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Thomas-Fermi approximation applied to calculation of equations of state and thermodynamic functions at high pressure from differential equations of statistical atom model
The effects on calculated lower-level population densities of the truncation of Na and Sr(+) model atoms are determined in the context of the present spectral diagnostic scheme for solar prominences and spicules. It is shown that neglect of the upper atomic levels in Na, in particular, leads to overestimates in electron density and gas pressure by factors of about 2 and about 4, respectively, and to underestimates in the degree of hydrogen ionization and in the line-of-sight thickness of emitting material again by factors of about 2 and about 4, respectively. The implications of the revised emitting region extents, in particular, on the validity of the diagnostic method for these features are discussed.
The paper presents the results from a validation study undertaken as a part of the NASA s fundamental aeronautics initiative on high altitude emissions in order to assess the accuracy of several atomization models used in both non-superheat and superheat spray calculations. As a part of this investigation we have undertaken the validation based on four different cases to investigate the spray characteristics of (1) a flashing jet generated by the sudden release of pressurized R134A from cylindrical nozzle, (2) a liquid jet atomizing in a subsonic cross flow, (3) a Parker-Hannifin pressure swirl atomizer, and (4) a single-element Lean Direct Injector (LDI) combustor experiment. These cases were chosen because of their importance in some aerospace applications. The validation is based on some 3D and axisymmetric calculations involving both reacting and non-reacting sprays. In general, the predicted results provide reasonable agreement for both mean droplet sizes (D32) and average droplet velocities but mostly underestimate the droplets sizes in the inner radial region of a cylindrical jet.
Photoionization fronts play a dominant role in many astrophysical environments but remain difficult to achieve in a laboratory experiment. Recent papers have suggested that experiments using a nitrogen medium held at ten atmospheres of pressure which is irradiated by a source with a radiation temperature of T R ~ 100 eV can produce viable photoionization fronts. We present a suite of one-dimensional numerical simulations using the Helios multimaterial radiation hydrodynamics code that models these conditions and the formation of a photoionization front. We study the effects of varying the atomic kinetics and radiative transfer model on the hydrodynamics and ionization state of the nitrogen gas, finding that more sophisticated physics, in particular, a multi-angle long characteristic radiative transfer model and a collisional-radiative atomics model, dramatically changes the atomic kinetic evolution of the gas. A photoionization front is identified by computing the ratios between the photoionization rate, the electron impact ionization rate, and the total recombination rate. We find that due to the increased electron temperatures found using more advanced physics that photoionization fronts are likely to form in our nominal model. We report the results of several parameter studies. In one of these, the nitrogen pressure is fixed at ten atmospheres and the source radiation temperature is varied, while in another, the temperature is fixed at 100 eV and the nitrogen pressure is varied. In conclusion, lower nitrogen pressures increase the likelihood of generating a photoionization front while varying the peak source temperature has little effect.
Modern density functional theory (DFT) is a powerful tool for accurately predicting self-consistent material properties such as equations of state, transport coefficients and opacities in high energy density plasmas, but it is generally restricted to conditions of local thermodynamic equilibrium (LTE) and produces only averaged electronic states instead of detailed configurations. We propose a simple modification to the bound-state occupation factor of a DFT-based average-atom model that captures essential non-LTE effects in plasmas—including autoionization and dielectronic recombination—thus extending DFT-based models to new regimes. Finally, we then expand the self-consistent electronic orbitals of the non-LTE DFT-AA model to generate multi-configuration electronic structure and detailed opacity spectra. This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.
TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B24, 63–76]. The results of a TLS refinement are T, L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both procedures are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.
Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
This project addresses the systematic lack of predictive capabilities by spray models within engine CFD codes. We develop a new modeling approach to predict the breakup of diesel sprays based on recent literature showing that liquid turbulence plays a fundamental role in spray atomization. A new body of quantitative validation data is also developed as a critical element of the project, leveraging the joint capabilities of Georgia Tech’s high-pressure continuous-flow spray chamber and Argonne National Lab’s near-nozzle x-ray diagnostics at the Advanced Photon Source. This project contributes spatially-resolved measurements of drop size distribution within well-characterized diesel injectors, Spray A and D, from the Engine Combustion Network (ECN) to the engine combustion community for the first time. Utilizing this new body of measurements, we validate and demonstrate a new spray model for diesel sprays, termed the KH-Faeth model, that predicts global and local spray characteristic more accurately than the widely adopted and employed KH model. Predicted drop size distributions are seen to predict measured drops sizes both quantitatively and predictively, with accurate response in droplet size distributions over a wide range of ambient density, injection pressure, and injector nozzle size (Spray A and D) without model tuning. The KH-Faeth model can reduce error in the predicted centerline droplet size profile by up to 80% for ECN Spray D simulations when compared to use of the widely employed KH model.
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The study of atomization in supersonic flow is critical to ensuring reliable ignition of scramjet combustors under startup conditions. Numerical methods incorporating surface tension effects have largely focused on the incompressible regime as most atomization applications occur at low Mach numbers. Simulating surface tension effects in compressible flow requires robust numerical methods that can handle discontinuities caused by both shocks and material interfaces with high density ratios. In this work, a shock and interface capturing scheme is developed that uses the Harten–Lax–van Leer–Contact (HLLC) Riemann solver while a Tangent of Hyperbola for INterface Capturing (THINC) interface reconstruction scheme retains the fluid immiscibility condition in the volume fraction and phasic densities in the context of the five equation model. The approach includes the effects of compressibility, surface tension, and molecular viscosity. One and two-dimensional benchmark problems demonstrate the desirable interface sharpening and conservation properties of the approach. Simulations of secondary atomization of a cylindrical water column after its interaction with a shockwave show good qualitative agreement with experimentally observed behavior. Three-dimensional examples of primary atomization of a liquid jet in a Mach 2 crossflow demonstrate the robustness of the method.
Graded density impactors (GDIs) are multi-material composite impactors used in gas gun experiments to tailor the drive conditions imparted to a sample test material. Previous graded density impactors generally rely on thin, but discrete, layers of different materials. The thinner and the greater number of layers will result in smoother compression. Taken to the limit of very thin layers would be pure material 1 at one surface, such as the front surface of an impactor, smoothly transitioning at the atomic scale to pure material 2 on the back surface. Such an impactor can initially shock, then smoothly compresses a material during a dynamic experiment. This type of experiment can serve to explore a larger region of thermodynamic space than a single or even multi-shock experiments. An overview of how graded density impactors are made is reviewed and sample results are given. Additionally, a strategy for modeling these kinds of impactors is presented. The length scales of constituent mixing are given from the experimental build through electrochemical-deposition. Equation of state models for pure constituents and their subsequent mixtures are presented. It is demonstrated that the time scales for pressure and temperature equilibration, for atomically mixed GDIs, are short enough to be a justifiable closure for the resulting multiphase flow. Furthermore, we present simulation results of dynamic shock followed by a ramp compression, utilizing a silver/gold graded density impactor, onto a tantalum sample.
The well-known anti-corrosive property of stainless steels is largely attributed to the addition of Cr, which can assist in forming an inert film on the corroding surface. To maximize the corrosion-resistant ability of Cr, a thorough study dealing with the passivation behaviors of this metal, including the structure and composition of the passive film as well as related reaction mechanisms, is required. In this work, continuous electrochemical adsorptions of OH-groups of water molecules onto Cr terraces in acid solutions are investigated using DFT methods. Different models with various surface conditions are applied. Passivation is found to begin in the active region, and a fully coated surface mainly with oxide is likely to be the starting point of the passive region. The measured limiting potentials are in reasonable agreement with passivation potentials observed via experiment.
The physical mechanisms characterizing the breakup of a diesel spray into droplets are still unknown. This gap in knowledge has largely been due to the challenges of directly imaging this process or quantitatively measuring the outcomes of spray breakup, such as droplet size. Recent x-ray measurements by Argonne National Laboratory, utilized in this work, provide needed information about the spatial evolution of droplet sizes in selected regions of the spray under a range of injection pressures (50–150 MPa) and ambient densities (7.6–22.8 kg/m3) relevant for diesel operating conditions. Ultra-small angle x-ray scattering (USAXS) measurements performed at the Advanced Photon Source are presented, which quantify Sauter mean diameters (SMD) within optically thick regions of the spray that are inaccessible by conventional droplet sizing measurement techniques, namely in the near-nozzle region, along the spray centerline, and within the core of the spray. To quantify droplet sizes along the periphery of the spray, a complementary technique is proposed and introduced, which leverages the ratio of path-integrated x-ray and visible laser extinction (SAMR) measurements to quantify SMD. The SAMR and USAXS measurements are then utilized to evaluate current spray models used for engine computational fluid dynamic (CFD) simulations. We explore the ability of a carefully calibrated spray model, premised on aerodynamic wave growth theory, to capture the experimentally observed trends of SMD throughout the spray. The spray structure is best predicted with an aerodynamic primary and secondary breakup process that is represented with a slower time constant and larger formed droplet size than conventionally recommended for diesel spray models. Additionally, spray model predictions suggest that droplet collisions may not influence the resultant droplet size distribution along the spray centerline in downstream regions of the spray.
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Antifouling polymer brushes are well-known for their exceptional resistance to unwanted protein adsorption. While experimental studies have extensively characterized protein–polymer brush interactions, computational investigations remain limited, largely due to the challenges in accurately modeling and integrating these complex, multicomponent systems without resorting to oversimplification. To address this challenge, this study presents one of the most comprehensive and realistic model systems to date, comprising the substrate, grafted polymers, and proteins. Our work interprets the interactions between polymer brush and protein based on realistic modeling without simplification. In particular, this study utilizes molecular modeling and simulation of polycationic and polyzwitterionic brushes─poly(dimethylaminoethyl methacrylate) (PDMAEMA), poly(2-(N-oxide-N,N-dimethylamino)ethyl methacrylate) (PNOMA), and poly(2-(N-3-sulfopropyl-N,N-dimethylammonium)ethyl methacrylate) (PSBMA)─grafted onto α-quartz substrates via polymerization initiator linkers. The brush models were developed to closely replicate experimentally synthesized samples and to provide detailed insights into structural and dynamical changes at the molecular level during protein adsorption. Using steered molecular dynamics simulations, we show that the PSBMA brush, due to its high local density, exhibits the greatest resistance to protein insertion. Cα root-mean-square deviation and interaction pattern analyses further reveal that the PSBMA brush also induces the most significant destabilization of lysozyme, while the PDMAEMA brush enhances protein stability through ion-mediated interactions. The PNOMA brush, while requiring the lowest force for protein adsorption, induces greater protein destabilization than the PDMAEMA brush, primarily due to electrostatic repulsion caused by a short carbon spacer length. Hydration analysis reveals that both the PSBMA brush and the lysozyme interacting with it exhibit the most rapid dehydration, attributed to the brush’s high local chain density, which results in the greatest lysozyme destabilization and the highest adsorption force. These findings highlight the dual role of antifouling polymer brushes: resisting protein adsorption and modulating protein structural dynamics. In conclusion, this study provides valuable insights for the rational design of next-generation antifouling materials and offers a framework for realistic model development in complex multicomponent systems.
A T-box regulator or riboswitch actively monitors the levels of charged/uncharged tRNA and participates in amino acid homeostasis by regulating genes involved in their utilization or biosynthesis. It has an aptamer domain for cognate tRNA recognition and an expression platform to sense the charge state and modulate gene expression. These two conserved domains are connected by a variable linker that harbors additional secondary structural elements, such as Stem III. The structural basis for specific tRNA binding is known, but the structural basis for charge sensing and the role of other elements remains elusive. To gain new structural insights on the T-box mechanism, a molecular envelope was calculated from small angle X-ray scattering data for the Bacillus subtilis glyQS T-box riboswitch in complex with an uncharged tRNAGly. A structural model of an antiterminated glyQS T-box in complex with its cognate tRNAGly was derived based on the molecular envelope. It shows the location and relative orientation of various secondary structural elements. The model was validated by comparing the envelopes of the wild-type complex and two variants. The structural model suggests that in addition to a possible regulatory role, Stem III could aid in preferential stabilization of the T-box anti-terminated state allowing read-through of regulated genes.