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At least 1,657 records · Page 92

Constructing the Mechanism of Dinoflagellate Luciferin Bioluminescence Using Computation

Dinoflagellate luciferin bioluminescence is unique since it does not rely on decarboxylation but is poorly understood compared to that of firefly, bacteria, and coelenterata luciferins. Here, in this work, we computationally investigate possible protonation states, stereoisomers, a chemical mechanism, and the dynamics of the bioluminescence intermediate that is responsible for chemiexcitation. Using semiempirical dynamics, time-dependent density functional theory static calculations, and a correlation diagram, we find that the intermediate’s functional group that is likely responsible for chemiexcitation is a 4-member ring, a dioxetanol, that undergoes [2π + 2π] cycloreversion and the biolumiphore is the cleaved structure. The simulated emission spectra and luciferase-dependent absorbance spectra agree with the experimental data, giving support to our proposed mechanism and biolumiphore. We also compute circular dichroism spectra of the intermediate’s four stereoisomers to guide future experiments in differentiating them.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Water Catalysis of the Reaction of Methanol with OH Radical in the Atmosphere is Negligible

Abstract Faced with the contradictory results of two recent experimental studies [Jara‐Toro et al., Angew. Chem. Int. Ed . 2017 , 56 , 2166 and Chao et al., Angew. Chem. Int. Ed . 2019 , 58 , 5013] of the possible catalytic effect of water vapor on CH 3 OH + OH reaction, we report calculations that corroborate the conclusion made by Chao et al. and extend the rate constant evaluation down to 200 K. The rate constants of the CH 3 OH + OH reaction catalyzed by a water molecule are computed as functions of temperature and relative humidity using high‐level electronic structure and kinetics calculations. The Wuhan–Minnesota Scaling (WMS) method is used to provide accurate energetics to benchmark a density functional for direct dynamics. Both high‐frequency and low‐frequency anharmonicities are included. Variational and tunneling effects are treated by canonical variational transition state theory with multidimensional small‐curvature tunneling. And, most significantly, we include multistructural effects in the rate constant calculations. Our calculations show that the catalytic effect of water vapor is not observable at 200–400 K.

Wu, Junjun↗

A unified non-equilibrium phase change model for injection flow modeling

The homogenous relaxation model (HRM) is one of the most widely used models to describe the liquid- gas phase transition. However, in its original formulation, it is unable to handle multispecies vapor-liquid equilibrium (VLE), which limits its applicability to single-component fluids. In this work, a unified non-equilibrium phase change model that considers the VLE of multicomponent mixtures is proposed building upon the HRM's structure. A time factor is introduced to mimic the effect of different phase change timescales due to different mechanisms, e.g., cavitation, flash-boiling, and evaporation. Here to assess the model's performance, computational fluid dynamics simulations of the internal and near-nozzle injection flow of the Engine Combustion Network's Spray G injector were performed using the nine-component PACE-20 fuel with both the unified model and the original HRM. The predicted fuel density in the near-nozzle region matched well with X-ray tomography measurements. The simulation results indicated that, whereas the HRM failed to capture the vaporization due to convective mixing between the fuel and ambient gas, the unified model performed well in predicting the mixing-driven vaporization and the corresponding evaporative cooling. Further comparisons using the nine-component fuel formula and a single-component fuel surrogate demonstrated the unified model's ability to predict preferential vaporization, which affects the predictions of local mixture composition and rate of vaporization. Finally, it is shown that the unified model is capable of representing multiple phase change mechanisms, and the relaxation time factor plays an important role in determining the degree of phase change due to the different mechanisms.

33 ADVANCED PROPULSION SYSTEMS↗

Magnetic-Field-Driven Electron Dynamics in Graphene

Graphene exhibits unique optoelectronic properties originating from the band structure at the Dirac points. It is an ideal model structure to study the electronic and optical properties under the influence of the applied magnetic field. In graphene, electric field, laser pulse, and voltage can create electron dynamics which is influenced by momentum dispersion. However, computational modeling of momentum-influenced electron dynamics under the applied magnetic field remains challenging. In this work, we perform computational modeling of the photoexcited electron dynamics achieved in graphene under an applied magnetic field. Our results show that magnetic field leads to local deviation from momentum conservation for charge carriers. With the increasing magnetic field, the delocalization of electron probability distribution increases and forms a cyclotron-like trajectory. Our work facilitates understanding of momentum resolved magnetic field effect on non-equilibrium properties of graphene, which is critical for optoelectronic and photovoltaic applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties

De novo protein design provides a framework to test our understanding of protein function and build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small-molecule reactive species. Because excited-state dynamics are influenced by the dynamics and hydration of a photooxidant’s environment, it was important to not only design a binding site but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDI Binding Protein), that held a naphthalenediimide (NDI), a powerful photooxidant, in a programmable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein using ultrafast pump–probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein labeling.

carbonyls↗

Realizing mechanical frustration at the nanoscale using DNA origami

Structural designs inspired by physical and biological systems have been previously utilized to develop mechanical metamaterials with enhanced properties based on clever geometric arrangement of constituent building blocks. Here, we use the DNA origami method to realize a nanoscale metastructure exhibiting mechanical frustration, a counterpart of the well-known phenomenon of magnetic frustration. By selectively actuating reconfigurable struts, it adopts either frustrated or non-frustrated states, each characterized by distinct free energy profiles. While the non-frustrated state distributes the strain homogeneously, the frustrated mode concentrates it at a specific location. Molecular dynamics simulations reconcile the contrasting behaviors and provide insights into underlying mechanics. We explore the design space further by tailoring responses through structural modifications. Our work combines programmable DNA self-assembly with mechanical design principles to overcome engineering limitations encountered at the macroscale to design dynamic, deformable nanostructures with potential applications in elastic energy storage, nanomechanical computation, and allosteric mechanisms in DNA-based nanomachinery.

DNA nanostructures↗

A Simulated Evaluation of Powder Flowability Through a Partially Obstructed Consumable in Blown Powder Directed Energy Deposition Systems

Abstract In the interest of continued industrialization of metal additive manufacturing in modern production environments, cost is often referenced as a primary deterrent to new adopters. Conventional economic models for additive systems, processes, and supply chains often focus on specific process applications with little generalizability, or they neglect significant costs associated with production such as machine maintenance and consumable part replacement. Compounding the latter issue are substantial knowledge gaps in consumable part wear characterization for additive and other convergent manufacturing systems. In coaxial blown powder directed energy deposition systems, gas atomized metal powder is wasted during material deposition at a rate that is partly dependent on present wear phenomena in a consumable nozzle housed in the cladding head assembly. The price and lead time required to replace the nozzle incentivizes its reuse even when visibly worn. Often this initiates a process quality decline in the form of underbuilt geometry and internal defects due to losses in powder catchment efficiency. While depositing H13 steel using a hybrid manufacturing machine tool equipped with such a deposition system, a unique partial clog with a bridge-like structure formed at the consumable nozzle exit when supporting argon gas flows failed mid-process. To further understand coaxial multi-phase powder flow in the event of support gas failure, a computational fluid dynamics simulation is tailored to relevant process parameters, H13 powder material profile, and machine operator observations collected after the incident. The resulting differences in powder flow compared to control gas flow parameters is presented and discussed. The powder flowability and performance of the clogged nozzle is then assessed by using an optical profilometer to extract the profile of the clog and recreate the clog geometry within the simulation environment. In past work this simulation has been experimentally validated for a 316L steel powder material profile and used specifically for analyzing powder stream geometry and catchment efficiency. After the initial powder flow characterization, the clog is removed, and the nozzle is reprofiled. After removing the obstructing clog, the newly unobstructed nozzle geometry, the original off the shelf nozzle geometry, and additional nozzle profiles exploring different consumable refurbishment strategies are reevaluated in the simulation. Powder catchment efficiency for all variant nozzle geometries and relevant flow variables are compared and discussed, along with potential mitigation strategies for optimizing powder flowability with worn consumables. This work expands on the known morphology of blown powder obstructions and wear defects present in consumable coaxial nozzles while discussing pragmatic simulation driven responses to unanticipated subsystem failure in hybrid manufacturing machining platforms.

DeWitte, Lisa↗

gdess: A framework for evaluating simulated atmospheric CO 2 in Earth System Models

Atmospheric carbon dioxide (CO 2 ) plays a key role in the global carbon cycle and global warming. Climate-carbon feedbacks are often studied and estimated using Earth System Models (ESMs), which couple together multiple model components—including the atmosphere, ocean, terrestrial biosphere, and cryosphere—to jointly simulate mass and energy exchanges within and between these components. Despite tremendous advances, model intercomparisons and benchmarking are aspects of ESMs that warrant further improvement (Fer et al., 2021; Smith et al., 2014). Such benchmarking is critical because comparing the value of state variables in these simulations against observed values provides evidence for appropriately refining model components; moreover, researchers can learn much about Earth system dynamics in the process (Randall et al., 2019). We introduce `gdess` (a.k.a., Greenhouse gas Diagnostics for Earth System Simulations), which parses observational datasets and ESM simulation output, combines them to be in a consistent structure, computes statistical metrics, and generates diagnostic visualizations. In its current incarnation, `gdess` facilitates evaluating a model's ability to reproduce observed temporal and spatial variations of atmospheric CO 2 . The diagnostics implemented modularly in `gdess` support more rapid assessment and improvement of model-simulated global CO 2 sources and sinks associated with land and ocean ecosystem processes. We intend for this set of automated diagnostics to form an extensible, open source framework for future comparisons of simulated and observed concentrations of various greenhouse gases across Earth system models.

97 MATHEMATICS AND COMPUTING↗

User's Manual for Computer Program ROTOR

A detailed description of a computer program to calculate tilt-rotor aircraft dynamic characteristics is presented. This program consists of two parts: (1) the natural frequencies and corresponding mode shapes of the rotor blade and wing are developed from structural data (mass distribution and stiffness distribution); and (2) the frequency response (to gust and blade pitch control inputs) and eigenvalues of the tilt-rotor dynamic system, based on the natural frequencies and mode shapes, are derived. Sample problems are included to assist the user.

Yasue, M.↗

Dynamic analysis using superelements for a large helicopter model

Using superelements (substructures), modal and frequency response analysis was performed for a large model of the Advanced Attack Helicopter developed for the U.S. Army. Whiffletree concept was employed so that the residual structure along with the various superelements could be represented as beam-like structures for economical and accurate dynamic analysis. A very large DMAP alter to the rigid format was developed so that the modal analysis, the frequency response, and the strain energy in each component could be computed in the same run.

Patel, M. P.↗

Large eddy simulation of turbulent channel flow: ILLIAC 5 calculation

The capabilities of large eddy simulation in the prediction and analyses of wall-bounded turbulent shear flows are demonstrated. The dynamical equations for large scale field motions are derived. The computational grid network is described and its relation to the observed physical length scales in the flow are discussed. Some aspects of the mechanics and structure of the flow are examined both in the vicinity of the wall and in regions away from the wall. An attempt is made to correlate numerical results with laboratory observations. Other significant observations and conclusions are presented.

Kim, J.↗

A stochastic-dynamic model for global atmospheric mass-field statistics

Global atmospheric mass field error correlations based on satellite observations and on numerical forecasts show strong and systematic latitude dependence. A model for the latitude dependent spatial correlation structure of mass field forecast errors is derived from dynamical considerations. Three methods of solution were tested. In the first method, the equation was solved by expansion in spherical harmonics, and the correlation function was computed analytically using the expansion coefficients. In the second method, the finite difference equivalent of the equation was solved using a fast poisson solver. The correlation function was computed using stratified sampling of the individual realizations. In the third method, a higher order equation was derived, and solved directly in finite differences by two successive applications of the fast poisson solver. The three methods were compared for accuracy and efficiency, and the third method was chosen as clearly superior.

Ghil, M.↗

Comprehensive rotorcraft analysis methods

The development and application of comprehensive rotorcraft analysis methods in the field of rotorcraft technology are described. These large scale analyses and the resulting computer programs are intended to treat the complex aeromechanical phenomena that describe the behavior of rotorcraft. They may be used to predict rotor aerodynamics, acoustic, performance, stability and control, handling qualities, loads and vibrations, structures, dynamics, and aeroelastic stability characteristics for a variety of applications including research, preliminary and detail design, and evaluation and treatment of field problems. The principal comprehensive methods developed or under development in recent years and generally available to the rotorcraft community because of US Army Aviation Research and Technology Activity (ARTA) sponsorship of all or part of the software systems are the Rotorcraft Flight Simulation (C81), Dynamic System Coupler (DYSCO), Coupled Rotor/Airframe Vibration Analysis Program (SIMVIB), Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics (CAMRAD), General Rotorcraft Aeromechanical Stability Program (GRASP), and Second Generation Comprehensive Helicopter Analysis System (2GCHAS).

Stephens, Wendell B.↗

Characterization of damped structural connections for multi-component systems

The inability to model connections adequately has historically limited the ability to predict overall system dynamic response. Connections between structural components are often mechanically complex and difficult to accurately model analytically. Improved analytical models for connections are needed to improve system dynamic predictions. This study explores combining Component Mode Synthesis methods for coupling structural components with Parameter Identification procedures for improving the analytical modeling of the connections. Improvements in the connection stiffness and damping properties are computed in terms of physical parameters so the physical characteristics of the connections can be better understood, in addition to providing improved input for the system model.

Lawrence, Charles↗

Characterization of damped structural connections for multi-component systems

The inability to model connections adequately has historically limited the ability to predict overall system dynamic response. Connections between structural components are often mechanically complex and difficult to accurataely model analytically. Improved analytical models for connections are needed to improve system dynamic predictions. This study explores combining Component Mode Synthesis methods for coupling structural components with Parameter Identification procedures for improving the analytical modeling of the connections. Improvements in the connection stiffness and damping properties are computed in terms of physical parameters so the physical characteristics of the connections can be better understood, in addition to providing improved input for the system model.

Lawrence, Charles↗

Preliminary efforts toward development of data handling and analysis software for unsteady flow measurements: An application for aeroelastic transonic flow configurations

A few years ago the Structural Dynamics Division at LaRC started ambitious experimental research efforts known as the Benchmark Models Program. The primary objective of this program was to provide experimental data that may serve as a calibration source for computational fluid dynamics (CFD) efforts that deal with aeroelastic unsteady flow configurations. It also focuses on the understanding of complex flow phenomenon associated with unsteady flow developments. The overall plan for the program has been described by Bennett, including a presentation of initial test results of flutter of a rigid wing mounted on flexible supports. An example of a test model employed to measure the dynamic response along with corresponding pressure distributions is shown. This model incorporates eighty pressure transducers distributed along two spanwise stations. In addition, the models are equipped with four accelerometers and two strain gages. The data handling system for the Benchmark Model Program is under development. Several interactive computer routines designed for the user interface, dynamic memory allocation, unsteady flow measurements data extraction, and further data processing were developed. To present a few examples of measured data, the unsteady pressure distributions and the wing model dynamic response were plotted.

Finaish, Fathi↗

Calculation of AGARD Wing 445.6 Flutter Using Navier-Stokes Aerodynamics

An unsteady, 3D, implicit upwind Euler/Navier-Stokes algorithm is here used to compute the flutter characteristics of Wing 445.6, the AGARD standard aeroelastic configuration for dynamic response, with a view to the discrepancy between Euler characteristics and experimental data. Attention is given to effects of fluid viscosity, structural damping, and number of structural model nodes. The flutter characteristics of the wing are determined using these unsteady generalized aerodynamic forces in a traditional V-g analysis. The V-g analysis indicates that fluid viscosity has a significant effect on the supersonic flutter boundary for this wing.

Lee-Rausch, Elizabeth M.↗