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At least 1,117 records · Page 62

Simulations of the Biodegradation of Citrate Based Polymers for Artificial Scaffolds Using Accelerated Reactive Molecular Dynamics

Here, we explore the reactivity and mechanical properties of poly(1,6-hexanediol-co-Citric acid) via ReaxFF molecular dynamics simulations. We implement an accelerated scheme within the ReaxFF framework to study the hydrolysis reaction of the polymer which is provided with sufficient amount of energy known as the restrain energy after a suitable pre-transition state configuration is obtained to overcome the activation energy barrier and the desired product is obtained. The validity of the ReaxFF force field is established by comparing the ReaxFF energy barriers of ester and ether hydrolysis with benchmark DFT values in literature. We perform chemical and mechanical degradation of polymer chain bundles at 300 K. We find that ester hydrolyzes faster than ether due to lower activation energy barrier of the reaction. The selectivity of the bond-boost scheme has been demonstrated by lowering the boost parameters of the accelerated simulation which almost stops the ether hydrolysis. Mechanical degradation of pre-hydrolyzed and intermittent hydrolyzed polymer bundles is performed along the longitudinal direction at two different strain rates. We find that the tensile modulus of the polymers are increases with increase in strain rates which shows that polymers show a strain dependent behavior. The tensile modulus of the Polyester-ether is higher than Polyester yet reaches yield-stress faster than Polyester. This makes Polyester more ductile than Polyester-ether.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic nanodomains dictate macroscopic properties in lead halide perovskites

Lead halide perovskites have emerged as promising materials for solar energy conversion and X-ray detection owing to their remarkable optoelectronic properties. However, the microscopic origins of their superior performance remain unclear. Here we show that low-symmetry dynamic nanodomains present in the high-symmetry average cubic phases, whose characteristics are dictated by the A-site cation, govern the macroscopic behaviour. We combine X-ray diffuse scattering, inelastic neutron spectroscopy, hyperspectral photoluminescence microscopy and machine-learning-assisted molecular dynamics simulations to directly correlate local nanoscale dynamics with macroscopic optoelectronic response. Our approach reveals that methylammonium-based perovskites form densely packed, anisotropic dynamic nanodomains with out-of-phase octahedral tilting, whereas formamidinium-based systems develop sparse, isotropic, spherical nanodomains with in-phase tilting, even when crystallography reveals cubic symmetry on average. We demonstrate that these sparsely distributed isotropic nanodomains present in formamidinium-based systems reduce electronic dynamic disorder, resulting in a beneficial optoelectronic response, thereby enhancing the performance of formamidinium-based lead halide perovskite devices. By elucidating the influence of the A-site cation on local dynamic nanodomains, and consequently, on the macroscopic properties, we propose leveraging this relationship to engineer the optoelectronic response of these materials, propelling further advancements in perovskite-based photovoltaics, optoelectronics and X-ray imaging.

Materials Science↗

Dissociation dynamics of the diamondoid adamantane upon photoionization by XUV femtosecond pulses

This work presents a photodissociation study of the diamondoid adamantane using extreme ultraviolet femtosecond pulses. The fragmentation dynamics of the dication is unraveled by the use of advanced ion and electron spectroscopy giving access to the dissociation channels as well as their energetics. To get insight into the fragmentation dynamics, we use a theoretical approach combining potential energy surface determination, statistical fragmentation methods and molecular dynamics simulations. We demonstrate that the dissociation dynamics of adamantane dications takes place in a two-step process: barrierless cage opening followed by Coulomb repulsion-driven fragmentation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Investigation of flow regimes in arc plasma–gas interactions using a two-temperature arc in crossflow model

The perpendicular impingement of a gas stream on an electric arc, a configuration known as the arc in crossflow, is of primary relevance in the study of plasma-gas interactions, as well as in industrial applications such as circuit breakers and wire-arc spraying. The flow dynamics in the arc in crossflow are the result of coupled fluid-thermal-electromagnetic phenomena accompanied by large property gradients, which can produce significant deviations from Local Thermodynamic Equilibrium (LTE) among electrons and gas species. These characteristics can lead to the establishment of distinct flow regimes depending on the relative values of the controlling parameters of the system, such as inflow velocity, arc current, and inter-electrode spacing. A two-temperature non-LTE (NLTE) model is used to investigate the arc dynamics and the establishment of flow regimes in the arc in crossflow. The plasma flow model is implemented within a nonlinear Variational Multiscale (VMS) numerical discretization approach that is less dissipative, and hence better suited to capture unstable behavior, than traditional VMS methods commonly used in computational fluid dynamics simulations. The Reynolds and the Enthalpy dimensionless numbers, characterizing the relative flow strength and arc strength, respectively, are chosen as the controlling parameters of the system. Simulation results reveal the onset of dynamic behavior and the establishment of steady, periodic, quasi-periodic, and chaotic or potentially turbulent, regimes, as identified by distinct spatiotemporal fluctuations. The computational findings reveal the role of increasing the relative arc strength on enhancing flow stability by delaying the growth of fluctuating and unstable flow behavior.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Discovery of enhanced lattice dynamics in a single-layered hybrid perovskite

Layered hybrid perovskites exhibit emergent physical properties and exceptional functional performances, but the coexistence of lattice order and structural disorder severely hinders our understanding of these materials. One unsolved problem regards how the lattice dynamics are affected by the dimensional engineering of the inorganic frameworks and their interaction with the molecular moieties. Here, we address this question by using a combination of spontaneous Raman scattering, terahertz spectroscopy, and molecular dynamics simulations. This approach reveals the structural dynamics in and out of equilibrium and provides unexpected observables that differentiate single- and double-layered perovskites. While no distinct vibrational coherence is observed in double-layered perovskites, an off-resonant terahertz pulse can drive a long-lived coherent phonon mode in the single-layered system. This difference highlights the dramatic change in the lattice environment as the dimension is reduced, and the findings pave the way for ultrafast structural engineering and high-speed optical modulators based on layered perovskites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bulb-style Kaplan Turbine - Run-of-the-river (ror) Hydro Governor And Turbine Model

This software package includes hydro governor and turbine models developed in Simulink (Mathworks Inc.) and RSCAD (RTDS Technologies) for low-head bulb-style Kaplan turbine hydropower plants. The model developed in Simulink has been designed and tuned to match the governor-turbine response for a real-world hydropower unit owned by Idaho Falls Power (IFP). The Simulink and RSCAD models enable real-time testing in a hardware-in-the-loop (HIL) implementation using OPAL-RT and RTDS digital real-time simulators, respectively. An automatic initialization for dynamic simulation has also been integrated to each model in both Simulink and RSCAD. The RSCAD initialization involves a novel python-based interfacing for automatic modification of the initial conditions in the model. The parameters of these models can be tuned to match other hydropower plants in this class.

Alam, SMShafiul↗

GridOPTICS/GridPACK

GridPACK is a software framework consisting of a set of modules designed to simplify the development of programs that model the power grid and run on parallel, high performance computing platforms. It also contains several fully developed applications, including powerflow, dynamic simulation, state estimation, Kalman filter analysis (dynamic state estimation), contingency analysis and real time path rating. These applications can be used either standalone or as components in more complicated workflows that combine several different types of application together. The framework modules are available as a combination of libraries and software templates and consist of components for setting up and distributing power grid networks, support for modeling the behavior of individual buses and branches in the network, converting the network models to the corresponding algebraic equations, and parallel routines for manipulating and solving large algebraic systems. The framework also contains a module for distributing tasks evenly amongst computing resources, even if individual tasks vary widely in their execution times. Additional modules support input and output, basic statistical analysis of contingency based calculations, distributed data structures, as well as basic profiling and error management.

Palmer, Bruce↗

Investigation of the Impact of Lipid Acyl Chain Saturation on Fusion Peptide Interactions with Lipid Bilayers

The interaction of many peptides with lipid bilayer membranes strongly depends on the lipid composition. Here, a study of the impact of unsaturated lipid acyl chains on the interaction of a derivative of the HIV-1 fusion peptide with lipid bilayer vesicles is presented. Lipid bilayer vesicles composed of mixtures of lipids with two saturated acyl chains and lipids and one saturated and one unsaturated acyl chain, but identical head groups, were studied. The dependence of the peptide conformation on the unsaturated lipid content was probed by circular dichroism spectroscopy, while the impact of the peptide on the bilayer structure was determined by small-angle neutron scattering. The impact of the peptide on the lipid bilayer vesicle dynamics was investigated using neutron spin echo spectroscopy. Molecular dynamics simulations were used to characterize the behavior of the systems studied to determine if there were clear differences in their physical properties. The results reveal that the peptide–bilayer interaction is not a simple function of the unsaturated lipid acyl chain content of the bilayer. Instead, the peptide behavior is more consistent with that seen for the bilayer containing only unsaturated lipids, which is supported by lipid-specific interactions revealed by the simulations.

59 BASIC BIOLOGICAL SCIENCES↗

The design and operation of a planet emitted and albedo radiation simulator

A simulator is described, which provides a dynamic simulation of planetary albedo and planet-emitted thermal radiation. The simulator was designed for model tests of advanced thermal control concepts, the development of space hardware, and flight qualification of small payloads. The simulator was designed to be used in a vacuum chamber equipped with liquid nitrogen cold walls and a solar simulator. The simulator consists of two major components: a gimbaled model support system and an array of quartz infrared lamps. Tests indicate that the apparatus will satisfactorily simulate the secondary radiation on a 0.92-meter spherical body in near-earth orbits. Calculations indicate that other shapes can be accommodated without structural modifications.

Sweet, G. E.↗

Global crop production forecasting - A simulation analysis of the data system problems and their solutions

Alternative data systems for a global crop production forecasting system were studied with the aid of a unique simulation facility called the Data System Dynamic Simulator (DSDS). Information system requirements were determined and compared with existing and planned data systems, and deficiencies were identified and analyzed. A first step was to determine the data load for an operational global crop production forecasting system as a function of data frequency, crop types, biophases, cloud coverage, and number of satellites. The DSDS was used to correlate the interrelated influence of orbital parameters, crop calendars, and cloud conditions to generate global data loading profiles. Some of the more important conclusions and the main features of the simulation system are presented.

Golden, H.↗

A summary of the Dynamics Explorer /DE/-2 spacecraft attitude control operations and dynamics

A summary of attitude control operations and observed attitude dynamics for the Dynamics Explorer (DE)-2 spacecraft is presented. By performing a systematic analysis of spacecraft drift and through optimization of modeling parameters in dynamics simulators, insight is given into spacecraft dynamics, techniques for reducing drift, and methods for streamlining operational procedures. This paper discusses how attitude and momentum drift were reduced for DE-2 by changing spacecraft geometry, altering operational procedures and making timely use of the control modes available. Attempts to correlate spacecraft drift activity with known environmental variables are made with only limited success.

Stengle, T. H.↗

Control response measurements of the Skyship-500 airship

An examination is conducted of the Skyship 500's dynamic response to control inputs from elevators, rudders, and throttles at zero, 25, and 40 kts indicated airspeed. Input frequency sweeps were made with pitch and turn controls at 25 and 40 kts, ranging in frequency from about 0.03 to 1.5 Hz. FFT data analysis was then applied to compute describing functions for each run. Frequency responses are noted to be very smooth, and comparisons between repeat runs indicate excellent agreement. Summary plots of the faired describing functions from each run form the core of the data presented. These data constitute a comprehensive and reliable data base on which to predicate future dynamic simulation mathematical models of small airship dynamic response.

Jex, H. R.↗

On the mechanics of filament winding. I - A generalized model

In this paper the filament winding process was analyzed to relate process variables to structural parameters. An analytical model has been developed for a filament wound preform by determining the necessary geometric and kinematic conditions. An equation of motion of winding was developed to predict layer by layer geometry using the mandrel shape as the initial boundary condition. This model provides the laws of motion of the traverse stroke relative to the mandrel to ensure that the filament laydown is of the predetermined geodesic path over the mandrel, that the winding density is distributed over the mandrel in the prearranged manner, and that the winding build is being formed to reproduce the preassigned shape or contour of the preform. From this analysis, the winding process parameters can be controlled accordingly to produce any given shape. The analytical model was used to produce computer simulation of the winding process. The dynamic simulation of the winding process visualizes and inspects the layer by layer path of the tow and provides process variables required to produce preforms of optimum structural parameters.

Hamouda, Hechmi↗

Impact of DER Communication Delay in AGC: Cyber-Physical Dynamic Co-Simulation: Preprint

Distributed energy resource (DER) frequency regulations are promising technologies for future grid operation. Unlike conventional generators, DERs might require open communication networks to exchange signals with control centers, possibly through DER aggregators; therefore, the impacts of the communication variations including the latency on the system frequency stability need to be investigated. This paper develops a cyber-physical dynamic simulation (CPDS) model based on the Hierarchical Engine for Large-Scale Co-Simulation (HELICS) to evaluate the impact of the communication variations, such as delays in DER frequency regulations. The feasible delay range can be obtained under different AGC parameter settings. The results show that the risk of instability generally increases with the communication delay and that the difference of AGC provided from DER and conventional generation units should be recognized when designing frequency regulation controllers.

61 RADIATION PROTECTION AND DOSIMETRY↗

Time reversal symmetry breaking and odd viscosity in active fluids: Green–Kubo and NEMD results

Active fluids, which are driven at the microscale by non-conservative forces, are known to exhibit novel transport phenomena due to the breaking of time reversal symmetry. Recently, Epstein and Mandadapu [arXiv:1907.10041 (2019)] obtained Green-Kubo relations for the full set of viscous coefficients governing isotropic chiral active fluids, including the so-called odd viscosity, invoking Onsager's regression hypothesis for the decay of fluctuations in active non-equilibrium steady states. In this Communication, we test these Green-Kubo relations using molecular dynamics simulations of a canonical model system consisting of actively torqued dumbbells. We find the resulting odd and shear viscosity values from the Green-Kubo relations to be in good agreement with values measured independently through non-equilibrium molecular dynamics flow simulations. This provides a test of the Green-Kubo relations and lends support to the application of the Onsager regression hypothesis in relation to viscous behaviors of active matter systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Three-dimensional structure determination and prediction of proteins with intrinsically disordered regions, unstructured regions, conformational flexibility, and lacking homologous structures are challenging. We previously predicted and refined an in silico structure of a plant cellulose synthase from cotton (GhCESA1), and more recently, cryo-electron microscopy (cryo-EM) has resolved a majority of the lengths of two CESA structures from poplar (PttCESA8) and cotton (GhCESA7). However, 26–30% of these cryo-EM structures remain unresolved, including the N-terminal domain, half of the class-specific region, the gating loop region, and the C-terminal domain. Here, we describe the generation and evaluation of a full-length hybrid GhCESA1 model based on this cryo-EM PttCESA8 structure, with unresolved regions completed using this in silico refined GhCESA1 model. All-atom molecular dynamics simulations and subsequent energy minimizations were performed for the in silico and hybrid GhCESA1 models in a lipid bilayer-water-ion environment, and structural stability, dynamics, energetics, contacts, and quality were evaluated. The unresolved regions were found to be the most dynamic, in agreement with their poor electron density with cryo-EM. The hybrid model exhibited a higher total secondary structure content, more favorable intra-protein and protein-lipid interaction energies, and improved quality metrics. Moreover, hydrogen bonding was revealed to be a primary mechanism for intra-protein and protein-lipid contacts. These results demonstrate that in silico structure prediction and refinement may be useful to augment experimental structure determination, especially for disordered and unstructured regions. Furthermore, this hybrid model can serve as a steppingstone to derive full-length homology models of other CESAs found in more experimentally tractable organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling the aqueous interface of amorphous TiO 2 using deep potential molecular dynamics

Amorphous titanium dioxide (a-TiO 2 ) is widely used as a coating material in applications such as electrochemistry and self-cleaning surfaces where its interface with water has a central role. However, little is known about the structures of the a-TiO 2 surface and aqueous interface, particularly at the microscopic level. In this work, we construct a model of the a-TiO 2 surface via a cut-melt-and-quench procedure based on molecular dynamics simulations with deep neural network potentials (DPs) trained on density functional theory data. After interfacing the a-TiO 2 surface with water, we investigate the structure and dynamics of the resulting system using a combination of DP-based molecular dynamics (DPMD) and ab initio molecular dynamics (AIMD) simulations. Both AIMD and DPMD simulations reveal that the distribution of water on the a-TiO 2 surface lacks distinct layers normally found at the aqueous interface of crystalline TiO 2 , leading to an ~10 times faster diffusion of water at the interface. Bridging hydroxyls (Ti 2 –O b H) resulting from water dissociation decay several times more slowly than terminal hydroxyls (Ti–O w H) due to fast Ti–O w H 2 → Ti–O w H proton exchange events. These results provide a basis for a detailed understanding of the properties of a-TiO 2 in electrochemical environments. Moreover, the procedure of generating the a-TiO 2 -interface employed here is generally applicable to studying the aqueous interfaces of amorphous metal oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗