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Results for “mesoscale modeling”
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Distinguishing Mesoscale Polar Order (Unidirectional vs Bidirectional) of Cellulose Microfibrils in Plant Cell Walls Using Sum Frequency Generation Spectroscopy
Cellulose in plant cell walls are synthesized as crystalline microfibrils with diameters of 3–4 nm and lengths of around 1–10 μm. These microfibrils are known to be the backbone of cell walls, and their multiscale three-dimensional organization plays a critical role in cell wall functions including plant growth and recalcitrance to degradation. The mesoscale organization of microfibrils over a 1–100 nm range in cell walls is challenging to resolve because most characterization techniques investigating this length scale suffer from low spatial resolution, sample preparation artifacts, or inaccessibility of specific cell types. Here, we report a sum frequency generation (SFG) study determining the mesoscale polarity of cellulose microfibrils in intact plant cell walls. SFG is a nonlinear optical spectroscopy technique sensitive to the molecular-to-mesoscale order of noncentrosymmetric domains in amorphous matrices. However, the quantitative theoretical model to unravel the effect of polarity in packing of noncentrosymmetric domains on SFG spectral features has remained unresolved. In this work, we show how the phase synchronization principle of the SFG process is used to predict the relative intensities of vibrational modes with different polar angles from the noncentrosymmetric domain axis. Applying this model calculation for the first time and employing SFG microscopy, we found that cellulose microfibrils in certain xylem cell walls are deposited unidirectionally (or biased in one direction) instead of the bidirectional polarity which was believed to be dominant in plant cell walls from volume-averaged characterizations of macroscopic samples. Here, with this advancement in SFG analysis, one can now determine the relative polarity of noncentrosymmetric domains such as crystalline biopolymers interspersed in amorphous polymer matrices, which will open opportunities to study new questions that have not been conceived in the past.
Evaluating Diurnal and Semi-Diurnal Cycle of Precipitation in CMIP6 Models Using Satellite- and Ground-Based Observations
We report the diurnal and semi-diurnal cycle of precipitation simulated from CMIP6 models during 1996-2005 are evaluated globally between 60°S and 60°N, as well as at ten selected locations representing three categories of diurnal cycle of precipitation: (1) afternoon precipitation over land, (2) early morning precipitation over ocean, and (3) nocturnal precipitation over land. Three satellite-based and two ground-based rainfall products are used to evaluate the climate models. Globally, the ensemble mean of CMIP6 models shows a diurnal phase of 3 to 4 hours earlier over land and 1 to 2 hours earlier over ocean, when compared with the latest satellite products. These biases are in line with what were found in previous versions of climate models but reduced compared to the CMIP5 ensemble mean. Analysis at the selected locations complimented with in-situ measurements further reinforces these results. Several CMIP6 models have shown a significant improvement in the diurnal cycle of precipitation compared to their CMIP5 counterparts, notably on delaying afternoon precipitation over land. This can be attributed to the use of more sophisticated convective parameterizations. Most models are still unable to capture the nocturnal peak associated with elevated convection and propagating mesoscale convective systems, with a few exceptions that allow convection to be initiated above the boundary layer to capture nocturnal elevated convection. We also quantify an encouraging consistency between the satellite- and ground-based precipitation measurements despite differing spatiotemporal resolutions and sampling periods, which provides confidence in using them to evaluate the diurnal and semi-diurnal cycle of precipitation in climate models.
Anisotropic Motions of Fibrils Dictated by Their Orientations in the Lamella: A Coarse-Grained Model of a Plant Cell Wall
Plant cell walls are complex systems that exhibit the characteristics of both rigid and soft material depending on their external perturbations. The three main polymeric components in a plant primary cell wall are cellulose fibrils, hemicellulose, and pectins. These components interact in a hierarchical fashion giving rise to mesoscale structural features such as cellulose bundles, lamella stacking, and so on. Although several studies have focused on understanding these unique structural features, a clear picture linking them to cell wall mechanics is still lacking. As a first step toward this goal, a phenomenological model of plant cell wall has been developed in this work by using available experimental data to investigate the underlying connections between mesoscale structural features and the motions of fibrils during deformation. In this model cellulose fibrils exhibit motions such as angular reorientations and kinking upon forced stretching. Furthermore, these motions are dependent on the orientation of fibrils with respect to the stretch direction, i.e., fibrils that are at an angle to the stretch direction exhibit predominant angular reorientations, while fibrils transverse to the stretch direction undergo kinking as a result of transverse compression. Varying the chain length of pectin had negligible effects on these motions. One of the main contributions from this work is the development of a simple model that can be easily fine-tuned to test other hypotheses and extended to include additional experimental knowledge about the structural aspects of cell walls in the future.
Optimization and Evaluation of Stochastic Unified Convection Using Single-Column Model Simulations at Multiple Observation Sites
We extend the previously developed stochastic unified convection scheme (UNICON) for shallow convection to deep convection by parameterizing the impact of mesoscale organized flow on updraft properties. The extended stochastic UNICON parameterizes thermodynamic properties of updrafts at the near-surface as a multivariate Gaussian distribution, where the variances of the distribution are the summation of variances from non-organized turbulence and mesoscale organized flow. The distribution of updraft radius is parameterized as a power-law distribution with a scale break which is parameterized as a linear function of the strength of mesoscale organized flow. The proposed parameterization is validated using a series of large-eddy simulations of deep convection. The free parameters introduced in the formulation of stochastic UNICON are optimized using 10 cases of single-column model simulations over the ocean. Stochastic UNICON with the optimized parameters significantly reduces the biases of thermodynamic profiles and surface precipitation rates simulated in the original UNICON for tropical convection cases. The simulation of the variation in anomalies of temperature and moisture associated with the Madden-Julian oscillation is also improved. The overall improvements in simulated thermodynamic profiles are found to be due to the increased heating and drying tendencies by convective processes in stochastic UNICON. An additional simulation of an idealized deep convection case shows that stochastic UNICON produces enhanced cloud variabilities with dependency on updraft radius, indicating its ability to represent the coexistence of shallow and deep convection.
Characteristics of Precipitation and Mesoscale Convective Systems Over the Peruvian Central Andes in Multi 5‐Year Convection‐Permitting Simulations
Abstract Using the Weather Research and Forecasting model with two planetary boundary layer schemes, ACM2 and MYNN, convection‐permitting model (CPM) regional climate simulations were conducted for a 6‐year period, including a one‐year spin‐up period, at a 15‐km grid spacing covering entire South America and a nested convection‐permitting 3‐km grid spacing covering the Peruvian central Andes region. These two CPM simulations along with a 4‐km simulation covering South America produced by National Center for Atmospheric Research (NCAR), three gridded precipitation products, and rain gauge data in Peru and Brazil, are used to document the characteristics of precipitation and mesoscale convective systems (MCSs) in the Peruvian central Andes region. Results show that all km‐scale simulations generally capture the spatiotemporal patterns of precipitation and MCSs at both seasonal and diurnal scales, although biases exist in aspects such as precipitation intensity and MCS frequency, size, propagation speed, and associated precipitation intensity. The 3‐km simulation using MYNN scheme generally outperforms the other simulations in capturing seasonal and diurnal precipitation over the mountain, while both it and the 4‐km simulation demonstrate superior performance in the western Amazon Basin, based on the comparison to the gridded precipitation products and gauge data. Dynamic factors, primarily low‐level jet and terrain‐induced uplift, are the key drivers for precipitation and MCS genesis along the east slope of the Andes, while thermodynamic factors control the precipitation and MCS activity in the western Amazon Basin and over elevated mountainous regions. The study suggests model improvements and better model configurations for future regional climate projections.
A Machine Learning Assisted Development of a Model for the Populations of Convective and Stratiform Clouds
Abstract Traditional parameterizations of the interaction between convection and the environment have relied on an assumption that the slowly varying large‐scale environment is in statistical equilibrium with a large number of small and short‐lived convective clouds. They fail to capture nonequilibrium transitions such as the diurnal cycle and the formation of mesoscale convective systems as well as observed precipitation statistics and extremes. Informed by analysis of radar observations, cloud‐permitting model simulation, theory, and machine learning, this work presents a new stochastic cloud population dynamics model for characterizing the interactions between convective and stratiform clouds, with the goal of informing the representation of these interactions in global climate models. Fifteen wet seasons of precipitating cloud observations by a C‐band radar at Darwin, Australia are fed into a machine learning algorithm to obtain transition functions that close a set of coupled equations relating large‐scale forcing, mass flux, the convective cell size distribution, and the stratiform area. Under realistic large‐scale forcing, the derived transition functions show that, on the one hand, interactions with stratiform clouds act to dampen the variability in the size and number of convective cells and therefore in the convective mass flux. On the other, for a given convective area fraction, a larger number of smaller cells is more favorable for the growth of stratiform area than a smaller number of larger cells. The combination of these two factors gives rise to solutions with a few convective cells embedded in a large stratiform area, reminiscent of mesoscale convective systems.
A sensitivity analysis of twinning crystal plasticity finite element model using single crystal and poly crystal Zircaloy
The popularity of crystal plasticity finite element method (CPFEM) models is increasing due to their ability to predict the mechanical response of crystalline materials such as metals and metal alloys more accurately than traditional continuum mechanics models. This is since the crystal plasticity models consider the effect of atomic structure, microstructural morphology, and properties of individual grains. These CPFEM models use a large number of material parameters in order to capture the mesoscale physics which comes with the downside of the tedious calibration process. In this paper, a CPFEM code was developed to include the twinning induced grain reorientation and subsequent crystallographic slip for HPC material. The developed code is incorporated in a large-scale, parallelized nonlinear solver WARP3D. Further, a sensitivity analysis with respect to 22 material parameters was then conducted using single crystal and polycrystal representative volume element (RVE) of Zircaloy material. Loading was applied along five different crystallographic orientations for single crystal RVE and along three directions namely, rolling (RD), transverse (TD), and normal (ND) direction for polycrystal RVE. Results obtained from the sensitivity analysis were used for the calibration of material parameters for Zircaloy. Finally, developed code along with calibrated material parameters was used to investigate the effect of the hydride phase formation in Zircaloy which is a typical case observed for nuclear applications. It was found that the volume fraction of the hydride phase has a significant impact on the mechanical properties of Zircaloy.
Quantifying UAS Observation Error Variance Used in Data Assimilation Systems and Its Impact on Predictive Skill
Observation error determines the weights of the observations and background state used in data assimilation to generate analyses. Quantifying observation error is critical for the optimal assimilation of observational data sets. Uncrewed Aircraft System (UAS) observations have shown potential benefits in filling observational gaps in the lower atmosphere; however, characterization of their error characteristics has been limited. To optimize the use of UAS observations in numerical weather prediction, UAS observation error is estimated based on the 3‐cornered hat diagnostic approach which uses three independent estimates of the atmospheric state. This approach is applied to data from the 2018 Lower Atmospheric Profiling Studies at Elevation‐a Remotely‐piloted Aircraft Team Experiment field campaign using collocated UAS and rawinsonde observations along with output from a set of convection‐permitting model simulations. The estimated observation error values for UAS temperature, wind, and relative humidity measurements were found to be only weakly dependent on height AGL with mean values equal to 0.5°C, 0.8 m s −1 , and 3%, respectively. Only the newly estimated observation error for temperature differed from that previously used to assimilate commercial aircraft observations into global models (1.0°C). However, using this reduced temperature observation error produced more accurate mesoscale analyses and forecasts of both terrain‐driven flows and convection initiation generated by colliding outflow boundaries within the San Luis Valley of Colorado.
Mesoscale to Microscale Coupling for Wind Energy Applications: Addressing the Challenges
The purpose of the US DOE's Mesoscale to Microscale Coupling (MMC) Project is to develop, verify, and validate physical models and modeling techniques that bridge the most important atmospheric scales that determine wind plant performance and reliability. The project seeks to create a new predictive numerical simulation capability that represents a range of dynamic atmospheric flow conditions impacting wind plant performance.
Cabana: A Performance Portable Library for Particle-Based Simulations
Particle-based simulations are ubiquitous throughout many fields of computational science and engineering, spanning the atomistic level with molecular dynamics (MD), to mesoscale particle-in-cell (PIC) simulations for solid mechanics, device-scale modeling with PIC methods for plasma physics, and massive N-body cosmology simulations of galaxy structures, with many other methods in between (Hockney & Eastwood, 1989). While these methods use particles to represent significantly different entities with completely different physical models, many low-level details are shared including performant algorithms for short- and/or long-range particle interactions, multi-node particle communication patterns, and other data management tasks such as particle sorting and neighbor list construction. Cabana is a performance portable library for particle-based simulations, developed as part of the Co-Design Center for Particle Applications (CoPA) within the Exascale Computing Project (ECP) (Alexander et al., 2020). The CoPA project and its full development scope, including ECP partner applications, algorithm development, and similar software libraries for quantum MD, is described in (Mniszewski et al., 2021). Cabana uses the Kokkos library for on-node parallelism (Edwards et al., 2014; Trott et al., 2022), enabling simulation on multi-core CPU and GPU architectures, and MPI for GPU-aware, multi-node communication. Cabana provides particle simulation capabilities on almost all current Kokkos backends, including serial execution, OpenMP (including OpenMP-Target for GPUs), CUDA (NVIDIA GPUs), HIP (AMD GPUs), and SYCL (Intel GPUs), providing a clear path for the coming generation of accelerator-based exascale hardware. Cabana builds on Kokkos by providing new particle data structures and particle algorithms resulting in a similar execution policy-based, node-level programming model that is intended to be used in addition to the core Kokkos library within an application. Cabana is designed as an application and physics agnostic, but particle-specific toolkit which can either be used to generate a new application, or to be used as needed in existing applications at various levels of invasiveness including through interfaces that wrap user memory in existing data structures.
SULI Intern Final Report: Computationally Investigating Hydrogen Thermo-Diffusion in Yttrium Hydride Using Multiscale Methods
The renaissance of nuclear energy has arrived, heralding an age of abundant inexpensive clean energy, and renewed space exploration. In nuclear-powered spacecraft and microreactors, safety and size are of utmost importance. Yttrium Hydride (YHx) is being researched for its utility as a neutron moderator in nuclear reactors; the hydrogen in YHx slows down neutrons, enabling a continuous nuclear reaction in the reactor. This has the benefit of allowing reactors to be more safe, compact, and efficient. The goal of this effort is to computationally predict the coefficient of temperature-dependent hydrogen diffusion within YHx, the Soret coefficient. This parameter is essential for determining the safe operating modes of YHx moderators. Zirconium Hydride (ZrHx) is used in the Training, Research, Isotopes, General Atomics (TRIGA) reactor, is the reference material for these calculations. In this work, nanoscale atomic modeling in the Vienna Ab initio Simulation Package (VASP) is combined with the mesoscale finite element phase-field module in the Multiphysics Object-Oriented Simulation Environment (MOOSE); this culminates in a new multiscale computational method to simulate Soret diffusion of hydrogen in YHx. This data is useful for predicting experimental outcomes. This workflow involves convergence testing followed by static, Nudged Elastic Band (NEB), Quasi-Harmonic Approximation (QHA), and Molecular Dynamics (MD) calculations - linked with phase field simulation. NEB simulates hydrogen migration, while QHA and MD predict temperature-dependent properties. The static calculations align with literature, and preliminary NEB and QHA calculations yield accurate results. Once the atomic calculations are complete, we will incorporate Electron Backscatter Diffraction (EBSD) images and VASP-generated parameters into the phase field module to simulate intra- and intergranular transport of hydrogen in ZrHx and YHx. Future research will extend our approach to fuel-moderator materials systems such as Uranium-Yttrium Hydride (U-YHx). This work contributes to the development of advanced nuclear energy solutions for space travel.
Ice-shelf freshwater triggers for the Filchner–Ronne Ice Shelf melt tipping point in a global ocean–sea-ice model
Some ocean modeling studies have identified a potential tipping point from a low to a high basal melt regime beneath the Filchner–Ronne Ice Shelf (FRIS), Antarctica, with significant implications for subsequent Antarctic ice sheet mass loss. To date, investigation of the climate drivers and impacts of this possible event have been limited because ice-shelf cavities and ice-shelf melting are only now starting to be included in global climate models. Using a global ocean–sea-ice configuration of the Energy Exascale Earth System Model (E3SM) that represents both ocean circulations and melting within ice-shelf cavities, we explore freshwater triggers (iceberg melt and ice-shelf basal melt) of a transition to a high-melt regime at FRIS in a low-resolution (30 km in the Southern Ocean) global ocean–sea-ice model. We find that a realistic spatial distribution of iceberg melt fluxes is necessary to prevent the FRIS melt regime change from unrealistically occurring under historical-reanalysis-based atmospheric forcing. Further, improvement of the default parameterization for mesoscale eddy mixing significantly reduces a large regional fresh bias and weak Antarctic Slope Front structure, both of which precondition the model to melt regime change. Using two different stable model con figurations, we explore the sensitivity of FRIS melt regime change to regional ice-sheet freshwater fluxes. Through a series of sensitivity experiments prescribing incrementally increasing melt rates from the smaller, neighboring ice shelves in the eastern Weddell Sea, we demonstrate the potential for an ice-shelf melt “domino effect” should the upstream ice shelves experience increased melt rates. The experiments also reveal that modest ice-shelf melt biases in a model, especially at coarse ocean resolution where narrow continental shelf dynamics are not well resolved, can lead to an unrealistic melt regime change at downstream ice shelves. Thus, we find that remote connections between melt fluxes at different ice shelves are sensitive to baseline model conditions. Our results highlight both the potential and the peril of simulating prognostic Antarctic ice-shelf melt rates in a low-resolution global model.
Ice-shelf freshwater triggers for the Filchner–Ronne Ice Shelf melt tipping point in a global ocean–sea-ice model
Abstract. Some ocean modeling studies have identified a potential tipping point from a low to a high basal melt regime beneath the Filchner–Ronne Ice Shelf (FRIS), Antarctica, with significant implications for subsequent Antarctic ice sheet mass loss. To date, investigation of the climate drivers and impacts of this possible event have been limited because ice-shelf cavities and ice-shelf melting are only now starting to be included in global climate models. Using a global ocean–sea-ice configuration of the Energy Exascale Earth System Model (E3SM) that represents both ocean circulations and melting within ice-shelf cavities, we explore freshwater triggers (iceberg melt and ice-shelf basal melt) of a transition to a high-melt regime at FRIS in a low-resolution (30 km in the Southern Ocean) global ocean–sea-ice model. We find that a realistic spatial distribution of iceberg melt fluxes is necessary to prevent the FRIS melt regime change from unrealistically occurring under historical-reanalysis-based atmospheric forcing. Further, improvement of the default parameterization for mesoscale eddy mixing significantly reduces a large regional fresh bias and weak Antarctic Slope Front structure, both of which precondition the model to melt regime change. Using two different stable model configurations, we explore the sensitivity of FRIS melt regime change to regional ice-sheet freshwater fluxes. Through a series of sensitivity experiments prescribing incrementally increasing melt rates from the smaller, neighboring ice shelves in the eastern Weddell Sea, we demonstrate the potential for an ice-shelf melt “domino effect” should the upstream ice shelves experience increased melt rates. The experiments also reveal that modest ice-shelf melt biases in a model, especially at coarse ocean resolution where narrow continental shelf dynamics are not well resolved, can lead to an unrealistic melt regime change at downstream ice shelves. Thus, we find that remote connections between melt fluxes at different ice shelves are sensitive to baseline model conditions. Our results highlight both the potential and the peril of simulating prognostic Antarctic ice-shelf melt rates in a low-resolution global model.
Mesoscale structural gradients in human tooth enamel
The outstanding mechanical and chemical properties of dental enamel emerge from its complex hierarchical architecture. An accurate, detailed multiscale model of the structure and composition of enamel is important for understanding lesion formation in tooth decay (dental caries), enamel development (amelogenesis) and associated pathologies (e.g., amelogenesis imperfecta or molar hypomineralization), and minimally invasive dentistry. Although features at length scales smaller than 100 nm (individual crystallites) and greater than 50 µm (multiple rods) are well understood, competing field of view and sampling considerations have hindered exploration of mesoscale features, i.e., at the level of single enamel rods and the interrod enamel (1 to 10 µm). Here, we combine synchrotron X-ray diffraction at submicrometer resolution, analysis of crystallite orientation distribution, and unsupervised machine learning to show that crystallographic parameters differ between rod head and rod tail/interrod enamel. This variation strongly suggests that crystallites in different microarchitectural domains also differ in their composition. Thus, we use a dilute linear model to predict the concentrations of minority ions in hydroxylapatite (Mg 2+ and CO 3 2- /Na + ) that plausibly explain the observed lattice parameter variations. While differences within samples are highly significant and of similar magnitude, absolute values and the sign of the effect for some crystallographic parameters show interindividual variation that warrants further investigation. In conclusion, by revealing additional complexity at the rod/interrod level of human enamel and leaving open the possibility of modulation across larger length scales, these results inform future investigations into mechanisms governing amelogenesis and introduce another feature to consider when modeling the mechanical and chemical performance of enamel.
The COMBLE campaign: a study of marine boundary-layer clouds in Arctic cold-air outbreaks
One of the most intense air mass transformations on Earth happens when cold air flows from frozen surfaces to much warmer open water in cold-air outbreaks (CAOs), a process captured beautifully in satellite imagery. Despite the ubiquity of the CAO cloud regime over high-latitude oceans, we have a rather poor understanding of its properties, its role in energy and water cycles, and its treatment in weather and climate models. The Cold-air Outbreaks in the Marine Boundary Layer Experiment (COMBLE) was conducted to better understand this regime and its representation in models. COMBLE aimed to examine the relations between surface fluxes, boundary-layer structure, aerosol, cloud and precipitation properties, and mesoscale circulations in marine CAOs. Processes affecting these properties largely fall in a range of scales where boundary-layer processes, convection, and precipitation are tightly coupled, which makes accurate representation of the CAO cloud regime in numerical weather prediction and global climate models most challenging. COMBLE deployed an Atmospheric Radiation Measurement Mobile Facility at a coastal site in northern Scandinavia (69°N), with additional instruments on Bear Island (75°N), from December 2019 to May 2020. CAO conditions were experienced 19% (21%) of the time at the main site (on Bear Island). A comprehensive suite of continuous in situ and remote sensing observations of atmospheric conditions, clouds, precipitation, and aerosol were collected. Because of the clouds’ well-defined origin, their shallow depth, and the broad range of observed temperature and aerosol concentrations, the COMBLE dataset provides a powerful modeling test bed for improving the representation of mixed-phase cloud processes in large-eddy simulations and large-scale models.
Variability of bottom carbonate chemistry over the deep coral reefs in the Florida Straits and the impacts of mesoscale processes
Not provided.
Flow Reduction in Pore Networks of Packed Silica Nanoparticles: Insights from Mesoscopic Fluid Models
A modified many-body dissipative particle dynamics (mDPD) model is rigorously calibrated to achieve realistic fluid–fluid/solid interphase properties and applied for mesoscale flow simulations to elucidate the transport mechanisms of heptane liquid and water, respectively, through pore networks formed by packed silica nanoparticles with a uniform diameter of 30 nm. Two million CPU core hours were used to complete the simulation studies. Results show reduction of permeability by 54–64% in heptane flow and by 88–91% in water flow, respectively, compared to the Kozeny–Carman equation. In these nanopores, a large portion of the fluids are in the near-wall regions and thus not mobile due to the confinement effect, resulting in reduced hydraulic conductivity. Moreover, intense oscillations in the calculated flow velocities also indicate the confinement effect that contests the external driven force to flow. Here, the generic form of Darcy’s law is considered valid for flow through homogeneous nanopore networks, while permeability depends collectively on pore size and surface wettability. This fluid-permeability dependency is unique to flow in nanopores. In addition, potential dependence of permeability on pore connectivity is observed when the porosity remains the same in different core specimens.