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At least 919 records · Page 51

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized here a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

74 ATOMIC AND MOLECULAR PHYSICS↗

Insights into the Reactivity of Brookite TiO 2 Nanorods in Liquid Water from Ab Initio Molecular Dynamics Simulations

Brookite TiO 2 , a rare natural polymorph of TiO 2 , has been reported to be an excellent photocatalyst for the production of hydrogen from water and aqueous alcohol solutions, especially when it is reduced and synthesized in the form of nanorods. Here, we investigate the reactivity of stoichiometric and reduced brookite nanorods in liquid water using ab initio molecular dynamics and hybrid density functional theory calculations. Our simulations show a much higher water dissociation fraction on reduced nanorods than on stoichiometric ones, with an accumulation of the resulting bridging hydroxyls (O br H) and terminal hydroxyls (Ti –OH) on different facets of the nanorod. ObrH groups accumulate preferentially on low-energy (210) facets, where they are stabilized by adjacent reduced Ti (Ti 3+ ) sites, while Ti –OH groups prefer to form at the four-fold coordinated Ti atoms on high-energy (010) facets. This hydroxylation pattern also favors the spatial localization of excited holes on the (010) facets. This coupling between water-induced surface chemistry and charge separation underpins the enhanced photocatalytic activity of brookite nanorods, providing useful information for the design of more efficient TiO2-based nanostructures for solar-driven hydrogen evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of vibration frequency on vibration-assisted nano-scratch process of mono-crystalline copper via molecular dynamics simulation

It has always been a critical issue to understand the material removal behavior of Vibration-Assisted Machining (VAM), especially on atomic level. To find out the effects of vibration frequency on material removal response, a three-dimensional molecular dynamics (MD) model has been established in this research to investigate the effects of scratched groove, crystal defects on the surface quality, comparing with the Von Mises shear strain and tangential force in simulations during nano-scratching process. Comparisons are made among the results of simulations from different vibration frequency with the same scratching feed, depth, amplitude and crystal orientation. Copper potential in this simulation is Embedded-Atom Method (EAM) potential. Interaction between copper and carbon atoms is Morse potential. Simulational results show that higher frequency can make groove smoother. Simulation with high frequency creates more dislocations to improve the machinability of copper specimen. The changing frequency does not have evident effects on Von Mises shear strain. Higher frequency can decrease the tangential force to reduce the consumption of cutting energy and tool wear. In conclusion, higher vibration frequency in VAM on mono-crystalline copper has positive effects on surface finish, machinablility and tool wear reduction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Dynamic Simulation of a Sub-Critical Coal Fired Power Plant

In order to address the demanding operating conditions for remaining coal-fired power plants, a dynamic model and a suite of tools have been developed for studying load cycling and to find optimization opportunities. A sub-critical steam cycle power plant was modeled in a flow-sheet modeling tool, APROS™. The model represented the firing system, economizer, evaporator, superheat, and reheat systems. Four loads from 100% TMCR to 25% TMCR were calibrated and tested such that low-to-high cycling could be studied. The model was run through various load cycles; one of which is presented here. This modeling is a prototype for general use in developing cutting edge controls products and for maximizing economic, low-emissions, and efficient operation of the existing coal power fleet.

Braun, Timothy↗

Validation of Small Satellite Dynamics Simulation Modules using ASTERIA Flight Data

ASTERIA (Arcsecond Space Telescope Enabling Research in Astrophysics) was a CubeSat space telescope that operated in low-Earth orbit, having been deployed from the International Space Station in 2017. The spacecraft has achieved sub-arcsecond pointing stability and millikelvin thermal stability over 20-minute observations. A key enabling feature of the ASTERIA mission is the low level of pointing error that has been demonstrated under ASTERIA’s fine pointing control mode. Prior to launch, the ASTERIA mission performed analysis and simulations to estimate the in-flight pointing performance. This analysis used reaction wheel models provided by JPL’s Small Satellite Dynamics Testbed (SSDT), which had performed Kistler table testing to characterize the jitter caused by the reaction wheels of the Blue Canyon Technologies XACT attitude control unit within ASTERIA. These models were subsequently incorporated into the SSDT simulation. The main source of jitter, the high-frequency attitude disturbance over the camera exposure time, on ASTERIA is the set of rotating reaction wheels that are used for maintaining fine pointing during observations. The reaction wheels impart disturbance forces and torques continuously that cause unwanted motion during imaging. Increased jitter consequently leads to blurring of the image. Therefore, to benefit all SmallSat missions devoted to photometric or spectroscopic astrophysics applications, an on-orbit flight data acquisition and jitter testing campaign was performed in an attempt to help validate the SSDT’s simulation models. This paper describes the process used to validate several simulation models and attempt to characterize the ASTERIA jitter by analyzing the size of the resulting spot size for the target stars as a function of wheel speed, having commanded four wheel speeds for each of three stars of known brightness. After summarizing the on-orbit observation and jitter level measurement process, this paper compares the results obtained from the flight operational environment to the corresponding set of simulation jitter levels. Though the flight data obtained during this experiment was not sufficient to validate the simulation’s jitter model, other models have been validated with flight data, including the magnetic field, orbit propagation, sun position, and long-duration orbit decay models, which may be used by all other projects that use the SSDT’s simulation to increase system capability knowledge.

Mohan, Swati↗

Molecular dynamics simulation of graphene growth at initial stage on Ni(100) facet for low flux C energy by CVD

In this study, atomic simulation for graphene growth on Ni (100) at initial stage via chemical vapor deposition method has been developed. The C-C atoms interaction was performed by Terasoff potential mean while Ni-Ni interaction was specified by EAM (Embedded Atom Modified). On the other hand, we used very simple interatomic potential to describe Ni-C interaction during deposition process. From this simulation, it shows that the formation of graphene is not occurs through a combined deposition mechanism on Ni substrate but via C segregation. It means, Ni-C amorphous is source for graphene growth when cooling down of Ni substrate. This result is appropriate with experiments, tight binding and quantum mechanics simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Accelerating structural dynamics simulations with localised phenomena through matrix compression and projection‐based model order reduction

In this work, a novel approach is introduced for accelerating the solution of structural dynamics problems in the presence of localised phenomena, such as cracks. For this category of problems, conventional projection-based Model Order Reduction (MOR) methods are either limited with respect to the range of system configurations that can be represented or require frequent solutions of the Full Order Model (FOM) to update the low-dimensional spaces, in which solutions are represented. In the proposed approach, low-dimensional spaces, constructed for the healthy structure, are enriched with appropriately selected columns of the flexibility matrix of the system. It can be shown that these spaces contain the solution to the original problem for the static case, while their dimension is much smaller. In order to allow their online construction for arbitrary localised features, the full flexibility matrix of the system should be available. To this end, a hierarchical representation is used for the matrices involved, allowing to compute the flexibility matrix efficiently and with reduced memory requirements. The resulting method offers significant speedups, without sacrificing the flexibility and accuracy of the full order model. The performance and limitations of the approach are studied through a series of examples in structural dynamics.

fracture mechanics↗

Ab initio molecular dynamics simulation of Na-doped aluminosilicate glasses and glass-water interaction

The structure and properties of sodium aluminosilicate (NAS) glasses are investigated using ab initio molecular dynamics and density functional calculations. Four NAS glass models of about 700 atoms with composition (SiO 2 ) 0.6 (Al 2 O 3 ) 0.4-x (Na 2 O) x with Na/Al ratio R = 0.0, 0.5, 1.0 and 1.5 are constructed corresponding to x = 0, 0.135, 0.20 and 0.24. Detailed information on network coordination, electronic structure, interatomic bonding and partial charge distribution, mechanical and optical properties of these models are presented and fully analyzed. The structural details for each R are discussed in terms of short- and intermediate-range order manifested in the coordination number, atomic pair and bond angle distributions. It is shown that the mechanical strength of NAS glasses decreases with increasing Na content, indicating that pure aluminosilicate glass is stronger than the alkali-doped glasses. We use the novel concept of total bond order density to characterize the internal cohesion of the NAS glasses. In the case of R = 1 NAS model, 12 water molecules are added to investigate the solvation effect and hydrolysis in NAS glass.

36 MATERIALS SCIENCE↗

Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A simplified rotor system mathematical model for piloted flight dynamics simulation

The model was developed for real-time pilot-in-the-loop investigation of helicopter flying qualities. The mathematical model included the tip-path plane dynamics and several primary rotor design parameters, such as flapping hinge restraint, flapping hinge offset, blade Lock number, and pitch-flap coupling. The model was used in several exploratory studies of the flying qualities of helicopters with a variety of rotor systems. The basic assumptions used and the major steps involved in the development of the set of equations listed are described. The equations consisted of the tip-path plane dynamic equation, the equations for the main rotor forces and moments, and the equation for control phasing required to achieve decoupling in pitch and roll due to cyclic inputs.

Chen, R. T. N.↗

An Alternative Frictional Boundary Condition for Computational Fluid Dynamics Simulation of Friction Stir Welding

For better application of numerical simulation in optimization and design of friction stir welding (FSW), this paper presents a new frictional boundary condition at the tool/workpiece interface for computational fluid dynamics (CFD) modeling of FSW. The proposed boundary condition is based on an implementation of the Coulomb friction model. Using the new boundary condition, the CFD simulation yields non-uniform distribution of contact state over the tool/workpiece interface, as validated by the experimental weld macrostructure. It is found that interfacial sticking state is present over large area at the tool-workpiece interface, while significant interfacial sliding occurs at the shoulder periphery, the lower part of pin side, and the periphery of pin bottom. Due to the interfacial sticking, a rotating flow zone is found under the shoulder, in which fast circular motion occurs. The diameter of the rotating flow zone is smaller than the shoulder diameter, which is attributed to the presence of the interfacial sliding at the shoulder periphery. For the simulated welding condition, the heat generation due to friction and plastic deformation makes up 54.4 and 45.6% of the total heat generation rate, respectively. In conclusion, the simulated temperature field is validated by the good agreement to the experimental measurements.

36 MATERIALS SCIENCE↗

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Examining the Effect of Exchange-Correlation Approximations in First-Principles Dynamics Simulation of Interfacial Charge Transfer

We examine the extent to which the exchange-correlation (XC) approximation influences modeling interfacial charge transfer using fewest-switches surface hopping (FSSH) simulations within the single-particle description. A heterogeneous interface between a lithium ion and an extended boron-nitride sheet was considered here, being an extreme case in which wave function localization and energy level alignments are highly sensitive to the XC approximation. The PBE0 hybrid XC approximation yields nonadiabatic couplings (NACs) that are significantly smaller than the values obtained from the PBE-GGA approximation by an order of magnitude for localized electronic states. This difference between the two XC functionals for the calculated NACs was found to derive mainly from the wave function characteristics rather than from the lattice movement although first-principles molecular dynamics trajectories, along which NACs are obtained, differ noticeably between the two XC functionals. Using the NACs and single-particle energy level alignments at different levels of theory, FSSH simulations were performed to model the electron transfer dynamics at the interface. Here, the electron transfer time scale was found to vary as much as, but not more than, 1 order of magnitude. The time scale was found to be quite sensitive to both NACs and energy level alignments. While the order of magnitude consistency for the charge transfer rate is encouraging even for this rather extreme model of heterojunction interface, continued advancement in electronic structure methods is required for quantitatively accurate determination of the transfer rate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular dynamics simulation of water in and around carbon nanotubes: A coarse-grained description

In the present study, we intend to investigate behaviour of water in and around hydrophobic open ended carbon nanotubes (CNTs) using a coarse-grained, core-softened model potential for water. The model potential considered here for water has recently been shown to successfully reproduce dynamic, thermodynamic and structural anomalies of water. The epitome of the study is to understand the incarceration of this coarse-grained water in a single-file carbon nanotube. In order to examine the effect of fluid-water van der Waals interaction on the structure of fluid in and around the nanotube, we have simulated three different CNT-water systems with varying degree of solute-water dispersion interaction. The analyses of the radial one-particle density profiles reveal varying degree of permeation and wetting of the CNT interior depending on the degree of fluid-solute attractive van der Waals interaction. A peak in the radial density profile slightly off the nanotube axis signifies a zigzag chain of water molecule around the CNT axis. The average numbers of water molecules inside the CNT have been shown to increase with the increase in fluid-water attractive dispersion interaction.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Molecular Dynamics Simulations of Helium Bubble Formation in Palladium Tritides [Slides]

Pd readily absorbs hydrogen and its isotopes, and can be used to purify gas mixtures involving tritium. Tritium decays to He, forming He bubbles. Bubbles causes possible PCT effects swelling, He release, all leading to failures. Radioactive decay experiments take many years. Molecular dynamics (MD) studies can be quickly done. No previous MD methods can simulate He bubble nucleation and growth.

74 ATOMIC AND MOLECULAR PHYSICS↗

Molecular Dynamics Simulations of Helium Bubble Formation in Palladium Tritides [Slides]

Pd readily absorbs hydrogen and its isotopes, and can be used to purify gas mixtures involving tritium. Tritium decays to He, forming He bubbles. Bubbles causes possible PCT effects swelling, He release, all leading to failures. Radioactive decay experiments take many years. Molecular dynamics (MD) studies can be quickly done. No previous MD methods can simulate He bubble nucleation and growth.

74 ATOMIC AND MOLECULAR PHYSICS↗

Computational Fluid Dynamics Simulations to Assess Spatial Variability and Optimal Ventilation Scenarios for Biological Laboratory Exposures

A significant amount of uncertainty exists regarding potential human exposure to laboratory biomaterials and organisms in Biosafety Level 2 (BSL-2) research laboratories. Computational fluid dynamics (CFD) modeling is proposed as a way to better understand potential impacts of different combinations of biomaterials, laboratory manipulations, and exposure routes on risks to laboratory workers. Here, in this study, we use CFD models to simulate airborne concentrations of contaminants in an actual BSL-2 laboratory under different configurations. Results show that ventilation configuration, sampling location, and contaminant source location can significantly impact airborne concentrations and exposures. Depending on the source location and airflow patterns, the transient and time-integrated concentrations varied by several orders of magnitude. Contaminant plumes from sources located near a return vent (or exhaust like a fume hood or ventilated biosafety cabinet) are likely to be more contained than sources that are further from the exhaust. Having a direct flow between the source and the exhaust (through-flow condition) may reduce potential exposures to individuals outside the air flow path. Designing a BSL-2 room with ventilation and airflow patterns that maximize through-flow conditions to the return/exhaust vents and minimize dispersion and mixing throughout the room is, therefore, recommended. CFD simulations can also be used to assist in characterizing the impacts of supply and return vent locations, room layout, and source locations on spatial and temporal contaminant concentrations. In addition, proper placement of particle sensors can also be informed by CFD simulations to provide additional characterization and monitoring of potential exposures in BSL-2 facilities.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗