SEARCH · Engineering Papers

Results for “model communities”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71

All sources NASA NTRS DOE OSTI

NASA NTRS2018

Improvement of Stratospheric Aerosol Extinction Retrieval from OMPS/LP Using a New Aerosol Model

The Ozone Mapping and Profiler Suite Limb Profiler (OMPS/LP) has been flying on the Suomi National Polar-orbiting Partnership (S-NPP) satellite since October 2011. It is designed to produce ozone and aerosol vertical profiles at 2-kilometer vertical resolution over the entire sunlit globe. Aerosol extinction profiles are computed with Mie theory using radiances measured at 675 nanometers. The operational Version 1.0 (V1.0) aerosol extinction retrieval algorithm assumes a bimodal lognormal aerosol size distribution (ASD) whose parameters were derived by combining an in situ measurement of aerosol microphysics with the Stratospheric Aerosol and Gas Experiment (SAGE II) aerosol extinction climatology. Internal analysis indicates that this bimodal lognormal ASD does not sufficiently explain the spectral dependence of LP-measured radiances. In this paper we describe the derivation of an improved aerosol size distribution, designated Version 1.5 (V1.5), for the LP retrieval algorithm. The new ASD uses a gamma function distribution that is derived from Community Aerosol and Radiation Model for Atmospheres (CARMA)-calculated results. A cumulative distribution fit derived from the gamma function ASD gives better agreement with CARMA results at small particle radii than bimodal or unimodal functions. The new ASD also explains the spectral dependence of LP-measured radiances better than the V1.0 ASD. We find that the impact of our choice of ASD on the retrieved extinctions varies strongly with the underlying reflectivity of the scene. Initial comparisons with collocated extinction profiles retrieved at 676 nanometers from the SAGE III instrument on the International Space Station (ISS) show a significant improvement in agreement for the LP V1.5 retrievals. Zonal mean extinction profiles agree to within 10 percent between 19 and 29 kilometers, and regression fits of collocated samples show improved correlation and reduced scatter compared to the V1.0 product. This improved agreement will motivate development of more sophisticated ASDs from CARMA results that incorporate latitude, altitude and seasonal variations in aerosol properties.

Ozone Mapping Profiler Suite Limb Profiler (OMPS/L↗

DOE OSTI2021

Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling

Significance Soil organic matter contains a large fraction of global C whose fate is largely governed by soil microbial communities. Global C-cycle models can be improved using information about microbial processes in soil, but the inner workings of soil communities remain largely hidden from view. We used stable isotopes to characterize the guild structure of soil bacteria based on how they assimilated C from different sources. Guild structure corresponded with growth dynamics and rrn copy number. We also show that this guild structure explains microbial biogeographical patterns at continental and global scales. These results suggest that microbial contributions to soil C cycling are largely governed by an anabolic process that governs energy allocation to growth, competition, and survival.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1994

Workshop on Computational Turbulence Modeling

The purpose of this meeting was to discuss the current status and future development of turbulence modeling in computational fluid dynamics for aerospace propulsion systems. Various turbulence models have been developed and applied to different turbulent flows over the past several decades and it is becoming more and more urgent to assess their performance in various complex situations. In order to help users in selecting and implementing appropriate models in their engineering calculations, it is important to identify the capabilities as well as the deficiencies of these models. This also benefits turbulence modelers by permitting them to further improve upon the existing models. This workshop was designed for exchanging ideas and enhancing collaboration between different groups in the Lewis community who are using turbulence models in propulsion related CFD. In this respect this workshop will help the Lewis goal of excelling in propulsion related research. This meeting had seven sessions for presentations and one panel discussion over a period of two days. Each presentation session was assigned to one or two branches (or groups) to present their turbulence related research work. Each group was asked to address at least the following points: current status of turbulence model applications and developments in the research; progress and existing problems; and requests about turbulence modeling. The panel discussion session was designed for organizing committee members to answer management and technical questions from the audience and to make concluding remarks.

Shabbir, A.↗

DOE OSTI2020

Model Exploration of an Information-Based Healthcare Intervention Using Parallelization and Active Learning

This paper describes the application of a large-scale active learning method to characterize the parameter space of a computational agent-based model developed to investigate the impact of CommunityRx, a clinical information-based health intervention that provides patients with personalized information about local community resources to meet basic and self-care needs. Additionally, the diffusion of information about community resources and their use is modeled via networked interactions and their subsequent effect on agents' use of community resources across an urban population. A random forest model is iteratively fitted to model evaluations to characterize the model parameter space with respect to observed empirical data. We demonstrate the feasibility of using high-performance computing and active learning model exploration techniques to characterize large parameter spaces; by partitioning the parameter space into potentially viable and non-viable regions, we rule out regions of space where simulation output is implausible to observed empirical data. We argue that such methods are necessary to enable model exploration in complex computational models that incorporate increasingly available micro-level behavior data. We provide public access to the model and high-performance computing experimentation code.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Toward more mechanistic representations of biogeochemical processes in river networks: Implementation and demonstration of a multiscale model

A recently introduced multiscale model for representing the effects of small-scale hyporheic-zone biogeochemical processes is extended from the reach scale to river network scales. The model uses advection-dispersion-reaction equations for the channel network and one-dimensional advection-reaction subgrid models for the hyporheic zone. We summarize implementation in the integrated surface/subsurface hydrology modeling system Amanzi-ATS. The extension uses topologically defined meshes to represent stream/river networks and associates a hyporheic subgrid model with each channel grid cell. Biogeochemical reaction modeling capability residing in community software is accessed through an application programming interface. The implementation is verified against independent numerical solutions on a single reach. Mesh convergence studies show that commonly used semi-distributed representations can introduce significant spatial discretization error. Denitrification of farm runoff in a subbasin of the Portage River Basin in Ohio, USA is used to demonstrate the general-purpose reactive transport capability.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Community Based Data of Potentiometric Titration of Iron Oxides: Ferrihydrite (HFO), Goethite, Hematite, Magnetite

This data release includes experimental data of potentiometric titration for iron oxides. The data in the provided .csv files is not our own experimental data but have been compiled from the multiple literature sources. The master database is L-SCIE (LLNL Surface Complexation/Ion Exchange) database, and the provided .csv files are extracted data from L-SCIE. The .csv files were obtained by using the Lawrence Livermore National Laboratory Surface Complexation Database Converter (SCDC) code written in the R programming language (free licensing available at https://ipo.llnl.gov/technologies/software/llnl-surface-complexation-database-converter-scdc).The released data was used for developing a comprehensive community data-driven surface complexation modeling (SCM) framework for simulating potentiometric titration of mineral surfaces. Compiled community data for ferrihydrite, goethite, hematite, and magnetite are fit to produce representative protolysis constants that can reproduce potentiometric titration data collected from multiple literature sources.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1989

The Antarctic dry valley lakes: Relevance to Mars

The similarity of the early environments of Mars and Earth, and the biological evolution which occurred on early Earth, motivates exobiologists to seriously consider the possiblity of an early Martian biota. Environments are being identified which could contain Martian life and areas which may presently contain evidence of this former life. Sediments which were thought to be deposited in large ice-covered lakes are present on Mars. Such localities were identified within some of the canyons of the Valles Marineris and more recently in the ancient terrain in the Southern Hemisphere. Perennially ice-covered Antarctic lakes are being studied in order to develop quantitative models that relate environmental factors to the nature of the biological community and sediment forming processes. These models will be applied to the Martian paleolakes to establish the scientific rationale for the exobiological study of ancient Martian sediments.

Wharton, R. A., Jr.↗

NASA NTRS2022

Uncertainty Models for the Hybrid Parametric Variation Method of Uncertainty Quantification; Analysis

There is some level of uncertainty in every finite element model (FEM), which flows to a level of uncertainty in predicted results. The purpose of uncertainty quantification (UQ) is to provide statistical bounds on prediction accuracy based on model uncertainty. This is distinct from model updating, which attempts to modify models to improve their accuracy. UQ does not improve the accuracy of models, but accepts that the models are inherently inaccurate and attempts to quantify the impact of that inaccuracy on predicted results. Previously, an alternate method for UQ, called the Hybrid Parametric Variation (HPV) method, was applied to Space Launch System (SLS) Hurty/Craig-Bampton (HCB) components to predict system-level statistics for launch vehicle attitude control transfer functions and core stage section loads due to buffet. The HPV method combines a parametric variation of the HCB fixed-interface (FI) modal frequencies with a nonparametric variation (NPV) method that randomly varies the HCB mass and stiffness matrices as Wishart random matrix distributions using random matrix theory (RMT). Alternatively, the most common method for modeling uncertainty in the structural dynamics community is a parametric approach, which varies physical parameters in the model. However, there are several disadvantages associated with the parametric method. Determining a reduced set of parameters that have a significant impact on the system response can be time consuming, and the selected parameter probability distributions are rarely reliably known. Therefore, in practice, the parameters are surrogates for the actual errors, and the link to parameter uncertainty is unknown. Another major drawback is that the uncertainty that can be represented is limited to the form of the nominal FEM. It is the experience of the authors that based on numerous aerospace programs, almost all FEM errors are in form rather than parameter values. This hypothesis is supported by the observation of the authors that it is almost never possible to ‘tune’ a FEM to match modal test results by only modifying model parameters. Model-form uncertainty cannot be directly represented by FEM input parameters nor included in a parametric approach. However, model-form uncertainty can be modeled using RMT, where a probability distribution is developed for the matrix ensemble of interest. The major advantage of the NPV method is that it covers errors in model form. The HPV method anchors uncertainty at the HCB component level to component modal test results by matching the HCB and test modes based on mode descriptions or other methods, and then applying differing levels of frequency variation. The specific variations depend on the confidence to which a component FEM has been validated through modal testing. The NPV method is layered on the frequency variation to match modal test self-orthogonality and cross-orthogonality (XO) results. Once the component uncertainty models are identified, they are assembled, and the uncertainty is propagated to the system level using a Monte Carlo (MC) analysis approach that generates statistics for system-level predictions This provides a UQ method that can be traced to test data, which can be updated as additional data and improved correlated models become available. The purpose of this paper is to collect and present all of the theory for HPV that has been previously published in reports and papers and to present examples of its application. Specifically, component uncertainty models based on the dispersion of corresponding mass and stiffness matrices using proposed test/analysis correlation metrics are investigated. The first example is purely academic so that the true answers are known, and the validity of the HPV method and the corresponding uncertainty models can be determined. The purpose of this paper is to collect and present all of the theory for HPV that has been previously published in reports and papers and to present examples of its application. Specifically, component uncertainty models based on the dispersion of corresponding mass and stiffness matrices using proposed test/analysis correlation metrics are investigated. The first example is purely academic so that the true answers are known, and the validity of the HPV method and the corresponding uncertainty models can be determined. The second example is an application to a component that is design specific to the SLS. Based on this work and other assessments, the HPV method provides another tool to the toolset used for complex system UQ analysis. From experience gathered to date using the HPV method, additional design specific applications must be investigated to provide further confidence in the validity of the HPV method of UQ analysis.

Uncertainty quantification↗

NASA NTRSDate not supplied

AI Foundation Models for Science: An Open Collaborative Initiative

Foundation Models (FMs), AI models designed to replace task-specific models, are increasingly being recognized for their versatility across numerous downstream applications. These models, trained using self-supervised techniques on any type of sequence data, circumvent the need for large annotated datasets, a major bottleneck in traditional AI model development. FMs can be applied to downstream tasks using few-shot learning and fine-tuning, significantly reducing the need for large labeled training datasets and computational resources. However, the development of FMs requires substantial resources, including access to data and compute power, expertise in the latest models, and specialized scientific knowledge for systematic evaluation. It is challenging for a single group to possess all these capabilities. To address this, NASA IMPACT has initiated an open collaborative effort, leveraging partnerships with the private sector and other groups within and outside NASA, to jointly build FMs. The overarching goal is to develop a consistent and collaborative approach to building FMs for high-value science datasets. This initiative has fostered collaboration within NASA and with external partners, including IBM Research, Clark University, DOE’s ORNL, ESA, and USGS. The effort focuses on identifying key datasets with a wide range of downstream applications, pretraining and building FMs using modified transformer architectures, evaluating compute infrastructure needs, and sharing models, pretraining and fine-tuning code, and data with the community. Furthermore, it aims to train the Earth science community to fine-tune these models for various downstream applications. Our initial effort resulted in the creation of a 100 million parameter HLS Geospatial Model within six months, which was released on HuggingFace. We are now expanding our scope to include data from weather and climate models and investigating multimodal models. We invite those interested in participating in this effort to join us by sharing their use cases, expertise, or data.

Rahul Ramachandran↗

DOE OSTI2023

G4CMP: Condensed matter physics simulation using the G$\scriptsize{\mathrm{EANT}}$4 toolkit

G4CMP simulates phonon and charge transport in cryogenic semiconductor crystals using the Geant4 toolkit. The transport code is capable of simulating the propagation of acoustic phonons as well as electron and hole charge carriers. Herein processes for anisotropic phonon propagation, oblique charge-carrier propagation, and phonon emission by accelerated charge carriers are included. The simulation reproduces theoretical predictions and experimental observations such as phonon caustics, heat-pulse propagation times, and mean charge-carrier drift velocities. In addition to presenting the physics and features supported by G4CMP, this report outlines example applications from the dark matter and quantum information science communities. These communities are applying G4CMP to model and design devices for which the energy transported by phonons and charge carriers is germane to the performance of superconducting instruments and circuits placed on silicon and germanium substrates. The G4CMP package is available to download from GitHub: github.com/kelseymh/G4CMP.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Microbial community diversity changes during voltage reversal repair in a 12-unit microbial fuel cell

Microbial fuel cell stacks (MFC-Stack) are often confronted with voltage reversals, likely due to an interplay between microbial community dynamics and insufficient electric circuit balancing. Herein, we provide new insight into voltage reversals by examining the microbiomes of twelve MFC units of a 12-liter Pilot-MFC-Stack during repair. Different biofilm repair methods (self-healing, electrostimulation, and re-acclimatization upon cross-inoculation) were used to evaluate the microbial community response. In addition, MFC-Stack simulation was performed based on Kirchhoff’s Second Law to predict values for source potentials and post-evaluate internal resistances. Analysis of the 16S rRNA amplicon sequencing data suggests that the biofilm repair methods could slowly heal damaged biofilms. Notably, severely voltage reversed MFC units had low electrogen relative abundances (18%) and positive anode potentials, while strong bioanodes and contained more than 50% electrogens and had negative anode potentials. Between-community analyses (beta diversity ordination and multinomial regression) of the voltage reversed MFC units revealed differences among biofilms in contrast to healthy/strong MFC units. Permutational multivariate analysis of variance (PERMANOVA) confirmed that reversed biofilms were, indeed, significantly (p < 0.05) different from stronger ones. Overall, these analyses demonstrated the utility of combining electrotechnical and microbial community analyses, especially beta diversity ordination and multinomial regression, to understand problematic MFC units and the potential success of a biofilm repair method. Finally, thicker biofilms were usually healthier and stronger, although thickness was no guarantee for proper structure and power function as all factors were interdependent. There was an evolutionary trend that strong anodes became stronger/healthier and others weaker. This spontaneous trend has to be considered to avoid irreversible voltage reversals and to repair electrogenic biofilms in an MFC-Stack.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Combining Observations and Models: A Review of the CARDAMOM Framework for Data‐Constrained Terrestrial Ecosystem Modeling

The rapid increase in the volume and variety of terrestrial biosphere observations (i.e., remote sensing data and in situ measurements) offers a unique opportunity to derive ecological insights, refine process‐based models, and improve forecasting for decision support. However, despite their potential, ecological observations have primarily been used to benchmark process‐based models, as many past and current models lack the capability to directly integrate observations and their associated uncertainties for parameterization. In contrast, data assimilation frameworks such as the CARbon DAta MOdel fraMework (CARDAMOM) and its suite of process‐based models, known as the Data Assimilation Linked Ecosystem Carbon Model (DALEC), are specifically designed for model‐data fusion. This review, motivated by a recent CARDAMOM community workshop, examines the development and applications of CARDAMOM, with an emphasis on its role in advancing ecosystem process understanding. CARDAMOM employs a Bayesian approach, using a Markov Chain Monte Carlo algorithm to enable data‐driven calibration of DALEC parameters and initial states (i.e., carbon pool sizes) through observation operators. CARDAMOM's unique ability to retrieve localized model process parameters from diverse datasets—ranging from in situ measurements to global satellite observations—makes it a highly flexible tool for analyzing spatially variable ecosystem responses to environmental change. However, assimilating these data also presents challenges, including data quality issues that propagate into model skill, as well as trade‐offs between model complexity, parameter equifinality, and predictive performance. We discuss potential solutions to these challenges, such as reducing parameter equifinality by incorporating new observations. This review also offers community recommendations for incorporating emerging datasets, integrating machine learning techniques, strengthening collaboration with remote sensing, field, and modeling communities, and expanding CARDAMOM's relevance for localized ecosystem monitoring and decision‐making. CARDAMOM enables a deep, mechanistic understanding of terrestrial ecosystem dynamics that cannot be achieved through empirical analyses of observational datasets or weakly constrained models alone.

Bayesian inference↗

NASA NTRS2025

Integrating the Interconnections Between Groundwater and Land Surface Processes Through the Coupled NASA Land Information System and ParFlow Environment

Understanding the interactions between the atmosphere, the land, and the subsurface is fundamental to hydrology and is critical for a better assessment of the impacts of climate change and human management on hydrological systems. However, many land surface models simplify the subsurface hydrology and thereby these interactions. In this study, we couple the land surface model Noah-MP included in the NASA Land Information System (LIS) with the integrated hydrologic model ParFlow (ParFlow-LIS) using the Earth System Modeling Framework (ESMF) and the National United Operational Prediction Capability (NUOPC). This coupling improves the simulation of water and energy cycle processes by adding the three-dimensional variably saturated and heterogeneous flow in the subsurface using sophisticated and nonlinear physics-based equations as well as the advances in satellite remote sensing-based data assimilation of the land surface, thereby benefiting the integrated hydrologic modeling and data assimilation community. We use the High Plains aquifer, located in the central United States, as a testbed to evaluate the coupled ParFlow-LIS system. The new ParFlow-LIS system accounts for the effects of topographically driven flows on the land surface, producing more fine-scale patterns of land surface states and fluxes than standalone LIS. In addition, ParFlow-LIS enables the consideration of the effect of subsurface water storage on evapotranspiration. This is particularly important in areas and times with dry soils, such as during drought conditions or in the presence of a cone of depression due to pumping.

land surface modeling↗

NASA NTRS2006

Simulated convective systems using a cloud resolving model: Impact of large-scale temperature and moisture forcing using observations and GEOS-3 reanalysis

The GCE (Goddard Cumulus Ensemble) model, which has been developed and improved at NASA Goddard Space Flight Center over the past two decades, is considered as one of the finer and state-of-the-art CRMs (Cloud Resolving Models) in the research community. As the chosen CRM for a NASA Interdisciplinary Science (IDS) Project, GCE has recently been successfully upgraded into an MPI (Message Passing Interface) version with which great improvement has been achieved in computational efficiency, scalability, and portability. By basically using the large-scale temperature and moisture advective forcing, as well as the temperature, water vapor and wind fields obtained from TRMM (Tropical Rainfall Measuring Mission) field experiments such as SCSMEX (South China Sea Monsoon Experiment) and KWAJEX (Kwajalein Experiment), our recent 2-D and 3-D GCE simulations were able to capture detailed convective systems typical of the targeted (simulated) regions. The GEOS-3 [Goddard EOS (Earth Observing System) Version-3] reanalysis data have also been proposed and successfully implemented for usage in the proposed/performed GCE long-term simulations (i.e., aiming at producing massive simulated cloud data -- Cloud Library) in compensating the scarcity of real field experimental data in both time and space (location). Preliminary 2-D or 3-D pilot results using GEOS-3 data have generally showed good qualitative agreement (yet some quantitative difference) with the respective numerical results using the SCSMEX observations. The first objective of this paper is to ensure the GEOS-3 data quality by comparing the model results obtained from several pairs of simulations using the real observations and GEOS-3 reanalysis data. The different large-scale advective forcing obtained from these two kinds of resources (i.e., sounding observations and GEOS-3 reanalysis) has been considered as a major critical factor in producing various model results. The second objective of this paper is therefore to investigate and present such an impact of large-scale forcing on various modeled quantities (such as hydrometeors, rainfall, and etc.). A third objective is to validate the overall GCE 3-D model performance by comparing the numerical results with sounding observations, as well as available satellite retrievals.

Shie, C.-L.↗

DOE OSTI2024

Advancing quantitative models of soil microbiology, ecology, and biochemistry

Rapid advances in soil biology are increasingly reflected in mathematical models. From molecular to global scales, models contribute to fundamental understanding and prediction of critical soil processes, such as carbon sequestration. Recent models explicitly incorporate microbial control over soil carbon and nutrient cycling, an approach that offers greater biological realism but raises new challenges in model parameterization and stability. Although they have proliferated at community and ecosystem scales, microbial-explicit models have yet to be incorporated into most Earth system models. Applying soil models across scales requires integration with data to support parameterization and validation using approaches such as Bayesian data assimilation. In conclusion, to catalyze future progress, we recommend breaking down barriers between modeling and empirical disciplines while broadening access to the computational infrastructure that supports soil biological modeling.

Xie, Wally↗

DOE OSTI2022

Geological activity shapes the microbiome in deep-subsurface aquifers by advection

Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Multi-Scale Modeling Framework for Mercury Biogeochemistry

Multi-Scale modeling of mercury (Hg) geochemical speciation and reactions has been performed by integrating atomistic quantum chemical calculations with continuum scale speciation models. Major progress has been made in the improvement of quantum chemical models to calculate critical thermodynamic data for Hg complexes in aquatic environments. Rapid and reliable quantum chemical approaches have been developed for calculating acid dissociation constants (pK a ) and stability constants (log K), with calculated mean unsigned errors of 0.5 and 1.5 log units, respectively for ligand molecules and Hg complexes. At the continuum scale, systematic analysis of uncertainty propagation in mercury (Hg) speciation modeling has been conducted and was used to identify environmental conditions under which thermodynamic constant uncertainties are significant and recommended to be accounted for. The integrated framework for multi-scale modeling of mercury geochemistry is open to the research community through the web-based multiscale modeling aqueous speciation resource, AQUA-MER. The improved quantum chemical approaches for thermodynamic constant calculations are accessible through AQUA-MER and can be used to provide the missing constants in the continuum scale speciation calculations. In addition to low molecular mass Hg complex speciation, modeling natural aquatic environments also involve the transport of high molecular weight dissolved organic matter (DOM) in reactive flows simultaneously with equilibrium and kinetic reactions. To this end, atomistic MD simulations were performed to capture the details of aggregation, mechanisms and distribution of functional groups in DOM at the molecular level. The elemental composition and calculated bulk properties of the DOM models are in close agreement with experimental measurements. A travel-time based reactive transport model in the hyporheic zone of stream corridors was established for the multicomponent Hg-DOM-S system and implemented through PFLOTRAN.

54 ENVIRONMENTAL SCIENCES↗