Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “atomistic transitions”

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.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Single Residue K12 Governs the Exceptional Voltage Sensitivity of Mitochondrial Voltage-Dependent Anion Channel Gating

The voltage-dependent anion channel (VDAC) is a β-barrel channel of the mitochondrial outer membrane (MOM) that passively transports ions, metabolites, polypeptides, and single-stranded DNA. VDAC responds to a transmembrane potential by “gating,” i.e. transitioning to one of a variety of low-conducting states of unknown structure. The gated state results in nearly complete suppression of multivalent mitochondrial metabolite (such as ATP and ADP) transport, while enhancing calcium transport. Voltage gating is a universal property of β-barrel channels, but VDAC gating is anomalously sensitive to transmembrane potential. Here, we show that a single residue in the pore interior, K12, is responsible for most of VDAC’s voltage sensitivity. Using the analysis of over 40 μs of atomistic molecular dynamics (MD) simulations, we explore correlations between motions of charged residues inside the VDAC pore and geometric deformations of the β-barrel. Residue K12 is bistable; its motions between two widely separated positions along the pore axis enhance the fluctuations of the β-barrel and augment the likelihood of gating. Single channel electrophysiology of various K12 mutants reveals a dramatic reduction of the voltage-induced gating transitions. The crystal structure of the K12E mutant at a resolution of 2.6 Å indicates a similar architecture of the K12E mutant to the wild type; however, 60 μs of atomistic MD simulations using the K12E mutant show restricted motion of residue 12, due to enhanced connectivity with neighboring residues, and diminished amplitude of barrel motions. We conclude that β-barrel fluctuations, governed particularly by residue K12, drive VDAC gating transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Computational Methods in Heterogeneous Catalysis

The unprecedented ability of computations to probe atomic-level details of catalytic systems holds immense promise for the fundamentals-based bottom-up design of novel heterogeneous catalysts, which are at the heart of the chemical and energy sectors of industry. Here, we critically analyze recent advances in computational heterogeneous catalysis. First, we will survey the progress in electronic structure methods and atomistic catalyst models employed, which have enabled the catalysis community to build increasingly intricate, realistic, and accurate models of the active sites of supported transition-metal catalysts. We then review developments in microkinetic modeling, specifically mean-field microkinetic models and kinetic Monte Carlo simulations, which bridge the gap between nanoscale computational insights and macroscale experimental kinetics data with increasing fidelity. Here, we finally review the advancements in theoretical methods for accelerating catalyst design and discovery. Throughout the review, we provide ample examples of applications, discuss remaining challenges, and provide our outlook for the near future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Effect of relative humidity on the interlayer spacing of phosphate intercalated Mg, Al layered double hydroxide (hydrotalcite‐like) crystals

Abstract The availability of water and the type of interlayer anions present affect the arrangement and interlayer spacing of layered double hydroxide (LDH). A systematic study of the effect of relative humidity (RH) on the basal spacing of phosphate intercalated, magnesium aluminum LDHs (MgAl–PO 4 LDH) was conducted, confirming that MgAl‐PO 4 LDH exhibit distinct interlayer spacing corresponding to separate low‐ and high‐hydration states produced when exposed to low and high humidity conditions. The transition from the low‐ to high‐hydration form begins when RH exceeds 33% and is accompanied by the transition from one to two interlayers of water. An improved understanding of the effect of RH on MgAl–PO 4 LDHs will enable more accurate atomistic modeling and experimental characterization of MgAl–PO 4 LDHs and may lead to improvements in the tunability of MgAl‐PO 4 LDHs for commercial applications such as slow‐release fertilizer.

Reed, Titus↗
DOE OSTI2025

CHEMREASONER: Heuristic Search over a Large Language Model’s Knowledge Space using Quantum-Chemical Feedback

The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided computational screening framework unifying linguistic reasoning with quantum-chemistry based feedback from 3D atomistic representations. Our approach formulates catalyst discovery as an uncertain environment where an agent actively searches for highly effective catalysts via the iterative combination of large language model (LLM)-derived hypotheses and atomistic graph neural network (GNN)-derived feedback. Identified catalysts in intermediate search steps undergo structural evaluation based on spatial orientation, reaction pathways, and stability. Scoring functions based on adsorption energies and barriers steer the exploration in the LLM's knowledge space toward energetically favorable, high-efficiency catalysts. We introduce planning methods that automatically guide the exploration without human input, providing competitive performance against expert-enumerated chemical descriptor-based implementations. By integrating language-guided reasoning with computational chemistry feedback, our work pioneers AI-accelerated, trustworthy catalyst discovery.

artificial intelligence↗
DOE OSTI2021

Elastic Properties and Deformation Mechanisms in the van der Waals Single-Crystalline Indium Selenide

The bulk van der Waals (vdW) single-crystalline indium selenide (β-InSe) displays exceptional plasticity in a layered crystalline form at both micro- and macroscale. However, the nanoscale origin of plasticity remains unclear. Herein, an atomic-level study on the deformation mechanisms of InSe by using first-principles calculations is reported. Remarkable anisotropic elasticity is observed in the vdW InSe layered crystal, and the stiffness is dramatically softened because of the vdW gap in the layered structure. The simulations capture the distinct fracture modes in the uniaxial tensile deformation, depending on the loading directions—brittle fracture in the [100] and [110] directions while ductile failure in the [001] direction. The InSe layered crystal structure exhibits superplastic deformability under uniaxial compression. Different transition pathways, including interlayer tangling, amorphization, and cross-linking, are tracked along respective deformation directions. The unprecedented plasticity of InSe layered crystals can be attributed to the phase transition coupled with interlayer gliding and cross-layer dislocation slipping. Here, this study deepens our understanding of the deformation mechanisms of layered materials at the atomistic level and provides insights into tailoring material properties for low-dimensional material design based on its deformation mechanisms.

2D materials↗
DOE OSTI2020

Direct Visualization of Electric-Field-Induced Structural Dynamics in Monolayer Transition Metal Dichalcogenides

Layered transition metal dichalcogenides offer many attractive features for next-generation low-dimensional device geometries. Due to the practical and fabrication challenges related to in situ methods, the atomistic dynamics that give rise to realizable macroscopic device properties are often unclear. Here in this study, in situ transmission electron microscopy techniques are utilized in order to understand the structural dynamics at play, especially at interfaces and defects, in the prototypical film of monolayer MoS 2 under electrical bias. Through our sample fabrication process, we clearly identify the presence of mass transport in the presence of a lateral electric field. In particular, we observe that the voids present at grain boundaries combine to induce structural deformation. The electric field mediates a net vacancy flux from the grain boundary interior to the exposed surface edge sites that leaves molybdenum clusters in its wake. Following the initial biasing cycles, however, the mass flow is largely diminished and the resultant structure remains stable over repeated biasing. We believe insights from this work can help explain observations of nonuniform heating and preferential oxidation at grain boundary sites in these materials.

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

Kinetic Growth of Multicomponent Microcompartment Shells

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Altogether, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

defects↗
DOE OSTI2022

Grain incompatibility determines the local structure of amorphous grain boundary complexions

Amorphous grain boundary complexions lack long-range crystalline order but are not featureless, as distinct gradients in structural short-range order have been reported through their thickness. In this work, we test the hypothesis that the distribution of short-range order is determined by the confining crystals using atomistic simulations of both Cu-Zr bicrystals and a random polycrystal. Voronoi polyhedra with structures similar to that of perfect face-centered cubic serve as signatures of high structural order and are only found at the amorphous-crystalline transition regions. The density of the ordered structural motifs within a specific amorphous-crystalline transition region is found to not be directly determined by the orientation and symmetry of the grain which touches it, but rather by the incompatibility between the two confining grains. Further, ordered polyhedra density is found to be inversely related to grain incompatibility, meaning that large incompatibilities between the confining crystals lead to less order in the amorphous-crystalline transition region. The finding that the entire grain-film-grain system must be considered to understand local structure unequivocally demonstrates that amorphous complexions are not simply a collection of independent phases which happen to nucleate at a grain boundary. Rather, an amorphous grain boundary complexion is a single entity that finds a local equilibrium configuration.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Insight into the nanostructure of “water in salt” solutions: A SAXS/WAXS study on imide-based lithium salts aqueous solutions

"Water-in-salt " electrolyte (WISE) series have been studied for lithium-ion batteries and supercapacitor applications, but so far, most of the focus has been on the LiTFSI salt-based systems. Herein, we used small-angle X-ray scattering/wide-angle X-ray scattering (SAXS/WAXS) and molecular dynamics (MD) simulation to investigate the solvation structure of a series of lithium salts with four different symmetric anions: (bis(fluoro sulfonyl)imide (FSI), bis(trifluoromethane sulfonyl)imide (TFSI), bis(pentafluoroethane sulfonyl) imide (BETI) and bis(nonafluorobutane sulfonyl)imide (BNTI)), which have similar parent structures but different lengths of the fluorocarbon chains. Two competing structures were found in the four lithium salts aqueous solutions: anion solvated structure and anion network. The anion network plays a crucial role in obtaining a stable and enlarged electrochemical window. The d spacing of the anion solvated structure follows a linear correlation with the number of carbons in the fluorocarbon chains and an exponential correlation with the concentrations. Further, we also observed that the transition from one structure to another is predominantly controlled by the salt volume fraction for all imide-based aqueous solutions. This work provides a systematic study of the atomistic scale structures of a series of imide-based lithium salt aqueous solutions that could extend the knowledge of WIS electrolytes.

25 ENERGY STORAGE↗
DOE OSTI2025

Structure-dependent clustering-to-declustering solute segregation transitions near disconnections

Grain-boundary disconnections, characterized by a step and a dislocation, are pervasive interfacial line defects that play a critical role in governing the properties and performance of nanocrystalline alloys. Although segregation of alloying elements is frequently observed at GB disconnections, the underlying mechanisms remain poorly understood, particularly at elevated temperatures and non-dilute conditions. In this study, we employ atomistic simulations to study the segregation behavior of Ag at various faulted disconnections in Cu as a model material system. Our results demonstrate a pronounced size and compactness effect on the segregation behavior: more compact faulted disconnection structures promote the formation of Ag segregation clusters due to a highly localized tensile field, whereas more spread faulted disconnection structures (i.e., with wider partial dislocation spacing) exhibit much weaker clustering tendencies. Furthermore, with increasing temperature, Ag clustering in small disconnections initially intensifies and then disappears, indicating a thermally driven transition from clustering to declustering segregation behavior.

Disconnections↗
DOE OSTI2025

Atomistically resolved hot exciton relaxation dynamics in CdSe quantum dots: Experiment and theory

Semiconductor quantum dots (QDs) are well known to give rise to a quantum confined structure of excitons. Because of this quantum confinement, new physics of hot exciton relaxation dynamics arises. Decades of work using transient absorption (TA) spectroscopy have yielded initial simple observations, such as estimates of the cooling rate from single pump photon energy experiments. More detailed TA experiments employed variable pump photon energies to measure excitonic state-resolved transition rates. These TA measurements, usually the simplest form, have been employed to characterize QDs and their relaxation dynamics to this day. Yet, these TA measurements are fundamentally lacking in their ability to measure energy-resolved hot exciton cooling, which requires observation of the full cooling history through the real excitonic manifold. Here, we employ coherent multi-dimensional spectroscopy (CMDS) to perform an atomistically directed study of hot exciton cooling in CdSe QDs, revealing energy resolved relaxation dynamics. CMDS experiments are compared with simulations and prior TA measurements and simpler theories. Our findings reveal a hot exciton relaxation dynamics landscape. This relaxation dynamics landscape is a linear or sub-linear function of excess energy for different structures of QDs, with a strong size dependence. Our model simulations parameterized by the empirical pseudopotential model reproduces the experimental functional form and the dependence upon QD diameter and shell.

Atomistic simulations↗
DOE OSTI2024

Anomalous temperature dependence of elastic limit in metallic glasses

Abstract Understanding the atomistic mechanisms of inelastic deformation in metallic glasses (MGs) remains challenging due to their amorphous structure, where local carriers of plasticity cannot be easily defined. Using molecular dynamics (MD) simulations, we analyzed the onset of inelastic deformation in CuZr MGs, specifically the temperature dependence of the elastic limit, in terms of localized shear transformation (ST) events. We find that although the ST events initiate at lower strain with increasing temperature, the elastic limit increases with temperature in certain temperature ranges. We explain this anomalous behavior through the framework of an energy-strain landscape (ESL) constructed from high-throughput strain-dependent energy barrier calculations for the ST events identified in the MD simulations. The ESL reveals that the anomalous behavior is caused by the transition of ST events from irreversible to reversible with increasing temperature. An analytical formulation is developed to predict this transition and the temperature dependence of the elastic limit.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Designing polar textures with ultrafast neuromorphic features from atomistic simulations

This review summarizes recent works, all using a specific atomistic approach, that predict and explain the occurrence of key features for neuromorphic computing in three archetypical dipolar materials, when they are subject to THz excitations. The main ideas behind such atomistic approach are provided, and illustration of model relaxor ferroelectrics, antiferroelectrics, and normal ferroelectrics are given, highlighting the important potential of polar materials as candidates for neuromorphic computing. Some peculiar emphases are made in this Review, such as the connection between neuromorphic features and percolation theory, local minima in energy path, topological transitions and/or anharmonic oscillator model, depending on the material under investigation. By considering three different and main polar material families, this work provides a complete and innovative toolbox for designing polar-based neuromorphic systems.

THz pulses↗
DOE OSTI2023

Diffusion, atomic transport, and ordering in Al-Zr alloys: FCC and liquid phases

Additive manufacturing of materials with controlled microstructure demands knowledge of atomic scale properties near the solid-liquid transition state. Many of these properties are not affordable by experimental techniques and computer modeling is the possible solution to the problem. In this paper, we present the results of an extended atomistic study of intrinsic atomic transport due to vacancy diffusion in FCC and L12 solid phases and diffusion in the liquid phase of Al-Zr alloys. A deceleration of the overall self-diffusion was observed when Zr was added to Al. The effect was stronger in the solid and weaker in the liquid. Additionally, the effect was strongly temperature dependent in the solid phases, but not in the liquid. Atomic transport was chemically biased: transport of Zr atoms was significantly slower than that of Al atoms, and this bias effect was stronger in the solid phases. The overall diffusion and chemical ordering processes in the liquid state were five to six orders in magnitude faster than in the solid. Chemical short-range order parameters in the liquid saturated at values close to those in the ordered L12 structure of Al3Zr. Chemical and structural ordering in the solid phases was negligible over the modeled microsecond time scale. Here, the results are discussed in view of optimizing additive manufacturing parameters for the controlled formation of metastable L1 2 precipitates.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Interfacial tuning of chiral magnetic interactions for large topological Hall effects in LaMnO 3 /SrIrO 3 heterostructures

Chiral interactions in magnetic systems can give rise to rich physics manifested, for example, as nontrivial spin textures. The foremost interaction responsible for chiral magnetism is the Dzyaloshinskii-Moriya interaction (DMI), resulting from inversion symmetry breaking in the presence of strong spin-orbit coupling. However, the atomistic origin of DMIs and their relationship to emergent electrodynamic phenomena, such as topological Hall effect (THE), remain unclear. Here, we investigate the role of interfacial DMIs in 3 d –5 d transition metal-oxide-based LaMnO 3 /SrIrO 3 superlattices on THE from a chiral spin texture. By additively engineering the interfacial inversion symmetry with atomic-scale precision, we directly link the competition between interfacial collinear ferromagnetic interactions and DMIs to an enhanced THE. The ability to control the DMI and resulting THE points to a pathway for harnessing interfacial structures to maximize the density of chiral spin textures useful for developing high-density information storage and quantum magnets for quantum information science.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Molecular Dynamics of High Pressure Tin Phases I: Strength and deformation evaluations of empirical potentials [Slides]

Multi-phase problems have so many more unknowns, we’d like to have a tool to constrain some open questions related to microstructure and twin & dislocation behavior. We want an atomistic scale perspective on aspects of strength. Some multi-scale questions accessible to atomistic study: What lattice-specific behavior influences dislocation production/mobility and/or twinning? Do the phase transformations wipe-out, modify or preserve grain size and orientation? Does plastic strain reset at phase transition? If so under what conditions? Tin is the material chosen for the effort because it is non-hazardous and has multiple accessible solid phases at relatively low pressures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Calcium silicate hydrate colloid at different humidities: Microstructure, deformation mechanism, and mechanical properties

Calcium silicate hydrate (C-S-H) is the main hydration product of Portland cement, while fundamental questions persist regarding its colloidal structure and water content. In this work, we developed a full atomistic C-S-H colloid model and investigated the physical and mechanical properties at different gel water concentrations. Water confined in nanometer gel pores degrades the mechanical properties of C-S-H because of its hydrolysis effect. A “ductile to brittle” transition was observed in the C-S-H colloid model with increasing gel water contents, evolving from transgranular failure to intergranular fracture. The gel water confined in nanometer-sized pores displays glassy characteristics, and it acts as a lubricant and facilitates structure distortions during the deformation. We elucidated the topology effect of the hydrogen bond network on the evolution of the viscoelasticity of C-S-H at different humidities. In conclusion, this work sheds light on the role of water in C-S-H colloids from nanostructure perspectives.

36 MATERIALS SCIENCE↗
DOE OSTI2025

What is the Role of Relative Humidity on Conductivity in Polymer Electrolytes?

Ion transport properties in polymer electrolytes have been widely studied under rigorously dry and highly water-swollen conditions. However, the transition between these extremes, i.e., the low hydration regime, is still poorly understood at the molecular level and relevant to applications ranging from battery electrolytes to electrophoretic separations. Here, in this study, we apply atomistic molecular dynamics simulations to probe the role of hydration on ion mobilities and conductivities in LiTFSI-doped polyethers at low water content (less than 10% water by volume), which corresponds to 0−80% relative humidity conditions. With increasing water content, Li + ions exhibit two distinct regimes in their mobilities. At low water content, the majority of the Li + ions are weakly hydrated (two or fewer water molecules per Li + ion), maintaining strong interactions with their polymer solvation cage, and therefore exhibit only a weak increase in mobility relative to dry conditions. As water content increases, Li + ions form complete hydration shells, residing within water-rich domains that promote faster mobilities. Further, Li + mobilities increase more significantly in polymer electrolytes composed of more hydrophilic polymers and higher salt concentrations due to the formation of larger water-rich domains. In contrast, TFSI − has comparatively weak interactions with both the polymer and water, exhibiting a monotonic increase in mobility as a function of water content. Overall, these results help clarify the molecular mechanisms underlying ionic mobilities and conductivities in polymer electrolytes at low water content.

36 MATERIALS SCIENCE↗