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NASA NTRS2020

Ion Channels – From Structure to Electrophysiology and Back

A reliable way to establish whether our understanding of a channel is satisfactory is to reproduce its measured ionic conductance over a broad range of applied voltages in computer simulations. In molecular dynamics (MD), this can be done by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive, we have developed a markedly more efficient alternative in which MD is combined with the electrodiffusion (ED) equation. In this approach, the assumptions of the ED equation can be rigorously tested, and the precision and consistency of the calculated conductance can be determined. We have demonstrated that the full current/voltage dependence and the underlying free energy profile for a simple channel can be reliably calculated from equilibrium or non-equilibrium MD simulations at a single voltage. Free energy profiles can be obtained from non-equilibrium simulations without a loss of accuracy even without the knowledge of diffusion coefficient. To carry out MD simulations, a structural model of a channel has to be assumed, which is an important constraint, considering that high-resolution structures are available for only very few simple channels. If the comparison of calculated ionic conductance with electrophysiological data is satisfactory, it greatly increases our confidence that the structure and the function are described sufficiently accurately. We examined the validity of the ED for several channels embedded in phospholipid membranes - four naturally occurring channels: trichotoxin, alamethicin, p7 from hepatitis C virus (HCV) and Vpu from the HIV-1 virus, a synthetic, hexameric channel, formed by a 21-residue peptide that contains only leucine and serine and a bacterial pentameric ligand-gated ion channel, GLIC. All these channels mediate transport of potassium and chloride ions. It was found that the ED equation is satisfactory for these systems. In some of them, experimental and calculated electrophysiological properties are in good agreement, whereas in others there are strong indications that the structural models are incorrect.

Pohorille, Andrew↗
NASA NTRS2024

Looking to the Future: A Call to Action for Advanced GNC Algorithm Verification and Validation

Future space systems will rely on autonomous Guidance, Navigation, and Control (GNC) functions to efficiently manage safe and precise self-directed operations in uncertain complex environments. Fundamentally, the GNC system plays a key role in mission performance and safety because it computes the ideal trajectory (Guidance), determines the actual trajectory (Navigation), and executes the ideal trajectory (Control) of a vehicle’s position and attitude. Our current GNC systems are highly automated and already have a high degree of complexity. As missions become more ambitious, GNC systems for launch vehicles and space platforms (e.g., spacecraft, probes, and landers) will require higher levels of performance and autonomous operation than previously encountered, for example, this includes GNC for optimizing aerodynamic and/or propulsion performance during planetary entry. This GNC Verification and Validation (V&V) paper highlights concerns with what undoubtedly will be a trend towards increased complexity as fully autonomous GNC systems are developed for future space missions. Clearly, complex GNC systems pose challenges in the prelaunch V&V phase, which is a relatively expensive part of a mission’s life cycle. Essentially the V&V phase is focused on checking that the system effectively meets all the design and operational requirements for the mission. The authors of this paper (i.e., the Inter-Agency Working Group of GNC subject matter experts) focused on this fundamental question over the past few years: Will the GNC engineering community of practice be sufficiently prepared to perform the necessary V&V on evolving GNC architectures that are driven by very demanding requirements for autonomy, resiliency, reconfigurability, adaptability, and mission cost-benefit balance? It is the viewpoint of our Inter-Agency team that the GNC V&V approaches and processes needed to address the next generation of complex GNC systems, which likely will employ various forms of modern GNC technology, are not currently established to the level the community will need in the future. While researchers and practitioners have made some progress in developing new GNC V&V methods for modern GNC systems, a good deal of work remains to be done to codify such methods in a comprehensive and systematic manner. Thus, the Inter-Agency team’s partner organizations [the National Aeronautics and Space Administration (NASA), the European Space Agency (ESA), the National Centre for Space Studies (CNES), the German Aerospace Center (DLR), the French Aerospace Lab (ONERA), and ISAE-SUPAERO] have conducted preliminary investigations into advancing GNC V&V techniques, which resulted in the identification of the need for education, new V&V tools, and benchmark problems for the GNC community. The necessary proactive steps to be taken to meet the challenges and fill the gaps in GNC V&V are summarized in this paper. The first steps include identifying advanced analysis tools, developing a GNC V&V roadmap, and expanding education and training programs for GNC practitioners. This paper is a call to action and proposes a comprehensive set of recommended actions for all our stakeholders: space agencies, researchers, and industry.

Samir Bennani↗
DOE OSTI2023

Prediction and uncertainty quantification of shale well performance using multifidelity Monte Carlo

Uncertainty quantification is an integral component of reservoir management, especially considering the inherent uncertainty in subsurface systems. While a standard practice to estimate the uncertainty, Monte Carlo (MC) simulation is computationally intense when the sampling population comprises high-fidelity simulations. Alternatively, the Multi-fidelity Monte Carlo (MFMC) simulation overcomes this computational intensity by integrating low- and high-fidelity simulations. Our goal is to minimize the number of expensive high-fidelity simulations while maintaining accuracy and using numerous fast and cheap low-fidelity simulations to efficiently sample to input parameter space of interest. We selected gas production from unconventional wells to demonstrate the potential speedups and accuracy of the MFMC approach. The model fidelity usually determines the trade-off between accuracy and efficiency. While the high-fidelity model is more accurate, the low-fidelity model is more efficient. Our high-fidelity simulation includes reservoir simulations of a hydraulically fractured well. On the other hand, our low-fidelity model comprises the parallel-plate flow model. We used differential programming to efficiently solve the 1D flow model, where automatic differentiation is used to efficiently compute the gradients. We matched the production profile of high-fidelity simulations with our low-fidelity simulations. Then, we used a support vector regression to map the high- and low-fidelity input parameters. The mapping function is essential to tune the low-dimensional parameter space of the low-fidelity model to the high-dimensional parameter space of the high-fidelity model. We found that we can use a combination of 9 high fidelity and 10,000 low fidelity simulations to efficiently and accurately simulate pressure management. This method is at least two orders of magnitude faster than only using high-fidelity simulations. Finally, from a broader perspective, MFMC could efficiently estimate the uncertainty of various systems and models, integrating low- and high-fidelity models.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2023

Trajectory sampling and finite-size effects in first-principles stopping power calculations

Abstract Real-time time-dependent density functional theory (TDDFT) is presently the most accurate available method for computing electronic stopping powers from first principles. However, obtaining application-relevant results often involves either costly averages over multiple calculations or ad hoc selection of a representative ion trajectory. We consider a broadly applicable, quantitative metric for evaluating and optimizing trajectories in this context. This methodology enables rigorous analysis of the failure modes of various common trajectory choices in crystalline materials. Although randomly selecting trajectories is common practice in stopping power calculations in solids, we show that nearly 30% of random trajectories in an FCC aluminum crystal will not representatively sample the material over the time and length scales feasibly simulated with TDDFT, and unrepresentative choices incur errors of up to 60%. We also show that finite-size effects depend on ion trajectory via “ouroboros” effects beyond the prevailing plasmon-based interpretation, and we propose a cost-reducing scheme to obtain converged results even when expensive core-electron contributions preclude large supercells. This work helps to mitigate poorly controlled approximations in first-principles stopping power calculations, allowing 1–2 order of magnitude cost reductions for obtaining representatively averaged and converged results.

36 MATERIALS SCIENCE↗
NASA NTRS2026

Benchmarking Bayesian Optimization Frameworks and Acquisition Strategies for Materials Discovery and Autonomous Laboratories

Bayesian optimization (BO) can accelerate materials discovery by guiding expensive experiments toward the most promising processing conditions. We systematically compare five BO surrogate and framework combinations (Gaussian processes in Ax, Gaussian processes and Monte-Carlo neural networks in BayBE, random forests in Lolopy, and tree-structured Parzen (TPE) estimators in Hyperopt) on three benchmarks that mimic common materials design tasks (a discrete solid-electrolyte composition space, a hybrid discrete/continuous laminate-composite design problem solved with micromechanics modeling, and the continuous Ishigami analytic function which is a standard optimization benchmark). Each BO surrogate is paired with posterior mean, probability of improvement, and expected improvement acquisition functions and run for 100 trials from randomized initial samples with uniform random search providing a control. Across five random seeds per setting, BayBE’s Gaussian-process surrogate with expected improvement consistently reached ≥95 % of the known optimum in the fewest evaluations, while Lolopy’s random forest matched or exceeded GP performance on purely categorical or mixed spaces at a higher computational cost. Posterior mean alone often stagnated at local optima, underscoring the need for exploration, whereas probability and expected improvement balanced exploration and exploitation leading to better optimization in fewer trials. Execution times ranged from milliseconds for TPE to minutes for neural-network and random-forest surrogates. These results establish baseline expectations for BO in automated materials laboratories and highlight expected improvement with Gaussian processes as a reliable first choice, with random forests offering a strong alternative when categorical variables dominate. The benchmark suite and code are released to facilitate future surrogate, acquisition, and constraint-handling research in data-driven materials optimization.

Bayesian optimization↗
DOE OSTI2016

Sensitivity Analysis of Passive Heat Removal Capability of FHR Based on Efficient Surrogate Model and GenFlow

Code Scaling, Applicability and Uncertainty Evaluation Methodology (CSAU) is used for quantifying reactor safety margins and works as an alternative method for licensing nuclear power plant. In the framework of CSAU, sensitivity and uncertainty analysis (SA and UA) should be performed. However, for large-scale complicated thermal hydraulics analysis simulated by code (e.g. RELAP5, CFD and subchannel analysis, the sensitivity and uncertainty analysis is really time-consuming. Furthermore, sometimes it is not feasible to perform SA and UA. Specifically, the computation time for Monte Carlo sampling or advanced LHS sampling can be neglected, but the computation time for thermal hydraulics code makes up main part of time during SA and UA process. In order to accelerate the speed of SA and UA, thermal hydraulics code can be improved based on advanced mathematic algorithm or using parallel method. However, the development for new mathematic method needs long time and strict verification and validation process is needed for a new code, which usually takes a couple of years or even longer time to have an approved code that can be used in nuclear industry. An alternative way to improve the speed of SA and UA is using surrogate model. The surrogate model is derived from the input as well as output data of the original code, assuming the code as a black box. The most common method is using response surface method (RSM) as a surrogate for the code, the input parameters are then sampled from their assumed distribution and the corresponding value of the response surface function is calculated. However, a couple of input parameters need hundreds or even thousands of original code calculations. The large number of runs is an obvious disadvantage of this method. Besides, the second disadvantage is an appropriate response surface function must be selected (e.g. quadratic, cubic, quartic, with or without cross product terms, or using a non-polynomial form) to avoid the overfit and underfit problem. This process is time consuming and expensive. Polynomial chaos expansion method is a reasonably fast and attractive alternative, stochastic model. The chaos expansion provides an efficient high-order method of including non-linear effects in stochastic analysis. Usually, the information about the model parameters and their probability distribution is limited and the dependence between them is not known. However, if arbitrary polynomial chaos is used, instead of assuming probability distribution for input parameters which may introduces additional subjectivity into the analysis, the available information can directly and most purely be used in stochastic analysis based on arbitrary data distribution. Thus, it is not necessary to know the exact probability density functions to perform SA and UA based on arbitrary polynomial chaos (aPC). The aPC has been applied for uncertainty quantification in many fields (e.g. in solid mechanics, fluid flows, thermal sciences), and become widely used in nuclear industry recently. Mk1 PB-FHR is a small modular fluoride-salt-cooled, high-temperature reactors (FHRs) that is a concept design by University of California, Berkeley (UCB). It has inherently safe features like natural-circulation-driven systems (e.g. direct reactor auxiliary cooling system (DRACS)) to passively remove decay heat from the reactor core during design basis and beyond design. It is necessary to perform SA and UA, since the licensing process of this new kind of reactor is under way and there are many design parameters that have not been fixed. Current nuclear commercial codes, such as RELAP5, have mainly been developed for light water reactors, which require the use of comprehensive two-phase flow models. This capability is not required to simulate single-phase flow phenomena in FHRs, whose baseline coolant, flibe, remains liquid up to 1430 deg. C at atmospheric pressure. The FHR advanced natural circulation analysis (FANCY) code has been developed specifically for FHR technology modeling and validation work has been performed by using CIET data in UCB. The code has been renamed General Flow (GenFlow) because it has been further developed to have the capability to model complicated pipework system based on object-oriented concept for user friendly purpose. Besides, it can be used to simulate both the force circulation as well as natural circulation. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2026

Evaluating lightweight unsupervised online IDS for masquerade attacks in CAN

Vehicular controller area networks (CANs) are susceptible to masquerade attacks by malicious adversaries. In masquerade attacks, adversaries silence a targeted ID and then send malicious frames with forged content at the expected timing of benign frames. As masquerade attacks could seriously harm vehicle functionality and are the stealthiest attacks to detect in CAN, recent work has devoted attention to compare frameworks for detecting masquerade attacks in CAN. However, most existing works report offline evaluations using CAN logs already collected using simulations that do not comply with the domain’s real-time constraints. Here we contribute to advance the state of the art by presenting a comparative evaluation of four different non-deep learning (DL)-based unsupervised online intrusion detection systems (IDS) for masquerade attacks in CAN. Our approach differs from existing comparative evaluations in that we analyze the effect of controlling streaming data conditions in a sliding window setting. In doing so, we use realistic masquerade attacks being replayed from the ROAD dataset. We show that although evaluated IDS are not effective at detecting every attack type, the method that relies on detecting changes in the hierarchical structure of clusters of time series produces the best results at the expense of higher computational overhead. We discuss limitations, open challenges, and how the evaluated methods can be used for practical unsupervised online CAN IDS for masquerade attacks.

Anomaly detection↗
DOE OSTI2022

Clean Condensing Gas Furnace

Natural gas furnaces are the most common space heating equipment in the U.S. residential and commercial building markets. However, current residential natural gas condensing furnaces generate substantial acidic condensate as well as significant emissions of sulfur oxides (SOx), nitrogen oxides (NOx), carbon monoxide (CO), hydrocarbons (HC), and methane (CH 4 ) contributing to environmental degradation of air, water, and soil. This report describes a novel solution to reduce the environmental impact of natural gas condensing furnaces based on the technology of a monolithic acidic gas reduction (AGR) catalyst for SOx trapping, NOx redox to nitrogen, and oxidation of formic acid, CO, HC, and CH 4 . The AGR technology offers the following benefits: (1) a neutral furnace condensate with a pH of ~7, allowing its safe release into the sewer system thus eliminating a second drainage system; (2) trapping and removing nearly all SOx emissions; (3) NOx emissions nearly at nearly 1-2 ng/J, more than 95% lower than new emissions standards in California; (4) the use of a low-cost heat exchanger as a condensing heat exchanger (HX) since the condensate is not acidic, avoiding the need for expensive stainless steel alloys; and (5) unburnt fuel energy recovery to boost efficiency.The AGR component and AGR-enabled furnace performance were broadly tested to determine their effects on long-term reliability and durability, as well as SOx storage and regeneration activity. The AGR regeneration does not impair the performance in achieving neutral condensate and ultra-low NOx emissions, and the AGR catalyst subjected to regeneration activities continued to function well and achieved slightly better annual fuel utilization efficiency (AFUE). The 400-hour reliability and durability test of the retrofitted condensing furnace with the AGR component shows that the furnace unit still achieves a neutral furnace condensate with a pH of ~7 and enables 0~3 ng/J of NOx emissions. However, the 400-hour operation slightly degraded the AFUE because of soot particle accumulation caused by frequent incomplete combustion owing to inappropriate condensate drainage during testing. Thus, proper condensate drainage is critical for AGR-enabled furnaces. Furthermore, neutron computed tomography was employed to survey the aged AGR component and demonstrate high-resolution 2D and 3D representations for the nondestructive diagnosis of the AGR component. The tomography showed that the AGR component did not deform or suffer broken AGR channels. A new AGR catalyst with low precious metal loading was preliminarily explored to identify a pathway of optimizing AGR material loading and maximizing acidic gas reduction at low cost. The new AGR component can reduce precious metal loading by 38% and still achieve neutral condensate and ultralow NOx emissions. The furnace with the AGR component of low Pt/Rh loading enables a maximum AFUE of 97%, which is meaningfully higher than the original furnace. Long-duration testing for the furnace enabled with the low precious metal loading AGR component will be vital in future research. Although the current work demonstrates a proof of concept for the AGR-enabled furnace, the AGR assembly needs to be optimized and integrated into the design of new OEM furnace products. Furthermore, the AGR technology can be applied not only for residential gas furnaces, but also for commercial rooftop units, gas heat pumps, gas-fired water heaters, combustion boilers, and other systems.

03 NATURAL GAS↗
NASA NTRS2005

Safety Verification of the Small Aircraft Transportation System Concept of Operations

A critical factor in the adoption of any new aeronautical technology or concept of operation is safety. Traditionally, safety is accomplished through a rigorous process that involves human factors, low and high fidelity simulations, and flight experiments. As this process is usually performed on final products or functional prototypes, concept modifications resulting from this process are very expensive to implement. This paper describe an approach to system safety that can take place at early stages of a concept design. It is based on a set of mathematical techniques and tools known as formal methods. In contrast to testing and simulation, formal methods provide the capability of exhaustive state exploration analysis. We present the safety analysis and verification performed for the Small Aircraft Transportation System (SATS) Concept of Operations (ConOps). The concept of operations is modeled using discrete and hybrid mathematical models. These models are then analyzed using formal methods. The objective of the analysis is to show, in a mathematical framework, that the concept of operation complies with a set of safety requirements. It is also shown that the ConOps has some desirable characteristic such as liveness and absence of dead-lock. The analysis and verification is performed in the Prototype Verification System (PVS), which is a computer based specification language and a theorem proving assistant.

Carreno, Victor↗
DOE OSTI2026

Comparison of DeePMD, MTP, GAP, ACE and MACE Machine‐Learned Potentials for Radiation‐Damage Simulations: A User Perspective

Accurate and efficient interatomic potentials are essential for molecular dynamics (MD) simulations of radiation damage, gas diffusion, and phase stability in complex ceramics such as LiAlO 2 , especially under extreme conditions relevant to tritium production. Here, we evaluate the performance of six machine-learned interatomic potentials (MLIPs), moment tensor potential (MTP), Gaussian approximation potential, deep potential (DeePMD), atomic cluster expansion (ACE), message-passing ACE (multilayer atomic cluster expansion (MACE) pretrained) and MACE (trained from-scratch), all trained on the same density functional theory dataset with inclusion of tritium. The MLIPs are benchmarked against traditional Buckingham and ReaxFF potentials in terms of energy accuracy, density predictions, thermal equilibration behavior, threshold displacement energy (E d ), tritium diffusivity, and computational cost. Among the models, MTP shows the best overall balance between efficiency and accuracy, with low force and energy errors and realistic E d values for Li and Al. The ACE and MACE (pretrained and trained from scratch) models exhibit high E d (>200 eV) and unphysical pair interactions. DeePMD underestimates Ed due to overly repulsive behavior even at equilibrium distances. All models over-estimate tritium diffusion but the pretrained MACE model behaves well during tritium-diffusion simulations up to 500 K, maintaining diffusivities in the physically consistent 10 −11 m 2 /s range. Finally, we quantify the computational cost of each potential in large-scale atomic/molecular massively parallel simulator, finding that only MTP is more efficient than traditional empirical potentials, while others are significantly more expensive. These findings explain the trade-offs between accuracy and computational cost in MLIP development and provide essential guidance for use in high-throughput radiation damage and gas diffusion simulations in nuclear ceramics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Graph-Based Approaches for Predicting Solvation Energy in Multiple Solvents: Open Datasets and Machine Learning Models

The solvation properties of molecules, often estimated using quantum chemical simulations, are important in the synthesis of energy storage materials, drugs, and industrial chemicals. Here, we develop machine learning models of solvation energies to replace expensive quantum chemistry calculations with inexpensive-to-compute message-passing neural network models that require only the molecular graph as inputs. Our models are trained on a new database of solvation energies for 130,258 molecules taken from the QM9 dataset computed in five solvents (acetone, ethanol, acetonitrile, dimethyl sulfoxide, and water) via an implicit solvent model. Our best model achieves a mean absolute error of 0.5 kcal/mol for molecules with nine or fewer non-hydrogen atoms and 1 kcal/mol for molecules with between 10 and 14 non-hydrogen atoms. We make the entire dataset of 651,290 computed entries openly available and provide simple web and programmatic interfaces to enable others to run our solvation energy model on new molecules. This model calculates the solvation energies for molecules using only the SMILES string and also provides an estimate of whether each molecule is within the domain of applicability of our model. We envision that the dataset and models will provide the functionality needed for the rapid screening of large chemical spaces to discover improved molecules for many applications.

25 ENERGY STORAGE↗
DOE OSTI2020

Multi-Model and Multi-Scale Global Sensitivity Analysis for Identifying Controlling Processes of Complex Systems

An environmental model consists of multiple process level sub-models, and each sub-model represents a process that is key to the operation of the simulated system. Global sensitivity analysis methods have been widely used to identify important processes for system model development and improvement. The existing methods of global sensitivity analysis only consider parametric uncertainty, and are not capable of handling model uncertainty caused by multiple process models that arise from competing hypotheses about one or more processes. To address this problem, this project develops a new method to probe model output sensitivity to competing process models by integrating model averaging methods with variance-based global sensitivity analysis to address uncertainty in process models and parameters. The new method yields three process sensitivity indices. The first one is called first-order process sensitivity index, and it is derived as a single summary measure of relative process importance. Evaluating the index is computationally expensive, because it relies in a Monte Carlo scheme that requires thousands and even millions of model executions. To reduce computational cost, this project develops a computationally efficient, quasi Monte Carlo method, and this method is presented in Chapter 2 of this report with and a numerical example for demonstration. The numerical example shows that the results of the quasi Monte Carlo method are substantially close to those of the full Monte Carlo method, but the computational cost of the quasi Monte Carlo method is only 0.7% of that of the full Monte Carlo method. The second index is called total-effect process sensitivity index, and it measures interactions between different processes. Therefore, this sensitivity index includes the first-order process sensitivity index, and can be used to identify influential processes. On the other hand, the total-effect process sensitivity index can also be used to screen non-influential processes. This is demonstrated by two numerical examples using the Sobol-G* functions and groundwater flow models that consider recharge process, geological process, and snowmelt process. The numerical examples shows that the total-effect process sensitivity index is more informative than the first-order process sensitivity. The derivation of the process sensitivity index and the numerical examples are discussed in Chapter 3. Chapter 4 presents two computationally efficient methods for screening non-influential processes to exclude them from further investigation. The two methods are the multi-model difference-based sensitivity (MMDS) analysis method, which can be implemented using the Latin Hypercube Sampling. The second one is the implementation of MMDS method using a binning method. The numerical example for the Sobol-G* function indicates the two methods are capable of identifying non-influential models, and the numerical examples for the groundwater flow and reactive transport show that the two methods are effective for groundwater problems. However, it should be noted that the two methods are numerical approximations, and they can only be used for screening non-influential processes, not for ranking importance of system processes. All the sensitivity analysis methods are implemented by developing python codes, and the codes are in a software called SAMMPY: a python package for process sensitivity analysis under multiple models. The SAMMPY design and structure are discussed in Chapter 5, and the package is released to the public for free download.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1986

Sensitivity analysis and approximation methods for general eigenvalue problems

Optimization of dynamic systems involving complex non-hermitian matrices is often computationally expensive. Major contributors to the computational expense are the sensitivity analysis and reanalysis of a modified design. The present work seeks to alleviate this computational burden by identifying efficient sensitivity analysis and approximate reanalysis methods. For the algebraic eigenvalue problem involving non-hermitian matrices, algorithms for sensitivity analysis and approximate reanalysis are classified, compared and evaluated for efficiency and accuracy. Proper eigenvector normalization is discussed. An improved method for calculating derivatives of eigenvectors is proposed based on a more rational normalization condition and taking advantage of matrix sparsity. Important numerical aspects of this method are also discussed. To alleviate the problem of reanalysis, various approximation methods for eigenvalues are proposed and evaluated. Linear and quadratic approximations are based directly on the Taylor series. Several approximation methods are developed based on the generalized Rayleigh quotient for the eigenvalue problem. Approximation methods based on trace theorem give high accuracy without needing any derivatives. Operation counts for the computation of the approximations are given. General recommendations are made for the selection of appropriate approximation technique as a function of the matrix size, number of design variables, number of eigenvalues of interest and the number of design points at which approximation is sought.

Murthy, D. V.↗
DOE OSTI2022

Influence of Aerosol Embedded in Shallow Cumulus Cloud Fields on the Surface Solar Irradiance

Ubiquitous shallow cumulus clouds are associated with complex variability in surface solar irradiance (SSI). Aerosol embedded in the cloud field typically has a much smaller overall radiative effect, but can significantly perturb the shape of the SSI probability density function (PDF). These perturbations have important implications for several applications that utilize SSI, but are poorly quantified and are the subject of this study. Multiple cases of shallow cumulus cloud fields with embedded aerosol are simulated at the Southern Great Plains Atmospheric Observatory using large eddy simulation (LES). The LES-derived cloud and aerosol fields are then ingested into Monte Carlo three-dimensional (3D) radiative transfer to simulate SSI. We find a variety of perturbations to the SSI PDF that depend on aerosol presence and optical properties. The processes leading to these perturbations include extinction of the direct beam that often increases from the clear-sky region toward cloud edge due to aerosol hygroscopic growth, and scattering of radiation by aerosol into cloud shadows. The ability to predict the SSI PDF in the presence of aerosol is assessed by adding three representative aerosol optical properties into an existing machine learning framework. We show that machine learning accurately predicts the SSI PDF across a wide range of conditions with negligible computational expense. Importance metrics reveal the relatively high influence of aerosol optical properties in making the predictions. These new findings highlight the important role that aerosol plays in SSI variability for highly 3D cloud-aerosol environments and provides a computationally efficient route forward for its simulation.

3D radiative transfer↗
DOE OSTI2024

A Corrected Score Function Framework for Modelling Circadian Gene Expression

Many biological processes display oscillatory behaviour based on an approximately 24 h internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic studies have identified associations between gene expression during a 24 h period and an individual's health. A challenge with analysing data from these studies is that each individual's internal timing system is offset relative to the 24 h day-night cycle, where day–night cycle time is recorded for each collected sample. Laboratory procedures can accurately determine each individual's offset and determine the internal time of sample collection. However, these laboratory procedures are labour-intensive and expensive. Here, in this paper, we propose a corrected score function framework to obtain a regression model of gene expression given internal time when the offset of each individual is too burdensome to determine. A feature of this framework is that it does not require the probability distribution generating offsets to be symmetric with a mean of zero. Simulation studies validate the use of this corrected score function framework for cosinor regression, which is prevalent in circadian transcriptomic studies. Illustrations with data from three circadian transcriptomic studies further demonstrate that the proposed framework consistently mitigates bias relative to using a score function that does not account for this offset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A Kriging Surrogate Model for Computing Gas Mixture Equations of State

Accurate simulation of the complex flow following the detonation of an explosive material is a challenging problem. In these flows, the detonation products of the explosive must be treated as a real gas while the surrounding air is treated as an ideal gas. As the detonation process unfolds and the blast wave moves into the surrounding ambient air, the products of detonation expand outward and interact with the air creating a mixture region. In this region, both of the state equations for air and the products must be satisfied. One of the most accurate, yet computationally expensive, methods to handle this problem is an algorithm that iterates between the equations of state until both pressure and temperature reach an equilibrium inside of a computational cell. Since this mixture region moves and grows over time, this algorithm must be performed millions, or even billions, of times in a typical detonation simulation. As such, these calculations can account for a large percentage of the overall solution time. This work aims to use a kriging surrogate model to replace this process. The iterative method solves a nonlinear system of equations created from the gas mixture density, internal energy, and composition using a Broyden iterative solver to obtain an output pressure and temperature. Kriging is used to produce curve fits which interpolate selected pressures and temperatures from this solver from appropriate ranges of the mixture input quantities. Using a finite volume hydrocode, the performance of the model with respect to the iterative solver is demonstrated in the simulation of a pentaerythritol tetranitrate (PETN) charge detonation. The model's computational speed and accuracy are quantified as a function of the choice of sampling points in order to try optimize the combination as well as to show the benefits of this novel approach.

Engineering↗
DOE OSTI2021

Internal Conversion between Bright (1 1 B $^+_u$) and Dark (21 A $^-_g$) States in s- trans -Butadiene and s- trans -Hexatriene

Internal conversion (IC) between the two lowest singlet excited states, 1 1 B$_u^+$ and 2 1 A$_g^–$, of s-trans-butadiene and s-trans-hexatriene is investigated using a series of single- and multi- reference wave function and density functional theory (DFT) methodologies. Three independent types of the equation-of-motion coupled-cluster (EOMCC) theory capable of providing an accurate and balanced description of one- as well as two-electron transitions, abbreviated as δ-CR-EOMCC(2,3), DIP-EOMCC(4h2p){N o }, and DEA-EOMCC(4p2h){N u } or DEA-EOMCC(3p1h,4p2h){N u }, consistently predict that the 1 1 B$_u^+$/2 1 A$_g^–$ crossing in both molecules occurs along the bond length alternation coordinate. However, the analogous 1 1 B$_u^+$ and 2 1 A$_g^–$ potentials obtained with some multireference approaches, such as CASSCF and MRCIS(D), as well as with the linear-response formulation of time-dependent DFT (TDDFT), do not cross. Hence, caution needs to be exercised when studying the low-lying singlet excited states of polyenes with conventional multiconfigurational methods and TDDFT. The multistate many-body perturbation theory methods, such as XMCQDPT 2 , do correctly reproduce the curve crossing. Among the simplest and least expensive computational methodologies, the DFT approaches that incorporate the contributions of doubly excited configurations, abbreviated as MRSF (mixed reference spin-flip) TDDFT and SSR( 4,4 ), accurately reproduce our best EOMCC results. This is highly promising for nonadiabatic molecular dynamics simulations in larger systems.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Modeling of canonical and C2'- O -thiophenylmethyl modified hexamers of RNA. Insights into the nature of structural changes and thermal stability

Modifying the ribose ring or the nucleobase within oligonucleotides of RNA is a strategy that has regained attention due to its potential to provide chemical stability, increase affinity towards a target, or introduce groups with bioorthogonal reactivity, among other applications. However introducing groups via synthetic routes can be a daunting process and may result in unexpected physical properties and structural variations. In addition, characterizing the effects of a modification within an oligonucleotide can be time consuming and expensive, e.g., NMR, crystallography. Thus the development of models that are accurate, reasonably priced and carried out over short periods of time is essential to the development of this field. In this paper we report on the development and validation of computational models that explain the nature of the structural and stability changes induced by the presence of a C2'-O-methylthiophene group at various positions within duplexes conformed by two 6-mers of modified RNA as well as random coils containing the same modification(s). Through analysis of the obtained models it was concluded that the presence of the methylthiophene moiety on two strands of RNA induces a conformational change around the torsion angle (κ°) that leads to lower values in the pseudorotational angle (δ°), thus resulting in an A-form α-helix with shorter distances between phosphates than those in canonical RNA. These results provide a reasonable explanation for the experimental observations, which display the thermal stabilization of the duplexes, and are guiding efforts from our groups to control the structure and function of RNA, i.e., via functionalization of the RNA structure for attaining thermal stability while retaining the structural properties of an A-form duplex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗