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At least 1,207 records · Page 67

A simulation of the intracluster medium with feedback from cluster galaxies

We detail method and report first results from a three-dimensional hydrodynamical and N-body simulation of the formation and evolution of a Coma-sized cluster of galaxies, with the intent of studying the history of the hot, X-ray emitting intracluster medium. Cluster gas, galaxies, and dark matter are included in the model. The galaxies and dark matter fell gravitational forces; the cluster gas also undergoes hydrodynamical effects such as shock heating and PdV work. For the first time in three dimensions, we include modeling of ejection of processed gas from the simulated galaxies by winds, including heating and heavy element enrichment. For comparison, we employ a `pure infall' simulation using the same initial conditions but with no galaxies or winds. We employ an extreme ejection history for galactic feedback in order to define the boundary of likely models. As expected, feedback raises the entropy of the intracluster gas, preventing it from collapsing to densities as high as those attained in the infall model. The effect is more pronounced in subclusters formed at high redshift. The cluster with feedback is always less X-ray luminous, but experiences more rapid luminosity evolution, than the pure infall cluster. Even employing an extreme ejection model, the final gas temperature is only approximately 15% larger than in the infall model. The radial temperature profile is very nearly isothermal within 1.5 Mpc. The cluster galaxies in the feedback model have a velocity dispersion approximately 15% lower than the dark matter. This results in the true ratio of specific energies in galaxies to gas being less than one, beta(sub spec) approximately 0.7. The infall model predicts beta(sub spec) approximately 1.2. Large excursions in these values occur over time, following the complex dynamical history of the cluster. The morphology of the X-ray emission is little affected by feedback. The emission profiles of both clusters are well described by the standard beta-model with beta(sub fit) approximately equal to 0.7 - 0.9. X-ray mass estimates based on the assumptions of hydrostatic equilibrium and the applicability of the beta-model are quite accurate in both cases. A strong, radial iron abundance gradient is present, which develops as a consequence of the steepening of the galaxy density profile over time. Spectroscopic observations using nonimaging detectors with wide (approximately 45 min) fields of view dramatically smear the gradient. Observations with arcminute resolution, made available with the ASCA satellite, would readily resolve the gradient.

Metzler, Christopher A.↗

Plasma-Catalytic Ammonia Synthesis beyond the Equilibrium Limit

In this work, we explore the consequences of nonthermal plasma-activation on product yields in catalytic ammonia synthesis, a reaction that is equilibrium-limited at elevated temperatures. We employ a minimal microkinetic model that incorporates the influence of plasma-activation on N 2 dissociation rates to predict NH 3 yields into and across the equilibrium-limited regime. NH 3 yields are predicted to exceed bulk thermodynamic equilibrium limits on materials that are thermal-rate-limited by N 2 dissociation. In all cases, yields revert to bulk equilibrium at temperatures at which thermal reaction rates exceed plasma-activated ones. Beyond-equilibrium NH 3 yields are observed in a packed bed dielectric barrier discharge reactor and exhibit sensitivity to catalytic material choice in a way consistent with model predictions. The approach and results highlight the opportunity to exploit synergies between nonthermal plasmas and catalysts to affect transformations at conditions inaccessible through thermal routes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing Domains of Equilibration In Highly Metamorhposed Eucrites

This study assesses how petrographic textures and trace element distributions, combined with thermodynamic models, can act as indicators of metamorphic equilibrium and/or trace element mobility in highly metamorphosed eucrite, Elephant Moraine (EET) 90020.

Thermodynamic modelling↗

A review of Reynolds stress models for turbulent shear flows

A detailed review of recent developments in Reynolds stress modeling for incompressible turbulent shear flows is provided. The mathematical foundations of both two-equation models and full second-order closures are explored in depth. It is shown how these models can be systematically derived for two-dimensional mean turbulent flows that are close to equilibrium. A variety of examples are provided to demonstrate how well properly calibrated versions of these models perform for such flows. However, substantial problems remain for the description of more complex turbulent flows where there are large departures from equilibrium. Recent efforts to extend Reynolds stress models to nonequilibrium turbulent flows are discussed briefly along with the major modeling issues relevant to practical naval hydrodynamics applications.

Speziale, Charles G.↗

A simple nonlinear model for the return to isotropy in turbulence

A quadratic nonlinear generalization of the linear Rotta model for the slow pressure-strain correlation of turbulence is developed. The model is shown to satisfy realizability and to give rise to no stable nontrivial equilibrium solutions for the anisotropy tensor in the case of vanishing mean velocity gradients. The absence of stable nontrivial equilibrium solutions is a necessary condition to ensure that the model predicts a return to isotropy for all relaxational turbulent flows. Both the phase space dynamics and the temporal behavior of the model are examined and compared against experimental data for the return to isotropy problem. It is demonstrated that the quadratic model successfully captures the experimental trends which clearly exhibit nonlinear behavior. Direct comparisons are also made with the predictions of the Rotta model and the Lumley model.

Sarkar, Sutanu↗

The Grell-Freitas Convection Parameterization: Recent Developments and Applications Within the NASA GEOS Global Model

We implemented and began to evaluate an alternative convection parameterization for the NASA Goddard Earth Observing System (GEOS) global model. The parameterization is based on the mass flux approach with several closures, for equilibrium and non-equilibrium convection, and includes scale and aerosol awareness functionalities. Recently, the scheme has been extended to a tri-modal spectral size approach to simulate the transition from shallow, mid, and deep convection regimes. In addition, the inclusion of a new closure for non-equilibrium convection resulted in a substantial gain of realism in model simulation of the diurnal cycle of convection over the land. Here, we briefly introduce the recent developments, implementation, and preliminary results of this parameterization in the NASA GEOS modeling system.

GEO↗

Unfolding of the Villin Headpiece Domain: Revealing Structural Heterogeneity with Time‐Resolved X‐Ray Solution Scattering and Markov State Modeling

Understanding protein folding pathways is crucial to deciphering the principles of protein structure and function. Here, the unfolding dynamics of the 35‐residue villin headpiece (HP35) and a norleucine‐substituted variant (2F4K) using a combination of experimental and computational techniques is investigated. Time‐resolved X‐ray solution scattering coupled with equilibrium molecular dynamics simulations and Markov state modeling reveals distinct unfolding mechanisms between the two variants: HP35 and 2F4K. Specifically, HP35 exhibits a two‐state unfolding process, whereas an intermediate state is identified for the 2F4K mutant. A Markov state model constructed from simulations is used to map atomic‐level transitions to experimental observations, providing insights into the role of sequence variations in modulating folding pathways. The findings underscore the importance of integrating experimental and computational approaches to unravel protein unfolding mechanisms between heterogenous structural ensembles.

Nijhawan, Adam K. [Department of Chemistry Northwe↗

CNO abundances and hydrodynamic models of the nova outburst.

We have used a fully implicit, Lagrangian, hydrodynamic computer code incorporating a nuclear reaction network to follow thermonuclear runaways in the hydrogen-rich envelopes of white dwarfs in order to produce a nova outburst. Because of the short time-scales and the high nuclear burning rates produced in our models, the nuclear reactions are far out of equilibrium and the beta-plus unstable nuclei become the most abundant nuclei in the envelope except for hydrogen and helium. Our models have ejected 1.00017 solar mass with kinetic energies of 8 times 10 to the 44-th power ergs, a value that agrees quite closely with the observed values for novae.

Starrfield, S.↗

Molecular structure models of amorphous bismuth and cerium carboxylate catalyst precursors

As our societal need for materials and energy has grown, so has our need for catalyst processes in hydrogen production. A major function in these applications, for both homogenous and heterogeneous catalysis processes, is the synthesis of an active metal catalyst. It must first be soluble to control the physical properties of the metal being used. Recent work in metal precursors has begun to turn toward these metal carboxylate types of material. Here, structural models are proposed for bismuth 2-ethylhexanoate and 2,2-dimethyloctanoate and cerium 2-ethylhexanoate. The bismuth compounds have been characterized at different ratios of bismuth to carboxylate as solutions of the free acids. Their structures are most consistent with a Bi 4 (RCO 2 ) 12 motif where the Bi ions are arranged in a flattened tetrahedron with Bi – Bi distances of about 4.3 Å. There is evidence for Bi – O – Bi linkages at low free acid concentrations. The cerium compound is most consistent with a linear tetracerium molecule where the Ce – Ce distances repeat at about 4.3 Å out to 16.4 Å. The models were generated by analogy with known crystal structures and compared to high-energy x-ray scattering data. To further evaluate the models, DFT calculations were made, and the equilibrium geometries were compared. The vibrational spectra calculated from those geometries are presented and compared to the experimental results. Magnetization vs. temperature data was collected on the cerium compound, and its behavior was consistent with the proposed model. A geometrical approach to determining the dimensionality and relative positions of the metal ions in these structures is presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Protein solubility modeling

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

Proteins/chemistry↗

Evaluation of thermodynamic closure models for partially reacted two-phase mixture of condensed phase explosives

One of the key fundamental issues that is crucial in the continuum modeling of reactive flow phenomena is the thermodynamically consistent description of reaction mixture properties. To define the mixture properties, thermodynamic closure rules that relate the properties of the individual reaction components to the mixture properties are required. In the context of reactive two-phase modeling approaches, various strategies to define the thermodynamic closures have been adopted such as pressure temperature (PT) equilibrium between the individual reaction components, pressure (specific) volume (PV) equilibrium, etc. The choice of closure rules determines the relative distribution of specific volume and energy across the reaction components that comprise the mixture. Therefore, depending on the choice of the closure, the mixture thermodynamic behavior can vary. The present work examines the effect of different closure approaches on the thermodynamic properties of the reaction mixture. The analysis is performed for a condensed phase HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) based plastic bonded explosive (PBX) 9501 explosive using four different thermodynamic closures, viz., PT equilibrium, PV equilibrium, volume temperature (VT) equilibrium, and pressure (P) equilibrium with reactants on an isentrope. Furthermore, the relative variations in the thermodynamic properties of the mixture are analyzed and compared under both compression and expansion loading regimes. It is shown that out of the four closure models, only PT equilibrium and P equilibrium closures lead to a thermodynamically accurate description of the mixture under both compression and expansion.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Virtual Tokamak for Test and Development of Plasma Control Applied to NSTX-U

Safe and efficient operation of tokamak experiments depends on shot preparation prior to the experiment to maximize performance and avoid issues that are predictable consequences of known physics. The General Atomics TokSys toolbox is used to test and develop the plasma control system (PCS) on numerous tokamaks around the world. Tokamaks that use a version of the DIII-D PCS can connect it to a TokSys simulation and control a virtual version of the tokamak with the real PCS. Recent upgrades to the simulation include more detailed profile and transport modeling to support design and implementation of optimized scenarios. The simulation combines a module called “Profiles” that simulates the 1D profiles of density, pressure, and current and a module called “GSevolve'' that evolves the 2D Grad-Shafranov equilibrium. The “Profiles'' module primarily uses simplified models for fueling, heating, and current. The TRANSP code provides precomputed diffusion coefficients and heating/current drive profiles from radio-frequency and neutral beam sources for the scenarios being simulated. The fidelity of a simulation can be enhanced by analyzing it with TRANSP and making corrections to the precomputed values and iterating until convergence. Simulations of the National Spherical Torus Upgrade (NSTX-U) are presented. It is shown that the simulation reproduces the experimental profile evolution. Here, the simulation has also been upgraded to reproduce the experimental outcome at points of bifurcation. This is demonstrated with a simulation of vertical displacement in NSTX-U.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Surface roughness effects on equilibrium temperature.

An analysis is presented for evaluation of equilibrium temperature distribution on radiatively adiabatic, adjoint planes which are uniformly irradiated by a collimated solar flux. The analysis employs a semigrey spectral model. Radiation properties for surface emitted radiation are obtained from the expressions of electromagnetic theory for smooth surfaces. Rough surface properties for solar radiation are given by the Beckmann bidirectional reflectance model. Numerical solutions to the governing equations yield equilibrium temperature distributions for a range of the influencing parameters. Surface roughness has little influence on equilibrium temperature for materials with high values for solar absorptance. However, for low or intermediate values of solar absorptance, roughness effects on the spatial distribution of reflected solar radiation can significantly alter equilibrium temperature particularly at surface elements where radiant interaction is small.

Houchens, A. F.↗

A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins

Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain. While accepted conformations must preserve the sequential bonding of the protein chain model and excluded volume among its units, the moves themselves may take the chain across itself. We call this a break in linear topology preservation. In this manuscript, we show, using simple protein models, that there is no difference in equilibrium properties calculated with a move set that preserves linear topology and one that does not. However, for complex structures, such as those of deeply knotted proteins, the preservation of linear topology provides correct equilibrium results but only after long relaxation. In any case, to analyze folding pathways, knotting mechanisms and folding kinetics, the preservation of linear topology may be an unavoidable requirement.

Especial, João N. C. (ORCID:0000000254765370)↗

On Computationally Efficient Radiative Transfer Calculations for Three-dimensional Entry Problems

The current work presents an efficient simulation framework for rigorously modeling radiative fields emanating from non-equilibrium planetary entry flows in complex three-dimensional domains. Key to this endeavor is adoption of finite-volume discretization in lieu of brute-force ray tracing. This change in conjunction with mesh sweeping and Lebedev-type quadrature for angular integration allows spatial-angular resolution of radiative transfer to be performed in a computationally tractable manner. Additionally, a new methodology has been established to build standalone reduced-order spectral databases for non-equilibrium radiative properties that can be applied to a broad range of hypersonic planetary entry problems with minimal loss in accuracy. The efficacy of the new framework has been demonstrated on the atomic nitrogen radiative system. The resulting reduced-order model requires three orders-of-magnitude fewer spectral evaluations and results in a 95% decrease in memory footprint. A comparative study for representative forebody and afterbody lines-of-sight from Stardust, FIRE II, and meteor entries into the Earth atmosphere indicates that both total intensity variation and detailed spectra can be retrieved with as few as 625 reduced-order groups (contrasting with the 100,000 frequencies in the original full set model). Similarly, three-dimensional predictions of radiative heating experienced by the Orion forebody are in excellent agreement with legacy radiation solvers while requiring only a sliver (roughly 0.5%) of computing wall time.

3D radiation↗

On Computationally Efficient Radiative Transfer Calculations for Three-Dimensional Entry Problems

The current work presents an efficient simulation framework for rigorously modeling radiative fields emanating from non-equilibrium planetary entry flows in complex three-dimensional domains. Key to this endeavor is adoption of finite-volume discretization in lieu of brute-force ray tracing. This change in conjunction with mesh sweeping and Lebedev-type quadrature for angular integration allows spatial-angular resolution of radiative transfer to be performed in a computationally tractable manner. Additionally, a new methodology has been established to build standalone reduced-order spectral databases for non-equilibrium radiative properties that can be applied to a broad range of hypersonic planetary entry problems with minimal loss in accuracy. The efficacy of the new framework has been demonstrated on the atomic nitrogen radiative system. The resulting reduced-order model requires three orders-of-magnitude fewer spectral evaluations and results in a 95% decrease in memory footprint. A comparative study for representative forebody and afterbody lines-of-sight from Stardust, FIRE II, and meteor entries into the Earth atmosphere indicates that both total intensity variation and detailed spectra can be retrieved with as few as 625 reduced-order groups (contrasting with the 100,000 frequencies in the original full set model). Similarly, three-dimensional predictions of radiative heating experienced by the Orion forebody are in excellent agreement with legacy radiation solvers while requiring only a sliver (roughly 0.5%) of computing wall time.

3D radiation↗

Thermodynamic stability versus kinetic accessibility: Pareto fronts for programmable self-assembly

A challenge in designing self-assembling building blocks is to ensure the target state is both thermodynamically stable and kinetically accessible. These two objectives are known to be typically in competition, but it is not known how to simultaneously optimize them. We consider this problem through the lens of multi-objective optimization theory: we develop a genetic algorithm to compute the Pareto fronts characterizing the tradeoff between equilibrium probability and folding rate, for a model system of small polymers of colloids with tunable short-ranged interaction energies. We use a coarse-grained model for the particles' dynamics that allows us to efficiently search over parameters, for systems small enough to be enumerated. For most target states there is a tradeoff when the number of types of particles is small, with medium-weak bonds favouring fast folding, and strong bonds favouring high equilibrium probability. Additionally, the tradeoff disappears when the number of particle types reaches a value m *, that is usually much less than the total number of particles. This general approach of computing Pareto fronts allows one to identify the minimum number of design parameters to avoid a thermodynamic–kinetic tradeoff. However, we argue, by contrasting our coarse-grained model's predictions with those of Brownian dynamics simulations, that particles with short-ranged isotropic interactions should generically have a tradeoff, and avoiding it in larger systems will require orientation-dependent interactions.

36 MATERIALS SCIENCE↗

Nozzle flow with vibrational nonequilibrium

This research concerns the modeling and numerical solutions of the coupled system of compressible Navier-Stokes equations in cylindrical coordinates under conditions of equilibrium and nonequilibrium thermodynamics. The problem considered was the modeling of a high temperature diatomic gas N2 flowing through a converging-diverging high expansion nozzle. The problem was modeled in two ways. The first model uses a single temperature with variable specific heats as functions of this temperature. For the second model we assume that the various degrees of freedom all have a Boltzmann distribution and that there is a continuous redistribution of energy among the various degrees of freedom as the gas passes through the nozzle. Each degree of freedom is assumed to have its own temperature and, consequently, each system state can be characterized by these temperatures. This suggests that formulation of a second model with a vibrational degree of freedom along with a rotational-translation degree of freedom, each degree of freedom having its own temperature. Initially the vibrational degree of freedom is excited by heating the gas to a high temperature. As the high temperature gas passes through the nozzle throat there is a sudden drop in temperature along with a relaxation time for the vibrational degree of freedom to achieve equilibrium with the rotational-translation degree of freedom. That is, we assume that the temperature change upon passing through the throat is so great that the changes in the vibrational degree of freedom occur at a much slower pace and consequently lags behind the rotational-translational energy changes. This lag results in a finite relaxation time. In this context the term nonequilibrium is used to denote the fact that the energy content of the various degrees of freedom are characterized by two temperatures. We neglect any chemical reactions which could also add nonequilibrium effects. We develop the energy equations for the nonequilibrium model from first principles. The resulting equations, which model the nozzle flow, can be expressed in various forms. In most forms the resulting equations are coupled systems of nonlinear partial differential equations subject to certain boundary conditions. To solve the resulting coupled system of nonlinear partial differential equations, several numerical techniques were investigated: (1) the explicit MacCormack method, (2) the explicit-implicit MacCormack method, (3) the method of operator splitting, (4) factorization schemes, and (5) the Steger-Warming scheme.

Heinbockel, J. H.↗