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Self-mixing in microtubule-kinesin active fluid from nonuniform to uniform distribution of activity

Active fluids have applications in micromixing, but little is known about the mixing kinematics of systems with spatiotemporally-varying activity. To investigate, UV-activated caged ATP is used to activate controlled regions of microtubule-kinesin active fluid and the mixing process is observed with fluorescent tracers and molecular dyes. At low Péclet numbers (diffusive transport), the active-inactive interface progresses toward the inactive area in a diffusion-like manner that is described by a simple model combining diffusion with Michaelis-Menten kinetics. At high Péclet numbers (convective transport), the active-inactive interface progresses in a superdiffusion-like manner that is qualitatively captured by an active-fluid hydrodynamic model coupled to ATP transport. Results show that active fluid mixing involves complex coupling between distribution of active stress and active transport of ATP and reduces mixing time for suspended components with decreased impact of initial component distribution. This work will inform application of active fluids to promote micromixing in microfluidic devices.

59 BASIC BIOLOGICAL SCIENCES↗

Cosmology with matter diffusion

We construct a viable cosmological model based on velocity diffusion of matter particles. In order to ensure the conservation of the total energy-momentum tensor in the presence of diffusion, we include a cosmological scalar field φ which we identify with the dark energy component of the universe. The model is characterized by only one new degree of freedom, the diffusion parameter σ. The standard ΛCDM model can be recovered by setting σ = 0. If diffusion takes place (σ > 0) the dynamics of the matter and of the dark energy fields are coupled. We argue that the existence of a diffusion mechanism in the universe may serve as a theoretical motivation for interacting models. We constrain the background dynamics of the diffusion model with Supernovae, H(z) and BAO data. We also perform a perturbative analysis of this model in order to understand structure formation in the universe. We calculate the impact of diffusion both on the CMB spectrum, with particular attention to the integrated Sachs-Wolfe signal, and on the matter power spectrum P(k). The latter analysis places strong constraints on the magnitude of the diffusion mechanism but does not rule out the model.

79 ASTRONOMY AND ASTROPHYSICS↗

A Monte Carlo model for determination of binary diffusion coefficients in gases

A Monte Carlo method has been developed for the calculation of binary diffusion coefficients in gas mixtures. The method is based on the stochastic solution of the linear Boltzmann equation obtained for the transport of one component in a thermal bath of the second one. Anisotropic scattering is included by calculating the classical deflection angle in binary collisions under isotropic potential. Model results are compared to accurate solutions of the Chapman-Enskog equation in the first and higher orders. We have selected two different cases, H{sub 2} in H{sub 2} and O in O{sub 2}, assuming rigid spheres or using a model phenomenological potential. Diffusion coefficients, calculated in the proposed approach, are found in close agreement with Chapman-Enskog results in all the cases considered, the deviations being reduced using higher order approximations.

97 MATHEMATICS AND COMPUTING↗

Effective Stochastic Model For Reactive Transport

We propose an effective stochastic advection-diffusion-reaction (SADR) model. Unlike traditional advection-dispersion-reaction models, the SADR model describes mechanical and diffusive mixing as two separate processes. In the SADR model, the mechanical mixing is driven by random advective velocity with the variance given by the coefficient of mechanical dispersion. The diffusive mixing is modeled as a fickian diffusion with the effective diffusion coefficient. Both coefficients are given in terms of Peclet number (Pe) and the coefficient of molecular diffusion. We use the experimental results of \cite{Gramling} to demonstrate that for transport and bimolecular reactions in porous media the SADR model is significantly more accurate than the traditional dispersion model, which overestimates the mass of the reaction product by as much as 25\%.

stochastic equations, mixing controlled reactions,↗

Theoretical Analysis of Experimental Data of Sodium Diffusion in Oxidized Molybdenum Thin Films

In this work, the diffusion process of sodium (Na) in molybdenum (Mo) thin films while it was deposited on soda lime glass (SLG) was studied. A small amount of oxygen was present in the chamber while the direct-current (DC) magnetron sputtering was used for the deposition. The substrate temperatures were varied to observe its effect. Such molybdenum films, with or without oxidations, are often used in thin film solar cells, either as back contact or as hole transport layers. Secondary ion mass spectrometry (SIMS) was used to quantify the concentration of the species. A grain diffusion mechanistic model incorporating the effect of grain and grain boundary geometrical shape and size was developed. The model was used to provide an in-depth theoretical analysis of the sodium diffusion in molybdenum thin films that lead to the measured SIMS data. It was observed that not only diffusion coefficients should be considered when analyzing diffusion processes in thin films but also the ratio of grain boundary size to grain size. Both depend on substrate temperature and directly affect the amount of diffused species in the film. The data were analyzed under the light of the film growth speed versus diffusion front speed, the effect of oxygen content, and the effect of substrate temperature on the overall diffusion process. The temperature inversely affects the ratio of grain boundary size and grain size and directly affects the diffusion coefficient, which leads to a preferable temperature at which the highest amount of alkali can be found in the film.

36 MATERIALS SCIENCE↗

Eddy diffusivity operator in homogeneous isotropic turbulence

Here, we use the recently developed macroscopic forcing method to compute the scale-dependent eddy diffusivity characterizing ensemble-averaged scalar and momentum transport in incompressible homogeneous isotropic turbulence. For scales larger than the energy containing eddies, eddy diffusivity is found to be constant and consistent with the Boussinesq approximation. However, for small scales eddy diffusivity is found to vanish inversely proportional to the wave number. Behavior at all scales is reasonably captured by a nonlocal eddy diffusivity operator modeled as D/$\sqrt{I - l^2∇^2}$, where D is the eddy diffusivity in the Boussinesq limit, and l is a constant on the order of the large-eddy length. These results present a direct measurement of eddy diffusivity in turbulence with implications in turbulence modeling.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On the Representation of Hyporheic Exchange in Models for Reactive Transport in Stream and River Corridors

Efforts to include more detailed representations of biogeochemical processes in basin-scale water quality simulation tools face the challenge of how to tractably represent mass exchange between the flowing channels of streams and rivers and biogeochemical hotspots in the hyporheic zones. Multiscale models that use relatively coarse representations of the channel network with subgrid models for mass exchange and reactions in the hyporheic zone have started to emerge to address that challenge. Two such multiscale models are considered here, one based on a stochastic Lagrangian travel time representation of advective pumping and one on multirate diffusive exchange. The two models are formally equivalent to well-established integrodifferential representations for transport of non-reacting tracers in steady stream flow, which have been very successful in reproducing stream tracer tests. Despite that equivalence, the two models are based on very different model structures and produce significantly different results in reactive transport. In a simple denitrification example, denitrification is two to three times greater for the advection-based model because the multirate diffusive model has direct connections between the stream channel and transient storage zones and an assumption of mixing in the transient storage zones that prevent oxygen levels from dropping to the point where denitrification can progress uninhibited. By contrast, the advection-based model produces distinct redox zonation, allowing for denitrification to proceed uninhibited on part of the hyporheic flowpaths. These results demonstrate that conservative tracer tests alone are inadequate for constraining representation of mass transfer in models for reactive transport in streams and rivers.

54 ENVIRONMENTAL SCIENCES↗

γ -ray Constraints on Decaying Dark Matter and Implications for IceCube

Utilizing the Fermi measurement of the γ -ray spectrum toward the Inner Galaxy, we derive some of the strongest constraints to date on the dark matter (DM) lifetime in the mass range from hundreds of MeV to above an EeV. Our profile-likelihood-based analysis relies on 413 weeks of Fermi Pass 8 data from 200 MeV to 2 TeV, along with up-to-date models for diffuse γ -ray emission within the Milky Way. We model Galactic and extragalactic DM decay and include contributions to the DM-induced γ -ray flux resulting from both primary emission and inverse-Compton scattering of primary electrons and positrons. For the extragalactic flux, we also calculate the spectrum associated with cascades of high-energy γ rays scattering off of the cosmic background radiation. We argue that a decaying DM interpretation for the 10 TeV–1 PeV neutrino flux observed by IceCube is disfavored by our constraints. Our results also challenge a decaying DM explanation of the AMS-02 positron flux. In conclusion, we interpret the results in terms of individual final states and in the context of simplified scenarios such as a hidden sector glueball model.

79 ASTRONOMY AND ASTROPHYSICS↗

Theoretical analysis of mixing in liquid clouds – Part IV: DSD evolution and mixing diagrams

Evolution of droplet size distribution (DSD) due to mixing between cloudy and dry volumes is investigated for different values of the cloud fraction and for different initial DSD shapes. The analysis is performed using a diffusion–evaporation model which describes time-dependent processes of turbulent diffusion and droplet evaporation within a mixing volume. Time evolution of the DSD characteristics such as droplet concentration, LWC and mean volume radii is analyzed. The mixing diagrams are plotted for the final mixing stages. It is shown that the difference between the mixing diagrams for homogeneous and inhomogeneous mixing is insignificant and decreases with an increase in the DSD width. The dependencies of the normalized cube of the mean volume radius on the cloud fraction were compared with those on normalized droplet concentration and found to be quite different. If the normalized droplet concentration is used, mixing diagrams do not show any significant dependence on relative humidity in the dry volume. The main conclusion of the study is that traditional mixing diagrams cannot serve as a reliable tool for analysis of mixing type.

54 ENVIRONMENTAL SCIENCES↗

A simplified model for thermal-wave cavity self-consistent measurement of thermal diffusivity

A simplified theoretical model was developed for the thermal-wave cavity (TWC) technique in this study. This model takes thermal radiation into account and can be employed for absolute measurements of the thermal diffusivity of gas and liquid samples without any knowledge of geometrical and thermal parameters of the components of the TWC. Using this model and cavity-length scans, thermal diffusivities of air and distilled water were accurately and precisely measured as (2.191 ± 0.004) × 10{sup −5} and (1.427 ± 0.009) × 10{sup −7} m{sup 2} s{sup −1}, respectively, in very good agreement with accepted literature values.

42 ENGINEERING↗

Geochemical modeling of leaching of Ca, Mg, Al, and Pb from cementitious waste forms

Results from extraction tests on cement-waste samples were simulated with a thermodynamic equilibrium model using a consistent database, to which lead data were added. Subsequent diffusion tests were modeled by means of a 3D diffusive transport model combined with the geochemical model derived from the extraction tests. Modeling results of the leached major element concentrations for both uncarbonated and (partially) carbonated samples agreed well with the extraction test using the set of pure minerals and solid solutions present in the database. The observed decrease in Ca leaching with increasing carbonation level was qualitatively predicted. Simulations also revealed that Pb leaching is not controlled by dissolution/precipitation only. The addition of the calcite-cerrusite solid solution and adsorption reactions on amorphous Fe- and Al-oxides improved the predictions and are considered to control the Pb leaching during the extractions tests. The dynamic diffusive leaching tests were appropriately modeled for Na, K, Ca and Pb.

36 MATERIALS SCIENCE↗

Improved Prediction of Cold-Air Pools in the Weather Research and Forecasting Model Using a Truly Horizontal Diffusion Scheme for Potential Temperature

The terrain-following vertical coordinate system used by many atmospheric models, including the Weather Research and Forecasting (WRF) Model, is prone to errors in regions of complex terrain. These errors stem, in part, from the calculation of horizontal gradients within the diffusion term of the momentum or scalar evolution equations. In WRF, such gradients can be calculated along coordinate surfaces, or using metric terms that help account for grid skewness. However, neither of these options ensures a truly horizontal gradient calculation, especially if a grid cell is skewed enough that the heights of the neighboring grid points used in the calculation fall outside the vertical range of the cell. In this work, an improved scheme that uses Taylor series approximations to vertically interpolate variables to the level necessary for a truly horizontal gradient calculation is implemented in WRF for the diffusion of potential temperature. The scheme is validated using an atmosphere-at-rest configuration, in which spurious flows develop only as a result of numerical errors and can thus be used as a proxy for model performance. Following validation, the method is applied to the simulation of cold-air pools (CAPs), which occur in regions of complex terrain and are characterized by strong near-surface temperature gradients. Using the truly horizontal scheme, idealized simulations demonstrate reduced numerical mixing in a quiescent CAP, and a realistic case study in the Columbia River basin shows a reduction in positive wind speed bias by up to roughly 20% compared to observations from the Second Wind Forecast Improvement Project.

54 ENVIRONMENTAL SCIENCES↗

Mass dependence of overshooting beneath convective envelopes

State of the art stellar evolution codes [Paxton et al., 2010, Demarque et al., 2004, Weiss and Schlattl, 2008, Siess et al., 2013, Christensen-Dalsgaard, 2008] evoke a diffusive process to model convective overshooting. The diffusion coefficient [Freytag et al., 1996, Pratt et al., 2017] used in the model can be set to change with the classification of the convective zone as non-burning, H-burning, He-burning, or metal-burning. It can also be set to change at defined evolutionary points, such as the bottom of the asymptotic giant branch, or during the third dredge up [Herwig, 2000, Lugaro et al., 2003]. Aside from these abrupt changes, the diffusion coefficient is typically locked to a percentage of the pressure scale height measured at the convective boundary. However, there is no theoretical reason for convective overshooting, or indeed other convective properties, to change in the same way that the pressure scale height changes as a star evolves.

79 ASTRONOMY AND ASTROPHYSICS↗

The GeV Excess Shining Through: Background Systematics for the Inner Galaxy Analysis

Recently, a spatially extended excess of gamma rays collected by the Fermi-LAT from the inner region of the Milky Way has been detected by different groups and with increasingly sophisticated techniques. Yet, any final conclusion about the morphology and spectral properties of such an extended diffuse emission are subject to a number of potentially critical uncertainties, related to the high density of cosmic rays, gas, magnetic fields and abundance of point sources. We will present a thorough study of the systematic uncertainties related to the modelling of diffuse background and to the propagation of cosmic rays in the inner part of our Galaxy. We will test a large set of models for the Galactic diffuse emission, generated by varying the propagation parameters within extreme conditions. By using those models in the fit of Fermi-LAT data as Galactic foreground, we will show that the gamma-ray excess survives and we will quantify the uncertainties on the excess emission morphology and energy spectrum.

79 ASTRONOMY AND ASTROPHYSICS↗

Dynamics of deuterium retention and desorption from plasma-facing materials in fusion reactor-relevant conditions

Hydrogen isotopes retention and desorption during and after discharges in fusion devices are still not well understood due to the complex device conditions and limitations of in-situ diagnostics and measurements. Here, we simulated well-diagnosed recent experiments at the DIII-D facility to benchmark our ITMC-DYN integrated package of modeling deuterium diffusion, retention, and desorption during and after D discharge irradiation. Modeling results were compared with detail experimental data of D desorption fluxes for various irradiation conditions. We predicted the temporal evolution of free and trapped D distribution in tungsten (W) plasma-facing material (PFM). Effects of key parameters namely diffusion coefficient, recombination rate, trapping energies against different defect types, were examined in these simulations. Existing experimental data of these parameters in literature varies significantly which makes it harder to identify key mechanisms and physics responsible for hydrogen isotope retention and desorption. The purpose of this work is to accurately simulate recent well-diagnosed reactor experiments given the uncertainties in such parameters and identify mechanisms responsible for the retention and desorption. We implemented the best identified diffusion, recombination, and trapping parameters in ITMC-DYN package that integrate both various collisional and thermal processes. We predicted, for example, that sample cooling between discharges in DIII-D operations can significantly affect the spatial distribution of trapped D in W under reactor irradiation conditions. Correct prediction of desorption spectra from samples irradiated during 10 DIII-D discharges showed that up to 35% of D can be retained in high binding energy defects such as vacancy clusters or voids.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ICAT: A numerical scheme to minimize numerical diffusion in advection-dispersion modeling and its application in identifying flow channeling

The advection-dispersion equation for scalar transport is essential for the numerical modeling of many fluid dynamics problems. However, solutions from numerical schemes always suffer from numerical diffusion and/or oscillation. In this study, we develop an Intra-Cell Advection Tracking (ICAT) scheme to minimize numerical diffusion and preserve monotonicity for advection-dispersion modeling. The key idea is to introduce “queues” in each discretized cell, and using a sequential transport rule and a flow distribution mechanism to track the scalar transport in these queues temporally and spatially. The capability and limitations of ICAT are first investigated through three test cases. Compared with the results obtained from other numerical schemes, the results from ICAT show substantially reduced numerical diffusion and agree better with analytical solutions. We also employ ICAT to simulate the transport process of a conservative tracer in a fracture with a highly heterogeneous aperture distribution. We report discrete flow channels in the fracture are better discerned by ICAT than by other numerical schemes, indicating the suitability of ICAT for modeling tracer transport in channelized flow fields.

15 GEOTHERMAL ENERGY↗

Generative models on phase space

Deep generative models such as diffusion and flow matching are powerful machine learning tools capable of learning and sampling from high-dimensional distributions. They are particularly useful when the training data appears to be concentrated on a submanifold of the data embedding space. For high-energy physics data, consisting of collections of relativistic energy-momentum 4-vectors, this submanifold can enforce extremely strong physically-motivated priors, such as energy and momentum conservation. If these constraints are learned only approximately, rather than exactly, this can inhibit the interpretability and reliability of such generative models. To remedy this deficiency, we introduce generative models which are, by construction, confined at every step of their sampling trajectory to the manifold of massless N-particle Lorentz-invariant phase space in the center-of-momentum frame. In the case of diffusion models, the "pure noise" forward process endpoint corresponds to the uniform distribution on phase space, which provides a clear starting point from which to identify how correlations among the particles emerge during the reverse (de-noising) process. We demonstrate that our models are able to learn both few-particle and many-particle distributions with various singularity structures, paving the way for future interpretability studies using generative models trained on simulated jet data.

Bogorad, Zachary [Fermilab]↗

On the asymptotic preserving property of the unified gas kinetic scheme for the diffusion limit of linear kinetic models

The unified gas kinetic scheme (UGKS) of K. Xu et al. (2010) [37], originally developed for multiscale gas dynamics problems, is applied in this paper to a linear kinetic model of radiative transfer theory. While such problems exhibit purely diffusive behavior in the optically thick (or small Knudsen) regime, we prove that UGKS is still asymptotic preserving (AP) in this regime, but for the free transport regime as well. Moreover, this scheme is modified to include a time implicit discretization of the limit diffusion equation, and to correctly capture the solution in case of boundary layers. Contrary to many AP schemes, this method is based on a standard finite volume approach, it does neither use any decomposition of the solution, nor staggered grids. Several numerical tests demonstrate the properties of the scheme.

97 MATHEMATICS AND COMPUTING↗