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At least 1,441 records · Page 80

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. In this paper, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.

59 BASIC BIOLOGICAL SCIENCES↗

Guidance of Nonlinear Systems

The paper describes a method for guiding a dynamic system through a given set of points. The paradigm is a fully automatic aircraft subject to air traffic control (ATC). The ATC provides a sequence of way points through which the aircraft trajectory must pass. The way points typically specify time, position, and velocity. The guidance problem is to synthesize a system state trajectory which satisfies both the ATC and aircraft constraints. Complications arise because the controlled process is multi-dimensional, multi-axis, nonlinear, highly coupled, and the state space is not flat. In addition, there is a multitude of possible operating modes, which may number in the hundreds. Each such mode defines a distinct state space model of the process by specifying the state space coordination, the partition of the controls into active controls and configuration controls, and the output map. Furthermore, mode transitions must be smooth. The guidance algorithm is based on the inversion of the pure feedback approximations, which is followed by iterative corrections for the effects of zero dynamics. The paper describes the structure and modules of the algorithm, and the performance is illustrated by several example aircraft maneuvers.

Meyer, George↗

Guidance of Nonlinear Systems

The paper describes a method for guiding a dynamic system through a given set of points. The paradigm is a fully automatic aircraft subject to air traffic control (ATC). The ATC provides a sequence of way points through which the aircraft trajectory must pass. The way points typically specify time, position, and velocity. The guidance problem is to synthesize a system state trajectory which satisfies both the ATC and aircraft constraints. Complications arise because the controlled process is multi-dimensional, multi-axis, nonlinear, highly coupled, and the state space is not flat. In addition, there is a multitude of possible operating modes, which may number in the hundreds. Each such mode defines a distinct state space model of the process by specifying the state space coordinatization, the partition of the controls into active controls and configuration controls, and the output map. Furthermore, mode transitions must be smooth. The guidance algorithm is based on the inversion of the pure feedback approximations, which is followed by iterative corrections for the effects of zero dynamics. The paper describes the structure and modules of the algorithm, and the performance is illustrated by several example aircraft maneuvers.

Meyer, George↗

Coupled machine learning–ecosystem ensemble models substantially improve predictions of nitrous oxide (N 2 O) fluxes from US croplands

Nitrous oxide (N 2 O) is a potent and persistent greenhouse gas, with rising atmospheric concentrations driven in part by inefficient use of synthetic nitrogen (N) fertilizers in agriculture. Predicting soil N 2 O emissions is challenging due to high spatial and temporal variability arising from complex soil biogeochemical processes. Process-based ecosystem models and standalone machine learning (ML) approaches without extensive site-specific calibration often miss high-emission episodes. Here, we show how an Ensemble Modeling System (EMS) based on outputs from an ensemble of ecosystem models coupled to an ensemble of ML models can improve predictions and understanding of N 2 O fluxes from US cropland. Trained and validated on ~12,000 N 2 O chamber measurements at 17 US Midwest sites (six crops, 35 management practices), the EMS accurately predicted daily fluxes of N 2 O at both training (R 2 = 0.84, RMSE = 16.4 g N ha −1 d −1 ) and held-out testing sites (R 2 = 0.84, RMSE = 6.2 g N ha −1 d −1 ). Analyses identified six dominant N 2 O drivers: soil organic carbon (SOC), NH 4 + , NO 3 - , water-filled pore space, temperature, and aboveground biomass production. Wet, warm soils produced large N 2 O peaks only with sufficient SOC and mineral N; in low-SOC soils, fluxes remained low. Incorporating these drivers into process-based models might significantly improve their predictive capacity. The EMS demonstrates a strong potential to predict N 2 O fluxes at unseen sites, enabling more reliable regional inventories, improved gap-filling where measurements are sparse, and enhanced understanding of mechanisms to advance targeted mitigation strategies in food, feed, and bioenergy crops.

AI↗

Towards machine-learning a fully-coupled constitutive model for thermal-hydraulic fracture in geothermal systems: phase I (Final Report)

This project, entitled “Towards machine-learning a fully-coupled constitutive model for thermal-hydraulic fracture in geothermal systems: phase I,” addresses challenges in understanding and controlling subsurface fracture networks, which are crucial for applications like deep geothermal heat mining and deep-crustal minerals/metals/hydrogen extraction. The research focuses on advancing the understanding of coupled thermal-hydro-mechanical-chemical (THMC) processes in geologic materials, particularly under the high temperature and pressure conditions found in the deep crust. This seed grant focused specifically on thermal cracking and the development of new constitutive models. Significant progress was made in both experimental and theoretical domains. To study micro-scale fracture formation, the project demonstrated the ability to create thermal cracking under stress in granite samples using a Paterson Gas-medium Deformation Apparatus.

15 GEOTHERMAL ENERGY↗

Extending accurate spectral induced polarization measurements into the kHz range: modelling and removal of errors from interactions between the parasitic capacitive coupling and the sample holder

SUMMARY Spectral induced polarization (SIP), describing the measurement of the frequency domain electrical impedance magnitude and phase of porous materials, has been widely used to characterize subsurface hydrological/biogeochemical properties and processes. SIP data collected at frequencies higher than 100 Hz are expected to describe the polarization of small particles providing insights into the physicochemical properties of clays, nanoparticles and microorganisms. However, the phase measurements at these high frequencies are often contaminated by errors due to the parasitic capacitive coupling of the SIP instrument, especially for lower conductivity samples. We developed a model showing the measured phase is the sum of the true sample phase and an error term ωCinZx, where ω is the angular frequency; Cin is the instrument input capacitance and Zx is a measurable impedance function related to the sample holder properties and the reference resistor. Based on this model, a new phase correction method is proposed that results in highly accurate SIP data up to 20 kHz as well as the determination of Cin. We tested the correction method using electric circuits, NaCl fluids and three unconsolidated samples (sand, sand-clay and sand-pyrite mixtures). The corrected phase for the circuit and NaCl fluid experiments showed excellent agreement with the theoretical phase response across the studied frequency range (errors <1 mrad). For unconsolidated samples, removal of errors results in phase spectra more consistent with expected polarization mechanisms, as based on phase peaks recorded for small pyrite and clay particles at high frequencies. These phase peaks could not be identified in the uncorrected data. Our approach can substantially enhance the value of the SIP method for the characterization of fine-grained sediments and rocks.

58 GEOSCIENCES↗

Prediction of local concentration fields in porous media with chemical reaction using a multi scale convolutional neural network

The study of solute transport in porous media is of interest in many chemical engineering systems. Some example applications include packed bed catalytic reactors, filtration devices, and batteries. The pore scale modeling of these systems is time consuming and may require large computing resources, for this reason computational fluid dynamics (CFD) simulations are not practical if a large number of simulations is required, like in multiscale modeling, where a model at a large scale calls for pore scale simulations. It has been shown that neural networks can be trained with a dataset of flow simulations and then predict fields orders of magnitude faster, and with less computational resources, in new domains. However, it is crucial to provide the neural network with an effective description of the domain and the undergoing operating conditions to be able to train models that generalize accurately in unseen samples. Therefore, research is needed to employ neural networks in new complex systems. The appropriate training of a network for predicting coupled flow and solute transport processes is an outstanding problem due to the complex interplay between geometry and operating conditions. In this work, we train a multi scale convolutional neural network (MSNet) with a diverse dataset of simulations of transport and chemical reaction in porous media to predict the local concentration fields in images of porous media. Our dataset contains a wide diversity of sphere pack arrangements under different operating conditions (Péclet and Reynolds numbers). Further, we train a robust model by employing different input descriptors that represent the medium and the different operating conditions of each system. Our trained model is able to provide nearly instantaneous predictions, compared to around twenty hours of the CFD workflow, with less than 3.5% error on new geometries and transport conditions. Thus the model could be easily integrated in a multiscale workflow where fast response is needed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Particle tracing modeling of ion fluxes at geosynchronous orbit

The initial results of a coupled MHD/particle tracing method to evaluate particle fluxes in the inner magnetosphere are presented. This setup is capable of capturing the earthward particle acceleration process resulting from dipolarization events in the tail region of the magnetosphere. On the period of study, the MHD code was able to capture a dipolarization event and the particle tracing algorithm was able to capture our results of these disturbances and calculate proton fluxes in the night side geosynchronous orbit region. The simulation captured dispersionless injections as well as the energy dispersion signatures that are frequently observed by satellites at geosynchronous orbit. Currently, ring current models rely on Maxwellian-type distributions based on either empirical flux values or sparse satellite data for their boundary conditions close to geosynchronous orbit. In spite of some differences in intensity and timing, the setup presented here is able to capture substorm injections, which represents an improvement regarding a reverse way of coupling these ring current models with MHD codes through the use of boundary conditions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Modeling aerosols and their interactions with shallow cumuli during the 2007 CHAPS field study

The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is used to simulate relationships between aerosols and clouds in the vicinity of Oklahoma City during the June 2007 Cumulus Humilis Aerosol Processing Study (CHAPS). The regional scale simulation completed using 2 km horizontal grid spacing evaluates four important relationships between aerosols and shallow cumulus clouds observed during CHAPS. First, the model reproduces the trends of higher nitrate volume fractions in cloud droplet residuals compared to interstitial non-activated aerosols, as measured using the Aerosol Mass Spectrometer. Comparing simulations with cloud chemistry turned on and off, we show that nitric acid vapor uptake by cloud droplets explains the higher nitrate content of cloud droplet residuals. Second, as documented using an offline code, both aerosol water and other inorganics (OIN), which are related to dust and crustal emissions, significantly affect predicted aerosol optical properties. Reducing the OIN content of wet aerosols by 50% significantly improves agreement of model predictions with measurements of aerosol optical properties. Third, the simulated hygroscopicity of aerosols is too high as compared to their hygroscopicity derived from cloud condensation nuclei and particle size distribution measurements, indicating uncertainties associated with simulating size-dependent chemical composition and treatment of aerosol mixing state within the model. Fourth, the model reasonably represents the observations of the first aerosol indirect effect where pollutants in the vicinity of Oklahoma City increase cloud droplet number concentrations and decrease the droplet effective radius. While previous studies have often focused on cloud-aerosol interactions in stratiform and deep convective clouds, this study highlights the ability of regional-scale models to represent some of the important aspects of cloud-aerosol interactions associated with fields of short-lived shallow cumuli.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geant4-based multiphysics simulation toolkit for analysis of radiation detector performance

Often only a single physical process or component is investigated in the simulation of radiation detector systems. The results are then considered to be representative of what is expected in the correlating physical experiment. Although singular assessments may serve as a good estimate, the overall performance of a radiation detector system depends on several physical processes and the performance of all components within the system. Our Geant4-based multiphysics simulation toolkit couples radiation transport with optical photon processes, providing simulations of radiation detector systems components from the scintillator through the photocathode of the photodetector. Work to incorporate the back-end detector components, including the complete photodetector and subsequent electronics (e.g., amplifiers, digitizers), is underway. Geant4 is used to model the radiation transport and optical photon processes that occur in the front-end detector system components when exposed to a chosen source. These components include the scintillator, detector housing, optical coupling to the photodetector, and photocathode of the photodetector. Characteristics of several detector systems that have been studied include time response; pulse height spectra; number of photoelectrons per MeV; detector efficiency versus incident quanta energy; and effects on detector response due to change in geometries, materials, and reflectivity. Comparison of these characteristics by means of this toolkit enables the selection of the optimal individual components; thus, it is possible to specify the radiation detector system best suited to meet the requirements of any physical experiment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Simulating the Effect of Fracture Connectivity on Repository Performance with GDSA Framework - 18589

This work examines the possible migration of radionuclides from a deep geologic nuclear waste repository sited in fractured crystalline host rock. The key safety concern is the potential effect on waste isolation of the inter-connectivity of the fracture network, which is primarily established by the temporal evolution of the temperature and stress fields at the time of original rock intrusion and cooling. Two end members are considered in these simulations, one with a high degree of connectivity to the biosphere, such that advective transport through the fracture and fault network controls radionuclide migration, and the other with a low degree of connectivity, such that slow diffusive transport through the crystalline rock matrix is the controlling process for radionuclide migration to the biosphere. Both end members have several areally extensive, high-transmissivity deformation zones, whose distance to the repository is an important factor for waste isolation capability. Uncertainties in fracture properties (transmissivity, orientation, radius) and fracture distribution also give rise to uncertainty in waste isolation capability (i.e., the overall connectivity of the repository with the surface biosphere). These types of natural system uncertainties are generally present in any geologic site-characterization program and thus represent an important factor in assessing repository performance in hard rock environments. The waste considered in these simulations are spent fuel rod assemblies from the U.S. commercial nuclear reactor fleet. Thermal output of the waste must be considered in the simulations and can influence the rate and timing of waste package failure, waste form degradation, and fluid flux due to thermal expansion around the repository horizon. To achieve a high-fidelity representation of radionuclide transport in fractures and rock matrix, combined with thermal energy transport and fluid flow in fractures and matrix, the mathematical model is solved numerically in a parallel high-performance computing (HPC) environment on a finite volume unstructured grid consisting of approximately 5 million cells, using Geologic Disposal Safety Assessment (GDSA) Framework (https://pa.sandia.gov), an open-source performance assessment tool for deep underground disposal of nuclear waste. GDSA Framework uses PFLOTRAN to solve the balance equations on a three-dimensional grid with heterogeneous properties, using multiple processors in a parallel configuration based on domain decomposition. The fracture networks in these simulations are originally generated as discrete fracture networks (DFNs), which are sets of two-dimensional planes distributed in a three-dimensional domain. The method used in GDSA Framework maps the stochastically generated DFN to an equivalent continuous porous medium (ECPM) domain that allows for the simulation of coupled heat flow, fluid flow, and radionuclide transport, including heat conduction through the matrix of the fractured rock, which is a process not easily modeled in a DFN representation. Computational efficiency is also greatly enhanced using the ECPM method, allowing for a realistic representation and analysis of uncertainties in a multi-realization performance assessment of a deep geologic repository. The effect of fracture connectivity on the waste isolation safety function, as brought to light by these GDSA Framework simulations, points to the importance of including a realistic representation of uncertainties in fracture properties and distribution (effectively, uncertainty in spatial heterogeneity) in repository safety assessment simulations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

IONIZATION IN ATMOSPHERES OF BROWN DWARFS AND EXTRASOLAR PLANETS. II. DUST-INDUCED COLLISIONAL IONIZATION

Observations have shown that continuous radio emission and also sporadic H{alpha} and X-ray emission are prominent in singular, low-mass objects later than spectral class M. These activity signatures are interpreted as being caused by coupling of an ionized atmosphere to the stellar magnetic field. What remains a puzzle, however, is the mechanism by which such a cool atmosphere can produce the necessary level of ionization. At these low temperatures, thermal gas processes are insufficient, but the formation of clouds sets in. Cloud particles can act as seeds for electron avalanches in streamers that ionize the ambient gas, and can lead to lightning and indirectly to magnetic field coupling, a combination of processes also expected for protoplanetary disks. However, the precondition is that the cloud particles are charged. We use results from DRIFT-PHOENIX model atmospheres to investigate collisional processes that can lead to the ionization of dust grains inside clouds. We show that ionization by turbulence-induced dust-dust collisions is the most efficient kinetic process. The efficiency is highest in the inner cloud where particles grow quickly and, hence, the dust-to-gas ratio is high. Dust-dust collisions alone are not sufficient to improve the magnetic coupling of the atmosphere inside the cloud layers, but the charges supplied either on grains or within the gas phase as separated electrons can trigger secondary nonlinear processes. Cosmic rays are likely to increase the global level of ionization, but their influence decreases if a strong, large-scale magnetic field is present as on brown dwarfs. We suggest that although thermal gas ionization declines in objects across the fully convective boundary, dust charging by collisional processes can play an important role in the lowest mass objects. The onset of atmospheric dust may therefore correlate with the anomalous X-ray and radio emission in atmospheres that are cool, but charged more than expected by pure thermal ionization.

79 ASTRONOMY AND ASTROPHYSICS↗

Modeling Isoprene Emission Response to Drought and Heatwaves Within MEGAN Using Evapotranspiration Data and by Coupling With the Community Land Model

We introduce two new drought stress algorithms designed to simulate isoprene emission with the Model of Emissions of Gases and Aerosols from Nature (MEGAN) model. The two approaches include the representation of the impact of drought on isoprene emission with a simple empirical approach for offline MEGAN applications and a more process-based approach for online MEGAN in Community Land Model (CLM) simulations. The two versions differ in their implementation of leaf-temperature impacts of mild drought. For the online version of MEGAN that is coupled to CLM, the impact of drought on leaf temperature is simulated directly and the calculated leaf temperature is considered for the estimation of isoprene emission. For the offline version, we apply an empirical algorithm derived from whole-canopy flux measurements for simulating the impact of drought ranging from mild to severe stage. In addition, the offline approach adopts the ratio ($f$ PET ) of actual evapotranspiration to potential evapotranspiration to quantify the severity of drought instead of using soil moisture. We applied the two algorithms in the CLM-CAM-chem (the Community Atmosphere Model with Chemistry) model to simulate the impact of drought on isoprene emission and found that drought can decrease isoprene emission globally by 11% in 2012. We further compared the formaldehyde (HCHO) vertical column density simulated by CAM-chem to satellite HCHO observations. We found that the proposed drought algorithm can improve the match with the HCHO observations during droughts, but the performance of the drought algorithm is limited by the capacity of the model to capture the severity of drought.

54 ENVIRONMENTAL SCIENCES↗

FVCOM-ICM4.0

FVCOM-ICM is a water quality model that simulates the influence of nutrients and carbon pollution on biogeochemical oceanographic processes such as phytoplankton primary productivity, nutrient consumption, mineralization, decay and settling of particulate organic matter and computes resulting dissolved oxygen (DO) concentrations and pH levels. An “offline” approach of coupling Finite Volume Coastal Ocean Model (FVCOM) hydrodynamic solutions to CE-QUAL-ICM biogeochemical model was used. FVCOM and CE-QUAL-ICM are public domain Fortran Codes that were developed independently by US Army Corps of Engineers and University of Massachusetts. PNNL developed FVCOM-ICM that has the ability to conduct water quality calculations using a previously computed hydrodynamic solution. The biogeochemical calculations using CE-QUAL-ICM kinetics are conducted over the same finite-volume mesh and in the FVCOM framework.

Khangaonkar, Tarang↗

Effect of Processing on Precipitation Kinetics in Nano Polycrystalline 7075 Aluminum Alloy

Fairmount Technologies (FT) seeks to optimize the thermomechanical processing of Aluminum Alloy 7075. The target yield strength is 20% higher than commercially available 7075-T6 temper sheet which will enable structural light weighting by a similar magnitude and reduce the carbon footprint of the transportation sector. To reduce processing cost and make this commercially viable, it is important to understand physical mechanisms driving microstructural changes. A mesoscale phase-field model seeded with experimentally measured microstructures and assessed thermodynamic and kinetic properties will be developed and exercised using HPC at PNNL. It will account for the effect of deformation, temperature, and chemistry on precipitation kinetics in nanocrystalline microstructures. Our objective is to understand this “stress-aging” coupling by performing parametric simulations with mesoscale models for a better understanding of GP zone and η' formation in nanocrystalline 7075 Al. This will help FT optimize processing schedules to achieve desired microstructures that increase both strength and ductility.

36 MATERIALS SCIENCE↗

Two-Way Integration of WRF and CCSM for Regional Climate Simulations

Under the support of the DOE award DE-SC0004670, we have successfully developed an integrated climate modeling system by nesting Weather Research and Forecasting (WRF) model within the Community Climate System Model (CCSM) and the ensuing new generation Community Earth System Model (CESM). The integrated WRF/CESM system is intended as one method of global climate modeling with regional simulation capabilities. It allows interactive dynamical regional downscaling in the computational flow of present or future global climate simulations. This capability substantially simplifies the process of dynamical downscaling by avoiding massive intermediate model outputs at high frequency that are typically required for offline regional downscaling. The inline coupling also has the advantage of higher temporal resolution for the interaction between regional and global model components. With the aid of the inline coupling, a capability has also been developed to ingest other global climate simulations (by CESM or other models), which otherwise may not have necessary intermediate outputs for regional downscaling, to realize their embedded regional details. It is accomplished by relaxing the global atmospheric state of the integrated model to that of the source simulations with an appropriate time scale. This capability has the potential to open a new venue for ensemble regional climate simulations using a single modeling system. Furthermore, this new modeling system provides an effective modeling framework for the studies of physical and dynamical feedbacks of regional weather phenomena to the large scale circulation. The projected uses of this capability include the research of up-scaling effect of regional weather system, and its use as an alternative physical representation of sub-scale processes in coarser-resolution climate models.

54 ENVIRONMENTAL SCIENCES↗

Computationally Efficient Multiscale Neural Networks Applied to Fluid Flow in Complex 3D Porous Media

Abstract The permeability of complex porous materials is of interest to many engineering disciplines. This quantity can be obtained via direct flow simulation, which provides the most accurate results, but is very computationally expensive. In particular, the simulation convergence time scales poorly as the simulation domains become less porous or more heterogeneous. Semi-analytical models that rely on averaged structural properties (i.e., porosity and tortuosity) have been proposed, but these features only partly summarize the domain, resulting in limited applicability. On the other hand, data-driven machine learning approaches have shown great promise for building more general models by virtue of accounting for the spatial arrangement of the domains’ solid boundaries. However, prior approaches building on the convolutional neural network (ConvNet) literature concerning 2D image recognition problems do not scale well to the large 3D domains required to obtain a representative elementary volume (REV). As such, most prior work focused on homogeneous samples, where a small REV entails that the global nature of fluid flow could be mostly neglected, and accordingly, the memory bottleneck of addressing 3D domains with ConvNets was side-stepped. Therefore, important geometries such as fractures and vuggy domains could not be modeled properly. In this work, we address this limitation with a general multiscale deep learning model that is able to learn from porous media simulation data. By using a coupled set of neural networks that view the domain on different scales, we enable the evaluation of large ( $$>512^3$$ > 512 3 ) images in approximately one second on a single graphics processing unit. This model architecture opens up the possibility of modeling domain sizes that would not be feasible using traditional direct simulation tools on a desktop computer. We validate our method with a laminar fluid flow case using vuggy samples and fractures. As a result of viewing the entire domain at once, our model is able to perform accurate prediction on domains exhibiting a large degree of heterogeneity. We expect the methodology to be applicable to many other transport problems where complex geometries play a central role.

36 MATERIALS SCIENCE↗