Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Mathematical methods”

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 37 records · Page 2

Experimental Observations of the Topology of Convolutional Neural Network Activations

Topological data analysis (TDA) is a branch of computational mathematics, bridging algebraic topology and data science, that provides compact, noise-robust representations of complex structures. Deep neural networks (DNNs) learn millions of parameters associated with a series of transformations defined by the model architecture resulting in high-dimensional, difficult to interpret internal representations of input data. As DNNs become more ubiquitous across multiple sectors of our society, there is increasing recognition that mathematical methods are needed to aid analysts, researchers, and practitioners in understanding and interpreting how these models' internal representations relate to the final classification. In this paper we apply cutting edge techniques from TDA with the goal of gaining insight towards interpretability of convolutional neural networks used for image classification. We use two common TDA approaches to explore several methods for modeling hidden layer activations as high-dimensional point clouds, and provide experimental evidence that these point clouds capture valuable structural information about the model's process. First, we demonstrate that a distance metric based on persistent homology can be used to quantify meaningful differences between layers and discuss these distances in the broader context of existing representational similarity metrics for neural network interpretability. Second, we show that a mapper graph can provide semantic insight as to how these models organize hierarchical class knowledge at each layer. These observations demonstrate that TDA is a useful tool to help deep learning practitioners unlock the hidden structures of their models.

topological data analysis, deep learning↗

DiaMonD: An Integrated Multifaceted Approach to Mathematics at the Interfaces of Data, Models, and Decisions

DiaMonD is a multi-institutional DOE MMICC effort that aims to address the challenges of end-to-end, data-to-decisions modeling and simulation for complex computational science and engineering problems in a unified, systematic, and integrated fashion. Institutions involved are Colorado State, Florida State, Los Alamos, MIT, Oak Ridge, Stanford, and UT-Austin. The goals of DiaMonD are (1) to develop advanced mathematical methods and analysis for multimodel, multiphysics, multiscale model problems driven by frontier DOE applications, including those in subsurface energy and environmental flows, materials for energy storage and conversion, and ice sheet dynamics; (2) to create theory and algorithms for integrated inversion, optimization, and uncertainty quantification for these complex problems; and (3) to disseminate the philosophy of an integrated end-to-end, data-to-decisions approach to modeling and simulation of complex problems to the broader applied math and computational science communities through workshops and other outreach.

42 ENGINEERING↗

Advanced Fuel Cycle Cost Basis Report: Supporting Documents 3 Cost Correlations

This chapter provides an overview of the drivers for developing correlation coefficients, status on efforts to develop partial correlation coefficients, and recommended next steps. Mathematical methods for developing and using correlation coefficients were previously documented by the FCO EWG in Chapters 6 and 7 of [Ganda 2014].

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Applications of Fuzzy Logic for Tritium Sensing Technology

Fuzzy Logic is a mathematical method that can represent human-like decisions by analyzing vagueness. The project is a practical approach for evaluating sensors using a fuzzy group best-worst method. Results What is the best sensor? The fuzzy logic methods give an answer to that through a selection system. The relationship between the inputs and the outputs gives consumers an understanding of how the best sensor was found through a scoring of each quality/criteria and their corresponding sub-criteria through expert opinion.

Holman, Allyson↗

The Local Topological Free Energy of the SARS-CoV-2 Spike Protein

The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its Spike protein. Understanding protein rearrangement and identifying specific amino acids where mutations affect protein rearrangement has attracted much attention for drug development. In this manuscript, we use a mathematical method to characterize the local topology/geometry of the SARS-CoV-2 Spike protein backbone. Our results show that local conformational changes in the FP, HR1, and CH domains are associated with global conformational changes in the RBD domain. The SARS-CoV-2 variants analyzed in this manuscript (alpha, beta, gamma, delta Mink, G614, N501) show differences in the local conformations of the FP, HR1, and CH domains as well. Finally, most mutations of concern are either in or in the vicinity of high local topological free energy conformations, suggesting that high local topological free energy conformations could be targets for mutations with significant impact of protein function. Namely, the residues 484, 570, 614, 796, and 969, which are present in variants of concern and are targeted as important in protein function, are predicted as such from our model.

60 APPLIED LIFE SCIENCES↗

Mapping Local Dissipation and Entropy Production in Complex and Active Fluids

While global entropy production provides a measure of irreversibility, its partitioning into contributions from local regions is key to understanding the mechanisms underlying time-reversal symmetry breaking in complex systems and active matter. Here, by analyzing local heat flows and fluxes, we propose a framework that enables the mapping of local dissipation and entropy production in a nonequilibrium system. We test this approach in simulations of fluids driven through complex environments and active systems. We connect the results across the local and global scales by showing that local dissipation and entropy production satisfy a local version of the usual (global) fluctuation theorem, which accounts for the correlations between the local region and its surroundings. Interestingly, in the case of the active fluid, our analysis reveals that these correlations are of opposite signs for the active (stochastic) and passive (deterministic) contributions to local dissipation.

Entropy↗

Emulating Quantum Entangled Biphoton Spectroscopy Using Classical Light Pulses

We show that for a class of quantum light spectroscopy (QLS) experiments using n = 0, 1, 2, ··· classical light pulses and an entangled photon pair (a biphoton state) where one photon acts as a reference without interacting with the matter sample, identical signals can be obtained by replacing the biphotons with classical-like coherent states of light, where these are defined explicitly in terms of the parameters of the biphoton states. An input-output formulation of quantum nonlinear spectroscopy is used to prove this equivalence. We demonstrate the equivalence numerically by comparing a classical pump–quantum probe experiment with the corresponding classical pump–classical probe experiment. This analysis shows that understanding the equivalence between entangled biphoton probes and carefully designed classical-like coherent state probes leads to quantum-inspired classical experiments that yield equivalent signals and provides insights for the future design of QLS experiments that could provide a true quantum advantage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluating the Importance of Conformers for Understanding the Vacuum-Ultraviolet Spectra of Oxiranes: Experiment and Theory

Vacuum-ultraviolet (VUV) absorption spectroscopy enables electronic transitions that offer the unambiguous identification of molecules. As target molecules become more complex, multifunctional species present a great challenge to both experimental and computational spectroscopy. This research reports both experimental and theoretical studies of oxiranes. Computationally, the nuclear ensemble approach has been used to accurately predict experimental spectra for a variety of molecules. However, this approach incurs great computational cost, as ensembles generally consist of thousands of geometries. The present study aims to drastically reduce the ensemble by evaluating the significance of the conformers to the predicted spectra. This approach was applied to 11 substituted oxiranes using the Conformer Rotamer Ensemble Sampling Tool (CREST) of Grimme to generate an ensemble of unique conformers determined by their Boltzmann populations. Five TD-DFT functionals (BMK, CAM-B3LYP, M06-2X, MN15, ωB97X-D) and EOM-CCSD were used to simulate the spectrum of each substituted oxirane ensemble. Computed spectra were then compared to the experiment using both qualitative and quantitative metrics. Based on these metrics, it was observed that certain conformers may not be necessary to characterize this set of oxiranes despite the temperature (323 K) of the experiment. A single conformer can then be used with TD-DFT and EOM-CCSD to replicate the experimental spectra of these medium-sized combustion species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗

Implementation of Genetic Algorithms to Optimize Metal–Organic Frameworks for CO 2 Capture

Metal-organic frameworks (MOFs) are promising materials for CO 2 capture with the potential to use less energy than current industrial CO 2 capture methods. MOFs are highly versatile sorbents, and there is an almost unlimited number of MOFs that could be synthesized. In this work, we used a genetic algorithm (GA) and grand canonical Monte Carlo (GCMC) simulations to efficiently search for high-performing MOFs for CO 2 capture. We analyzed the effects of important GA parameters, including the mutation probability, the number of MOFs per generation and the number of GA generations, on the GA performance. Here, we performed GCMC simulations on-the-fly during the GA procedure to determine the performance of proposed MOFs and optimized their structures using multiple objective functions across different topologies. The GA was able to determine top-performing MOFs balancing CO 2 selectivity versus working capacity and reduced the cost of molecular simulations by a factor of 25 versus brute-force screening of an entire database of structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Subnanometer Thick Native sp 2 Carbon on Oxidized Diamond Surfaces

Oxygen-terminated diamond has a wide breadth of applications, which include stabilizing near-surface color centers, semiconductor devices, and biological sensors. Despite the vast literature on characterizing functionalization groups on diamond, the chemical composition of the shallowest portion of the surface (<1 nm) is challenging to probe with conventional techniques like XPS and FTIR. In this work, we demonstrate the use of angleresolved XPS to probe the first ten nanometers of both oxygen and hydrogen terminated (100) single-crystalline diamond grown via chemical vapor deposition (CVD). With the use of consistent peakfitting methods, the peak identities and relative peak binding energies were identified for sp 2 carbon, ether, hydroxyl, carbonyl, and C−H groups for both of these diamond surface terminations. For the oxygen-terminated sample, we also quantified the thickness of the sp 2 carbon layer situated on top of the bulk sp 3 diamond bonded carbon to be 0.3 ± 0.1 nm, based on the analysis of the Auger electron spectra and D-parameter calculations. These results indicate that the majority of the oxygen is bonded to the sp 2 carbon layer on the diamond, and not directly to the sp 3 diamond bonded carbon.

Carbon↗

Elucidating Cycling Rate-Dependent Electrochemical Strains in Sodium Iron Phosphate Cathodes for Na-ion Batteries

Battery electrodes materials undergo significant mechanical instabilities which affects their longevity and exert rate-limitations during the cycling process. In this study, we investigate the rate-dependent mechanical response of sodium iron phosphate (NaFePO4, NFP) cathodes during Na intercalation via galvanostatic cycling at different rates by employing digital image correlation, electrochemical methods, and mathematical model. The mechanical behaviour of the electrode shows strong dependance on the applied scan rate. At slower rates, electrode shows asymmetrical strain generation between anodic and cathodic cycles, which is attributed to the formation of cathode-electrolyte interface layers. The electrode undergoes smaller strain generation when cycled at slower rates when the same amount of Na ions is removed or inserted into the electrode. A mathematical model was developed to predict strain evolution in the composite electrode as well as the concentration profile of the Na ions in the electrode particles. Rate-dependent and time dependent factors on the strain generation in the electrode are attributed to the capacity-dependent intercalation strains, rate-dependent mismatch strains, and time-dependent irreversible strains. The combination of in situ strain measurements with the analytical model provided new insight into the electrochemically induced mechanical deformations in Na-ion cathode electrodes.

Ozdogru, Bertan↗

Mathematical Models and Numerical Methods for High-Fidelity Simulation of Ignition of Reactive Mixtures by Nanosecond Plasma Discharges in Realistic Configurations

We present a newly developed framework for the numerical simulation of ignition of reactive mixtures using single or repeated nanosecond discharge pulses. The framework builds upon the AMReX library, using the existing compressible solver PeleC and low-Mach solver PeleLMeX and allowing for adaptive mesh refinement, complex geometries, and execution on next-generation high-performance computing (HPC) systems. High-fidelity elementary models are adopted for weakly-ionised plasma discharges with significant energy deposition, consistent with nanosecond discharge pulses, and then implemented in the solver. The treatment of non-thermal electrons and charged species, thermodynamics of non-equilbrium species, plasma kinetics, limiting time scales, and boundary conditions for charged species are discussed and addressed for computational efficiency. The framework is demonstrated for three relevant applications: single and multi-pulse discharges in air, single pulse ignition of an ethylene/air mixture, and a three-dimensional plasma discharge in air with temperature stratification. The successful application of the framework demonstrates the feasibility of high-fidelity simulation of ignition of air/hydrocarbon mixtures in three-dimensions with multiple discharge pulses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗