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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Simulation of the NaGd(MoO{sub 4}){sub 2}–NaEu(MoO{sub 4}){sub 2} and Na{sub 2}Gd{sub 4}(MoO{sub 4}){sub 7}–Na{sub 2}Eu{sub 4}(MoO{sub 4}){sub 7} Solid Solutions by the Interatomic Potential Method

Simulation of the solid solutions in the system of double sodium–gadolinium and sodium–europium molybdates, which are promising matrices for solid state lasers and phosphors has been carried out by the method of interatomic potentials. Two types of solid solutions have been studied, one of which contains finite components corresponding to the stoichiometric NaGd(MoO{sub 4}){sub 2}–NaEu(MoO{sub 4}){sub 2} compositions with statistical distribution of cations in the crystal lattice. Another object is a cation-deficient Na{sub 2}Gd{sub 4}(MoO{sub 4}){sub 7}–Na{sub 2}Eu{sub 4}(MoO{sub 4}){sub 7} system, in which we have examined the variants of statistical distribution and partial ordering of cations over structural positions. Atomistic simulation has been performed using the GULP 4.0.1 software package (General Utility Lattice Program). It is shown that when we pass from sodium-gadolinium molybdate to sodium-europium molybdate, both of stoichiometric and cation-deficient compositions, an increase in the unit cell volume is observed, while the density of the crystal, the energy of interatomic interactions in the structure, the vibrational entropy and the heat capacity decrease along with increasing europium content. The energy of interatomic interactions in the structure for cation-deficient solid solutions is less than for stoichiometric ones. Other aforementioned characteristics for cation-deficient solid solutions have greater values than for stoichiometric ones. The role of cluster europium centers in concentration quenching in NaGd(MoO{sub 4}){sub 2}–NaEu(MoO{sub 4}){sub 2} solid solutions has been examined.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Liquid crystal torons in Poiseuille-like flows

Three-dimensional (3D) simulations of the structure of liquid crystal (LC) torons, topologically protected distortions of the LC director field, under material flows are rare but essential in microfluidic applications. Here, we show that torons adopt a steady-state configuration at low flow velocity before disintegrating at higher velocities, in line with experimental results. Furthermore, we show that under partial slip conditions at the boundaries, the flow induces a reversible elongation of the torons, also consistent with the experimental observations. These results are in contrast with previous simulation results for 2D skyrmions under similar flow conditions, highlighting the need for a 3D description of this LC soliton in relation to its coupling to the material flow. These findings pave the way for future studies of other topological solitons, like hopfions and heliknotons, in flowing soft matter systems.

Science & Technology - Other Topics↗
DOE OSTI2017

Structure and lifetimes in ionic liquids and their mixtures

With the aid of molecular dynamics simulations, we study the structure and dynamics of different ionic liquid systems, with focus on hydrogen bond, ion pair and ion cage formation. To do so, we report here radial distribution functions, their number integrals, and various time–correlation functions, from which we extract well-defined lifetimes by means of the reactive flux formalism. We explore the influence of polarizable force fields vs. non-polarizable ones with downscaled charges (±0.8) for the example of 1-butyl-3-methylimidazolium bromide. Furthermore, we use 1-butyl-3-methylimidazolium trifluoromethanesulfonate to investigate the impact of temperature and mixing with water as well as with the chloride ionic liquid. Smaller coordination numbers, larger distances, and tremendously accelerated dynamics are observed when the polarizable force field is applied. The same trends are found with increasing temperature. Adding water decreases the ion–ion coordination numbers whereas the water–ion and water–water coordination is enhanced. A domain analysis reveals that the nonpolar parts of the ions are dispersed and when more water is added the water clusters increase in size. The dynamics accelerate in general upon addition of water. In the ionic liquid mixture, the coordination number around the cation changes between the two anions, but the number integrals of the cation around the anions remain constant and the dynamics slow down with increasing content of the chloride ionic liquid.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Realistic Ion Dynamics through Charge Renormalization in Nonaqueous Electrolytes

While many practically important electrolytes contain lithium ions, interactions of these ions are particularly difficult to probe experimentally because of their small X-ray and neutron scattering cross sections and large neutron absorption cross sections. Molecular dynamics (MD) is a powerful tool for understanding the properties of nonaqueous electrolyte solutions from the atomic level, but the accuracy of this computational method crucially depends on the physics built into the classical force field. In this study, we demonstrate that several force fields for lithium bistriflimide (LiTFSI) in acetonitrile yield a solution structure that is consistent with the neutron scattering experiments, yet these models produce dramatically different ion dynamics in solution. Such glaring discrepancies indicate that inadequate representation of long-range interactions leads to excessive ionic association and ion-pair clustering. We show that reasonable agreement with the experimental observations can be achieved by renormalization of the ion charges using a “titration” method suggested herewith. This simple modification produces realistic concentration dependencies for ionic diffusion and conductivity in <2 M solutions, without loss in quality for simulation of the structure.

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

Localization of Excitations near a Thin Structured Spacer between Linear and Nonlinear Crystals

It has been shown that localized and semi-localized stationary states exist near a thin structured defect layer between a linear medium and a Kerr nonlinear medium. Localized states are described by a monotonically decreasing amplitude of the field on the both sides of the interface between the media. Semilocalized states are characterized by the field that has the form of a standing wave in the linear medium and decreases monotonically in the nonlinear medium. Kerr media with self-focusing and defocusing are considered. The proposed model is described by a system of the linear and nonlinear Schrödinger equations with a specific potential simulating a thin structured defect layer. It has been shown that localized and semi-localized states exist in different energy ranges in the case of contact of the linear medium with the self-focusing medium. In the case of contact of the linear medium with the defocusing medium, two types of localized and semi-localized states differing in energy and field profile can exist in different energy ranges. In particular cases, expressions for energies of states of these types have been obtained and conditions of their applicability have been indicated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Predictions of Boron Phase Stability Using an Efficient Bayesian Machine Learning Interatomic Potential

Thermodynamic phase stability of three elemental boron allotropes, i.e., α-B, β-B, and γ-B, was investigated using a Bayesian interatomic potential trained via a sparse Gaussian process (SGP). SGP potentials trained with datasets from on-the-fly active learning achieve quantum mechanical level accuracy when employed in molecular dynamics simulations to predict wide-ranging thermodynamic, structural, and vibrational properties. The simulated phase diagram (500~1400 K and 0~16 GPa) agrees with experimental measurements. The SGP-based MD simulations also successfully predicted that the B13 defect is critical in stabilizing β-B below 700 K. At higher temperatures, the entropy becomes the dominant factor, making β-B the more stable phase over α-B. Furthermore, this Letter demonstrates that SGP potentials based on a training set consisting of defect-free-only systems could make correct predictions of defect-related phenomena in solid-state crystals, paving the path to investigate crystal phase stability and transitions.

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

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Abstract Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Galaxy formation with wave/fuzzy dark matter: The core-halo structure and the solitonic imprint

Dark matter-dominated cores have long been claimed for the well-studied local group dwarf galaxies. More recently, extended stellar halos have been uncovered around several of these dwarfs through deeper imaging and spectroscopy. Such core-halo structures (inner flat core and a characteristic r −3 asymptotic outer halo profile) are not a feature of conventional cold dark matter (CDM). In contrast, smooth and prominent dark matter cores are predicted for wave/fuzzy dark matter (ψDM). The question arises as to what extent the visible stellar profiles should reflect this dark matter core structure. Here we compare cosmological hydrodynamical simulations of CDM, “WDM” (model used as a proxy for ψDM) & ψDM, aiming to predict the stellar profiles for these three DM scenarios. We show that cores surrounded by extended halos are distinguishable for ψDM, where the stellar density is enhanced in the core due to the presence of the relatively dense soliton. Our analysis demonstrates that, in our simulations, a distinctive core-halo structure does not appear in the case of CDM in the DM, gas, or stars. Whereas we do find a core-halo transition for DM, gas, and stars for ψDM, and the scale of this transition is in line with the predicted core radius set by the soliton scale anticipated for the adopted boson mass of 2.5×10 −22 eV. The presence of a core-halo structure in the stellar profile for Galaxy 1 for ψDM is visible for the most massive and the first galaxy to form in the simulation. Clearly, further simulations are needed to establish how strict this possible relationship is between the DM and stellar core-halo profile as a potential observational discriminator. Furthermore, we observe the anticipated asymmetry for ψDM due to the soliton's motion (jumping and random walk), a distinctive characteristic not found in the symmetric distributions of stars in the warm and CDM models.

dark matter↗
DOE OSTI2024

Complex Structure of Molten FLiBe (2 Li F – Be F 2 ) Examined by Experimental Neutron Scattering, X-Ray Scattering, and Deep-Neural-Network Based Molecular Dynamics

The use of molten salts as coolants, fuels, and tritium breeding blankets in the next generation of fission and fusion nuclear reactors benefits from furthering the characterization of the molecular structure of molten halide salts, paving the way to predictive capability of the chemical and thermophysical properties of molten salts. Due to its neutronic, chemical, and thermochemical properties, 2 Li F - Be F 2 is a candidate molten salt for several fusion- and fission-reactor designs. We performed neutron and x-ray total-scattering measurements to determine the atomic structure of liquid 2 Li F - Be F 2 . We also performed and neural-network molecular-dynamics simulations to predict the structure obtained by neutron- and x-ray-diffraction experiments. The use of machine learning provides improvements to the efficiency in predicting the structure at a longer length scales than is achievable with simulations at significantly lower computational expense while retaining near accuracy. We found that the NNMD simulations accurately predicted the Be F 4 2 − oligomer formations seen in the experimental first-structure-factor peak. Our combination of high-resolution measurements with large-scale molecular dynamics provided an avenue to explore and experimentally verify the intermediate-range ordering beyond the first-nearest neighbor that has posed too many experimental and computational challenges in previous works. With a deeper understanding of the salt structure and ion ordering, the evolution of salt chemistry over the lifetime of a reactor can be better predicted, which is crucial to the licensing and operation of advanced fission and fusion reactors that employ molten salts. To this end, this work will serve as a reference for future studies of salt structure and macroscopic properties with and without the addition of solutes. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

A fully-integrated lattice Boltzmann method for fluid–structure interaction

Here we present a fully-integrated lattice Boltzmann (LB) method for fluid–structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples finite-strain solids to the LB fluid on the same fixed computational grid with the reference map technique (RMT). An integral part of the LBRMT is a new LB boundary condition for moving deformable interfaces across different densities. With this fully Eulerian solid–fluid coupling, the LBRMT is well-suited for parallelization and simulating multi-body contact without remeshing or extra meshes. We validate its accuracy via a benchmark of a deformable solid in a lid-driven cavity, then showcase its versatility through examples of soft solids rotating and settling. The LBRMT achieves a spatial convergence rate between first-order and second-order for FSI simulations and is designed for low to intermediate Reynolds number flows with finite inertia at small Mach numbers. With simulations of complex suspensions mixing, we highlight the potential of the LBRMT for studying collective behavior in soft matter and biofluid dynamics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10– 30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conformation at 50°C. We also found that the presence of glycan moieties did not influence the observed protein dynamics. Nevertheless, the closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Smoothened stimulation by membrane sterols drives Hedgehog pathway activity

Hedgehog signalling is fundamental to embryonic development and postnatal tissue regeneration. Aberrant postnatal Hedgehog signalling leads to several malignancies, including basal cell carcinoma and paediatric medulloblastoma. Hedgehog proteins bind to and inhibit the transmembrane cholesterol transporter Patched-1 (PTCH1), which permits activation of the seven-transmembrane transducer Smoothened (SMO) via a mechanism that is poorly understood. Here we report the crystal structure of active mouse SMO bound to both the agonist SAG21k and to an intracellular binding nanobody that stabilizes a physiologically relevant active state. Analogous to other G protein-coupled receptors, the activation of SMO is associated with subtle motions in the extracellular domain, and larger intracellular changes. In contrast to recent models, a cholesterol molecule that is critical for SMO activation is bound deep within the seven-transmembrane pocket. We propose that the inactivation of PTCH1 by Hedgehog allows a transmembrane sterol to access this seven-transmembrane site (potentially through a hydrophobic tunnel), which drives the activation of SMO. Overall, these results—combined with signalling studies and molecular dynamics simulations—delineate the structural basis for PTCH1–SMO regulation, and suggest a strategy for overcoming clinical resistance to SMO inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Elucidating the formation mechanisms of zeolites using data-driven modelling and in-situ characterization

Zeolites are the main solid catalysts used by the chemical industry. The use of zeolites in separations and as shape selective catalysts requires control of the width and connectivity of their pores. 235 distinct zeolite frameworks have been synthesized to date, of over 2 million that have been proposed. Recent work indicates that the limitation is in large part kinetic: new synthetic pathways are required to access new zeolites. Organic cations are used to direct the synthesis towards specific zeolites. However, the molecular mechanisms by which cations direct the nucleation towards specific zeolites is not known. Elucidating these mechanisms is key to realize new zeolites for catalysis and separations, and is the focus of this project. This project developed and implemented a synergistic, data-driven computational and experimental approach to resolve the molecular pathways of nucleation, growth, and polymorph selection of zeolites and the role of organic cations in directing their formation. The project developed computationally efficient and accurate models for the study of the nucleation and growth of pure silica zeolites in molecular simulations, using machine learning with data from experiments. Simulations with these models were integrated with scanning tunneling electron microscopy, computer vision, and deep learning to unveil the molecular pathways of formation of a zeolite. Of particular interest in this project was to elucidate the role of amorphous precursors in the nucleation of the zeolite. Previous experiments indicate that zeolites are born within non-crystalline aggregates in which the silicates and organic cations have local and medium range order similar to that of the zeolite. The organic cations that direct the formation of zeolites and those that direct the formation of ordered mesoporous silicas are similar. We hypothesized that the frustrated attraction that for large organic cations leads to the formation of stable mesophases that direct the synthesis of mesoporous silicas, could promote the formation of metastable mesophases that can assist in the nucleation and polymorph selection of zeolites. The simulations resolved how structure directing agents build crystalline order and showed that mesoscopic pre-ordering occurs is not required to facilitate the nucleation of zeolites, because the synthesis occurs at high driving forces, where the barriers for nucleation are negligible. This project unveiled that polymorph selection in zeolite synthesis occurs after nucleation, opening a distinct area of control through the kinetics of growth and not through nucleation barriers.

36 MATERIALS SCIENCE↗
DOE OSTI2024

An Open-Source Parallel EMT Simulation Framework

As the integration level of inverter-based resources (IBRs) increases, ensuring the reliable operation of the bulk power systems requires the use of electromagnetic transient (EMT) simulation tools to identify and mitigate system-wide stability risks. Conducting EMT studies for large-scale, IBR-rich grids, however, is challenging due to the inherent computational bottleneck caused by the underlying high-fidelity models and required small time steps. This paper introduces ParaEMT: an open-source, generic EMT simulation framework designed to accelerate simulations by leveraging advanced parallel computational technologies, such as high-performance computers. This paper presents a comprehensive exposition of ParaEMT, covering its modeling library, simulation strategy, framework structure, operational procedures, and auxiliary features, alongside its extensible parallel computational architecture. Notably, ParaEMT is a publicly accessible and modularized framework written in Python, thereby facilitating future development and the integration of new models and algorithms. The accuracy and efficiency of ParaEMT are demonstrated by rigorous validations via multiple case studies.

electromagnetic transient simulation↗
DOE OSTI2023

An Open-Source Parallel EMT Simulation Framework: Preprint

As the integration level of inverter-based resources (IBR) increases, ensuring the reliable operation of the bulk power systems requires the use of electromagnetic transient (EMT) simulation tools to identify and mitigate system-wide stability risks. Conducting EMT studies for large-scale, IBR-rich grids, however, is challenging due to the inherent computational bottleneck caused by the underlying high-fidelity models and required small time steps. This paper introduces ParaEMT: an open-source, generic EMT simulation framework designed to accelerate simulations by leveraging advanced parallel computational technologies, such as high-performance computers. This paper presents a comprehensive exposition of ParaEMT, covering its modeling library, simulation strategy, framework structure, operational procedures, and auxiliary features, alongside its extensible parallel computational architecture. Notably, ParaEMT is a publicly accessible and modularized framework written in Python, thereby facilitating future development and the integration of new models and algorithms. The accuracy and efficiency of ParaEMT are demonstrated by rigorous validations via multiple case studies.

electromagnetic transient simulation↗
DOE OSTI2025

Numerical Simulation Studies of Ultrasonic De-Icing for Heating, Ventilation, Air Conditioning, and Refrigeration Structures

Ice accumulation on heating, ventilation, air conditioning, and refrigeration (HVACR) structures presents significant operational challenges. These challenges include reduced efficiency, increased energy consumption, and potential damage to equipment. Traditional de-icing methods, such as chemical treatments, mechanical scraping, or heating-based techniques, are often labor-intensive, costly, and environmentally harmful. Here, this study uniquely investigates ultrasonic de-icing as an energy-efficient alternative for HVACR applications, focusing on the specific structural geometries found in these systems. A comprehensive numerical simulation framework was developed using finite element analysis to explore ultrasonic wave propagation across four distinct HVACR structures. Key parameters such as ultrasonic frequency, power levels, and the number and placement of actuators were examined for their impact on ice detachment efficiency. Results from simulations on a plate structure reveal that ultrasonic excitation can propagate effectively across large areas (at least 150 × 150 mm), enhancing the de-icing coverage. Lower frequency (e.g., 30 to 45 kHz) excitation results in greater displacement, improving de-icing performance, while increased actuator numbers with the same total power input also enhance effectiveness. Two actuators seem sufficient for the de-icing of a 300 × 300 mm plate. For tube-and-fin structures, specific high-power ultrasonic frequencies selectively excite the fin plates, demonstrating efficient ice removal when actuated on the tube. However, optimal performance requires careful design of actuator placement and vibration modes to accommodate the irregular shapes of these structures.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure of the Bastnäsite (001) Surface by Crystal Truncation Rod X-ray Diffraction and Ab Initio Molecular Dynamics: Implications for Separations of a Rare Earth Ore Mineral

Bastnäsite ((Ce,La)FCO 3 ) is the primary mineral source of light rare earth elements, but its surface structure is not well understood. This presents a major challenge in improving beneficiation strategies. In this work, a synergistic combination of X-ray scattering and ab initio molecular dynamics (AIMD) was used to gain atomistic insight into the interfacial structure of bastnäsite. Surface X-ray scattering was used to measure crystal truncation rods (CTRs) of the bastnäsite (001) surface, a significant crystal face with a previously unknown termination. The best-fit atomic-scale model of the CTR data features a carbonate layer at the surface, which is stabilized by the relaxation of carbonate groups from their bulk structural positions. AIMD simulations predict similar surface relaxations, which are shown to be influenced by the protonation of oxygen atoms at the surface. Evidence of ordered water at the interface is also observed in the best-fit model and AIMD simulations. Further, the presence of a carbonate layer at this dominant crystal surface is significant for improving separation technologies because most commonly used ligands utilize anionic functional groups to chelate metal cations at particle surfaces. Without modification, anionic ligands are expected to have poor affinity for the carbonate-terminated (001) surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗