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At least 649 records · Page 36

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NEAMS-ATF M3 Milestone Report: Literature Review of Modeling of Radiation-Induced Swelling in Fe-Cr-Al Steels

Fe-Cr-Al steels are proposed as accident-tolerant-fuel (ATF) cladding materials in light water reactors due to their excellent oxidation resistance at high temperatures. Currently, the understanding of their performance in reactor environment is still limited. In this review, firstly we reviewed the experimental studies of Fe-Cr-Al based alloys with particular focus on the radiation effects in these alloys. Although limited data are available in literature, several previous and recent experimental studies have shown that Fe-Cr-Al based alloys have very good void swelling resistance at low and moderate irradiation doses but the growth of dislocation loops is very active. Overall, the behavior of radiation damage evolution is similar to that in Fe-Cr ferritic/martensitic alloys. Secondly, we reviewed the rate theory-based modeling methods for modeling the coevolution of voids and dislocation loops in materials under irradiation such as Frenkel pair three-dimensional diffusion model (FP3DM) and cluster dynamics. Finally, we summarized and discussed our review and proposed our future plans for modeling radiation damage in Fe-Cr-Al based alloys.

36 MATERIALS SCIENCE↗

Characteristics of Fe Ablation Trials Observed During the 1998 Leonid Meteor Shower

Eighteen Fe ablation trails were observed during the 17/18 Nov 1998 Leonid meteor shower with an airborne Fe lidar aboard the National Simulation Facility/National Center for Atmospheric Research (NSF/NCAR) Electra aircraft over Okinawa. The average altitude of the 18 trails from the high velocity (72 km/s) Leonid meteors, 95.67 +/- 0.93 km, is approximately 6.7 km higher than previously observed for slower (approx. 30 km/s) sporadic meteors. This height difference is consistent with the assumption that meteors ablate when the kinetic energy imparted to the atmosphere reaches a critical threshold. The average age of the Fe trails, determined by a diffusion model, is 10.1 min. The youngest ages were observed below 92 km and above 98 km where chemistry and diffusion dominate, respectively. The average abundance of the trails is ten percent of the abundance of the background Fe layer. Observations suggest that the 1998 Leonid shower did not have a significant impact on the abundance of the background Fe layer.

Chu, Xin-Zhao↗

A model for Jupiter's proton radiation belt

A model for electron and proton energy and density in Jupiter's radiation belt is proposed. It is assumed that electrons diffuse inward from the solar wind. The Davis and Chang diffusion model, in which there is a very steep L-shell dependence in density and energy, is scaled outwards from the peak of the belts at about 1.5 to 2 Jupiter radii to the magnetopause as defined by the magnetic moment. The energetic electron density is calculated to be one billionth of the density in the solar wind, and that is assumed to be the trapping ratio of Jupiter's synchrotron belts. It is further assumed that the same figures apply to protons. The flux density at 80 MHz was measured by the Culgoora ring to be identical to that at 3000 MHz, implying a constant flux density of the synchrotron source of over 20 or 30 to 1 in frequency. It is suggested that the synchrotron spectrum is flat over more than an order of magnitude of frequency. Jupiter is an enormous synchrotron source and has a strong magnetic field, causing long diffusion times for electrons in the magnetosphere.

Warwick, J.↗

The AN neutron transport by nodal diffusion

The two group diffusion model combined to a nodal approach in space is the preferred scheme for the industrial simulation of nuclear water reactors. The main selling point is the speed of computation, allowing a large number of parametric studies. Anyway, the drawbacks of the underlying diffusion equation may arise with highly heterogeneous interfaces, often encountered in modern UO{sub 2} and MO{sub x} fuel loading patterns, and boron less controlled systems. This paper aims at showing how the simplified AN transport model, equivalent to the well known SPN, can be implemented in standard diffusion codes with minor modifications. Some numerical results are illustrated. (authors)

97 MATHEMATICS AND COMPUTING↗

Modeling MHD accretion-ejection—from the launching area to propagation scales

We present the results of axisymmetric magnetohydrodynamic simulations investigating the launching of jets and outflows from a magnetically diffusive accretion disk. The time evolution of the disk structure is self-consistently taken into account. In contrast to previous works, we have applied spherical coordinates for the numerical grid, implying substantial benefits concerning the numerical resolution and the stability of the simulation. Due to the new setup, we were able to run simulations for more than 150,000 dynamical times on a domain extending 1500 inner disk radii with a resolution of up to 24 cells per disk height in the inner disk. Depending on the disk magnetization, jet launching occurs in two different but complementary regimes—jets driven predominantly by centrifugal or magnetic forces. These regimes differ in the ejection efficiency concerning mass, energy, and angular momentum. We show that it is the actual disk magnetization and not so much the initial magnetization that best describes the disk-jet evolution. Considering the actual disk magnetization, we also find that simulations starting with different initial magnetization evolve in a similar—typical—way, due to advection and diffusion, as the magnetic flux in the disk evolves in time. Exploring a new, modified diffusivity model, we confirm the self-similar structure of the global jet-launching disk, obtaining power laws for the radial profiles of the disk physical variables such as density, magnetic field strength, or accretion velocity.

79 ASTRONOMY AND ASTROPHYSICS↗

High power density soft x-ray GaAs photodiodes with tailored spectral response

GaAs photodiode arrays have been designed for non-destructive monitoring of x-ray beam position in soft coherent beamline front ends in synchrotron light sources. A shallow p-on-n junction was employed to reduce the device photocurrent density to optimize the operation with beam power densities up to 20 W mm -2 , mainly coming from hard x-rays. With this approach, the photocurrent is primarily defined by the excess carriers generated by low-energy x-ray photons absorbed near the detector surface. The p–n junction structures were grown by molecular beam epitaxy and processed into 64-element linear photodiode arrays. The devices were characterized first in the visible range with a high-power Ar-ion laser and then tested in the soft and hard x-ray regions up to 10 keV at two beamlines of the National Synchrotron Light Source II. The responsivity was measured to be 0.16 A W -1 at 0.7 keV and 0.05 A W -1 at 6 keV in agreement with modeling. At higher x-ray energies the measured responsivity was lower than predicted in the framework of the carrier diffusion model; a possible explanation is discussed.

36 MATERIALS SCIENCE↗

Exhaust cloud rise and growth for Apollo Saturn engines.

Empirical and analytical results have been reduced from time-lapse photographs of exhaust clouds during the launch of Apollo 10, 14, 15, and 16 from the Kennedy Space Center. Theoretical predictions of the buoyant cloud rise and growth compare very favorably to actual measurements. The mathematical model predicts with engineering accuracy the terminal altitude and size of the clouds. A principal input to MSFC's multilayer diffusion model is top height of the exhaust cloud. It is this characteristic dimension that is the main subject of this report. An interesting occurrence during launch is the formation of bimodal exhaust cloud which is due to the north-south oriented flame trench directly beneath the base of the vehicle. This study has added considerable information on engine exhaust cloud rise and growth which is essential to the study of atmospheric dispersal in time and space.

Susko, M.↗

Boundary-layer analysis of subsonic inlet diffuser geometries for engines nacelles

Theoretical Mach number distributions and boundary-layer parameters are presented for subsonic nacelle inlet diffuser geometries with length to exit diameter ratios ranging from 0.4 to 1.6 and diffuser exit area to throat area ratios ranging from 1.1 to 2.0. The major portion of the study was done with a cubic diffuser contour with the inflection point at the midpoint of the diffuser, a diffuser throat Mach number of 0.6, and a free-stream Mach number of 0.12. Calculations were performed at both model (diffuser exit diameter, 30.5 cm) and full-scale (diffuser exit diameter, 183 cm) sizes. Separation limits were defined by establishing a separation boundary on plots of diffuser area ratio as a function of diffuser length to diameter ratio. The effects of diffuser contour, inlet lip geometry, and throat Mach number on the boundary-layer characteristics are illustrated. The major results of the study indicate that the separation boundary is shifted to greater area ratios by (1) increasing the diffuser length, (2) increasing the scale of the diffuser and, (3) moving the inflection point of the diffuser contour to or ahead of the midpoint of the diffuser.

Albers, J. A.↗

Spatial distribution of Compton-produced X-ray flux from rich and regular clusters of galaxies

The spatial distribution of radio and X-ray fluxes from rich and regular clusters of galaxies is discussed. A diffusion model is investigated in which high-energy electrons are ejected from a point source at the center of the cluster. While diffusing out, the electrons lose energy by Compton scattering with the universal blackbody photons, thus producing the X-ray emission. Traversing intracluster magnetic fields, the electrons emit synchrotron radio emission. For the Coma cluster of galaxies good agreement is found between the observed and predicted X-ray counting-rate distribution for the Compton model. From the observed radio data a value of about 3 by 10 to the -8th power gauss is deduced for the average magnetic-field strength in the central region of Coma.

Rephaeli, Y.↗

Interstitial and interlayer ion diffusion geometry extraction in graphitic nanosphere battery materials

Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermally annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Lastly, our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.

25 ENERGY STORAGE↗

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗

Numerical and experimental investigations of rarefied nozzle and plume flows of nitrogen

Numerical and experimental investigations are performed for the rarefied flow of nitrogen through a small nozzle which is expanded into near-vacuum conditions. Two different numerical studies are undertaken: the first employs a continuum approach in solving the Navier-Stokes equations, and the second employs a particle approach through use of the direct simulation Monte Carlo method (DSMC). The experimental investigation concerns the measurement of pressure, using a Pitot tube, in the nozzle exit plane and near-field of the plume. Comparison of the experimental and numerical data at the nozzle exit reveals that the DSMC technique provides the more accurate description of the expanding flow. It is discovered that the DSMC solutions are quite sensitive to the model employed to simulate the interaction between the gas and the nozzle wall surface. It is concluded that the simplistic fully diffuse model is quite satisfactory for the present application.

Boyd, Iain D.↗

The Role of Oxygen Concentration in Enabling High Gradients in Niobium SRF Cavities

We studied the role of O concentration with depth in the performance of Nb SRF cavities. An ensemble of electropolished 1.3 GHz cavities, which initially showed high field Q-slope (HFQS), was subjected to sequential testing and treatment with in-situ low temperature baking at various temperatures. We find that increasing the bake duration causes (i) an increase in the onset of HFQS until it is absent up to quench (ii) a non-monotonic relationship with the quench field (iii) an evolution of the RBCS toward a non-equilibrium behavior that drives anti-Q slope. Our data is qualitatively explained by assuming an O diffusion model and suggests that the mitigation of HFQS that arises from 120 C in-situ LTB is mediated by the diffusion of O from the native oxide which prevents the precipitation of proximity-coupled Nb nano-hydrides, in turn enabling higher quench fields. The decrease in quench field for cavities in which O has been diffused >90 nm from the RF surface may be due to a reduction of the field limit in the SS bilayer structure. We also suggest that the evolution of the RBCS occurs due to the absence of proximity coupled inclusions, bringing about non-equilibrium effects.

Bafia, D.↗

MoRE-Brain: Routed Mixture of Experts for Interpretable and Generalizable Cross-Subject fMRI Visual Decoding

Decoding visual experiences from fMRI offers a powerful avenue to understand human perception and develop advanced brain-computer interfaces. However, current progress often prioritizes maximizing reconstruction fidelity while overlooking interpretability, an essential aspect for deriving neuroscientific insight. To address this gap, we propose MoRE-Brain, a neuro-inspired framework designed for high-fidelity, adaptable, and interpretable visual reconstruction. MoRE-Brain uniquely employs a hierarchical Mixture-of-Experts architecture where distinct experts process fMRI signals from functionally related voxel groups, mimicking specialized brain networks. The experts are first trained to encode fMRI into the frozen CLIP space. A finetuned diffusion model then synthesizes images, guided by expert outputs through a novel dual-stage routing mechanism that dynamically weighs expert contributions across the diffusion process. MoRE-Brain offers three main advancements: First, it introduces a novel Mixture-of-Experts architecture grounded in brain network principles for neuro-decoding. Second, it achieves efficient cross-subject generalization by sharing core expert networks while adapting only subject-specific routers. Third, it provides enhanced mechanistic insight, as the explicit routing reveals precisely how different modeled brain regions shape the semantic and spatial attributes of the reconstructed image. Extensive experiments validate MoRE-Brain’s high reconstruction fidelity, with bottleneck analyses further demonstrating its effective utilization of fMRI signals, distinguishing genuine neural decoding from over-reliance on generative priors. Consequently, MoRE-Brain marks a substantial advance towards more generalizable and interpretable fMRI-based visual decoding.

Wei, Yuxiang [Georgia Institute of Technology]↗

Mathematical model of diffusion-limited evolution of multiple gas bubbles in tissue

Models of gas bubble dynamics employed in probabilistic analyses of decompression sickness incidence in man must be theoretically consistent and simple, if they are to yield useful results without requiring excessive computations. They are generally formulated in terms of ordinary differential equations that describe diffusion-limited gas exchange between a gas bubble and the extravascular tissue surrounding it. In our previous model (Ann. Biomed. Eng. 30: 232-246, 2002), we showed that with appropriate representation of sink pressures to account for gas loss or gain due to heterogeneous blood perfusion in the unstirred diffusion region around the bubble, diffusion-limited bubble growth in a tissue of finite volume can be simulated without postulating a boundary layer across which gas flux is discontinuous. However, interactions between two or more bubbles caused by competition for available gas cannot be considered in this model, because the diffusion region has a fixed volume with zero gas flux at its outer boundary. The present work extends the previous model to accommodate interactions among multiple bubbles by allowing the diffusion region volume of each bubble to vary during bubble evolution. For given decompression and tissue volume, bubble growth is sustained only if the bubble number density is below a certain maximum.

Evaluation Studies↗

Estimation of Sorption Behavior of Europium(III) Using Biotite Flakes - 13272

The interaction of biotite and Eu(III) (europium (III)) was examined by using secondary ion-microprobe mass spectrometer (SIMS), fluorescence emission spectrum and decay behavior of fluorescence emission spectrum in addition to the time-changes of Eu(III) and potassium ions concentrations in a solution, using the flake form samples. The results of SIMS showed that the intensity of Eu was gradually decreasing with depth, while the intensity of Eu in the case shaken for 30 days exceeded that in the case for 1 day. Furthermore, the spatial distribution of Eu(III) and potassium ions in the flake of biotite suggested that Eu ions diffuse mainly from the edges of biotite flake, while Eu ions can slightly diffuse through some small cracks existing on the flake surface far from the edges. Besides, the elution amount of potassium from the biotite flakes into a solution was proportional to the sorption amount of Eu(III). The changes nearly revealed ion exchange between these ions, while muscovite flake sample did not show such ion exchange reaction. In addition, from the time-change of Eu(III) concentration, an apparent diffusion coefficient was estimated to be 8.0x10{sup -12} m{sup 2}/s, by using two-dimensional diffusion model coupled with a film between the solid phase and the liquid phase. Furthermore, the fluorescent intensity decreased with the shaking (contacting) time. This means that Eu(III) gradually diffuses into the inside of biotite edges of the biotite flakes, after the sorption of Eu(III) in the edges. This tendency was observed also in the powder samples. The observed fluorescence decay (at 592 nm in wave length) showed almost similar curve in any samples, indicating a certain sorption form of Eu(III) onto the edges of the biotite flakes. These results mentioned above suggest that the diffusion processes through internal layer in biotite mainly control the sorption behavior of multivalent ions. Such diffusion processes affect the retardation-effects on fracture surfaces in the rock matrix, depending on the fluid flow velocity of groundwater. That is, a more reliable model considering the mass transfer in the internal layer of biotite may be required to estimate the sorption behavior of RNs with biotite which controls the whole sorption behavior of granite. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗