Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular simulation”

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 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Selective amorphization of SiGe in Si/SiGe nanostructures via high energy Si+ implant

Here, the selective amorphization of SiGe in Si/SiGe nanostructures via a 1 MeV Si + implant was investigated, resulting in single-crystal Si nanowires (NWs) and quantum dots (QDs) encapsulated in amorphous SiGe fins and pillars, respectively. The Si NWs and QDs are formed during high-temperature dry oxidation of single-crystal Si/SiGe heterostructure fins and pillars, during which Ge diffuses along the nanostructure sidewalls and encapsulates the Si layers. The fins and pillars were then subjected to a 3 × 10 15 ions/cm 2 1 MeV Si + implant, resulting in the amorphization of SiGe, while leaving the encapsulated Si crystalline for larger, 65-nm wide NWs and QDs. Interestingly, the 26-nm diameter Si QDs amorphize, while the 28-nm wide NWs remain crystalline during the same high energy ion implant. This result suggests that the Si/SiGe pillars have a lower threshold for Si-induced amorphization compared to their Si/SiGe fin counterparts. However, Monte Carlo simulations of ion implantation into the Si/SiGe nanostructures reveal similar predicted levels of displacements per cm 3 . Molecular dynamics simulations suggest that the total stress magnitude in Si QDs encapsulated in crystalline SiGe is higher than the total stress magnitude in Si NWs, which may lead to greater crystalline instability in the QDs during ion implant. The potential lower amorphization threshold of QDs compared to NWs is of special importance to applications that require robust QD devices in a variety of radiation environments.

36 MATERIALS SCIENCE↗
DOE OSTI2020

PDADMAC/PSS Oligoelectrolyte Multilayers: Internal Structure and Hydration Properties at Early Growth Stages from Atomistic Simulations

We analyze the internal structure and hydration properties of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligoelectrolyte multilayers at early stages of their layer-by-layer growth process. Our study is based on large-scale molecular dynamics simulations with atomistic resolution that we presented recently [Sánchez et al., Soft Matter 2019, 15, 9437], in which we produced the first four deposition cycles of a multilayer obtained by alternate exposure of a flat silica substrate to aqueous electrolyte solutions of such polymers at 0.1M of NaCl. In contrast to any previous work, here we perform a local structural analysis that allows us to determine the dependence of the multilayer properties on the distance to the substrate. We prove that the large accumulation of water and ions next to the substrate observed in previous overall measurements actually decreases the degree of intrinsic charge compensation, but this remains as the main mechanism within the interface region. We show that the range of influence of the substrate reaches approximately 3 nm, whereas the structure of the outer region is rather independent from the position. This detailed characterization is essential for the development of accurate mesoscale models able to reach length and time scales of technological interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

High-pressure hydrogen decompression in sulfur crosslinked elastomers

High-pressure storage and cyclic (de)pressurization of hydrogen gas is known to result in degradation and failure of gas canisters, hoses, linings, and O-rings as the relatively small hydrogen molecule can readily permeate most materials. Hence, identifying material compositions that are less susceptible to hydrogen-induced damage is of significant importance to the hydrogen energy infrastructure. Here, we use classical atomistic molecular dynamics simulations to study hydrogen exposed ethylene-propylene-diene monomer (EPDM) rubber, an elastomer typically used in O-rings. We make chemical modifications to the model by adjusting the crosslink density and report on gas solubility, diffusivity, and molecular restructuring in response to rapid decompression. Our simulations indicate that increases in crosslink density can reduce volumetric expansion during decompression and result in smaller free volume pore sizes. However, these favorable properties for sealing materials come with a tradeoff. At pressure, crosslinks introduce extra free volume, providing potential sites for gas localization, the precursor to cavitation-induced failure.

08 HYDROGEN↗
DOE OSTI2026

Elastic strain engineering of lattice thermal conductivity of silicon: An ab-initio study

Silicon (Si) is the most essential material in the semiconductor industry. It is important to manage the thermal properties of crystalline Si. Elastic strain engineering (ESE) has proven to be an effective tool in controlling the electrical conductivity of Si in strained-silicon technology; its effects on the thermal conductivity of silicon, therefore, warrants careful investigation. The ESE effect is much more pronounced for nanostructured materials due to the ultralarge elastic strains (on the order of 10%) achievable at the nanoscale. In this work, the lattice thermal conductivity (κ L ) of Si under hydrostatic, biaxial, and uniaxial strain states is studied with ab-initio simulations, and the values of strain-dependent κ L compare well with experimental results and existing molecular dynamics simulations. To understand the mechanisms of strain-modulated κ L , the phonon bands, scattering rate, and Grüneisen parameters of phonon modes are computed. It is shown that strain can significantly change the anharmonicity of the crystal system, thus changing phonon scattering rates and κ L . Our results demonstrate that ESE can reduce silicon κ L by up to approximately 90%. Furthermore, uniaxial and biaxial strains can induce highly anisotropic thermal conductivity in Si, with relative variations up to 58.5% and 14.5%, respectively.

Anisotropy in Thermal Conductivity↗
DOE OSTI2024

Surface molecular pump enables ultrahigh catalyst activity

The performance of electrocatalysts is critical for renewable energy technologies. While the electrocatalytic activity can be modulated through structural and compositional engineering following the Sabatier principle, the insufficiently explored catalyst-electrolyte interface is promising to promote microkinetic processes such as physisorption and desorption. By combining experimental designs and molecular dynamics simulations with explicit solvent in high accuracy, we demonstrated that dimethylformamide can work as an effective surface molecular pump to facilitate the entrapment of oxygen and outflux of water. Dimethylformamide disrupts the interfacial network of hydrogen bonds, leading to enhanced activity of the oxygen reduction reaction by a factor of 2 to 3. This strategy works generally for platinum-alloy catalysts, and we introduce an optimal model PtCuNi catalyst with an unprecedented specific activity of 21.8 ± 2.1 mA/cm 2 at 0.9 V versus the reversible hydrogen electrode, nearly double the previous record, and an ultrahigh mass activity of 10.7 ± 1.1 A/mg Pt .

Science & Technology - Other Topics↗
NASA NTRS2012

Observing Planets and Small Bodies in Sputtered High Energy Atom (SHEA) Fluxes

The evolution of the surfaces of bodies unprotected by either strong magnetic fields or thick atmospheres in the Solar System is caused by various processes, induced by photons, energetic ions and micrometeoroids. Among these processes, the continuous bombardment of the solar wind or energetic magnetospheric ions onto the bodies may significantly affect their surfaces, with implications for their evolution. Ion precipitation produces neutral atom releases into the exosphere through ion sputtering, with velocity distribution extending well above the particle escape limits. We refer to this component of the surface ejecta as sputtered high-energy atoms (SHEA). The use of ion sputtering emission for studying the interaction of exposed bodies (EB) with ion environments is described here. Remote sensing in SHEA in the vicinity of EB can provide mapping of the bodies exposed to ion sputtering action with temporal and mass resolution. This paper speculates on the possibility of performing remote sensing of exposed bodies using SHEA The evolution of the surfaces of bodies unprotected by either strong magnetic fields or thick atmospheres in the Solar System is caused by various processes, induced by photons, energetic ions and micrometeoroids. Among these processes, the continuous bombardment of the solar wind or energetic magnetospheric ions onto the bodies may significantly affect their surfaces, with implications for their evolution. Ion precipitation produces neutral atom releases into the exosphere through ion sputtering, with velocity distribution extending well above the particle escape limits. We refer to this component of the surface ejecta as sputtered high-energy atoms (SHEA). The use of ion sputtering emission for studying the interaction of exposed bodies (EB) with ion environments is described here. Remote sensing in SHEA in the vicinity of EB can provide mapping of the bodies exposed to ion sputtering action with temporal and mass resolution. This paper speculates on the possibility of performing remote sensing of exposed bodies using SHEA and suggests the need for quantitative results from laboratory simulations and molecular physic modeling in order to understand SHEA data from planetary missions. In the Appendix, referenced computer simulations using existing sputtering data are reviewed.

Milillo, A.↗
DOE OSTI2022

Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia

Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target–apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix–helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Large-Scale Atomistic Simulations: Investigating Free Expansion

The experiment investigates free expansion of a supercritical fluid into a two-phase liquid-vapor coexistence region. A huge molecular dynamics simulation (6 billion Lennard-Jones atoms) was run on 5760 GPUs (33% of LLNL Sierra) using LAMMPS/Kokkos software. This improved visualization workflow and started preliminary simulations of aluminum using SNAP machine learning potential.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Understanding Metal–Organic Framework Nucleation from a Solution with Evolving Graphs

A mechanistic understanding of metal–organic framework (MOF) synthesis and scale-up remains underexplored due to the complex nature of the interactions of their building blocks. In this work, we investigate the collective assembly of building units at the early stages of MOF nucleation, using MIL-101(Cr) as a prototypical example. Using large-scale molecular dynamics simulations, we observe that the choice of solvent (water and N,N-dimethylformamide), the introduction of ions (Na+ and F–) and the relative populations of MIL-101(Cr) half-secondary building unit (half-SBU) isomers have a strong influence on the cluster formation process. Additionally, the shape, size, nucleation and growth rates, crystallinity, and short and long-range order largely vary depending on the synthesis conditions. We evaluate these properties as they naturally emerge when interpreting the self-assembly of MOF nuclei as the time evolution of an undirected graph. Solution-induced conformational complexity and ionic concentration have a dramatic effect on the morphology of clusters emerging during assembly. While pure solvents lead to the rapid formation of a small number of large clusters, the presence of ions in aqueous solutions results in smaller clusters and slower nucleation. This diversity is captured by the key features of the graph representation. Principle component analysis on graph properties reveals that only a small number of molecular descriptors is needed to deconvolute MOF self-assembly. Furthermore, descriptors such as the average coordination number between half-SBUs and fractal dimension are of particular interest as they can be can be followed experimentally by techniques like by time-resolved spectroscopy. Ultimately, graph theory emerges as an approach that can be used to understand complex processes revealing molecular descriptors accessible by both simulation and experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Extemporaneous Mechanochemistry: Shock-Wave-Induced Ultrafast Chemical Reactions Due to Intramolecular Strain Energy

We report regions of energy localization referred to as hotspots are known to govern shock initiation and the run-to-detonation in energetic materials. Mounting computational evidence points to accelerated chemistry in hotspots from large intramolecular strains induced via the interactions between the shock wave and microstructure. However, definite evidence mapping intramolecular strain to accelerated or altered chemical reactions has so far been elusive. From a large-scale reactive molecular dynamics simulation of the energetic material 1,3,5-triamino-2,4,6-trinitrobenzene, we map decomposition kinetics to molecular temperature and intramolecular strain energy prior to reaction. Both temperature and intramolecular strain are shown to accelerate chemical kinetics. A detailed analysis of the atomistic trajectory shows that intramolecular strain can induce a mechanochemical alteration of decomposition mechanisms. The results in this paper could inform continuum-level chemistry models to account for a wide range of mechanochemical effects.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Species Separation and Hydrogen Streaming upon Shock Release from Polystyrene under Inertial Confinement Fusion Conditions

Shock release from inertial confinement fusion (ICF) shells poses a great challenge to single-fluid hydrodynamic equations, especially for describing materials composed of different ion species. This has been evidenced by a recent experiment [Haberberger et al., Phys. Rev. Lett. 123, 235001 (2019)], in which low-density plasmas ( 10 19 to 10 20 cm – 3 ) are measured to move far ahead of what radiation-hydrodynamic simulations predict. To understand such experimental observations, in this work we have performed large-scale nonequilibrium molecular-dynamics simulations of shock release in polystyrene (CH) at experimental conditions. These simulations revealed that upon shock releasing from the back surface of a CH foil, hydrogen can stream out of the bulk of the foil due to its mass being lighter than carbon. This released hydrogen, exhibiting a much broader velocity distribution than carbon, forms low-density plasmas moving in nearly constant velocities ahead of the in-flight shell, which is in quantitative agreement with the experimental measurements. Such kinetic effect of species separation is currently missing in single-fluid radiation-hydrodynamics codes for ICF simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Spatial arrangement of dynamic surface species from solid-state NMR and machine learning-accelerated MD simulations

Here, the surface arrangement of motional organic functionalities is explored by experimental dipolar coupling measurements and the prediction of motionally-averaged coupling constant from molecular dynamics simulations. The use of machine learning potentials was key to reaching the timescale required. The distance between dynamic surface species are important in cooperative heterogeneous catalysis.

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

Isolating Chemical Reaction Mechanism as a Variable with Reactive Coarse-Grained Molecular Dynamics: Step-Growth versus Chain-Growth Polymerization

Here we present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often group multiple atoms into a single “coarse-grained” interaction site, which leads to a loss of chemical resolution. In this work we convert this shortcoming into a feature and use identical coarse-grained models to represent molecules that share nonreactive characteristics but react by different mechanisms. As a proof of concept, we use this approach to simulate and investigate distinct, yet similar, trifunctional isocyanurate resin formulations that polymerize by either chain- or step-growth. Because the underlying molecular mechanics of these models are identical, all emergent differences are a function of the reaction mechanism only. We find that the microscopic morphologies resemble related all-atom simulations and that simulated mechanical testing reasonably agrees with experiment.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cooperativity in the Aldol Condensation Using Bifunctional Mesoporous Silica–Poly(styrene) MCM-41 Organic/Inorganic Hybrid Catalysts

This work explores the efficacy of silica/organic hybrid catalysts, where the organic component is built from linear aminopolymers appended to the silica support within the support mesopores. Specifically, the role of molecular weight and polymer chain composition in amine-bearing atom transfer radical polymerization-synthesized poly(styrene-co-2-(4-vinylbenzyl)isoindoline-1,3-dione) copolymers is probed in the aldol condensation of 4-nitrobenzaldehyde and acetone. Controlled polymerization produces protected amine-containing poly(styrene) chains of controlled molecular weight and dispersity, and a grafting-to thiol–ene coupling approach followed by a phthalimide deprotection step are used to covalently tether and activate the polymer hybrid catalysts prior to the catalytic reactions. Site-normalized batch kinetics are used to assess the role of polymer molecular weight and chain composition in the cooperative catalysis. Lower-molecular-weight copolymers are demonstrated to be more active than catalysts built from only molecular organic components or from higher-molecular-weight chains. Molecular dynamics simulations are used to probe the role of polymer flexibility and morphology, whereby it is determined that higher-molecular-weight hybrid structures result in congested pores that inhibit active site cooperativity and the diffusivity of reagents, thus resulting in lower rates during the reaction.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Probing C–I bond fission in the UV photochemistry of 2-iodothiophene with core-to-valence transient absorption spectroscopy

The UV photochemistry of small heteroaromatic molecules serves as a testbed for understanding fundamental photo-induced chemical transformations in moderately complex compounds, including isomerization, ring-opening, and molecular dissociation. Here, a combined experimental-theoretical study of 268 nm UV light-induced dynamics in 2-iodothiophene (C 4 H 3 IS) is performed. The dynamics are experimentally monitored with a femtosecond extreme ultraviolet (XUV) probe that measures iodine N-edge 4d core-to-valence transitions. Experiments are complemented by density functional theory calculations of both the pump-pulse induced valence excitations and the XUV probe-induced core-to-valence transitions. Possible intramolecular relaxation dynamics are investigated by ab initio molecular dynamics simulations. Furthermore, gradual absorption changes up to ~0.5 to 1 ps after excitation are observed for both the parent molecular species and emerging iodine fragments, with the latter appearing with a characteristic rise time of 160 ± 30 fs. Comparison of spectral intensities and energies with the calculations identifies an iodine dissociation pathway initiated by a predominant π → π* excitation. In contrast, initial excitation to a nearby n ⟂ → σ* state appears unlikely based on a significantly smaller oscillator strength and the absence of any corresponding XUV absorption signatures. Excitation to the π → π* state is followed by contraction of the C–I bond, enabling a nonadiabatic transition to a dissociative π→σ C-I * state. For the subsequent fragmentation, a relatively narrow bond-length region along the C–I stretch coordinate between 230 and 280 pm is identified, where the transition between the parent molecule and the thienyl radical + iodine atom products becomes prominent in the XUV spectrum due to rapid localization of two singly occupied molecular orbitals on the two fragments.

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

Efficient end-to-end simulation of time-dependent coherent X-ray scattering experiments

Physical optics simulations for beamlines and experiments allow users to test experiment feasibility and optimize beamline settings ahead of beam time in order to optimize valuable beam time at synchrotron light sources like NSLS-II. Further, such simulations also help to develop and test experimental data processing methods and software in advance. The Synchrotron Radiation Workshop ( SRW ) software package supports such complex simulations. We demonstrate how recent developments in SRW significantly improve the efficiency of physical optics simulations, such as end-to-end simulations of time-dependent X-ray photon correlation spectroscopy experiments with partially coherent undulator radiation (UR). The molecular dynamics simulation code LAMMPS was chosen to model the sample: a solution of silica nanoparticles in water at room temperature. Real-space distributions of nanoparticles produced by LAMMPS were imported into SRW and used to simulate scattering patterns of partially coherent hard X-ray UR from such a sample at the detector. The partially coherent UR illuminating the sample can be represented by a set of orthogonal coherent modes obtained by simulation of emission and propagation of this radiation through the coherent hard X-ray (CHX) scattering beamline followed by a coherent-mode decomposition. GPU acceleration is added for several key functions of SRW used in propagation from sample to detector, further improving the speed of the calculations. The accuracy of this simulation is benchmarked by comparison with experimental data.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Probing Carbon Mineralization Mechanisms in Pore and Bulk Fluids by Harnessing Architected Calcium Silicates

The ability to synthesize materials with well-controlled pore structures gives us unprecedented control over probing fluid interactions with reactive interfaces and advancing calibrated insights into coupled chemo-morphological interactions. One of the primary challenges in developing crystalline silicate materials lies in achieving ordered pore structures. Existing approaches of producing amorphous mesoporous metal silicates via sol–gel methods and heat-treatment of these materials to produce crystalline phases cause the pore structures in the amorphous phases to collapse. To overcome this challenge, carbon coating of amorphous mesoporous calcium silicate particles is carried out to retain the pore structure, while the material is heated to produce crystalline calcium silicate with calcium sulfate inclusions. The pore diameter in these materials is about 3.9 nm, with a surface area and a pore volume of 28.75 m 2 /g and 0.092 cm 2 /g, respectively. The mechanisms of carbon mineralization are investigated by reacting architected calcium silicate with 1 M Na 2 CO 3 and monitoring the evolution in the structural phases using operando wide-angle X-ray scattering (WAXS) measurements. Formation of stable calcium carbonate polymorph or calcite and metastable calcium carbonate polymorph or vaterite in pore and bulk fluids, respectively, resulting from the reaction between Na 2 CO 3 and CaSiO 3 , are noted. The mechanisms associated with carbon mineralization are delineated using ReaxFF molecular dynamics (MD) simulations. The surface dissolution reaction is initiated by 2H + ions that replace a Ca 2+ ion in the Ca–silicate matrix. Ca 2+ ions in the solution initially react with water to form calcium hydroxide and eventually form calcium (bi)carbonate. A slow and gradual increase in the formation of sodium silicate in the solution resulting from the reactions of silicic acid or the silicon dioxide reaction with sodium hydroxide is noted. When carbon mineralization occurs in environments bearing interfacial fluids, calcite is the dominant calcium carbonate polymorph, as determined using experiments with pore fluids and molecular-scale simulations. In conclusion, these studies provide fundamental insights into the mechanisms underlying the carbon mineralization of calcium silicate informed by experiments and molecular-scale simulations.

Calcium↗
DOE OSTI2022

Method to determine the electron–ion temperature relaxation rate from test particle distributions

Here a method to calculate the electron–ion energy exchange rate from the forces on and velocities of an ensemble of test particles is described. The essence of the method is that the energy exchange rate is related to the covariance between the distribution of velocities of test particles and the forces acting on them. The energy exchange rate is related to the electron–ion temperature relaxation rate in the limit of a low test particle speed. A proof of concept is conducted with first-principles molecular dynamics simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗