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At least 865 records · Page 48

A Mathematical Model of the Dynamics of Cytokine Expression and Human Immune Cell Activation in Response to the Pathogen Staphylococcus aureus

Cell-based mathematical models have previously been developed to simulate the immune system in response to pathogens. Mathematical modeling papers which study the human immune response to pathogens have predicted concentrations of a variety of cells, including activated and resting macrophages, plasma cells, and antibodies. This study aims to create a comprehensive mathematical model that can predict cytokine levels in response to a gram-positive bacterium, S. aureus by coupling previous models. To accomplish this, the cytokines Tumor Necrosis Factor Alpha (TNF-α), Interleukin 6 (IL-6), Interleukin 8 (IL-8), and Interleukin 10 (IL-10) are included to quantify the relationship between cytokine release from macrophages and the concentration of the pathogen, S. aureus, ex vivo. Partial differential equations (PDEs) are used to model cellular response and ordinary differential equations (ODEs) are used to model cytokine response, and interactions between both components produce a more robust and more complete systems-level understanding of immune activation. In the coupled cellular and cytokine model outlined in this paper, a low concentration of S. aureus is used to stimulate the measured cellular response and cytokine expression. Results show that our cellular activation and cytokine expression model characterizing septic conditions can predict ex vivo mechanisms in response to gram-negative and gram-positive bacteria. Our simulations provide new insights into how the human immune system responds to infections from different pathogens. Novel applications of these insights help in the development of more powerful tools and protocols in infection biology.

60 APPLIED LIFE SCIENCES↗

Coupled cluster and dislocation dynamics modeling of microstructure evolution in irradiated materials

We develop here a coupled cluster and dislocation dynamics framework to study the microstructure evolution of irradiated materials. The framework not only accounts for the three dimensional diffusion of radiation-generated clusters, but also their interaction with dislocation networks and the resultant climb motion of discrete dislocations within finite crystals. The framework is solved with a superposition solution scheme, and is applied to investigate the evolution of the irradiation-induced dislocation loops in zirconium (Zr), considering the effects of various bias factors including the diffusion anisotropy difference (DAD) of interstitials and interstitial clusters, the dislocation bias of defects to discrete dislocation segments, and the production bias of defects from the radiation cascade. We find that the DAD is the most critical factor influencing the kinetics of the loop evolution in Zr, while the recombination/interaction of mobile defects can induce a strong spatial dependence of the loop evolution together with the DAD. Here, the method is also adopted to study the evolution of interstitial $\langle$a$\rangle$ and vacancy $\langle$c$\rangle$ dislocation loop ensembles consistent with the microstructure observed during irradiation-induced growth of Zr. Our findings not only reveal the spatial dependence of the size and ellipticity of the dislocation loops, but also suggest a limit on the anisotropy factor of interstitials to reproduce the co-growth of $\langle$a$\rangle$ and $\langle$c$\rangle$ loops in zirconium, in good agreement with experimental observations and other simulation results.

Bias factors↗

Model comparisons for two-temperature plasma equations of state

When a plasma is generated in the laboratory, energy is often deposited preferentially into either the electrons or the ions, giving rise to a quasiequilibrium state in which the two species, electrons and ions, are well described by two effective temperatures, T e and T i . Accurate hydrodynamic modeling of such a two-temperature plasma requires an equation of state that captures the relevant many-body physics without assuming a strict local thermodynamic equilibrium. Several models have been proposed within the literature, which extend conventional statistical approaches, each employing a different combination of assumptions for modifying the equilibrium equations. Here, in this work, we compare the predictions for several models, presenting derivations of the internal energy and pressure for each microscopic model within a unified framework so that the assumptions of each model may be more easily compared to one another. We find that for sufficiently weak coupling, all models agree with one another. However, as the coupling strength is increased, the disagreement between the models becomes more pronounced. Moreover, the relative sizes of the corrections predicted by each model depend on which species has the higher temperature, T e >T i vs T e < T i .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Enhancing Lithium-Ion Battery Aging Simulations: Coupling a High-Resolution, 3D, Grain-Scale Electromechanical Model to a Single-Particle Model

One of the main goals in modeling lithium-ion batteries is to improve/predict longevity and resilience of new chemistries. Unfortunately, this requires simulation of thousands of charge/discharge cycles, which can be rather time consuming depending on the fidelity of the simulation. The purpose of this talk is to discuss a new modeling framework that couples a high-resolution, continuous damage model (CDM) to a single particle model (SPM) resulting in a good combination of speed and fidelity. In previous work, a 3D, continuum-level chemo-mechanical model was developed to investigate cracking within a single cathode particle comprised of hundreds to thousands of randomly oriented grains. The CDM predicted that particle fracture is primarily due to non-ideal grain interactions with slight dependence on high-rate charge demands. Essentially, when neighboring grains were misaligned, they expanded different rates relative to one another leading to high stresses and ultimately the formation of intraparticle cracks. The model predicted that small particles with large grains develop significantly less damage than larger particles with small grains. Finally, the model predicted most of the chemo-mechanical damage accumulates in the first charge after formation. This chemo-mechanical "damage saturation" effect indicated that initial particle fracture occurs within the first few cycles, while long-term cathode degradation is not solely chemo-mechanically induced. This led to a need for simulating fatigue-like mechanism that degrade the battery over longer time scales. In order to reach the time scales, need to resolve fatigue-like degradation, the CDM needs to be complemented by a faster model. Therefore, recent efforts have been focused on using results from the CDM to inform parameters within the SPM. These parameters are homogenization factors that are associated with diffusion, particle radius, and/or exchange current density. By coupling the CDM to the SPM, the aging simulation is broken up into two domains: short-term and long-term degradation. The short-term degradation occurs over a single cycle and is handled by the CDM due of its high fidelity, but relatively expensive computational cost. Such mechanism include break-in crack caused by mismatches in grain orientation. The long-term degradation occurs over tens of cycles and is handled by the SPM due it's computational efficiency. Most of the fatigue-like mechanism fall into this category. The eventual goal of this modeling framework is to upscale to a psudo-2D model allowing for full electrode simulation, which are informed by high-fidelity grain-scale simulations.

electrochemistry↗

Development of Time Lapse VSP Integration Workflow: A Case Study at Farnsworth CO2-EOR Project

Abstract This study aims to develop a 4D Vertical Seismic Profile (VSP) integration workflow to improve the prediction of subsurface stress changes. The selected study site is a 5-spot pattern within the ongoing CO2-EOR operations at the Farnsworth Field Unit FWU in Ochiltree County, Texas. The specific pattern has undergone extensive geological and geomechanical characterization through the acquisition of 3D seismic data, geophysical well logs, and core. This workflow constrains a numerical hydromechanical model by applying a penalty function formed between "modeled" versus "observed" time-lapse compressional and shear seismic velocity changes. Analyses of geophysical logs and ultra-sonic measurements on core exhibit measurable sensitivities to changes in both fluid saturation and mean effective stress. These data are used to develop a site-specific rock physics model and stress-velocity relationship, which inform the numerical models used to generate the "modeled" portion of the penalty function. The "observed" portion of the penalty function is provided by a novel elastic full-waveform inversion of the available 3D baseline and three monitor surveys to produce high-quality estimates of time-lapse compressional and shear seismic velocity changes. The modeling workflow accounts sequentially for fluid substitution and stress impacts. Hydrodynamic and geomechanical properties of the 3D coupled numerical model are estimated through geostatistical integration of well log and core data with 3D seismic inversion products. Changes in seismic velocities due to fluid substitution are computed using the Biot-Gassmann workflow and site-specific rock physics. Stress impacts on time-lapse seismic velocity changes are modeled from the effective stress output of the hydromechanical model and are initially based on the velocity versus effective stress relationship extracted from core mechanical testing. Based on the principle of superposition of seismic wavefields, seismic velocity changes attributed to fluid substitution and that due to changes in mean effective stress are treated as linearly additive. The modeled results are upscaled using Backus averaging to reconcile scale discrepancies between the modeled and measured datasets to formulate the penalty function. This manuscript presents the forward modeling process and concludes that for the base case, the seismic velocity changes due to mean effective stress dominates over the seismic velocity changes attributed to fluid substitution because of the extensive range of the pressure perturbations. Successful minimization of this penalty function calibrates the coupled hydrodynamic geomechanical numerical model and affirms the suitability of acoustic time-lapse measurements such as 4D-VSP for geomechanical calibration.

02 PETROLEUM↗

A new parameterization of ice heterogeneous nucleation coupled to aerosol chemistry in WRF-Chem model version 3.5.1: evaluation through ISDAC measurements

In the Arctic, during polar night and early spring, ice clouds are separated into two leading types of ice clouds (TICs): (1) TIC1 clouds characterized by a large concentration of very small crystals and TIC2 clouds characterized by a low concentration of large ice crystals. Using a suitable parameterization of heterogeneous ice nucleation is essential for properly representing ice clouds in meteorological and climate models and subsequently understanding their interactions with aerosols and radiation. Here, we describe a new parameterization for ice crystal formation by heterogeneous nucleation in water-subsaturated conditions coupled to aerosol chemistry in the Weather Research and Forecasting model coupled with chemistry (WRF-Chem). The parameterization is implemented in the Milbrandt and Yau (2005a, b) two-moment cloud microphysics scheme, and we assess how the WRF-Chem model responds to the run-time interaction between chemistry and the new parameterization. Well-documented reference cases provided us with in situ data from the spring 2008 Indirect and Semi-Direct Aerosol Campaign (ISDAC) over Alaska. Our analysis reveals that the new parameterization clearly improves the representation of the ice water content (IWC) in polluted or unpolluted air masses and shows the poor performance of the reference parameterization in representing ice clouds with low IWC. The new parameterization is able to represent TIC1 and TIC2 microphysical characteristics at the top of the clouds, where heterogenous ice nucleation is most likely occurring, even with the known bias of simulated aerosols by WRF-Chem over the Arctic.

54 ENVIRONMENTAL SCIENCES↗

Phase-field modeling of crack growth under coupled creep-fatigue

Crack growth under coupled creep-fatigue strongly influences service life of metallic components operating at high temperatures. However, there lack numerical models that enable direct simulations of crack growth and plasticity development under coupled creep-fatigue. Here, in this study, a unified phase-field model is developed for simulating crack growth under fatigue, creep, and coupled creep-fatigue. This model is able to reproduce the Paris laws for both brittle and ductile materials in pure fatigue mode, which shows that the degradation rate due to cyclic stress in ductile materials is generally larger than that in brittle materials. Fatigue simulations with different yield strengths demonstrate that plasticity facilitates crack growth in typical ductile materials. High-throughput simulations are performed under coupled creep-fatigue conditions, with varying hold-stress levels and hold-time. By analyzing crack growth rate under different hold-time, a creep-fatigue interaction term is obtained. Simulation results demonstrate that the creep-fatigue interaction is caused by smaller stress gradient and enhanced degradation rate ahead of the crack tips under coupled creep-fatigue, compared to the situation of pure fatigue. This work reveals the origin of different Paris-law exponents in brittle and ductile materials and demonstrates how the interplay between creep and fatigue affects crack growth.

36 MATERIALS SCIENCE↗

Explaining the extra crystal-field mode in 𝐴 ⁢Ce ⁢𝑋 2 (𝐴 = K, Rb, Na; 𝑋 = O, S, Se, Te)

A growing list of Ce-based magnets have shown an extra and heretofore unexplained crystal electric field (CEF) mode at high energies. We describe a process whereby an optical phonon can produce a split CEF mode well above the phonon energy. We use density functional theory and point-charge model calculations to estimate the phonon distortions and coupling to model this effect in KCeO 2 , showing that it accounts for the extra CEF mode observed. Furthermore, this mechanism is generic and may explain the extra modes observed on a variety of Ce 3+ compounds.

36 MATERIALS SCIENCE↗

Quantum Drude oscillators coupled with Coulomb potential as an efficient model for bonded and non-covalent interactions in atomic dimers

The quantum Drude oscillator (QDO) model has been widely used as an efficient surrogate to describe the electric response properties of matter as well as long-range interactions in molecules and materials. Most commonly, QDOs are coupled within the dipole approximation so that the Hamiltonian can be exactly diagonalized, which forms the basis for the many-body dispersion method [Phys. Rev. Lett. 108, 236402 (2012)]. The dipole coupling is efficient and allows us to study non-covalent many-body effects in systems with thousands of atoms. However, there are two limitations: (i) the need to regularize the interaction at short distances with empirical damping functions and (ii) the lack of multipolar effects in the coupling potential. In this work, we convincingly address both limitations of the dipole-coupled QDO model by presenting a numerically exact solution of the Coulomb-coupled QDO model by means of quantum Monte Carlo methods. We calculate the potential-energy surfaces of homogeneous QDO dimers, analyzing their properties as a function of the three tunable parameters: frequency, reduced mass, and charge. We study the coupled-QDO model behavior at short distances and show how to parameterize this model to enable an effective description of chemical bonds, such as the covalent bond in the H2 molecule.

Chemistry↗

Machine learning coupled multi-scale modeling for redox flow batteries

The reaction distribution in macro or device-scale has been studied for redox flow batteries. The reaction distribution on electrode pore-scale structure however is not well understood, lacking especially on how the reaction distribution on the pore-scale may impact the overall performance of a flow battery. This study introduces for the first time a framework of a multi-scale model that provides understanding of the relationship between the pore-scale electrode structure reaction and the device-scale electrochemical reaction uniformity within the flow battery. A reduced order model is constructed based on 128 pore-scale simulations, which provide a quantitative relationship between the battery operation conditions (inlet velocity, current density, inlet concentration) and the surface reaction uniformity for the pore-scale sample. The multi-scale framework upscales this pore-scale surface reaction uniformity to device-scale combined uniformity. Based on the multi-scale model, a time-varying optimization of the inlet velocity is established, leading to significant reduction on pump power consumption with targeted surface reaction uniformity. The multi-scale model establishes the critical link between the micro-structure of a flow battery component and its performance at the macro-scale, therefore providing rationale for further operational or material optimization.

flow batteries, machine learning, multi-scale mode↗

Coupled Thermo–Hydro–Mechanical Modeling of Hydro-Shearing Stimulation in an Enhanced Geothermal System in the Raft River Geothermal Field, USA

The Raft River Enhanced Geothermal System (EGS) demonstration project aims to improve the geothermal production by enhancing the reservoir permeability via shear stimulation in well RRG-9. In this paper, we performed a series of 3D thermo– hydro–mechanical (THM) simulations to investigate the influence of hydraulic and thermal effects on the development of this EGS. The model includes synthetic fracture populations based on borehole televiewer images and in-situ stress measurements from well RRG-9. Fracture permeability evolution is determined using an empirical permeability law developed from laboratory experiments. The model was calibrated by comparing the hydraulic response to field observations, including wellhead pressure, injection rate, and well injectivity. Particularly, we analyzed the enhancement of reservoir permeability and the spatial extent of the stimulation zone for the given injection schedule. Our results indicate that the permeability enhancement of fractured geothermal reservoir is caused by the combined effects of injection-induced cooling and fluid pressure increase. The decrease of temperature plays a dominant role in reactivation of natural fractures under the hydro-shearing mechanism, while the higher injection pressure promotes shear failure and enlarges the stimulation zone. Finally, for the specified extensional stress state, the model favors greatest permeability enhancement along the maximum horizontal principal stress, a moderate vertical enhancement, and a smaller gain along the minimum horizontal principal stress.

58 GEOSCIENCES↗

Sub-Diurnal Methane Variations on Mars Driven by Barometric Pumping and Planetary Boundary Layer Evolution

In recent years, the Tunable Laser Spectrometer within the Sample Analysis at Mars (TLS-SAM) instrument on board the Mars Science Laboratory (MSL) Curiosity rover has detected methane variations in the atmosphere at Gale crater. Methane concentrations appear to fluctuate seasonally as well as sub-diurnally, which is difficult to reconcile with an as-yet-unknown transport mechanism delivering the gas from underground to the atmosphere. To potentially explain the fluctuations, we consider barometrically induced transport of methane from an underground source to the surface, modulated by temperature-dependent adsorption. The subsurface fractured-rock seepage model is coupled to a simplified 1-D atmospheric mixing model to provide insights on the pattern of atmospheric methane concentrations in response to transient surface methane emissions, as well as to predict sub-diurnal variation in methane abundance for the northern summer period, which is a candidate time frame for a MSL Curiosity sampling campaign. Our analysis suggests that there is a lower limit to the subsurface fracture density that can produce the observed methane patterns, below which the atmospheric methane variations would be out of phase with the observations. The best-performing model scenarios indicate a significant, short-lived methane pulse just prior to sunrise, the detection of which by TLS-SAM would be a potential indicator of the contribution of barometric pumping to Mars' atmospheric methane variations.

54 ENVIRONMENTAL SCIENCES↗