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At least 433 records · Page 24

Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.

Menon, Madhu↗

Aladyn - Adaptive Neural Network Molecular Dynamics Simulation Code: Computational Materials Mini-Application

This report provides an overview and commands description of the Computational Materials mini-application, Aladyn. Aladyn is a simple molecular dynamics code written in FORTRAN 2008, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of quantum mechanics-based energy calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. The Aladyn code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing many core architectures based on graphic processing units (GPUs). The effort is related to the High Performance Computing Incubator (HPCI) project at NASA Langley Research Center.

Yamakov, Vesselin I.↗

Particlization in fluid dynamical simulations of heavy-ion collisions: The IS3D module

The IS3D particlization module simulates the emission of hadrons from heavy-ion collisions via Monte-Carlo sampling of the Cooper–Frye formula which converts fluid dynamical information into local phase-space distributions for hadrons. The code package includes multiple choices for the non-equilibrium correction to these distribution functions: the 14-moment approximation, first-order Chapman–Enskog expansion, and two types of modified equilibrium distributions. This makes it possible to explore to what extent heavy-ion experimental data are sensitive to different choices for δf n , presently the main source of theoretical uncertainty in the particlization stage. Here, we validate our particle sampler with a high degree of precision by generating several million hadron emission events from a longitudinally boost-invariant hypersurface and comparing the event-averaged particle spectra and space–time distributions to the Cooper–Frye formula.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Application and use of Multi Body Dynamic Simulations for In Space Mechanisms

The Thermal and Mechanical Analysis Branch of the Space System Department (ES22) is actively growing and expanding a new mechanical analysis capability. In recent years, there has been an increase in the demand for Multi Body Dynamics (MBD) analysis to support small ESPA ring size spacecraft, cubesats, lunar surface operations and large spacecraft with complex operations or deployables. Requirements can be balanced for both needs to ensure mechanism is verified for launch. Multi-body dynamics is the study of multiple rigid or flexible bodies that are linked together or are in contact and the associated kinematics and dynamics of the system. The typical outputs include performance information, loads, and deflections of mechanical systems. They routinely support the development of robotic mechanisms, deployment mechanisms, landing simulations, control systems, and conops planning.

Multi Body Dynamics Analysis↗

Effect of Mg and Ni impurities on tritium diffusion in lithium ceramics through cluster dynamics simulations

This study investigates the impact of Mg and Ni doping on tritium diffusion in LiAlO 2 and LiAl 5 O 8 ceramics, that are used in tritium-producing burnable absorber rods (TPBARs). Utilizing Centipede simulations across a broad temperature range (500 K to 1250 K), we explore the interplay between defect dynamics, cluster formation, and tritium mobility. In LiAlO 2 , Mg doping significantly enhances tritium diffusivity by increasing tritium interstitial concentrations and diffusion coefficients of key species, thereby doubling the overall tritium diffusivity. Ni doping, while shifting the dominant defect to Li vacancies, maintains high tritium mobility due to the low binding energy of Li vacancy-tritium complexes, which ensures effective tritium migration. In LiAl 5 O 8 , Mg and Ni doping results in a slight reduction in the diffusion coefficients of key species, yet the dramatic increase in tritium interstitial concentrations compensates, leading to a net small increase in tritium diffusivity. In conclusion, the findings highlight the critical role of defects in tritium transport and the effect of Mg and Ni defects on the performance of these ceramics in demanding nuclear environments.

Cluster dynamics↗

Exploring non-adiabaticity to CO reduction reaction through ab initio molecular dynamics simulation

Non-adiabatic chemical reaction refers to the electronic excitation during reactions. This effect cannot be modeled by the ground-state Born-Oppenheimer molecular dynamics (BO-MD), where the electronic structure is at the ground state for every step of ions' movement. Although the non-adiabatic effect has been explored extensively in gas phase reactions, its role in electrochemical reactions, such as water splitting and CO 2 reduction, in electrolyte has been rarely explored. On the other hand, electrochemical reactions usually involve electron transport; thus, a non-adiabatic process can naturally play a significant role. In this work, using one-step CO 2 reduction as an example, we investigated the role of the non-adiabatic effect in the reaction. The reaction barriers were computed by adiabatic BO-MD and non-adiabatic real-time time dependent density functional theory (rt-TDDFT). We found that by including the non-adiabatic effect, rt-TDDFT could increase the reaction barrier up to 6% compared to the BO-MD calculated barrier when the solvent model is used to represent water. Simulations were carried out using explicit water molecules around the reaction site under different overpotentials, and similar non-adiabatic effects were found.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.

59 BASIC BIOLOGICAL SCIENCES↗

Simulated dynamic response of a servovalve controlled hydraulic actuator

A general purpose math model of a servovalve controlled hydraulic actuator system is derived. The system consists of a linear actuator with unequal piston areas, a single stage servovalve, a gas charged hydraulic accumulator, and the interconnecting piping. The state equations are integrated using the Advanced Continuous Simulation Language (ACSL) for determining the system's dynamic response characteristics. Using this generalized hydraulic actuator system model, response characteristics were determined for various servovalve commands.

Babcock, Dale A.↗

Computer program system for dynamic simulation and stability analysis of passive and actively controlled spacecraft. Volume 1. Theory

A theoretical development and associated digital computer program system is presented. The dynamic system (spacecraft) is modeled as an assembly of rigid and/or flexible bodies not necessarily in a topological tree configuration. The computer program system may be used to investigate total system dynamic characteristics including interaction effects between rigid and/or flexible bodies, control systems, and a wide range of environmental loadings. Additionally, the program system may be used for design of attitude control systems and for evaluation of total dynamic system performance including time domain response and frequency domain stability analyses. Volume 1 presents the theoretical developments including a description of the physical system, the equations of dynamic equilibrium, discussion of kinematics and system topology, a complete treatment of momentum wheel coupling, and a discussion of gravity gradient and environmental effects. Volume 2, is a program users' guide and includes a description of the overall digital program code, individual subroutines and a description of required program input and generated program output. Volume 3 presents the results of selected demonstration problems that illustrate all program system capabilities.

Bodley, C. S.↗

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↗

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↗

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↗

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.↗

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↗

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↗