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Sweep-tracing algorithm: in silico slip crystallography and tension-compression asymmetry in BCC metals
Abstract Direct Molecular Dynamics (MD) simulations are being increasingly employed to model dislocation-mediated crystal plasticity with atomic resolution. Thanks to the dislocation extraction algorithm (DXA), dislocation lines can be now accurately detected and positioned in space and their Burgers vector unambiguously identified in silico, while the simulation is being performed. However, DXA extracts static snapshots of dislocation configurations that by themselves present no information on dislocation motion. Referred to as a sweep-tracing algorithm (STA), here we introduce a practical computational method to observe dislocation motion and to accurately quantify its important characteristics such as preferential slip planes (slip crystallography). STA reconnects pairs of successive snapshots extracted by DXA and computes elementary slip facets thus precisely tracing the motion of dislocation segments from one snapshot to the next. As a testbed for our new method, we apply STA to the analysis of dislocation motion in large-scale MD simulations of single crystal plasticity in BCC metals. We observe that, when the crystal is subjected to uniaxial deformation along its [001] axis, dislocation slip predominantly occurs on the {112} maximum resolved shear stress plane under tension, while in compression slip is non-crystallographic (pencil) resulting in asymmetric mechanical response. The marked contrast in the observed slip crystallography is attributed to the twinning/anti-twinning asymmetry of shears in the {112} planes relatively favoring dislocation motion in the twinning sense while hindering dislocations from moving in the anti-twinning directions.
Satellite Image Algorithms
Presented by Conner Hatton at SIAM UQ Conference in Trieste, Italy, on February 27th, 2024. Conference details available online at https://www.siam.org/conferences/cm/conference/uq24
Toward In Situ Synchrotron Mapping of Crystal Selection Processes during Crystal Growth
In this work, we present an automated and rapid method for non-destructive mapping of crystal grains in a rod-shaped sample. The approach was designed for application to in situ float-zone crystal growth experiments at an x-ray synchrotron source, but could be useful in other applications. The methods have been tested on a TiO 2 boule grown in an optical float zone furnace. The approach applies a statistical filter to polycrystalline diffraction patterns on 2D detectors to rapidly determine the degree of powder-quality 1of the signal. When larger crystals emerge in the growth, their position, size and shape can be tracked using an automated blob-tracking algorithm that follows individual Bragg peaks as a function of position in a grid-scan, even when multiple crystals are contributing spots to diffraction images. This method is found to be robust as the same crystal shape can be independently reconstructed using different sets of Bragg reflections. Image segmentation methods are then used to map out the polycrystalline grains. We also note that other information about crystal quality, such as mosaicity or strain state, may be inferred and mapped from the intensity variation of the Bragg peaks at different locations within the sample.
Aerial 3D Building Reconstruction from Drone Imagery (A3DBR) v1
This toolkit is composed of several modules for extracting buildings geometrical and thermal characteristics from RGB and thermal imagery captured using a drone. - Building 3D reconstruction module: leverage a photogrammetry software to construct a 3D point cloud from RGB drone imagery, which is then used in conjunction with image processing and geometric methods to extract building footprint and building height (i.e., 3D model of the building). - Windows to wall ratio estimation module: leverage deep learning semantic segmentation modeling to detect windows on 2D drone RGB images. The detected windows are then projected onto the extracted building 3D model (using building 3D reconstruction module) and their area is computed to obtain window to wall ratio estimation. - Thermal anomalies detection module: leverage image processing and machine learning algorithm to detect on 2D drone thermal images potential thermal anomalies within building's facades and roofs.
Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features
Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.
Mappymatch FKA: YAMM (Yet Another Map-Matcher) [SWR 22-38]
A surprisingly non-trivial technical challenge is to associate points in space (e.g., GPS data) with specific segments of a road network or map. The software package ( allows users to match GPS point data to a road network (commonly known as "map matching"). The software is designed such that a user could match a set of GPS points to a variety of different road network representations using a variety of map matching algorithms. There are currently several "built-in" road networks and map matching algorithms but the software has been designed to enable new ones to be added with minimal overhead.
Algorithm to extract direction in 2D discrete distributions and a continuous Frobenius norm
In this study, we present a novel algorithm for determining directionality in 2D distributions of discrete data. We compare a reference dataset with a known direction to a measured dataset with an unknown direction by the Frobenius norm of the difference (FND) to find the unknown direction. To generalize this concept, we develop a continuous Frobenius norm of the difference (CFND) as a continuous analog of the FND and derive its analytical expression. By relating fitted and normalized 2D Gaussian distributions, we show that the CFND approximates the FND, and we validate this relationship with computer simulations. We find that a first-order approximation of the CFND between two similar Gaussian distributions takes the form of an absolute sine function, offering a simple analytical form with potential applications in specialized areas such as segmented inverse beta decay neutrino detectors, astronomy, machine learning, and more. Our methodology consists of modeling a 2D Gaussian distribution, binning the data into a histogram, and encoding it as a square matrix. Rotating this matrix around its geometric center and comparing it to a measured dataset using the FND gives us rotational data that we fit with an absolute sine function. The location of the minimum of this fit is the angle closest to the true angle of the direction in the measured dataset. We present the derivation and discuss initial applications of the CFND in our novel algorithm, demonstrating its success in approximating directionality in 2D distributions.
Neutrino Physics with Deep Learning on NOvA
The NOvA experiment has made both νμ \nu_\mu disappearance and νe \nu_e appearance measurements in Fermilab's NuMI beam, and is working on cross section measurements using near detector data. At the core of NOvA's measurements is the use of deep learning algorithms for identification and reconstruction of the neutrino flavor and energy. These algorithms, used for the first time on NOvA in 2016, yielded large improvements in selection efficiency, and will be applied to our first anti-neutrino results to be released this year. Presented here is the extension of our deep learning efforts for identification of neutrino signal events, final state identification, single particle tagging, and reconstruction using instance segmentation techniques. We will describe the new implementations of modified Convolutional Neural Networks for anti-neutrino events, single particles and their performance for analysis final states selection, standard candle measurements, and reconstruction.
Exploring Physics of Ferroelectric Domain Walls in Real Time: Deep Learning Enabled Scanning Probe Microscopy
The functionality of ferroelastic domain walls in ferroelectric materials is explored in real-time via the in situ implementation of computer vision algorithms in scanning probe microscopy (SPM) experiment. The robust deep convolutional neural network (DCNN) is implemented based on a deep residual learning framework (Res) and holistically nested edge detection (Hed), and ensembled to minimize the out-of-distribution drift effects. The DCNN is implemented for real-time operations on SPM, converting the data stream into the semantically segmented image of domain walls and the corresponding uncertainty. Further the pre-defined experimental workflows perform piezoresponse spectroscopy measurement on thus discovered domain walls, and alternating high- and low-polarization dynamic (out-of-plane) ferroelastic domain walls in a PbTiO 3 (PTO) thin film and high polarization dynamic (out-of-plane) at short ferroelastic walls (compared with long ferroelastic walls) in a lead zirconate titanate (PZT) thin film is reported. This work establishes the framework for real-time DCNN analysis of data streams in scanning probe and other microscopies and highlights the role of out-of-distribution effects and strategies to ameliorate them in real time analytics.
Jacobian-scaled K-means clustering for physics-informed segmentation of reacting flows
This work introduces Jacobian-scaled K-means (JSK-means) clustering, which is a physicsinformed clustering strategy centered on the K-means framework. The method allows for the injection of underlying physical knowledge into the clustering procedure through a distance function modification: instead of leveraging conventional Euclidean distance vectors, the JSKmeans procedure operates on distance vectors scaled by matrices obtained from dynamical system Jacobians evaluated at the cluster centroids. The goal of this work is to show how the JSKmeans algorithm - without modifying the input dataset - produces clusters that capture regions of dynamical similarity, in that the clusters are redistributed towards high-sensitivity regions in phase space and are described by similarity in the source terms of samples instead of the samples themselves. The algorithm is demonstrated on a complex reacting flow simulation dataset (a channel detonation configuration), where the dynamics in the thermochemical composition space are known through the highly nonlinear and stiff Arrhenius-based chemical source terms. Interpretations of cluster partitions in both physical space and composition space reveal how JSK-means shifts clusters produced by standard K-means towards regions of high chemical sensitivity (e.g., towards regions of peak heat release rate near the detonation reaction zone). Furthermore, the findings presented here illustrate the benefits of utilizing Jacobian-scaled distances in clustering techniques, and the JSK-means method in particular displays promising potential for improving former partition-based modeling strategies in reacting flow (and other multi-physics) applications.
From pixels to patterns: Coupling Optical Coherence Tomography and machine learning for monitoring coastal wetland root systems
Coastal wetlands are crucial in shoreline stabilization, carbon sequestration, and storm protection. Yet, due to limitations in traditional destructive sampling techniques, the belowground biomass (live root mass) and necromass (dead and decaying roots) remain difficult to assess in coastal wetlands, limiting our understanding on coastal resilience, nutrient cycling, and soil structure. This study employs Optical Coherence Tomography (OCT) as a high-resolution imaging technique to analyze root biomass and necromass in the Terrebonne Basin, Louisiana. A Random Forest (RF) model was developed to classify root health states based on OCT-derived features, achieving an accuracy of 70% in distinguishing live from dead root segments. The results demonstrate that OCT, combined with ML, offers a promising novel approach to root analysis, providing fine-scale insights into root morphology and decay patterns that are not easily captured by conventional methods. This research lays the foundation for future integration of OCT with complementary imaging modalities such as X-ray Computed Tomography (XCT) and advanced ML algorithms to enhance classification accuracy and scalability. Future work aims to expand the dataset diversity across different wetland types and apply the methodology for large-scale, repeatable assessments of root biomass turnover and accumulation, with important implications for wetland monitoring, conservation, and restoration under changing environmental conditions.
Infrared-Fused Vision-Based Thermoregulation Performance Estimation for Personal Thermal Comfort-Driven HVAC System Controls
Thermal comfort is one of the primary factors influencing occupant health, well-being, and productivity in buildings. Existing thermal comfort systems require occupants to frequently communicate their comfort vote via a survey which is impractical as a long-term solution. Here, we present a novel thermal infrared-fused computer vision sensing method to capture thermoregulation performance in a non-intrusive and non-invasive manner. In this method, we align thermal and visible images, detect facial segments (i.e., nose, eyes, face boundary), and accordingly read the temperatures from the appropriate coordinates in the thermal image. We focus on the human face since it is often clearly visible to cameras and is not merged into a hot background (unlike hands). We use a regularized Gaussian Mixture model to track the thermoregulation changes over time and apply a heuristic algorithm to extract hot and cold indices. We present a personalized and a generalized comfort modeling method, selected based on the availability of the occupant historical indices measurements in a neutral environment, and use the time-series of the hot and cold indices to define corrections to HVAC system operations in the form of setpoint constraints. To evaluate the efficacy of our proposed approach in responding to thermal stimuli, we designed a series of controlled experiments to simulate exposure to cold and hot environments. While applying personalized modeling showed an acceptable average accuracy of 91.3%, the generalized model’s average accuracy was only 65.2%. This shows the importance of having access to physiological records in modeling and assessing comfort. We also found that individual differences should be considered in selecting the cooling and heating rates when some knowledge of the occupant’s overall thermal preference is available.
Localized keyhole pore prediction during laser powder bed fusion via multimodal process monitoring and X-ray radiography
Systematic fault detection and control during laser powder bed fusion (L-PBF) has been a long-standing objective for system manufacturers and researchers in the additive manufacturing (AM) industry. This manuscript investigates a data fusion approach for detection of keyhole porosity formation during laser irradiation of Ti-6Al-4V substrates by concurrent recording of thermally induced optical emission measured using both off-axis and coaxial photodiode sensors, and acoustic emission. Subsurface defect formation was monitored via high-speed synchrotron X-ray imaging at 20,000 frames per second, enabling temporal registration of keyhole pore formation events to the monitoring signals at a resolution of 50 µs. We developed data fusion machine learning (ML) models for localized prediction of keyhole pore formation at various time scales ranging from 0.5 ms to 2 ms. The signal segments were featurized using two independent approaches: (1) power spectral density (PSD) and (2) highly comparative time series analysis (HCTSA) framework. The extracted features from different sensor modalities were fused together to construct a multimodal feature space and sequential feature selection was used to determine the most informative features for training the ML models. The predictive performance was evaluated for three classifying algorithms: Support Vector Machine (SVM), K-Nearest Neighbor (KNN), and Gaussian Naive Bayes (GNB). As a result, pore formation events were predicted with up to 0.95 F1-score, 1.0 recall and 0.94 accuracy. The most heavily weighted features indicate that model performance is chiefly governed by the acoustic monitoring signal, with a secondary contribution from the optical emission sensors.
Integrable symplectic maps with a polygon tessellation
Identifying integrable dynamics remains a formidable challenge, and despite centuries of research, only a handful of examples are known to date. In this article, we explore a distinct form of area-preserving (symplectic) mappings derived from the stroboscopic Poincaré cross section of a kicked rotator—an oscillator subjected to an external force periodically switched on in short pulses. The significance of this class of problems extends to various applications in physics and mathematics, including particle accelerators, crystallography, and studies of chaos. Notably, Suris's theorem constrains the integrability within this category of mappings, outlining potential scenarios with analytic invariants of motion. In this paper, we challenge the assumption of the analyticity of the invariant by exploring piecewise linear transformations on a torus ( T 2 ) and associated systems on the plane ( R 2 ), incorporating arithmetic quasiperiodicity and discontinuities. Introducing a new automated technique, we discovered previously unknown scenarios featuring polygonal invariants that form perfect tessellations and, moreover, fibrations of the plane or torus. This work reveals a novel category of planar tilings characterized by discrete symmetries that emerge from the invertibility of transformations and are intrinsically linked to the presence of integrability. Our algorithm relies on the analysis of the Poincaré rotation number and its piecewise monotonic nature for integrable cases, contrasting with the noisy behavior in the case of chaos, thereby allowing for clear separation. Some of the newly discovered systems exhibit the peculiar behavior of “integrable diffusion,” characterized by infinite and quasirandom hopping between tiles while being confined to a set of invariant segments. Finally, through the implementation of a smoothening procedure, all mappings can be generalized to quasi-integrable scenarios with suppressed volume occupied by chaotic trajectories, thereby opening doors to potential practical applications. Published by the American Physical Society 2024
Algorithm to extract direction in 2D discrete distributions and a continuous Frobenius norm
In this study, we present a novel algorithm for determining directionality in 2D distributions of discrete data. We compare a reference dataset with a known direction to a measured dataset with an unknown direction by the Frobenius norm of the difference (FND) to find the unknown direction. To generalize this concept, we develop a continuous Frobenius norm of the difference (CFND) as a continuous analog of the FND and derive its analytical expression. By relating fitted and normalized 2D Gaussian distributions, we show that the CFND approximates the FND, and we validate this relationship with computer simulations. We find that a first-order approximation of the CFND between two similar Gaussian distributions takes the form of an absolute sine function, offering a simple analytical form with potential for specialized applications in segmented inverse beta decay (IBD) neutrino detectors, astronomy, machine learning, and more. Although this method may easily extend to 3D scalar fields, our focus here is on 2D real-valued fields as it directly applies to directionality. Our methodology consists of modeling a 2D Gaussian distribution, binning the data into a histogram, and encoding it as a square matrix. Rotating this matrix around its geometric center and comparing it to a measured dataset using the FND gives us rotational data that we fit with an absolute sine function. The location of the minimum of this fit is the angle closest to the true angle of the direction in the measured dataset. We present the derivation and discuss initial applications of the CFND in our novel algorithm, demonstrating its success in approximating directionality in 2D distributions.
A Virtual Space Vector Model Predictive Control for a Seven-Level Hybrid Multilevel Converter
This paper proposes a virtual space vector (VSV) model predictive control (MPC) for a three-phase seven-level (7L) hybrid multilevel converter (HMC), where each phase consists of an active-neutral-point-clamped converter with a floating H-bridge. To achieve the best current tracking, which is the primary goal of the proposed algorithm, a novel geometrical positioning approach is proposed to select the optimal voltage vector among all the realspace vectors and VSVs. Then, all the possible switching sequences that belong to the optimal voltage vector are evaluated to realize the dc capacitor voltage balancing and common-mode voltage reduction. Through an external modulator, the optimal voltage vector can be synthesized by using either one-, three-, or seven-segment switching sequence. Compared with the conventional MPC, the proposed VSV-MPC can reduce not only the computational burden but also the current THD. Both simulation and experimental results obtained on silicon carbide based 7L-HMC prototype are presented to validate the feasibility and effectiveness of the proposed VSVMPC strategy.
Electromagnetic Shower Reconstruction and Identification in FASER's Emulsion Detector for LHC Forward Neutrino Measurements
We present methods for electromagnetic shower reconstruction and identification in the FASERnu emulsion detector using 100 GeV and 200 GeV electron test-beam data from the CERN SPS H4 beamline. The reconstruction employs a clustering-based algorithm without energy-dependent tuning to determine shower axes. A multi-level identification chain comprising track pre-selection, a cut-based selection, and a BDT classifier achieves combined background rejection rates of 99.99% (100 GeV) and 99.94% (200 GeV). The method reaches total reconstruction and identification efficiencies of 58.9% (100 GeV) and 70.8% (200 GeV) evaluated from simulated samples. Energy reconstruction using the total number of reconstructed segments as the calorimetric estimator yields relative biases of +0.6% (100 GeV) and -0.8% (200 GeV), with resolutions of 25.4% and 22.6%, respectively. Systematic uncertainties on the energy reconstruction are dominated by variations in emulsion film detection efficiency, contributing (+10.9%/-8.2%) at 100 GeV and (+10.3%/-6.9%) at 200 GeV. The methodology provides a validated framework for electron neutrino identification with the FASERnu detector at the LHC.