanoate Biopolymers Using Molecular Dynamics Simulations

Polyhydroxyalkanoates (PHAs) have emerged as a promising class of biosynthesizable, biocompatible, and biodegradable polymers to replace petroleum-based plastics for addressing the global plastic pollution problem. Although PHAs offer a wide range of chemical diversity, the structure–property relationships in this class of polymers remain poorly established. In particular, the available experimental data on the mechanical properties is scarce. In this contribution, we have used molecular dynamics simulations employing a recently developed forcefield to predict chemical trends in mechanical properties of PHAs. Specifically, we make predictions for Young’s modulus, and yield stress for a wide range of PHAs that exhibit varying lengths of backbone and side chains as well as different side chain functional groups. Deformation simulations were performed at six different strain rates and six different temperatures to elucidate their influence on the mechanical properties. Our results indicate that Young’s modulus and yield stress decrease systematically with increase in the number of carbon atoms in the side chain as well as in the polymer backbone. In addition, we find that the mechanical properties were strongly correlated with the chemical nature of the functional group. The functional groups that enhance the interchain interactions lead to an enhancement in both the Young’s modulus and yield stress. Finally, we applied the developed methodology to study composition-dependence of the mechanical properties for a selected set of binary and ternary copolymers. Overall, our work not only provides insights into rational design rules for tailoring mechanical properties in PHAs, but also opens up avenues for future high throughput atomistic simulation studies geared towards identifying functional PHA polymer candidates for targeted applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mapping the structural–mechanical landscape of amorphous carbon with ReaxFF molecular dynamics

We use ReaxFF molecular dynamics (MD) to investigate the relationship between structural and mechanical properties in bulk and nanostructured amorphous carbon (a-C). The liquid-quench MD method is used to generate isotropic bulk samples with mass densities ranging from 0.96 to 3.29 g/cm3. Structural analysis identifies two types of structures with distinct short- and medium-range order: lower-density sp2-dominated a-C, which is characterized by a bimodal ring-size distribution, and higher-density sp3-dominated tetrahedral amorphous carbon (ta-C), exhibiting a unimodal ring-size distribution. Stress–strain MD simulations and analysis reveal how an atomistic structure impacts elastic properties and post-yield atomic rearrangements. All stretched structures demonstrate elastic isotropy and plasticity driven by a ring-size expansion mechanism reflected in changes in ring statistics. The plastic region is substantially larger in ta-C than in a-C due to the post-yield shift from sp3 to sp2 C dominant bonding. In both a-C and ta-C, ultimate failure occurs when a reactive crack, traversed by long sp chains, forms and propagates predominantly perpendicular to the direction of the applied strain. Oxygen infiltration into the fractured region significantly reduces stress resistance, primarily through the early rupture of long sp chains. MD simulations and analysis are extended to a-C slabs, a-C nanotubes, and partially a-C nanotubes. The latter nanostructure highlights the differences between the elastically isotropic a-C walls, which develop circumferential cracking, and the crystalline walls, which tear along crystallographic directions. These results provide a strong foundation for further computational characterization of a-C materials.

Dernov, A. (ORCID:0009000004220973)↗
DOE OSTI2021

Quantifying the Long‐Range Coupling of Electronic Properties in Proteins with ab initio Molecular Dynamics**

Abstract The delicate interplay of covalent and non‐covalent interactions in proteins is inherently quantum mechanical and highly dynamic in nature. To directly interrogate the evolving nature of the electronic structure of proteins, we carry out 100‐ps‐scale ab initio molecular dynamics simulations of three representative small proteins with range‐separated hybrid density functional theory. We quantify the nature and length‐scale of the coupling of residue‐specific charge probability distributions in these proteins. While some nonpolar residues exhibit expectedly narrow charge distributions, most polar and charged residues exhibit broad, multimodal distributions. Even for nonpolar residues, we observe sequence‐specific deviations corresponding to charge accumulation or depletion that would be challenging to capture in a fixed charge force field. We quantify the effect of residue‐residue interactions on charge distributions first with linear cross‐correlations. We then show how additional insight can be gained from evaluating the mutual information of charge distributions. We show that a significant number of residues couple most strongly with residues that are distant in both sequence and space over a range of secondary structures including α‐helical, β‐sheet, disulfide bridging, and lasso motifs. The mutual information analysis is necessary to capture coupling between some polar and charged residues that would be otherwise missed.

Yang, Zhongyue↗
DOE OSTI2024

The Ecosystem as Super-Organ/ism, Revisited: Scaling Hydraulics to Forests under Climate Change

Synopsis Classic debates in community ecology focused on the complexities of considering an ecosystem as a super-organ or organism. New consideration of such perspectives could clarify mechanisms underlying the dynamics of forest carbon dioxide (CO2) uptake and water vapor loss, important for predicting and managing the future of Earth’s ecosystems and climate system. Here, we provide a rubric for considering ecosystem traits as aggregated, systemic, or emergent, i.e., representing the ecosystem as an aggregate of its individuals or as a metaphorical or literal super-organ or organism. We review recent approaches to scaling-up plant water relations (hydraulics) concepts developed for organs and organisms to enable and interpret measurements at ecosystem-level. We focus on three community-scale versions of water relations traits that have potential to provide mechanistic insight into climate change responses of forest CO2 and H2O gas exchange and productivity: leaf water potential (Ψcanopy), pressure volume curves (eco-PV), and hydraulic conductance (Keco). These analyses can reveal additional ecosystem-scale parameters analogous to those typically quantified for leaves or plants (e.g., wilting point and hydraulic vulnerability) that may act as thresholds in forest responses to drought, including growth cessation, mortality, and flammability. We unite these concepts in a novel framework to predict Ψcanopy and its approaching of critical thresholds during drought, using measurements of Keco and eco-PV curves. We thus delineate how the extension of water relations concepts from organ- and organism-scales can reveal the hydraulic constraints on the interaction of vegetation and climate and provide new mechanistic understanding and prediction of forest water use and productivity.

Zoology↗
DOE OSTI2021

The effect of entrance flow development on vortex formation and wall shear stress in a curved artery model

In this work, we numerically investigate the effect of entrance condition on the spatial and temporal evolution of multiple three-dimensional vortex pairs and the wall shear stress distribution in a curved artery model. We perform this study using a Newtonian blood-analog fluid subjected to a pulsatile flow with two inflow conditions. The first flow condition is fully developed while the second condition is undeveloped (i.e., uniform). We discuss the connection along the axial direction between regions of organized vorticity observed at various cross sections of the model and compare results between the different entrance conditions. We model a human artery with a simple, rigid 180° curved pipe with a circular cross section and constant curvature, neglecting the effects of taper, torsion, and elasticity. Numerical results are computed from a discontinuous high-order spectral element flow solver. The flow rate used in this study is physiological. We observe differences in secondary flow patterns, especially during the deceleration phase of the physiological waveform where multiple vortical structures of both Dean-type and Lyne-type coexist. The results indicate that decreased axial velocities under an undeveloped condition produce smaller secondary flows that ultimately inhibit growth of any interior flow vortices. We highlight the effect of the entrance condition on the formation of these structures and subsequent appearance of abnormal inner wall shear stresses, which suggest there may be a lower prevalence of cardiovascular disease in curved arteries where the flow is rather undeveloped—a potentially physiologically significant result to help understand the influence of blood flow development on disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

C-C Coupling Mechanism on Cu(100) A Molecular Dynamics Study at 298K

The electrochemical reduction of carbon dioxide (CO2) into valuable fuels such as C1 (syngas, methane) and C2 (ethylene, ethanol) products is a key strategy for achieving a carbon-neutral economy. Computational studies of C-C coupling, a critical step in CO2 reduction, are essential for designing more efficient catalysts. However, simulating these processes under realistic electrochemical conditions, including temperature and solvent effects, is computationally demanding. In this work, we develop a machine learning-based atomistic potential to study CO2 reduction on Cu(100) surfaces, accounting for temperature and explicit water solvent effects. We compute thermodynamic free energies of the possible C-C coupling pathways, CO*+CO*→OCCO*, CO*+CHO*→OCCHO*, CO*+COH*→OCCOH*, CHO*+COH*→OHCCOH*, COH*-COH*→HOCCOH*, and CHO*-CHO*→OHCCHO*. Our results quantify the thermodynamic tendencies of these reactions and reveal that, in addition to the well-established CO* + CO* → OCCO* pathway, CHO* is a critical intermediate in the formation of C2 products on Cu(100). Furthermore, we demonstrate that the machine learning approach offers a cost-efficient framework for studying CO2 reduction on diverse catalysts under realistic electrochemical conditions.

machine learning↗
DOE OSTI2024

High pressure suppression of plasticity due to an overabundance of shear embryo formation

Abstract High pressure shear band formation is a critical phenomenon in energetic materials due to its influence on both mechanical strength and mechanochemical activation. While shear banding is known to occur in a variety of these materials, the governing dynamics of the mechanisms are not well defined for molecular crystals. We conduct molecular dynamics simulations of shock wave induced shear band formation in the energetic material 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) to assess shear band nucleation processes. We find, that at high pressures, the initial formation sites for shear bands, “embryos”, form in excess and rapidly lower deviatoric stresses prior to shear band formation and growth. This results in the suppression of plastic deformation. A local cluster analysis is used to quantify and contrast this mechanism with a more typical shear banding seen at lower pressures. These results demonstrate a mechanism that is reversible in nature and that supersedes shear band formation at increased pressures. We anticipate that these results will have a broad impact on the modeling and development of high-strain rate application materials such as those for high explosives and hypersonic systems.

36 MATERIALS SCIENCE↗