Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Parameterization”

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.

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

At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Yet another parameter-free shape optimization method

The use of node coordinates as design variables in shape optimization offers a larger design space than computer-aided design (CAD)-based shape parameterizations. It also allows for the optimization of legacy designs, i.e., a finite element mesh from an existing design can be readily optimized to meet new performance requirements without involving a CAD model. However, it is well known that the node coordinate parameterization method is fraught with numerical difficulties, which makes it impractical to use. This has led to several of “parameter-free” shape optimization methods that seek the advantages and avoid the pitfalls of the naïve node coordinate parameterization method. These methods come in two main varieties: sensitivity filtering (or gradient smoothing) and consistent filtering. The latter is analogous to the density filter method used in topology optimization (TO). In this work, we use the PDE filter from TO and energy-based filters to implement consistent shape optimization filtering schemes easily and efficiently. Numerical experiments demonstrate that consistent methods are more robust than sensitivity filtering methods.

42 ENGINEERING↗
DOE OSTI2020

Improving Time Step Convergence in an Atmosphere Model With Simplified Physics: The Impacts of Closure Assumption and Process Coupling

Convergence testing is a common practice in the development of dynamical cores of atmospheric models but is not as often exercised for the parameterization of sub-grid physics. An earlier study revealed that the stratiform cloud parameterizations in several predecessors of the Energy Exascale Earth System Model (E3SM) showed strong time-step sensitivity and slower-than-expected convergence when the model's time step was systematically refined. In this work, a simplified atmosphere model is configured that consists of the spectral-element dynamical core of the E3SM atmosphere model coupled with a large-scale condensation parameterization based on commonly used assumptions. This simplified model also resembles E3SM and its predecessors in the numerical implementation of process coupling and shows poor time-step convergence in short ensemble tests. We present a formal error analysis to reveal the expected time-step convergence rate and the conditions for obtaining such convergence. Numerical experiments are conducted to investigate the root causes of convergence problems. We show that revisions in the process coupling and closure assumption help to improve convergence in short simulations using the simplified model; the same revisions applied to a full atmosphere model lead to significant changes in the simulated long-term climate. This work demonstrates that causes of convergence issues in atmospheric simulations can be understood by combining analyses from physical and mathematical perspectives. Addressing convergence issues can help to obtain a discrete model that is more consistent with the intended representation of the physical phenomena.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Sub-Cloud Turbulence Explains Cloud-Base Updrafts for Shallow Cumulus Ensembles: First Observational Evidence

Sub-cloud turbulent kinetic energy has been used to parameterize the cloud-base updraft velocity (w b ) in cumulus parameterizations. The validity of this idea has never been proved in observations. Instead, it was challenged by recent Doppler Lidar observations showing a poor correlation between the two. We argue that the low correlation is likely caused by the difficulty of a fixed-point Lidar to measure ensemble properties of cumulus fields. Taking advantage of the stationarity and ergodicity of early afternoon convection, we developed a Lidar sampling methodology to measure w b of a shallow cumulus (ShCu) ensemble (not a single ShCu). By analyzing 128 ShCu ensembles over the Southern Great Plains, we show that the ensemble properties of sub-cloud turbulence explain nearly half of the variability in ensemble-mean wb, demonstrating the ability of sub-cloud turbulence to dictate w b . Lastly, the derived empirical formulas will be useful for developing cumulus parameterizations and satellite inference of w b .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Enhanced Convective Microphysics Scheme and Its Impacts on Mean Climate in E3SM

Abstract To improve the representation of microphysical processes in convective clouds and their interaction with aerosol and stratiform clouds, a two‐moment convective microphysics parameterization (CMP) scheme developed by Song and Zhang (2011, https://doi.org/10.1029/2010jd014833 ) is upgraded and implemented in E3SM. The new developments include: (a) implementing a parameterization for graupel to enhance the representation of ice‐phase microphysical processes; (b) representing the impact of spatial inhomogeneity of cloud droplets in cumulus ensembles on autoconversion and accretion processes to improve the representation of warm‐rain microphysical processes; (c) implementing a comprehensive Bergeron process parameterization to better represent mixed‐phase microphysical processes; and (d) representing the interactions between ice‐phase microphysics and cloud thermodynamics. Simulations show that the cloud microphysical properties simulated by the CMP are generally in good agreement with observations. It reasonably simulates the changes in droplets effective radius related to precipitation formation in convective clouds, as identified from satellite observations. It also successfully simulates the contrast in these processes between maritime and continental clouds, demonstrating its capability to simulate the impact of aerosols on convection. Analyses of the impact of CMP on climate mean state simulation demonstrate that the CMP slightly improves the simulations of precipitation, cloud macrophysical properties, longwave cloud radiative forcing, zonal wind, and temperature. However, a degradation in shortwave cloud radiative forcing occurs.

GCM↗
DOE OSTI2023

Implicit learning of convective organization explains precipitation stochasticity

Accurate prediction of precipitation intensity is crucial for both human and natural systems, especially in a warming climate more prone to extreme precipitation. Yet, climate models fail to accurately predict precipitation intensity, particularly extremes. One missing piece of information in traditional climate model parameterizations is subgrid-scale cloud structure and organization, which affects precipitation intensity and stochasticity at coarse resolution. Here, using global storm-resolving simulations and machine learning, we show that, by implicitly learning subgrid organization, we can accurately predict precipitation variability and stochasticity with a low-dimensional set of latent variables. Using a neural network to parameterize coarse-grained precipitation, we find that the overall behavior of precipitation is reasonably predictable using large-scale quantities only; however, the neural network cannot predict the variability of precipitation (R 2 ~ 0.45) and underestimates precipitation extremes. The performance is significantly improved when the network is informed by our organization metric, correctly predicting precipitation extremes and spatial variability (R 2 ~ 0.9). The organization metric is implicitly learned by training the algorithm on a high-resolution precipitable water field, encoding the degree of subgrid organization. The organization metric shows large hysteresis, emphasizing the role of memory created by subgrid-scale structures. We demonstrate that this organization metric can be predicted as a simple memory process from information available at the previous time steps. These findings stress the role of organization and memory in accurate prediction of precipitation intensity and extremes and the necessity of parameterizing subgrid-scale convective organization in climate models to better project future changes of water cycle and extremes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

An Improved Algorithm for Estimating Surface Shortwave Radiation: Preliminary Evaluation With MODIS Products

Cloud parameters, as key inputs in radiative transfer algorithms, have a critical impact on surface shortwave radiation (SSR) computation. By introducing a parameterization of cloud transmittance and reflectance, based on radiative transfer simulations, this study improves the accuracy of an existing physically based model which severely underestimates SSR under thick cloud conditions. The cloud parameterization adopts the single-layer cloud model and simulates cloud transmittances and reflectances by varying cloud optical thickness, cloud particle size, and solar zenith angle. The revised model is applied to estimate instantaneous SSR using Moderate-resolution Imaging Spectroradiometer (MODIS) atmospheric and land products. The retrieved SSR is evaluated against observation data from 41 Baseline Surface Radiation Network (BSRN) stations and is also compared with the MODIS official SSR product. The root mean square error (RMSE) of the estimated instantaneous radiation is approximately 52 and 98 W m -2 under clear-sky and all-sky conditions, respectively. The accuracy of the improved parameterization is higher than that of the original model, and there is no obvious underestimation of SSR in the case of high cloud optical thickness. Therefore, the new algorithm improves the accuracy of SSR estimates in the presence of thick clouds. Retrievals with the improved model also achieve higher accuracy than the MODIS official SSR product (MCD18A1). To conclude, the reliable performance of the scheme at most BSRN stations illustrates that the improved model can be used to map SSR on a global scale.

42 ENGINEERING↗
DOE OSTI2022

Object-Based Evaluation of Tropical Precipitation Systems in DYAMOND Simulations over the Maritime Continent

The present study uses an object-based evaluation metric to examine the precipitation bias over the Maritime Continent in the global cloud-resolving models. We specifically focus on the difference between the models that directly resolve convection and those using convection parameterization. The 40-day hindcast experiments of the DYnamics of the Atmospheric general circulation Modeled On Non-hydrostatic Domain (DYAMOND) intercomparison project are evaluated against the high-resolution satellite rainfall products. The hindcast of the Central Weather Bureau Global Forecast System (CWBGFS) under the DYAMOND protocol is also included. The results indicate that most models simulate insufficient numbers of large precipitation system [object-based precipitation system (OPS), > 370 km in scale], indicating weaker convection organization. The observation indicates that the maximum precipitation within the OPS intensifies with increasing object size. All of the models capture this positive relationship, but most of them overestimate the sensitivity. Most of the models overestimate both the frequency and intensity of small OPS (< 160 km), except for the models with convection parameterization [i.e., CWBGFS, European Centre for Medium-Range Weather Forecasts Integrated Forecasting System (IFS)-9 km]. Although most of the models can reproduce the observed peak time of diurnal precipitation over the land area in the Maritime Continent, the simulated fractional contribution of different sizes of OPS to the total precipitation varies from model to model, and their peak times do not follow the observed ones with delayed peak times as the size of OPS increases from small, mid-size, to large categories. Most of the models reasonably capture the mean diurnal cycle peak time, but only the models with convection parameterization and Model for Prediction Across Scales (MPAS) can represent the diurnal evolution of fractional contribution from different OPSs. The implications of the current results to the upscale processes of the tropical convection systems in the global models are also discussed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The impact of forest-controlled snow variability on late-season streamflow varies by climatic region and forest structure

Previous studies have documented how forests influence snow at fine spatial scales, but none have documented the influence that existing forest-snow variability has on streamflow. Here to test how much forest-controlled snow variability influences streamflow, a tiling parameterization based on classifications from high-resolution (1–3 m) vegetation maps was incorporated into the Distributed Hydrology and Soil Vegetation Model (DHSVM). Within each grid cell (90–150 m), the tiling parameterization simulated forest-snow variability with four independently evolving snowpacks. Each tile had unique radiation conditions to represent conditions underneath the canopy, in exposed areas, and along north- and south-facing forest edges. This tiled parameterization was used to test where and when detailed forest-snow modelling should be considered further and where and when the impacts are too small to be worth the effort. To test this, tiled model simulations of streamflow were compared to non-tiled model simulations in the Sierra Nevada, CA, the Jemez Mountains, NM, and the Eastern Cascades, WA. In Tuolumne, CA, the tiled model simulated little difference in grid cell average SWE, and late-season streamflow decreased by only 3%–4% compared to the non-tiled model. In Jemez, NM, the tiled model decreased late-season streamflow by 18% due to increased sublimation. In Chiwawa, WA, the tiled model increased late-season streamflow by 15% due to high shortwave radiation attenuation and less longwave radiation enhancement from the forest. Furthermore, within the Chiwawa, a substantial silvicultural practice was synthetically implemented to increase the north-facing edge's fractional area. This silvicultural experiment, which used the same fractional forest area in all simulations increased late-season streamflow by 35% compared to tiled model simulations that did not represent forest edges. In conclusion, representing forest-SWE variability had an effect on late-season streamflow in some watersheds but not in others based on the fractional area of the forest edges, forest characteristics, and climate conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Review of Coastal Fog Microphysics During C-FOG

The goal of this paper is to provide an overview the coastal fog microphysical measurements and to evaluate microphysical parameterizations based on the C-FOG (Toward Improving Coastal Fog Prediction) field project. C-FOG is designed to advance understanding of liquid fog formation, development, and dissipation over coastal environments to improve fog predictability and monitoring. The project took place in Eastern Canada (Nova Scotia, NS and Newfoundland, NL) coastlines and open water environments during August-October of 2018 where environmental conditions play an important role for late season’s fog formation. Visibility (Vis), wind speed (Uh), and turbulence along coastlines are the most critical weather- related parameters affecting marine transportation and aviation. In the analysis, microphysical observations are summarized first and then they are, together with 3D wind components, used for fog intensity (visibility) evaluation. Results suggest that detailed microphysical observations collected at the supersites and aboard Research Vessel (RV) Hugh R. Sharp are useful to develop microphysical parameterizations. The fog life cycle and turbulence kinetic energy dissipation rate were strongly related to each other. The magnitude of 3D wind fluctuations was higher during the formation and dissipation stages. An array of cutting-edge instruments used for data collection provided new insight into the variability and intensity of fog (visibility) and microphysics. It is concluded that further improvements in microphysical observations and parameterizations are needed to improve fog predictability of NWP (Numerical Weather Prediction) models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Bounded motion design in the Earth zonal problem using differential algebra based normal form methods

Establishing long-term relative bounded motion between orbits in perturbed dynamics is a key challenge in astrodynamics to enable cluster flight with minimum propellant expenditure. Herein, we present an approach that allows for the design of long-term relative bounded motion considering a zonal gravitational model. Entire sets of orbits are obtained via high-order Taylor expansions of Poincarè return maps about reference fixed points. The high-order normal form algorithm is used to determine a change in expansion variables of the map into normal form space, in which the phase space behavior is circular and can be easily parameterized by action–angle coordinates. The action–angle representation of the normal form coordinates is then used to parameterize the original Poincarè return map and average it over a full phase space revolution by a path integral along the angle parameterization. As a result, the averaged nodal period and drift in the ascending node are obtained, for which the bounded motion conditions are straightforwardly imposed. Sets of highly accurate bounded orbits are obtained, extending over several thousand kilometers, and valid for decades.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Simultaneous Optimization of Crystal Plasticity Hardening Parameters

Crystal plasticity models relate macroscopic deformation behavior to the evolution of slip systems strength, but their parameterization is often non-unique, with multiple parameter sets being able to describe the same macroscopic behavior. To address this issue, the present work adopts a Bayesian optimization framework for the parameterization of face-centered cubic plasticity models while simultaneously considering multiple experimental datasets from the literature. For single crystal Cu, parameter optimization was guided by the tensile stress–strain curves along several crystallographic orientations, with an adequate fit being found for five orientations at once. While additional parameters allowed for the consideration of more physical mechanisms, like different slip system interaction strengths or misorientations inherent to the experimental data, the extra dimensionality was found to limit the efficiency of the global minimization procedure. For polycrystalline Ni, multiple grain sizes were considered together in a representative polycrystalline model, with the optimization able to reconcile the model with the data for three grain sizes at once. As meaningful interpretation of parameters relies on the uniqueness of their values, incorporating multiple datasets into this discerning parameterization procedure enables more robust prediction and application of crystal plasticity models.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Simulation and Emulation of X-Ray Diffraction from Dynamic Compression Experiments

Many important aspects of the dynamic thermo-mechanical response of materials occur at the mesoscale, i.e. a physical scale of interactions smaller than what can be adequately described by homogenous behaviors, yet larger than the scale of the atomic lattice. Concurrent advancements in computational power, continuum theory, and experimental diagnostics are enabling unprecedented understanding of such interactions. However, we cannot develop a sufficient level of confidence in such mesoscale capability until the constitutive description of the underlying constituents is reliably representative of their actual physical behavior. Therefore, there is a strong need to combine experimental, modeling, and data-science techniques to validate models of the thermomechanical response of individual single crystals. One experimental diagnostic with high potential impact to shock physics and materials science is in-situ x-ray diffraction. This paper is primarily focused on simulation of x-ray diffraction in shock physics, but with an aim toward quantifying parametric uncertainty of simulation models. Here, we develop and demonstrate a data-science and model-driven approach to constrain the parameterization of continuum models of crystal lattice deformation associated with the shock response of crystalline materials. The framework is built around the connection between continuum hydrodynamic simulations of lattice deformation and a new Bragg diffraction simulation code, BarberShop. The dynamic deformation of a crystal lattice is modeled using the DiscoFlux model within an arbitrary Lagrangian-Eulerian hydrodynamic code, FLAG. These detailed continuum simulations of lattice deformation can be computationally slow, thus a statistical model is used to emulate the evolution of lattice deformation fields in time and across the considered model parameter space. Emulated lattice deformation fields can then be generated rapidly for any combination of physics model parameters. In turn, these fields can be fed into BarberShop to realize a rapid prediction of Bragg diffraction patterns associated with particular values of physics model parameters. The framework enables parameterization of the single crystal model to obtain Bragg diffraction patterns that most closely resemble a corresponding measurement. Furthermore, the framework naturally provides sensitivities of the lattice deformation to the physics parameters. We highlight the utility of this framework through the application to a synthetic closed-loop inverse problem leading to the parameterization of a single crystal material model. As a model problem, we consider the dynamic response of the energetic molecular crystal, cyclotrimethylenetrinitramine (or RDX), under dynamic compression induced by simulated flyer plate impact experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Machine learning based approach to predict ductile damage model parameters for polycrystalline metals

Damage models for ductile materials typically need to be parameterized, often with the appropriate parameters changing for a given material depending on the loading conditions. This can make parameterizing these models computationally expensive, since an inverse problem must be solved for each loading condition. Using standard inverse modeling techniques typically requires hundreds or thousands of high-fidelity computer simulations to estimate the optimal parameters. Additionally, the time of a human expert is required to set up the inverse model. Machine learning has recently emerged as an alternative approach to inverse modeling in these settings, where the machine learning model is trained in an offline manner and new parameters can be quickly generated on the fly, after training is complete. Here, this work utilizes such a workflow to enable the rapid parameterization of a ductile damage model called TEPLA with a machine learning inverse model. The machine learning model can efficiently estimate the model parameters much faster, as compared to previously employed methods, such as Bayesian calibration. The results demonstrate good accuracy on a synthetic test dataset and is validated against experimental data.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Large-scale simulation-based parametric analysis of an optimal precooling strategy for demand flexibility in a commercial office building

Achieving success with grid-interactive efficient buildings (GEBs) is closely tied to the utilization of flexible loads. A valuable strategy involves the implementation of precooling techniques before high-demand events, such as peak hours, by adjusting zone air temperature setpoints. This leads to a reduction in thermal loads and peak electricity demand during these times, as the building’s thermal mass stores and subsequently releases thermal energy. However, the effectiveness of the pre-cooling optimization is highly contingent on specific conditions such as building thermal properties, weather conditions, utility rate structure, HVAC equipment sizing, etc. Therefore, investigating the impacts of these condition-specific factors is crucial, especially when considering precooling strategies that utilize thermal mass in commercial buildings. In this paper, we first devised a novel heuristic control approach that incorporates parameterized optimal precooling thermostat schedules to enhance demand flexibility in a commercial office building. Subsequently, we conducted a thorough performance evaluation of this control strategy. Here, the optimal thermostat schedule was parameterized using three optimization variables: the precooling start time, the precooling end time, and the precooling temperature setpoint. Utilizing the DOE medium-sized office building as the virtual testbed, we showed that the parameterized schedule effectively approximates model predictive control and requires drastically reduced computational overhead. In addition, we investigated the impact of different influencing factors on the optimal precooling strategy. These factors include building thermal mass, outdoor air conditions, and energy price profiles. Using high-performance computing, we simulated a total of 225 scenarios, consisting of three levels of thermal mass, five typical outdoor air temperature profiles, and fifteen time-of-use price plans. The results demonstrate that optimal thermostat scheduling could save substantial energy cost in medium-sized office buildings with heavy thermal mass but with some energy penalty. Although the potential for cost savings is lower in buildings with low and medium thermal mass, the energy penalty remains consistent in all three thermal mass scenarios. The study also highlights the need to account for zone diversity and recognize that a one-size-fits-all-zone setpoint schedule may not be suitable for all zones and can lead to unnecessary energy wastage. Furthermore, the results highlight that while outdoor air conditions play a role in cost and energy performance, the cooling load exerts a more immediate and substantial influence on cost savings in precooling strategies. Although cost savings are comparable under certain conditions with the same cooling load, observed deviations in energy penalty indicate potential disparities in the efficiency of the HVAC system during the load-shifting process. In addition, the duration of peak pricing and the ratio between peak and off-peak times exhibit clear correlations with cost savings and energy consumption, aligning with intuitive expectations. These findings offer valuable insights for optimizing precooling strategies in office buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Synergistic learning with multi-task DeepONet for efficient PDE problem solving

Multi-task learning (MTL) is an inductive transfer mechanism designed to leverage useful information from multiple tasks to improve generalization performance compared to single-task learning. It has been extensively explored in traditional machine learning to address issues such as data sparsity and overfitting in neural networks. In this work, we apply MTL to problems in science and engineering governed by partial differential equations (PDEs). However, implementing MTL in this context is complex, as it requires task-specific modifications to accommodate various scenarios representing different physical processes. To this end, we present a multi-task deep operator network (MT-DeepONet) to learn solutions across various functional forms of source terms in a PDE and multiple geometries in a single concurrent training session. We introduce modifications in the branch network of the vanilla DeepONet to account for various functional forms of a parameterized coefficient in a PDE. Additionally, we handle parameterized geometries by introducing a binary mask in the branch network and incorporating it into the loss term to improve convergence and generalization to new geometry tasks. Our approach is demonstrated on three benchmark problems: (1) learning different functional forms of the source term in the Fisher equation; (2) learning multiple geometries in a 2D Darcy Flow problem and showcasing better transfer learning capabilities to new geometries; and (3) learning 3D parameterized geometries for a heat transfer problem and demonstrate the ability to predict on new but similar geometries. Finally, our MT-DeepONet framework offers a novel approach to solving PDE problems in engineering and science under a unified umbrella based on synergistic learning that reduces the overall training cost for neural operators.

42 ENGINEERING↗
DOE OSTI2022

Frame invariant neural network closures for Kraichnan turbulence

Numerical simulations of geophysical and atmospheric flows have to rely on parameterizations of subgrid scale processes due to their limited spatial resolution. Despite substantial progress in developing parameterization (or closure) models for subgrid scale (SGS) processes using physical insights and mathematical approximations, they remain imperfect and can lead to inaccurate predictions. In recent years, machine learning has been successful in extracting complex patterns from high-resolution spatio-temporal data, leading to improved parameterization models, and ultimately better coarse grid prediction. However, the inability to satisfy known physics and poor generalization hinders the application of these models for real-world problems. In this work, we put forth a frame invariant closure approach to improve the accuracy and generalizability of deep learning-based subgrid scale closure models by embedding physical symmetries directly into the structure of the neural network. Specifically, we utilized specialized layers within the convolutional neural network in such a way that desired constraints are theoretically guaranteed without the need for any regularization terms. We demonstrate our framework for a two-dimensional decaying turbulence test case mostly characterized by the forward enstrophy cascade. We show that our frame invariant SGS model (i) accurately predicts the subgrid scale source term, (ii) respects the physical symmetries such as translation, Galilean, and rotation invariance, and (iii) is numerically stable when implemented in coarse-grid simulation with generalization to different initial conditions and Reynolds number. This work opens up a possibility of connecting physics-based theories and data-driven modeling paradigms, and thus represents a promising step towards the development of physically consistent data-driven turbulence closure models.

42 ENGINEERING↗
DOE OSTI2022

Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model

Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks that can throttle back metabolic flow. By (i) elucidating internal metabolic fluxes in wild-type C. thermocellum grown on cellobiose via 13 C-metabolic flux analysis ( 13 C-MFA), (ii) parameterizing a core kinetic model, and (iii) subsequently deploying an ensemble-docking workflow for discovering substrate-level regulations, this paper aims to reveal some of these factors and expand our knowledgebase governing C. thermocellum metabolism. Generated 13 C labeling data were used with 13 C-MFA to generate a wild-type flux distribution for the metabolic network. Notably, flux elucidation through MFA alluded to serine generation via the mercaptopyruvate pathway. Using the elucidated flux distributions in conjunction with batch fermentation process yield data for various mutant strains, we constructed a kinetic model of C. thermocellum core metabolism (i.e. k-ctherm138). Subsequently, we used the parameterized kinetic model to explore the effect of removing substrate-level regulations on ethanol yield and titer. Upon exploring all possible simultaneous (up to four) regulation removals we identified combinations that lead to many-fold model predicted improvement in ethanol titer. In addition, by coupling a systematic method for identifying putative competitive inhibitory mechanisms using K-FIT kinetic parameterization with the ensemble-docking workflow, we flagged 67 putative substrate-level inhibition mechanisms across central carbon metabolism supported by both kinetic formalism and docking analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Development of Density Functional Tight-Binding Parameters Using Relative Energy Fitting and Particle Swarm Optimization

We provide a strategy to optimize density functional tight-binding (DFTB) parameterization for the calculation of the structures and properties of organic molecules consisting of hydrogen, carbon, nitrogen, and oxygen. We utilize an objective function based on similarity measurements and the Particle Swarm Optimization (PSO) method to find an optimal set of parameters. This objective function considers not only the common DFTB descriptors of binding energies and atomic forces but also incorporates relative energies of isomers into the fitting procedure for more chemistry-driven results. The quality in the description of the binding energies and atomic forces is measured based on the Ballester similarity index and relative energies through a similarity index induced by the Levenshtein edit distance to quantify the correct energetic order of isomers. Training and testing datasets were created to include all relevant chemical functional groups. Finally, the accuracy of this strategy is assessed, and its range of applicability is discussed by comparison against our previous parameterization. The improved performance of the new DFTB parameterization is validated with respect to the density functional theory large datasets QM-9 and ANI-1, where excellent agreement is found between the structures and properties available in these datasets, and the ones obtained with DFTB.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗