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At least 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Electromechanics of graphene spirals

Among the most fascinating nanostructure morphologies are spirals, hybrids of somewhat obscure topology and dimensionality with technologically attractive properties. Here, we investigate mechanical and electromechanical properties of graphene spirals upon elongation by using density-functional tight-binding, continuum elasticity theory, and classical force field molecular dynamics. It turns out that electronic properties are governed by interlayer interactions as opposed to strain effects. The structural behavior is governed by van der Waals interaction: in its absence spirals unfold with equidistant layer spacings, ripple formation at spiral perimeter, and steadily increasing axial force; in its presence, on the contrary, spirals unfold via smooth local peeling, complex geometries, and nearly constant axial force. These electromechanical trends ought to provide useful guidelines not only for additional theoretical investigations but also for forthcoming experiments on graphene spirals.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Role of Capping Agents in the Synthesis of Salicylate-Capped Zinc Oxide Nanoparticles

Capping agents are often used for controlling the size, aggregation, and properties of nanoparticles. To guide the design of improved nanomaterials for targeted performance, one can use mechanistic insights into the interactions between capping agents and nanoparticles. Here, we employ density functional theory (DFT), reactive force-field molecular dynamics (ReaxFF MD) simulations, and optical spectroscopy to study the interactions between salicylate, as a model capping agent, and zinc oxide (ZnO) nanoparticles. In this work, we find that salicylate strongly interacts with the nanoparticle via the formation of O–Zn bonds in a distorted six-membered coordination ring structure. We describe the mechanisms of capping of ZnO nanoparticles by salicylate via three different binding modes. Simulations indicate that salicylate undergoes dissociative adsorption at the highly active surface Zn sites via a hydrogen-transfer process, thereby forming a tridentate configuration. The water-mediated interaction also facilitates the dissociative adsorption, leading to two salicylate O atoms coordinating with a surface Zn atom, while the other salicylate O atom bonds with another surface Zn atom. For molecular adsorption, binding free energies indicate that salicylate binds more strongly to ZnO, often in a bidentate configuration, than water does. The formation of the salicylate–ZnO complex is substantiated by UV–visible and Fourier transform infrared spectra. We find that the C=O stretching mode of salicylate becomes softened when it interacts with the nanoparticle, suggesting chemisorption of salicylate on ZnO. Although DFT predicts strong interaction between salicylate and ZnO, ReaxFF MD simulation indicates the moderate interaction between these two components in aqueous solution. Water molecules in close contact with the nanoparticle surface undergo dissociation, thus resulting in a surface hydroxyl, a reactive oxygen species that may influence the nanoparticle’s catalytic properties. Overall, the atomic-level information provided here can guide the selection process of salicylate as an appropriate agent for ZnO nanoparticle synthesis when strong interactions of particles with capping agents are required.

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

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Shadow molecular dynamics for flexible multipole models

Shadow molecular dynamics provide an efficient and stable atomistic simulation framework for flexible charge models with long-range electrostatic interactions. Shadow molecular dynamics simulations are driven by approximate “shadow” Born–Oppenheimer potentials for which the exact charges and forces are directly accessible without relying on costly (and approximate) iterative solvers. While previous implementations have been limited to atomic monopole charge distributions, we extend this approach to flexible multipole models. We derive detailed expressions for the shadow energy functions, potentials, and force terms, explicitly incorporating monopole–monopole, dipole–monopole, and dipole–dipole interactions. In our formulation, both atomic monopoles and atomic dipoles are treated as extended dynamical variables alongside the propagation of the nuclear degrees of freedom. We demonstrate that introducing the additional dipole degrees of freedom preserves the stability and accuracy previously seen in monopole-only shadow molecular dynamics simulations. In addition, we present a shadow molecular dynamics scheme where the monopole charges are held fixed while the dipoles remain flexible. Our extended shadow dynamics provide a framework for stable, computationally efficient, and versatile molecular dynamics simulations involving long-range interactions between flexible multipoles. This is of particular current interest in combination with machine-learned interatomic potentials, including long-range electrostatic interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Sublethal doses of neonicotinoid imidacloprid can interact with honey bee chemosensory protein 1 (CSP1) and inhibit its function

As a frequently used neonicotinoid insecticide, imidacloprid can impair the chemoreceptive behavior of honey bees even at sublethal doses, while the physiochemical mechanism has not been further revealed. Here, multiple fluorescence spectra, thermodynamic method, and molecular docking were used to study the interaction and the functional inhibition of imidacloprid to the recombinant CSP1 protein in Asian honey bee, Apis cerana. The results showed that the fluorescence intensity (λ{sub em} = 332 nm) of CSP1 could be significantly quenched by imidacloprid in a dynamic mode. During the quenching process, ΔH > 0, ΔS > 0, indicating that the acting forces of imidacloprid with CSP1 are mainly hydrophobic interactions. Synchronous fluorescence showed that the fluorescence of CSP1 was mainly derived from tryptophan, and the hydrophobicity of tryptophan decreased with the increase of imidacloprid concentration. Molecular docking predicted the optimal pose and the amino acid composition of the binding process. Circular dichroism (CD) spectra showed that imidacloprid reduced the α-helix of CSP1 and caused the extension of the CSP1 peptide chain. In addition, the binding of CSP1 to floral scent β-ionone was inhibited by nearly 50% of the apparent association constant (K{sub A}) in the presence of 0.28–2.53 ng/bee of imidacloprid, and the inhibition rate of nearly 95% at 3.75 ng/bee of imidacloprid at sublethal dose level. This study initially revealed the molecular physiochemical mechanism that sublethal doses of neonicotinoid still interact and inhibit the physiological function of the honey bees' chemoreceptive system. - Highlights: • Sublethal doses of imidacloprid can directly interact with CSP1 in Apis cerana. • Sublethal imidacloprid can inhibit the function of CSP1 binding to semiochemicals. • The fluorescence intensity of CSP1 quenched by imidacloprid in a dynamic mode. • The binding between CSP1 and imidacloprid are driven by hydrophobic interactions. • Imidacloprid caused the extension of the CSP1 peptide chain.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1978

The driving force for magnetospheric convection

Viscously driven magnetospheric models, as well as a model involving interconnection between the geomagnetic field and the magnetic field in the solar wind, have been proposed to describe the driving force for magnetospheric convection. Lack of a satisfactory theory for the interconnection in the latter model and, in the case of the viscous interaction models, inadequacies in predicting the quantity of the driving force, make these two classes of models less than successful. Accordingly, a mechanically driven magnetospheric model is proposed: solar wind plasma enters the magnetosphere around the neutral points, covers the inner surface of the magnetopause and subsequently expands, driving convection as it escapes from the open tail.

Johnson, F. S.↗
DOE OSTI2015

Analysis of first order reversal curves in the thermal hysteresis of spin-crossover nanoparticles within the mechanoelastic model

The recently obtained spin-crossover nanoparticles are possible candidates for applications in the recording media industry as materials for data storage, or as pressure and temperature sensors. For these applications, the intermolecular interactions and interactions between spin-crossover nanoparticles are extremely important, as they may be essential factors in triggering the transition between the two stable phases: the high-spin and low-spin ones. In order to find correlations between the distributions in size and interactions and the transition temperatures distribution, we apply the FORC (First Order Reversal Curves) method, using simulations based on a mechanoelastic model applied to 2D triangular lattices composed of molecules linked by springs and embedded in a surfactant. We consider two Gaussian distributions: one is the size of the nanoparticles and another is the elastic interactions between edge spin-crossover molecules and the surfactant molecules. In order to disentangle the kinetic and non-kinetic parts of the FORC distributions, we compare the results obtained for different temperature sweeping rates. We also show that the presence of few larger particles in a distribution centered around much smaller particles dramatically increases the hysteresis width.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS2011

Overview of Experimental Investigations for Ares I Launch Vehicle Development

Another concern for the vehicle during its design trajectory was the separation of the first stage solid rocket booster from the upper stage component after it had depleted its solid fuel propellant. There has been some concern about the interstage of the first stage from clearing the nozzle of the J2-X engine. A detailed separation aerodynamic wind tunnel investigation was conducted in the AEDC VKF Tunnel A to help to investigate the interaction aerodynamic effects5. A comparison of the separation plane details between the Ares I architecture and the Ares I-X demonstration flight architecture is shown in figure 12. The Ares I design requires a more complex separation sequence and requires better control in order to avoid contact with the nozzle of the upper stage engine. The interstage, which houses the J2-X engine for the Ares I vehicle, must be able to separate cleanly to avoid contact of the J2-X engine. There is only about approximately 18 inches of buffer inside the interstage on each size of the nozzle so this is a challenging controlled separation event. This complex experimental investigation required two separate Ares I models (upper stage and first stage with interstage attached) with independent strain gauge balances installed in each model. It also required the Captive Trajectory System (CTS) that was needed to precisely locate the components in space relative to each other to fill out the planned test matrix. The model setup in the AEDC VKF Tunnel A is shown in figure 13. The CTS remotely positioned the first stage at the required x, y, and z positions and was able to provide interactions within 0.2" of the upper stage. A sample of the axial force on the first stage booster is shown in figure 14. These results, as a function of separation distance between the two stages, are compared to pre-test CFD results. Since this is a very challenging, highly unsteady flow field for CFD to correctly model, the experimental results have been utilized by GN&C discipline to more accurately represent the interaction aerodynamics. In addition to the integrated forces and moments obtained from the test, flow visualization data was obtained from this test in the form of Schlieren photographs, as shown in figure 15, which show the shock structure and interaction effects after the two stages separate during flight. This separation test was crucial in the successful flight test of the Ares I-X vehicle and provided the GN&C discipline with the unpowered proximity aerodynamic effect for a separation of the Ares I vehicle.

Tomek, William G.↗
DOE OSTI2023

Coexistence of Merons with Skyrmions in the Centrosymmetric Van Der Waals Ferromagnet Fe 5– x GeTe 2

Fe 5-x GeTe 2 is a centrosymmetric, layered van der Waals (vdW) ferromagnet that displays Curie temperatures T c (270–330 K) that are within the useful range for spintronic applications. However, little is known about the interplay between its topological spin textures (e.g., merons, skyrmions) with technologically relevant transport properties such as the topological Hall effect (THE) or topological thermal transport. Here, via high-resolution Lorentz transmission electron microscopy, it is shown that merons and anti-meron pairs coexist with Néel skyrmions in Fe 5-x GeTe 2 over a wide range of temperatures and probe their effects on thermal and electrical transport. A THE is detected, even at room T, that senses merons at higher T's, as well as their coexistence with skyrmions as T is lowered, indicating an on-demand thermally driven formation of either type of spin texture. Remarkably, an unconventional THE is also observed in absence of Lorentz force, and it is attributed to the interaction between charge carriers and magnetic field-induced chiral spin textures. Here these results expose Fe 5-x GeTe 2 as a promising candidate for the development of applications in skyrmionics/meronics due to the interplay between distinct but coexisting topological magnetic textures and unconventional transport of charge/heat carriers.

two-dimensional magnets↗
DOE OSTI2025

Layers Can Be Deceiving: A Hopping Model for Small Molecule Diffusion in TATB Crystal

Sorption of small molecule gases in materials can play a significant role in their long‐term stability and compatibility within multi‐material assemblies. While many material properties of the insensitive high explosive TATB (1,3,5‐triamino‐2,4,6‐trinitrobenzene) are well understood, very little is known regarding its permeability to gases. TATB crystal exhibits a graphitic‐like layered packing structure that evokes a mental schema in which the layers form nanoscopic channels, but it is unclear whether this structure promotes gas transport. Here, we use molecular dynamics (MD) simulations to predict transport of small molecules through TATB single crystal. An approach to fit classical force fields is developed to model TATB interactions with H 2 O, He, Ne, and Ar, which is then combined with steered MD to probe gas transport along selected directions in the crystal. We find that small molecule transport occurs via a hopping mechanism that exhibits distinct jumps between interstitial sites and is substantially faster normal to the layers as compared to through them. This result stems from the finding that intralayer junctions between adjacent TATB molecules are the most stable interstitial sites and that energetic barriers are lower for hopping between adjacent layers. An empirical model for diffusion rate based on the MD data shows that the rate decays exponentially with increasing molecular radius and is negligibly small for all molecules larger than He, including common atmospheric gases. These findings have implications for the interpretation of experiments that measure surface area, material response to extreme conditions, and are expected to help constrain models for material aging.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Editorial: The World Is Nonlocal

Nonlocal modeling has come a long way. Researchers in the continuum mechanics and computational mechanics communities increasingly recognize that nonlocality is critical in realistic mathematical models of many aspects of the physical world. Physical interaction over a finite distance is fundamental at the atomic and nanoscale level, in which atoms and molecules interact through multibody potentials. Long-range forces partially determine the mechanics of surfaces and the behavior of dissolved molecules and suspended particles in a fluid. Nonlocality is therefore a vital feature of any continuum model that represents these physical systems at small length scales.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2017

APBB1 reinforces cancer stem cell and epithelial-to-mesenchymal transition by regulating the IGF1R signaling pathway in non-small-cell lung cancer cells

Amyloid β precursor protein binding family B member 1(APBB1) was first identified as a binding partner of amyloid precursor protein during brain development, but its function in the context of cancer remain unclear. Here we show for the first time that APBB1 is partly associated with intensifying cancer stem cell(CSC) and epithelial-to-mesenchymal transition (EMT) and enhancing radiation-resistant properties of lung cancer cells. We found that APBB1 was highly expressed in ALDH1{sup high} CSC-like cells sorted from A549 lung cancer cells. In APBB1-deficient H460 cells with forced overexpression of APBB1, the protein directly interacted with IGF1Rβ, enhanced phosphorylation of IGF1Rβ/PI3K/AKT pathway(activation) and subsequently induced the phosphorylation of GSK3β(inactivation). This phosphorylation stabilized Snail1, a negative regulator of E-cadherin expression, and regulated β-catenin–mediated ALDH1 expression, which are representative markers for EMT and CSCs, respectively. In contrast, suppression of APBB1 expression with siRNA yielded the opposite effects in APBB1-rich A549 cells. We concluded that APBB1 partly regulates the expression of ALDH1. We also found that APBB1 regulates activation of nuclear factor-κB, which is involved in reducing various stresses including oxidative stress, which suggests that APBB1 is associated with γ-radiation sensitivity. Our findings imply that APBB1 plays an important role in the maintenance of EMT-associated CSC-like properties and γ-radiation resistance via activation of IGF1Rβ/AKT/GSK3β pathway in lung cancer cells, highlighting APBB1 as a potential target for therapeutic cancer treatment. - Highlights: • APBB1 was highly expressed in ALDH1{sup high} cells sorted from A549 cells. • APBB1 is associated with intensifying CSC and EMT and enhancing radiation-resistant properties of lung cancer cells. • APBB1 regulates EMT-associated CSC-like properties and γ-radiation resistance via activation of IGF1Rβ/AKT/GSK3β pathway. • APBB1 partly regulates the expression of ALDH1 via AKT/GSK3β-associated β-catenin pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Atomistic Insights into the Reactive Diffusion of CO 2 in Guanidine-Based Facilitated Transport Membranes

The pressing need to address climate change has led to significant advancements in carbon dioxide (CO 2 ) capture technologies. Notably, facilitated transport membranes (FTMs) are distinguished by their exceptional selectivity and permeance, attributed to their reversible chemical reactions with CO 2 . This study, for the first time, sheds light on the reactive diffusion mechanism of CO 2 in FTMs, utilizing 1,1,3,3-tetramethylguanidine (TMG) as a mobile carrier. Specifically, state-ofthe- art molecular dynamics (MD) simulations, augmented by a reparameterized reactive force field (ReaxFF) capable of describing atomistic interactions and reaction pathways, are conducted to investigate the transport of CO 2 in TMG. The analysis of mean squared displacement (MSD) and diffusion coefficients reveals a clear hierarchy in the mobility of reaction components. Our findings highlight a unique hopping diffusion mechanism between bicarbonate ions and TMG molecules, increasing the diffusivity of reacted CO 2 by 1.4 times. The hopping events observed not only enhance our understanding of molecular mobility but also offer a means to boost the performance of FTMs in CO 2 capture applications. Overall, this research lays the groundwork for the future design of FTMs with optimal carrier properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

How Useful Are Common Simulants of Chemical Warfare Agents at Predicting Adsorption Behavior?

We report that nanoporous materials such as metal–organic frameworks (MOFs) have attractive properties for selective capture of chemical warfare agents (CWAs). For obvious reasons, most research on adsorption of CWAs is performed with simulant molecules rather than real agents. This paper examines how effectively common CWA simulants mimic the adsorption properties of sarin and soman. To this end, we perform molecular simulations in the dilute adsorption limit for four simulants [dimethyl methylphosphonate (DMMP), diethyl chlorophosphate (DCP), diisopropyl fluorophosphate, and dimethyl p-nitrophenyl phosphate (DMNP)] and sarin and soman in a set of 2969 MOFs with experimentally known crystal structures. To establish the robustness of the conclusions with respect to the force field used in these simulations, each system was examined with two independent force fields, a “generic” force field and a density functional theory (DFT)-derived force field we established based on extensive dispersion-corrected DFT calculations of adsorption in the well-known MOF UiO-66. Our results show that when judging the performance of adsorbents using the heat of adsorption, DCP and DMMP are the best simulants for the adsorption of sarin, while DMNP is the best simulant for soman. The adsorption properties of DCP or DMMP show a strong correlation with sarin over a range of MOFs, but the correlation between DMNP and soman is considerably weaker. Finally, comparisons of results with both force fields indicate that our main conclusions are robust with respect to the force field used to define adsorbate–MOF interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Atomistic Insights into Nucleation and Formation of Hexagonal Boron Nitride on Nickel from First-Principles-Based Reactive Molecular Dynamics Simulations

Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multiscale modeling combining density functional theory (DFT) and reactive molecular dynamics. The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, BxNy (x, y = 1, 2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer. B can diffuse competitively on both the surface and in the sublayer, while N diffuses strictly on the substrate surface. The DFT data were then used to generate a classical description of the Ni–B and Ni–N pair interactions within the formulation of the reactive force field, ReaxFF. Using the potential developed from this work, the elementary nucleation and growth process of an hBN monolayer structure from elemental B and N is shown at the atomistic scale. The nucleation initiates from the growth of linear BN chains, which evolve into branched and then hexagonal lattices. Subsequent DFT calculations confirmed the structure evolution energetically and validate the self-consistency of this multiscale modeling framework. On the basis of this framework, the fundamental aspects regarding crystal quality and the role of temperature and substrates used during hBN growth can also be understood.

Liu, Song↗
DOE OSTI2023

Uncertainty-aware molecular dynamics from Bayesian active learning for phase transformations and thermal transport in SiC

Abstract Machine learning interatomic force fields are promising for combining high computational efficiency and accuracy in modeling quantum interactions and simulating atomistic dynamics. Active learning methods have been recently developed to train force fields efficiently and automatically. Among them, Bayesian active learning utilizes principled uncertainty quantification to make data acquisition decisions. In this work, we present a general Bayesian active learning workflow, where the force field is constructed from a sparse Gaussian process regression model based on atomic cluster expansion descriptors. To circumvent the high computational cost of the sparse Gaussian process uncertainty calculation, we formulate a high-performance approximate mapping of the uncertainty and demonstrate a speedup of several orders of magnitude. We demonstrate the autonomous active learning workflow by training a Bayesian force field model for silicon carbide (SiC) polymorphs in only a few days of computer time and show that pressure-induced phase transformations are accurately captured. The resulting model exhibits close agreement with both ab initio calculations and experimental measurements, and outperforms existing empirical models on vibrational and thermal properties. The active learning workflow readily generalizes to a wide range of material systems and accelerates their computational understanding.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Coulomb-free 1S0 p − p scattering length from the quasi-free p + d → p + p + n reaction and its relation to universality

Abstract The Coulomb-free 1 S 0 proton-proton ( p - p ) scattering length relies heavily on numerous and distinct theoretical techniques to remove the Coulomb contribution. Here, it has been determined from the half-off-the-energy-shell p - p scattering cross section measured at center-of-mass energies below 1 MeV using the quasi-free p + d → p + p + n reaction. A Bayesian data-fitting approach using the expression of the s-wave nucleon-nucleon scattering cross section returned a p - p scattering length $${a}_{pp}=-18.1{7}_{-0.58}^{+0.52}{| }_{stat}\pm 0.0{1}_{syst}$$ a p p = − 18.1 7 − 0.58 + 0.52 ∣ s t a t ± 0.0 1 s y s t fm and effective range r 0 = 2.80 ± 0.05 s t a t ± 0.001 s y s t fm. A model based on universality concepts has been developed to interpret this result. It accounts for the short-range interaction as a whole, nuclear and residual electromagnetic, according to what the s-wave phase-shift δ does in the description of low-energy nucleon-nucleon scattering data. We conclude that our parameters are representative of the short-range physics and propose to assess the charge symmetry breaking of the short-range interaction instead of just the nuclear interaction. This is consistent with the current understanding that the charge dependence of nuclear forces is due to different masses of up-down quarks and their electromagnetic interactions. This achievement suggests that these properties have a lesser than expected impact in the context of the charge symmetry breaking.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗