Predicting Fluid Dynamics in Physical-informed Mesh-reduced Space
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Earth Sciences Applications for Energy and Global Security: A Few Vignettes [Slides]
Understanding the physics of flow and transport in the subsurface environment is crucial to several National Security applications. In the Energy Security realm, some examples include characterizing radioactive waste disposal, exploring natural gas extraction and sequestering CO2. An example in the Global Security arena is to be able to distinguish between anthropogenic and naturally occurring seismic disturbances, the former being of particular concern as underground nuclear testing activity has seen an increase in recent years. A common theme across these applications is the ability to accurately model fluid flow in porous and/or fractured subsurface media. For decades, researchers have grappled with how to include the effects of uncertainties in these models, including but not limited to heterogeneity, unknown initial and boundary conditions and issues with scalability. More recently advances in computing and machine learning methodologies have allowed a broader exploration of the uncertainty space as we strive for real time decision making. I will present an overview of the field and discuss a few examples of how my own research in these topics has evolved over nearly two decades.
58 GEOSCIENCES↗
Partitioning of Large-Scale Power Electronics-Based Power Systems for Small-Signal Stability Analysis
The nodal admittance matrix (NAM)-based approach is suitable for analyzing the small-signal stability of large-scale power electronics-based power systems (PEPSs) as it preserves the system structure by utilizing the admittance matrix. Previously, NAM-based area partition has been proposed, which divides the system into various subareas and interconnections for easier analysis of the low-dimension matrix compared to the entire system-based high-dimension matrix. However, no partition algorithm has been presented for the NAM-based area partition method. This paper focuses on implementing the spectral partitioning algorithm for partitioning large-scale PEPSs into a low-dimension matrix to reduce the computation complexity of the analysis. These spectral components facilitate data transformation into a new space, enabling the application of traditional clustering methods like k-means. To evaluate the performance of the partitioning method, the subareas and interconnections obtained from the spectral clustering algorithm are incorporated into the NAM-based area partition method for a large system with 140 buses. The computational times of the original method, where the NAM-based criterion is directly applied to the entire system, are compared with those of the NAM-based partition method in MATLAB. PSCAD simulations of the whole system and the obtained subareas are conducted to validate the effectiveness of the proposed algorithm.
Nupur, Nupur↗
Exploring Gradient-Based Multi-directional Controls in GANs
Generative Adversarial Networks (GANs) have been widely applied in modeling diverse image distributions. However, despite its impressive applications, the structure of the latent space in GANs largely remains as a black-box, leaving its controllable generation an open problem, especially when spurious correlations between different semantic attributes exist in the image distributions. To address this problem, previous methods typically learn linear directions or individual channels that control semantic attributes in the image space. However, they often suffer from imperfect disentanglement, or are unable to obtain multi-directional controls. Furthermore, in this work, in light of the above challenges, we propose a novel approach that discovers nonlinear controls, which enables multi-directional manipulation as well as effective disentanglement, based on gradient information in the learned GAN latent space. More specifically, we first learn interpolation directions by following the gradients from classification networks trained separately on the attributes, and then navigate the latent space by exclusively controlling channels activated for the target attribute in the learned directions. Empirically, with small training data, our approach is able to gain fine-grained controls over a diverse set of bi-directional and multi-directional attributes, and we showcase its ability to achieve disentanglement significantly better than state-of-the-art methods both qualitatively and quantitatively.
97 MATHEMATICS AND COMPUTING↗
Unstructured global to coastal wave modeling for the Energy Exascale Earth System Model using WAVEWATCH III version 6.07
Wind-wave processes have generally been excluded from coupled Earth system models due to the high computational expense of spectral wave models, which resolve a frequency and direction spectrum of waves across space and time. Existing uniform-resolution wave modeling approaches used in Earth system models cannot appropriately represent wave climates from global to coastal ocean scales, largely because of tradeoffs between coastal resolution and computational costs. To resolve this challenge, we introduce a global unstructured mesh capability for the WAVEWATCH III (WW3) model that is suitable for coupling within the US Department of Energy's Energy Exascale Earth System Model (E3SM). The new unstructured WW3 global wave modeling approach can provide the accuracy of higher global resolutions in coastal areas at the relative cost of lower uniform global resolutions. This new capability enables simulation of waves at physically relevant scales as needed for coastal applications.
58 GEOSCIENCES↗
Exotic phases in finite-density ℤ 3 theories
Lattice ℤ 3 theories with complex actions share many key features with finite- density QCD including a sign problem and $\mathcal{CK}$ symmetry. Complex ℤ 3 spin and gauge models exhibit a generalized Kramers-Wannier duality mapping them onto chiral ℤ 3 spin and gauge models, which are simulatable with standard lattice methods in large regions of parameter space. The Migdal-Kadanoff real-space renormalization group (RG) preserves this duality, and we use it to compute the approximate phase diagram of both spin and gauge ℤ 3 models in dimensions one through four. Chiral ℤ 3 spin models are known to exhibit a Devil’s Flower phase structure, with inhomogeneous phases that can be thought of as ℤ 3 analogues of chiral spirals. Out of the large class of models we study, we find that only chiral spin models and their duals have a Devil’s Flower structure with an infinite set of inhomogeneous phases, a result we attribute to Elitzur’s theorem. We also find that different forms of the Migdal-Kadanoff RG produce different numbers of phases, a violation of the expectation for universal behavior from a real-space RG. We discuss extensions of our work to ℤ N models, SU(N) models and nonzero temperature.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Assessment of Mechanical Draft Cooling Tower Thermal Emissions from Visual Images of Plumes
Using a one-dimensional code, we computed the power (enthalpy discharge rate) of a twelve-cell mechanical draft cooling tower (MDCT) using over two hundred visible condensed water vapor plume volume measurements derived from images, weather data, and tower operating conditions. The plume images were simultaneously captured by multiple stationary digital cameras surrounding the cooling tower. An analysis technique combining structure from motion (SfM), a neural-network-based image segmentation algorithm, and space carving was used to quantify the volumes. Afterwards, the power output was computed using novel techniques in the one-dimensional code that included cooling tower exhaust plume adjacency effects implemented with a modified version of the entrainment function, weather data averaged from eleven stations, and fan operations at the times when plume volumes were measured. The model was then compared with the averaged observed power output, and it validated well with an average error ranging from 6 to 12%, depending on the meteorological data used in the simulations. This methodology can possibly determine power plant fuel consumption rates by applying visible imagery.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
GFCCLib: Scalable and efficient coupled-cluster Green's function library for accurately tackling many-body electronic structure problems
Coupled-cluster Green’s function (GFCC) calculation has drawn much attention in the recent years for targeting the molecular and material electronic structure problems from a many-body perspective in a systematically improvable way. However, GFCC calculations on scientific computing clusters usually suffer from expensive higher di- mensional tensor contractions in the complex space, expensive inter-process communi- cation, and severe load imbalance, which limits it’s routine use for tackling electronic structure problems. Here we present a numerical library prototype that is specifically designed for large-scale GFCC calculations. The design of the library is focused on a systematically optimal computing strategy to improve its scalability and efficiency. The performance of the library is demonstrated by the relevant profiling analysis of running GFCC calculations on remote giant computing clusters. The capability of the library is highlighted by computing a wide near valence band of a fullerene C60 molecule for the first time at the GFCCSD level that shows excellent agreement with the experimental spectrum.
Peng, Bo↗
A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop
The folding and unfolding of RNA stem-loops are critical biological processes; however, their computational studies are often hampered by the ruggedness of their folding landscape, necessitating long simulation times at the atomistic scale. Here, we adapted DeepDriveMD (DDMD), an advanced deep learning-driven sampling technique originally developed for protein folding, to address the challenges of RNA stem-loop folding. Although tempering- and order parameter-based techniques are commonly used for similar rare-event problems, the computational costs or the need for a priori knowledge about the system often present a challenge in their effective use. DDMD overcomes these challenges by adaptively learning from an ensemble of running MD simulations using generic contact maps as the raw input. DeepDriveMD enables on-the-fly learning of a low-dimensional latent representation and guides the simulation toward the undersampled regions while optimizing the resources to explore the relevant parts of the phase space. We showed that DDMD estimates the free energy landscape of the RNA stem-loop reasonably well at room temperature. Our simulation framework runs at a constant temperature without external biasing potential, hence preserving the information on transition rates, with a computational cost much lower than that of the simulations performed with external biasing potentials. Here, we also introduced a reweighting strategy for obtaining unbiased free energy surfaces and presented a qualitative analysis of the latent space. This analysis showed that the latent space captures the relevant slow degrees of freedom for the RNA folding problem of interest. Finally, throughout the manuscript, we outlined how different parameters are selected and optimized to adapt DDMD for this system. We believe this compendium of decision-making processes will help new users adapt this technique for the rare-event sampling problems of their interest.
Gupta, Ayush↗
Real-time dynamics of the Schwinger model as an open quantum system with Neural Density Operators
Ab-initio simulations of multiple heavy quarks propagating in a Quark-Gluon Plasma are computationally difficult to perform due to the large dimension of the space of density matrices. This work develops machine learning algorithms to overcome this difficulty by approximating exact quantum states with neural network parametrisations, specifically Neural Density Operators. As a proof of principle demonstration in a QCD-like theory, the approach is applied to solve the Lindblad master equation in the 1 + 1d lattice Schwinger Model as an open quantum system. Neural Density Operators enable the study of in-medium dynamics on large lattice volumes, where multiple-string interactions and their effects on string-breaking and recombination phenomena can be studied. Thermal properties of the system at equilibrium can also be probed with these methods by variationally constructing the steady state of the Lindblad master equation. Scaling of this approach with system size is studied, and numerical demonstrations on up to 32 spatial lattice sites and with up to 3 interacting strings are performed.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Theoretical modeling of a bottom-raised oscillating surge wave energy converter structural loadings and power performances
Here, this study presents theoretical formulations to evaluate the fundamental parameters and performance characteristics of a bottom-raised oscillating surge wave energy converter (OSWEC) device. Employing a flat plate assumption and potential flow formulation in elliptical coordinates, closed-form equations for the added mass, radiation damping, and excitation forces/torques in the relevant pitch-pitch and surge-pitch directions of motion are developed and used to calculate the system's response amplitude operator and the forces and moments acting on the foundation. The model is benchmarked against numerical simulations using WAMIT and WEC-Sim, showcasing excellent agreement. The sensitivity of plate thickness on the analytical hydrodynamic solutions is investigated over several thickness-to-width ratios ranging from 1:80 to 1:10. The results show that as the thickness of the benchmark OSWEC increases, the deviation of the analytical hydrodynamic coefficients from the numerical solutions grows from 3% to 25%. Differences in the excitation forces and torques, however, are contained within 12%. While the flat plate assumption is a limitation of the proposed analytical model, the error is within a reasonable margin for use in the design space exploration phase before a higher-fidelity (and thus more computationally expensive) model is employed. A parametric study demonstrates the ability of the analytical model to quickly sweep over a domain of OSWEC dimensions, illustrating the analytical model's utility in the early phases of design.
13 HYDRO ENERGY↗
Evolutionary multi-objective optimization and Pareto-frontal uncertainty quantification of interatomic forcefields for thermal conductivity simulations
Predictive Molecular Dynamics simulations of thermal transport require forcefields that can simultaneously reproduce several structural, thermodynamic and vibrational properties of materials like lattice constants, phonon density of states, and specific heat. This requires a multi-objective optimization approach for forcefield parameterization. Existing methodologies for forcefield parameterization use ad-hoc and empirical weighting schemes to convert this into a single-objective optimization problem. Here, we provide and describe software to perform multi-objective optimization of Stillinger–Weber forcefields (SWFF) for two-dimensional layered materials using the recently developed 3rd generation non-dominated sorting genetic algorithm (NSGA-III). NSGA-III converges to the set of optimal forcefields lying on the Pareto front in the multi-dimensional objective space. This set of forcefields is used for uncertainty quantification of computed thermal conductivity due to variability in the forcefield parameters. We demonstrate this new optimization scheme by constructing a SWFF for a representative two-dimensional material, 2H-MoSe 2 and quantifying the uncertainty in their computed thermal conductivity.
97 MATHEMATICS AND COMPUTING↗
Extensively Microtwinned Diamond with Nanolaminates of Lonsdaleite Formed by Flash Laser Heating of Glassy Carbon
Diamond’s unique properties on the nanoscale make it one of the most important materials for use in biosensors and quantum computing and for components that can withstand the harsh environments of space. We synthesize oriented, faceted diamond particles by flash laser heating of glassy carbon at 16 GPa and 2300 K. Detailed transmission electron microscopy shows them to consist of a mosaic of diamond nanocrystals frequently joined at twin boundaries forming microtwins. Striking 3-fold translational periodicity was observed in both imaging and diffraction. This periodicity was shown to originate from nanodimensional wedge-shaped overlapping regions of twinned diamond and not from a possible 9R polytype, which has also been reported in other group IVa elements and water ice. Extended bilayers of hexagonal layer stacking were observed, forming lonsdaleite nanolaminates. In conclusion, the particles exhibited optical fluorescence with a rapid quench time (<1 ns) attributed to their unique twinned microstructure.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase
Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.
archaea↗
From calibration to parameter learning: Harnessing the scaling effects of big data in geoscientific modeling
Abstract The behaviors and skills of models in many geosciences (e.g., hydrology and ecosystem sciences) strongly depend on spatially-varying parameters that need calibration. A well-calibrated model can reasonably propagate information from observations to unobserved variables via model physics, but traditional calibration is highly inefficient and results in non-unique solutions. Here we propose a novel differentiable parameter learning (dPL) framework that efficiently learns a global mapping between inputs (and optionally responses) and parameters. Crucially, dPL exhibits beneficial scaling curves not previously demonstrated to geoscientists: as training data increases, dPL achieves better performance, more physical coherence, and better generalizability (across space and uncalibrated variables), all with orders-of-magnitude lower computational cost. We demonstrate examples that learned from soil moisture and streamflow, where dPL drastically outperformed existing evolutionary and regionalization methods, or required only ~12.5% of the training data to achieve similar performance. The generic scheme promotes the integration of deep learning and process-based models, without mandating reimplementation.
54 ENVIRONMENTAL SCIENCES↗
Dissociative electron attachment to 5-bromo-uracil: non-adiabatic dynamics on complex-valued potential energy surfaces
Electron induced dissociation reactions are relevant to many fields, ranging from prebiotic chemistry to cancer treatments. However, the simulation of dissociation electron attachment (DEA) dynamics is very challenging because the auto-ionization widths of the transient negative ions must be accounted for. We propose an adaptation of the ab initio multiple spawning (AIMS) method for complex-valued potential energy surfaces, along the lines of recent developments based on surface hopping dynamics. Our approach combines models for the energy dependence of the auto-ionization widths, obtained from scattering calculations, with survival probabilities computed for the trajectory basis functions employed in the AIMS dynamics. The method is applied to simulate the DEA dynamics of 5-bromouracil in full dimensionality, i.e., taking all the vibrational modes into consideration. The propagation starts on the $π_{2}^{*}$ resonance state and describes the formation of Br - anions mediated by non-adiabatic couplings. The potential energies, gradients and non-adiabatic couplings were computed with the fractional-occupancy molecular orbital complete-active-space configuration-interaction method, and the calculated DEA cross section are consistent with the observed DEA intensities.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Model independent dark matter properties from cosmic growth
Dark matter dominates the matter budget of the universe but its nature is unknown. Deviations from the standard model, where dark matter clusters with the same gravitational strength as baryons, and has the same pressureless equation of state as baryons, can be tested by cosmic growth measurements. We take a model independent approach, allowing deviations in bins of redshift, and compute the constraints enabled by ongoing cosmic structure surveys through redshift space distortions and peculiar velocities. These can produce constraints at the 3-14% level in four independent redshift bins over z = [0,4].
79 ASTRONOMY AND ASTROPHYSICS↗
Data-driven profile prediction for DIII-D
A new, fully data-driven algorithm has been developed that uses neural networks to predict plasma pro les on a scale of τ E into the future given actuators and the present plasma state. The model was trained and tested on DIII-D data from the 2013-2018 experimental campaigns. The model is accurate on average, with q predictions the worst and pressure predictions the best. The model can run in milliseconds and is very simple to use. This makes it a potentially useful tool for operators and physicists when planning plasma scenarios. It also is a candidate for doing phase-space exploration without going through the DIIID database or complicated and computationally expensive simulation codes. Here, a reduced model using only realtime diagnostics has also been developed and formed the basis for a model-predictive control algorithm implemented and successfully tested on DIII-D.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗