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At least 595 records · Page 33

Molecular dynamics simulation of the effect of cooling rate on the structure and properties of lithium disilicate glass

The effects of cooling rate on the structure and properties of lithium disilicate (LS2) glass are investigated using molecular dynamics (MD) computer simulations. The evolution of structural features such as pair distribution function, bond angle distribution, and Li coordination distribution are determined, and correlated with dynamic and static properties to elucidate the effects of cooling rate. The density, elastic moduli, and diffusion coefficient are found to be highly sensitive to cooling rate, whereas the Si pair distribution function and bond angle distribution are weakly affected by the cooling rate. Additionally, the changes of Si-O-Si bond angle and Li coordination number suggest the formation of Li cluster at lower cooling rates. Furthermore, by comparing results from other simulations and reported experiments, we confirm that the increase of cooling rate leads to an increase of conductivity and a decrease of density. Finally, at very high cooling rates, we find that all the atoms in LS2-glass do not relax simultaneously, but do so in two distinct configurations.

36 MATERIALS SCIENCE↗

Molecular dynamics simulations of displacement cascades in LiAlO2 and LiAl5O8 ceramics

Abstract Molecular dynamics was employed to investigate the radiation damage due to collision cascades in LiAlO 2 and LiAl 5 O 8 , the latter being a secondary phase formed in the former during irradiation. Atomic displacement cascades were simulated by initiating primary knock-on atoms (PKA) with energy values = 5, 10 and 15 keV and the damage was quantified by the number of Frenkel pairs formed for each species: Li, Al and O. The primary challenges of modeling an ionic system with and without a core–shell model for oxygen atoms were addressed and new findings on the radiation resistance of these ceramics are presented. The working of a variable timestep function and the kinetics in the background of the simulations have been elaborated to highlight the novelty of the simulation approach. More importantly, the key results indicated that LiAlO 2 experiences much more radiation damage than LiAl 5 O 8 , where the number of Li Frenkel pairs in LiAlO 2 was 3–5 times higher than in LiAl 5 O 8 while the number of Frenkel pairs for Al and O in LiAlO 2 are ~ 2 times higher than in LiAl 5 O 8 . The primary reason is high displacement threshold energies (E d ) in LiAl 5 O 8 for Li cations. The greater E d for Li imparts higher resistance to damage during the collision cascade and thus inhibits amorphization in LiAl 5 O 8 . The presented results suggest that LiAl 5 O 8 is likely to maintain structural integrity better than LiAlO 2 in the irradiation conditions studied in this work.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Characterizing Porous and Nonporous Phenolic Resins from Molecular Dynamics Simulations

Phenolic resins are an important component of many ablative heat shield materials, which protect spacecrafts from the extreme temperatures reached during atmospheric entry. Examples include the high-density Heritage Carbon Phenolic (HCP) used in the Pioneer-Venus and Galileo missions, as well as the low-density Phenolic Impregnated Carbon Ablator (PICA) used in the Mars Science Laboratory and Mars 2020 missions. Additionally, recent developments within NASA have produced the mid-density Heatshield for Extreme Entry Environment Technology (HEEET) and its derivative 3D Woven Mid-Density Carbon Phenolic (3MDCP). Unlike the nonporous phenolic in HCP, PICA and HEEET/3MDCP are fabricated by infusing preforms with diluted phenolic formulations to obtain a lower density porous matrix. Despite the importance of the phenolic phase to the material response during entry, the variation in properties of porous and nonporous phenolic is not well understood. Here, we present an investigation of porous and nonporous phenolic resins using molecular dynamics (MD) simulations. Resin cure is mimicked in the simulations through the inclusion of representative reaction templates to generate accurate models of the complex crosslinked structures. To create porous models, explicit solvent molecules are included during the cure simulations. We observe nanoscale separation of the phenolic and solvent phases, which results in significant differences in the final structures of porous and nonporous models. In addition to a quantitative assessment of the network structure and porosity, we elucidate the effects of the phenolic formulation on the final material properties. These results are compared with experimental data as appropriate.

phenolic↗

Applying molecular dynamics simulations to the study of micro cold spray of yttria

Micro cold spray (MCS) is a novel manufacturing process with proven success depositing dense, thick films of technical ceramics without the need for elevated processing temperatures or chemical precursors. The process transforms a loose sub-micrometer powder into an adherent film with mechanical properties approaching that of the bulk material through a phenomenon known as room temperature impact consolidation. While this phenomenon has been demonstrated for a wide variety of ceramic materials and film substrates, yttria stands out as a material that is both well-characterized in experiments and of significant interest for industrial applications due to its excellent refractory properties. This dissertation seeks to investigate the fundamental mechanisms that enable room temperature impact consolidation by using molecular dynamics (MD) simulations of yttria particle impacts and characterizing the deformation behavior of the system.

36 MATERIALS SCIENCE↗

Computational Fluid Dynamics Simulations to Predict Oxidation in Heat Recovery Steam Generator Tubes

Heat Recovery Steam Generators (HRSGs) are widely used across United States in combined cycle power plants to recover waste heat from the gas turbine (GT). HRSGs are used either to generate electricity or to produce process steam for industrial applications. The primary components of HRSG consists of a duct and a heat exchanger (HX). It is known across the power industry that the high temperature oxidation and ensuing exfoliation problem is a major cause for the damage of HX materials of HRSG. Alloys and/or coatings that can prevent or mitigate oxidation are very expensive, therefore they must be used or applied on the select regions of the HX tubes where the tendency of oxide formation is the highest. The main goal of this project is to identify such regions through Computational Fluid Dynamics (CFD) simulations. Therefore, in this work, we developed a CFD framework using commercial code StarCCM+ for the prediction of the fluid flow and heat transfer in a HRSG and associated oxidation inside the tubes of the HX. The developed CFD framework was verified and validated with experimental data before deployment. We also developed an innovative method to model the effect of the fins on the heat transfer and the pressure drop using a porous media model (PMM) approach to keep the mesh size within reasonable limits. After validation, we performed high-fidelity CFD simulations of a real-scale HRSG using the PMM, with High Performance Computing (HPC) resources of ORNL. From the simulation results, we acquired oxide thickness maps for all the tubes of the select HX sections of HRSG prone to oxidation. These oxide maps can inform regions of the HX tubes that requires oxide-resistant coatings, thereby guiding engineers for cost-efficient manufacturing of the HX that can combat oxidation in HRSGs.

36 MATERIALS SCIENCE↗

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗

Molecular dynamics simulation of thermal transport in UO 2 containing uranium, oxygen, and fission-product defects

Uranium dioxide (UO 2 ) is the most commonly used fuel in light-water nuclear reactors and thermal conductivity controls the removal of heat produced by fission, thereby governing fuel temperature during normal and accident conditions. The use of fuel performance codes by the industry to predict operational behavior is widespread. A primary source of uncertainty in these codes is thermal conductivity, and optimized fuel utilization may be possible if existing empirical models are replaced with models that incorporate explicit thermal-conductivity-degradation mechanisms during fuel burn up. This approach is able to represent the degradation of thermal conductivity due to each individual defect type, rather than the overall burn-up measure typically used, which is not an accurate representation of the chemical or microstructure state of the fuel that actually governs thermal conductivity and other properties. To generate a mechanistic thermal conductivity model, molecular dynamics (MD) simulations of UO 2 thermal conductivity including representative uranium and oxygen defects and fission products are carried out. These calculations employ a standard Buckingham-type interatomic potential and a potential that combines the many-body embedded-atom-method potential with Morse-Buckingham pair potentials. Potential parameters for UO 2+x and ZrO 2 are developed for the latter potential. Physical insights from the resonant phonon-spin-scattering mechanism due to spins on the magnetic uranium ions are introduced into the treatment of the MD results, with the corresponding relaxation time derived from existing experimental data. High defect scattering is predicted for Xe atoms compared to that of La and Zr ions. Uranium defects reduce the thermal conductivity more than oxygen defects. For each defect and fission product, scattering parameters are derived for application in both a Callaway model and the corresponding high-temperature model typically used in fuel-performance codes. The model is validated by comparison to low-temperature experimental measurements on single-crystal hyperstoichiometric UO 2+x samples and high-temperature literature data. Furthermore, this work will enable more accurate fuel-performance simulations and will extend to new fuel types and operating conditions, all of which improve the fuel economics of nuclear energy and maintain high fuel reliability and safety.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Dynamic simulation, control, and performance evaluation of a synergistic solar and natural gas hybrid power plant

Solar power is considered among the leading renewable energy technologies. Abundant supply, flexibility of installation, and decreasing cost makes it an interesting renewable energy resource. However, there are challenges associated with the reliability of solar power due to its intermittent nature. This work demonstrates the synergies that exist in integrated hybrid systems, where a dispatchable fuel is used in conjunction with concentrated solar power. In this simulation-based study, a parabolic trough solar concentrator is used to collect solar energy. The heat collected from the solar field is used to generate steam in a Rankine cycle. The system also utilizes natural gas combustion in the steam generator to provide supplemental steam when the solar intensity is reduced due to cloud cover or at night. Natural gas is also used for superheating the steam, which allows the system to produce higher temperatures and achieve increased thermodynamic cycle efficiencies. This flexible design produces 100 MW at nominal conditions, while it is capable of producing a maximum of 140 MW when sufficient solar energy is available. The novel contributions of this work include a complete, systems-level, dynamic model of a hybrid solar plant. The model is complete with a control system that smoothly transitions the plant from pure natural gas mode at night to solar hybrid mode during the day. It evaluates innovative design features such as flexible fuel operation, steam superheating to boost efficiency, and preheating by solar or waste heat. Furthermore, this work demonstrates that by hybridizing a solar system with a dispatchable energy source, both the reliability and efficiency of the solar power production are increased. The annual solar-to-electric efficiency increases from 15.2% to 26.13% with hybridization, which indicates that utilization of the solar energy is effectively increased.

30 DIRECT ENERGY CONVERSION↗

Machine learning enabled quantification of the hydrogen bonds inside the polyelectrolyte brush layer probed using all-atom molecular dynamics simulations

The configuration of densely grafted charged polyelectrolyte (PE) brushes is strongly dictated by the properties and behavior of the counterions that screen the PE brush charges and the solvent molecules (typically water) that solvate the brush molecules and these screening counterions. Only recently, efforts have been made to study the PE brushes atomistically, thereby shedding light on the properties of brush-supported ions and water molecules. However, even for such efforts, there are limitations associated with using a generic definition to estimate certain properties of water and ions inside the brush layer. For example, water–water hydrogen bonds (HBs) will behave differently for locations outside and inside the brush layer, given the fact that the densely closely grafted PE brush molecules create a soft nanoconfinement where the water connectivity becomes highly disrupted: therefore, using the same definition to quantify the HBs inside and outside the brush layer will be unwise. In this paper, we address this limitation by employing an unsupervised machine learning (ML) approach to predict the water–water hydrogen bonding inside a cationic PE brush layer modeled using all-atom molecular dynamics (MD) simulations. Here, the ML method, which relies on a clustering approach and uses the equilibrium coordinates of the water molecules (obtained from the all-atom MD simulations) as the input, is capable of identifying the structural modification of water–water HBs (revealed through appropriate clustering of the data) inside the PE brush layer induced soft nanoconfinement. Such capabilities would not have been possible by using a generic definition of the HBs. Our calculations lead to four key findings: (1) the clusters formed inside and outside the brush layer are structurally similar; (2) the margin of the cluster is shorter inside the PE brush layer confirming the possible disruption of the HBs inside the PE brush layer; (3) the average “hydrogen–acceptor-oxygen–donor-oxygen” angle that defines the HB is reduced for the HBs formed inside the brush layer; (4) the use of the generic definition (definition usable for characterizing the HBs in brush-free bulk) leads to an overprediction of the number of HBs formed inside the PE brush layer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational strategies in the dynamic simulation of constrained flexible MBS

This research focuses on the computational dynamics of flexible constrained multibody systems. At first a recursive mapping formulation of the kinematical expressions in a minimum dimension as well as the matrix representation of the equations of motion are presented. The method employs Kane's equation, FEM, and concepts of continuum mechanics. The generalized active forces are extended to include the effects of high temperature conditions, such as creep, thermal stress, and elastic-plastic deformation. The time variant constraint relations for rolling/contact conditions between two flexible bodies are also studied. The constraints for validation of MBS simulation of gear meshing contact using a modified Timoshenko beam theory are also presented. The last part deals with minimization of vibration/deformation of the elastic beam in multibody systems making use of time variant boundary conditions. The above methodologies and computational procedures developed are being implemented in a program called DYAMUS.

Amirouche, F. M. L.↗

Test of a flexible spacecraft dynamics simulator

There are a number of approaches one can take to modeling the dynamics of a flexible body. While one can attempt to capture the full dynamical behavior subject to disturbances from actuators and environmental torques, such a detailed description often is unnecessary. Simplification is possible either by limiting the amplitude of motion to permit linearization of the dynamics equations or by restricting the types of allowed motion. In this work, we study the nonlinear dynamics of bending deformations of wire booms on spinning spacecraft. The theory allows for large amplitude excursions from equilibrium while enforcing constraints on the dynamics to prohibit those modes that are physically less relevant or are expected to damp out fast. These constraints explicitly remove the acoustic modes (i.e., longitudinal sound waves and shear waves) while allowing for arbitrary bending and twisting, motions which typically are of lower frequency. As a test case, a spin axis reorientation maneuver by the Polar Plasma Laboratory (POLAR) spacecraft has been simulated. POLAR was chosen as a representative spacecraft because it has flexible wire antennas that extend to a length of 65 meters. Bending deformations in these antennas could be quite large and have a significant effect on the attitude dynamics of the spacecraft body. Summary results from the simulation are presented along, with a comparison with POLAR flight data.

Dichmann, Donald↗

System dynamic simulation: A new method in social impact assessment (SIA)

Many complex social questions are difficult to address adequately with conventional methods and techniques, due to the complicated dynamics, and hard to quantify social processes. Despite these difficulties researchers and practitioners have attempted to use conventional methods not only in evaluative modes but also in predictive modes to inform decision making. The effectiveness of SIAs would be increased if they were used to support the project design processes. This requires deliberate use of lessons from retrospective assessments to inform predictive assessments. Social simulations may be a useful tool for developing a predictive SIA method. There have been limited attempts to develop computer simulations that allow social impacts to be explored and understood before implementing development projects. In light of this argument, this paper aims to introduce system dynamic (SD) simulation as a new predictive SIA method in large development projects. We propose the potential value of the SD approach to simulate social impacts of development projects. We use data from the SIA of Gareh-Bygone floodwater spreading project to illustrate the potential of SD simulation in SIA. It was concluded that in comparison to traditional SIA methods SD simulation can integrate quantitative and qualitative inputs from different sources and methods and provides a more effective and dynamic assessment of social impacts for development projects. We recommend future research to investigate the full potential of SD in SIA in comparing different situations and scenarios.

54 ENVIRONMENTAL SCIENCES↗

Quantifying Dimer and Trimer Formation by Tri- n -butyl Phosphates in n -Dodecane: Molecular Dynamics Simulations

Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential Mean Force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial Distribution Functions (RDF) of TBP suggests the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle and distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using FTIR technique. The new insights into the conformational behaviors of TBP molecule as a monomer and as part of an aggregate could greatly aid the understanding of the complexation between TBP and metal ions in solvent extraction system. The U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences funded the work performed by LXD.

equilibrium constants↗

Local structure analysis of low-temperature neutron pair distribution function coupled with molecular dynamics simulations of CH 4 and CO 2 hydrates from 2 to 210 K

CH 4 hydrates occur naturally and are an abundant potential fuel source with a corresponding risk of potent greenhouse gas release, due to their stability conditions at low temperature and high pressure. Byproduct CO 2 can be exchanged with CH 4 in these natural deposits and can potentially stabilize the hydrates at higher temperatures. CH 4 , CO 2 , and mixed CH 4 -CO 2 hydrates are studied with in situ neutron pair distribution function experiments from 2 to 210 K to investigate the impact of varying the CH 4 -CO 2 guest composition in the gas hydrate structure. These experiments combined with Reverse Monte Carlo analysis allow for the characterization of intermolecular CH 4 and CO 2 interactions with the water molecules which form the hydrate lattice and how they impact the local structure of the lattice itself. Results indicate that when CH 4 and CO 2 co-occupy the hydrate, the host is more strongly distorted than in the pure CH 4 and CO 2 hydrates, but this becomes less defined with increasing temperature. The presence of CO 2 in mixed hydrate increases the stability range and creates a barrier for CH 4 to completely leave the structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards computational polar-topotronics: Multiscale neural-network quantum molecular dynamics simulations of polar vortex states in SrTiO3/PbTiO3 nanowires

Recent discoveries of polar topological structures ( e.g ., skyrmions and merons) in ferroelectric/paraelectric heterostructures have opened a new field of polar topotronics. However, how complex interplay of photoexcitation, electric field and mechanical strain controls these topological structures remains elusive. To address this challenge, we have developed a computational approach at the nexus of machine learning and first-principles simulations. Our multiscale neural-network quantum molecular dynamics molecular mechanics approach achieves orders-of-magnitude faster computation, while maintaining quantum-mechanical accuracy for atoms within the region of interest. This approach has enabled us to investigate the dynamics of vortex states formed in PbTiO 3 nanowires embedded in SrTiO 3 . We find topological switching of these vortex states to topologically trivial, uniformly polarized states using electric field and trivial domain-wall states using shear strain. These results, along with our earlier results on optical control of polar topology, suggest an exciting new avenue toward opto-electro-mechanical control of ultrafast, ultralow-power polar topotronic devices.

Linker, Thomas↗

Accelerated molecular dynamics simulations of dislocation climb in nickel

We report the mechanical behavior of materials operating under high temperatures is strongly influenced by creep mechanisms such as dislocation climb, which is controlled by the diffusion of vacancies. However, atomistic simulations of these mechanisms have traditionally been impractical due to the long time scales required. To overcome these time scale challenges, we use Parallel Trajectory Splicing (ParSplice), an accelerated molecular dynamics method, to simulate dislocation climb in nickel. We focus on modeling the activity of a vacancy near a jog on an edge dislocation in order to observe vacancy pipe diffusion and vacancy absorption at the jog. From rigorously constructed trajectories encompassing more than 2000 vacancy absorption events over a simulation time of more than 4μs at 900 K, a comprehensive sampling of available atomistic mechanisms is collated and analyzed further with molecular statics calculations. We estimate average rates for pipe diffusion and vacancy absorption into the jog using data from the dynamic and static calculations, finding very good agreement. Our results strongly suggest that the dominant mechanism for vacancy absorption by jogs is via biased diffusion to the dislocation core followed by fast pipe diffusion to the jog.

36 MATERIALS SCIENCE↗