Direct Atomic Simulations of Facet Formation and Equilibrium Shapes of SiC Nanoparticles
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Equilibrium↗
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All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System
Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiate a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study structural and dynamical responses of biological pathways. In this work, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed (holo) and ligand-unbound open (apo) forms of STING in the membrane system by comparing their conformational and dynamical differences. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays ~174° rotation of the ligand-binding domain (LBD) relative to the open STING structure. The dynamical analysis of residue Cys148 located in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also demonstrate that using the full-length proteins is critical, since the MD simulations of the LBD portion alone cannot properly describe the global conformational properties of STING.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Optimization of Ag Electrocatalyst Performance for CO2 to CO Conversion: Pairing Atomic Simulations with Experiments
This invited presentation encapsulates computational investigation of nanostructured Ag electrocatalyst for CO2 to CO conversion to complement the surface science/electrochemical experiments.
catalysis↗
Optimization of Ag Electrocatalyst Performance for CO2 to CO Conversion: Pairing Atomic Simulations with Experiments
Density-functional theory- based calculations that complement our series of experimental efforts on optimizing Ag electrocatalyst performance for CO2 to CO conversion were presented. Three key findings are drawn out from the combined UHV surface science, STM and electrochemical measurements: (1) Using a series of Ag nanoparticles with 2-6 nm average diameters, CO2 reduction reaction (CO2RR) activity increases, with particle between 2 nm and ∼4 nm demonstrating the highest combination of activity and selectivity; (2) Electronic metal−support interactions (EMSIs) between Ag and C dramatically improve CO2RR performance as evidenced by a scaling relationship between particle size and the relative Ag−C EMSIs strength, which improves the CO2-to-CO Faradaic efficiency of sub-2 nm Ag particles from 2 to ∼100% and increases the CO turnover frequency ∼15-fold compared with similarly sized bare Ag particles; (3) The performance Ag electrocatalysts is improved when supported on S-doped C materials. Computational modeling of 1−10 nm Ag particles predicts a nearly identical size-dependent trend with maximum CO2RR activity predicted for 3.7nm particles. The calculations support the promotional effect of C materials, showing a large charge transfer of 1.02 e from Ag clusters to defective C and a 0.41 eV less endergonic step of forming COOH intermediate on Ag/defective-C compared to the Ag/C system. Calculations indicate a more favorable energetic pathway of CO2-to-CO at the C-S-Ag interface, consistent with experiments.
CO2 utilization↗
Evaluation of Thermal Control Coatings and Polymeric Materials Exposed to Ground Simulated Atomic Oxygen and Vacuum Ultraviolet Radiation
Numerous thermal control and polymeric samples with potential International Space Station applications were evaluated for atomic oxygen and vacuum ultraviolet radiation effects in the Princeton Plasma Physics Laboratory 5 eV Neutral Atomic Oxygen Facility and in the MSFC Atomic Oxygen Drift Tube System. Included in this study were samples of various anodized aluminum samples, ceramic paints, polymeric materials, and beta cloth, a Teflon-impregnated fiberglass cloth. Aluminum anodizations tested were black duranodic, chromic acid anodize, and sulfuric acid anodize. Paint samples consisted of an inorganic glassy black paint and Z-93 white paint made with the original PS7 binder and the new K2130 binder. Polymeric samples evaluated included bulk Halar, bulk PEEK, and silverized FEP Teflon. Aluminized and nonaluminized Chemfab 250 beta cloth were also exposed. Samples were evaluated for changes in mass, thickness, solar absorptance, and infrared emittance. In addition to material effects, an investigation was made comparing diffuse reflectance/solar absorptance measurements made using a Beckman DK2 spectroreflectometer and like measurements made using an AZ Technology-developed laboratory portable spectroreflectometer.
Kamenetzky, R. R.↗
3-D atomistic nanoelectronic modeling on high performance clusters: multimillion atom simulations
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quantum dot nanoelectronics sparse matrix-vector m↗
Evaluation of the Mechanical Properties of Innovative Spacecraft Materials under a LEO Simulated Atomic Oxygen Environment
External spacecraft materials are crucial for protecting satellites from the harsh space environment. This study evaluates the radiation effects of low Earth orbit (LEO) space weather, focusing on high-energy electron and atomic oxygen (AO) exposure, on several modern spacecraft materials. The materials under investigation are “flight duplicates" of samples scheduled for launch as part of the Materials International Space Station Experiment Flight Facility (MISSE-FF) mission in 2025. To observe changes in stress distribution within weathered polymers, the experimental setup based on the photo elasticity technique was developed
Yuliya Kuznetsova↗
Evaluation of the Mechanical Properties of Innovative Spacecraft Materials Under a Low Earth Orbit-Simulated Atomic Oxygen Environment
External spacecraft materials are crucial for protecting satellites from the harsh space environment. This study evaluates the radiation effects of low Earth orbit (LEO) space weather, focusing on high-energy electron and atomic oxygen (AO) exposure, on several modern spacecraft materials. The materials under investigation are “flight duplicates" of samples scheduled for launch as part of the Materials International Space Station Experiment Flight Facility (MISSE-FF) mission in 2025. To observe changes in stress distribution within weathered polymers, the experimental setup based on the photo elasticity technique was developed.
Yuliya Kuznetsova↗
Atomic Oxygen Environment, Effects and Simulation
Atomic oxygen is the most predominant constituent in the low Earth orbital environment between the altitudes of 180 and 650 km. It is also a major constituent of the Mars orbital environment. It is very chemically reactive and can oxidize materials on the outside of spacecraft. In many cases the reaction products are volatile which can lead to mechanical failure. Stable oxides can also form that change the optical or thermal properties of the material. The importance of understanding atomic oxygen reactions with materials has led to both flight experiments in low Earth orbit and ground-based testing in vacuum chambers containing atomic oxygen to study its’ effect on materials. This presentation will focus on defining atomic oxygen environments, discussing atomic oxygen effects on spacecraft materials, reviewing some methods of atomic oxygen simulation, and discussing differences in ground-based testing and space testing as well as synergistic effects.
atomic oxygen, space environment, ground-based tes↗
Modeling of deposit formation in mesoporous substrates via atomic layer deposition: Insights from pore‐scale simulation
Atomic layer deposition (ALD) has been a promising technique in fabricating membranes and tuning their properties with a precision at the atomic level. Fabrication of zeolitic imidazolate framework (ZIF) membranes using the ligand-induced permselectivation (LIPS) method starts with the formation of an oxide in a mesoporous substrate by ALD and is followed by the transformation of this oxide to ZIF using imidazolate vapor treatment. The objective of the ALD step is to block the mesopores with a thin deposit, that is, one with small penetration depth and small thickness on the top surface of the substrate. Unlike typical ALD on nonporous substrates, where all available sites react per ALD cycle, thin deposit formation in a mesoporous substrate requires that only a small fraction of the available deposition sites (i.e., close to the substrate surface) is subjected to ALD. Consequently, reactant dosing and duration of pulses are important process variables which, together with diffusion and reaction kinetics determine the deposit structure. Quantitative understanding of the interplay of these variables and phenomena can enable the rational design of ALD within mesoporous substrates. Here, we extend our earlier modeling effort considering the coexistence of ALD both inside the pores and on the external surface of the substrate. Finite-volume based models were developed and validated to simulate the two distinct modes of deposition cycle by cycle. The total mass uptake of the substrate with ALD cycles can be predicted using the combined surface deposition and pore reaction–diffusion models as affirmed by in situ quartz crystal microbalance experimental data. The ALD reactor model combined with the deposition model can accurately capture the number of ALD cycles needed to block the pores of the substrate. Based on the model, we designed a modified ALD process and examined the performance of the corresponding LIPS membranes. Furthermore, the present modeling work provides a new understanding of the deposit formation via ALD within mesoporous substrates for a variety of membrane applications.
atomic layer deposition↗
Neutralizer and sample chamber for the Atomic Oxygen Simulation System (AOSS)
A neutralizer system capable of converting a beam of oxygen ions (O(+) or O2(+)) into a beam of low-energy neutral oxygen atoms (O) was developed. The neutralizer system is to be designed to be compatible with the Atomic Oxygen Simulation System (AOSS) located in the Physical Science Branch of MSFC. The Center for Molecular and Atomic Studies at Surfaces (CMASS) at Vanderbilt University has met these objectives by developing a system that neutralizes the ions through electron transfer during a grazing-incidence reflection of an ion beam from a smooth nickel surface. The purpose is to describe the system, provide schematic representations of the system, and to discuss the use of the system in relation to the AOSS at the Physical Science Branch of MSFC.
Albridge, Royal G.↗
Davis Computational Spectroscopy Workflow—From Structure to Spectra
Here, we describe an automated workflow that connects a series of atomic simulation tools to investigate the relationship between atomic structure, lattice dynamics, materials properties, and inelastic neutron scattering (INS) spectra. Starting from the atomic simulation environment (ASE) as an interface, we demonstrate the use of a selection of calculators, including density functional theory (DFT) and density functional tight binding (DFTB), to optimize the structures and calculate interatomic force constants. We present the use of our workflow to compute the phonon frequencies and eigenvectors, which are required to accurately simulate the INS spectra in crystalline solids like diamond and graphite as well as molecular solids like rubrene. We have also implemented a machine-learning force field based on Chebyshev polynomials called the Chebyshev interaction model for efficient simulation (ChIMES) to improve the accuracy of the DFTB simulations. We then explore the transferability of our DFTB/ChIMES models by comparing simulations derived from different training sets. We show that DFTB/ChIMES demonstrates ~100× reduction in computational expense while retaining most of the accuracy of DFT as well as yielding high accuracy for different materials outside of our training sets. The DFTB/ChIMES method within the workflow expands the possibilities to use simulations to accurately predict materials properties of increasingly complex structures that would be unfeasible with ab initio methods.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
All-Atom Biomolecular Simulation in the Exascale Era
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML techniques, that model biomolecular motions over unprecedented length and time scales. This new capability holds the potential to revolutionize our understanding of fundamental biological processes. Herein we report on some of the major advances that were discussed at a recent CECAM workshop in Pisa, Italy, on the topic with a primary focus on atomic-level simulations. First, we highlight examples of current large-scale biomolecular simulations and the future possibilities enabled by crossing the exascale threshold. Next, we discuss challenges to be overcome in optimizing the usage of these powerful resources. Finally, we close by listing several grand challenge problems that could be investigated with this new computer architecture.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Low Earth orbit atomic oxygen simulation for durability evaluation of solar reflector surfaces
To evaluate the performance and durability of solar reflector surfaces in the atomic oxygen environment typical of low Earth orbit (LEO), one must expose the reflector surface either directly to LEO or to ground-laboratory atomic oxygen environments. Although actual LEO exposures are most desired, such opportunities are typically scarce, expensive, and of limited duration. As a result, ground-laboratory exposures must be relied upon as the most practical long-term durability evaluation technique. Plasma ashers are widely used as LEO simulation facilities by producing atomic oxygen environments for durability evaluation of potential spacecraft materials. Atomic oxygen arrival differs between ground and space exposure in that plasma asher exposure produces isotropic arrival and space solar tracking produces sweeping arrival. Differences in initial impact reaction probability occur, dependent upon the energy and species existing in these environments. Due to the variations in ground-laboratory and space atomic oxygen, quantification of in-space performance based on plasma asher testing is not straightforward. The various atomic oxygen interactions that can occur with reflector surfaces, such as undercutting in organic substrates at protective coating defect sites, ground-laboratory techniques recommended for evaluating the atomic oxygen durability of reflectors based on asher exposures, and computational techniques which make use of ground-laboratory atomic oxygen exposure to predict in-space LEO durability are addressed.
Degroh, Kim K.↗
A model for trapping and re-solution regarding intra-granular bubbles in UO 2 , linked to atomic-scale simulations
In the literature, a clear definition of the irradiation re-solution frequency of gas from bubbles in the UO 2 fuel is absent. Moreover, for intra-granular bubbles, a detailed calculation of the cumulated displaced gas quantities in function of the distance from the radius of the bubble after a re-solution event has never been published. The assessment of these two elements is very useful if we want to increase the adherence of fission gas release codes to our present knowledge of the behavior of fission gases. Hence, we suggest to link the definition of the re-solution frequency to atomic-scale simulations. Furthermore, we present the cumulated displaced gas quantities obtained from Molecular Dynamics calculations, from which we have derived a re-solution profile that can be exploited to better consider the irradiation re-solution phenomenon inside Fission Gas Release codes. On top of that, we have built a new trapping/re-solution model for intra-granular bubbles linked to Molecular Dynamics simulations that can be easily incorporated into Fission Gas Release codes. In conclusion, we also check that the model is properly built through the comparison of the new model against a reference.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)
Zeolites, an important class of 3-dimensional nanoporous materials, have been widely explored for a variety of applications including gas storage, separations, and catalysis. As the properties of these aluminosilicate materials depend on a number of factors (e.g., framework topology, Si/Al ratio, extra-framework cations etc.), detailed experiments (e.g., catalytic properties, adsorption capacities etc.) are often limited to only a handful of materials. Computational methods have played an important role in (1) providing molecular level insights to rationalize experimental observations, and (2) screening large libraries of zeolites to identify promising candidates for experimental synthesis and validation. Different levels of theory and computational chemistry codes are necessary to describe the range of relevant phenomena such as adsorption (e.g., grand canonical Monte Carlo), diffusion (e.g., molecular dynamics), and chemical reactions (e.g., density functional theory). Manipulation of atomic structures, handling of input files, and developing robust workflows becomes quite cumbersome. To mitigate these challenges, we describe the development of the Multiscale Atomic Zeolite Simulation Environment (MAZE) – a Python package that simplifies zeolite-specific calculation workflows by providing a user-friendly interface for systematically manipulating zeolite structures
97 MATHEMATICS AND COMPUTING↗