arXiv subjects

Mathew Cherukara

Publications and source records attributed to Mathew Cherukara.

14 recordsLinked to original sources

arXiv2026

An End-to-End Differentiable Forward Model for High-Energy Diffraction Microscopy

High-Energy Diffraction Microscopy (HEDM) recovers crystallographic orientation, strain, and grain position from rotating-crystal X-ray diffraction patterns. Existing forward models in far-field (FF), near-field (NF), and point-focused (pf) HEDM are not differentiable, which forecloses gradient-based joint parameter refinement, physics-informed regularisation, and Bayesian uncertainty quantification. We present the first end-to-end differentiable HEDM forward model covering all three geometries, implemented in PyTorch with pixel-exact agreement against the established MIDAS reference simulators (162/162 FF, 2304/2304 NF including a non-zero detector-tilt sweep, and 1088/1096 pf-HEDM spots matched). Three demonstrations validate the framework: joint orientation-strain-position recovery in NF-HEDM at ~6 nm precision; round-trip refinement on a real 214-grain alpha-Ti FF-HEDM dataset reaching 100% grain recovery from a 1.5 degree initial perturbation with residuals matching the production fit to 0.3%; and joint refinement of all per-detector geometry parameters and per-grain state on a synthetic four-panel FF-HEDM setup, recovering panel rotations about the beam axis to ~10 mu-rad and a global rotation-axis wedge to ~26 mu-rad. The framework is released as the open-source midas-diffract package (pip install midas-diffract).

cond-mat.mtrl-sci↗

arXiv2026

Materials Behavior as Mechanism Ensembles: A Probabilistic Framework for Emergent Behaviors

Materials behavior is often treated as a deterministic mapping from structure to properties, yet many important phenomena emerge from the conditional activation of multiple mechanisms across scales. This is especially evident in fatigue of metals, where crack growth is typically modeled as monotonic and irreversible process, despite evidence that local microstructure, loading history, and competing unit processes can shift the balance among propagation, arrest, and self-healing. Here we present a probabilistic framework that describes materials behavior as an ensemble of constituent mechanisms whose activation, interaction, and evolution determine emergent outcomes. The framework connects mechanism activation, state evolution, and macroscopic observables in a probabilistic way. In the case of fatigue crack propagation, it reframes damage tolerance as an inference problem over mechanism competition and provides a basis for integrating multiscale simulation, multimodal characterization, and machine learning. The same logic extends to other physical and chemical systems suggesting a portable framework for any system in which emergent behavior reflects mechanism competition under changing conditions. The broader ambition of this perspective review is a shift from correlating structure and performance after the fact to identifying, in advance, the conditions that make desired emergent behavior probable.

cond-mat.mtrl-sci↗

arXiv2025

Pty-Chi: A PyTorch-based modern ptychographic data analysis package

Ptychography has become an indispensable tool for high-resolution, non-destructive imaging using coherent light sources. The processing of ptychographic data critically depends on robust, efficient, and flexible computational reconstruction software. We introduce Pty-Chi, an open-source ptychographic reconstruction package built on PyTorch that unifies state-of-the-art analytical algorithms with automatic differentiation methods. Pty-Chi provides a comprehensive suite of reconstruction algorithms while supporting advanced experimental parameter corrections such as orthogonal probe relaxation and multislice modeling. Leveraging PyTorch as the computational backend ensures vendor-agnostic GPU acceleration, multi-device parallelization, and seamless access to modern optimizers. An object-oriented, modular design makes Pty-Chi highly extendable, enabling researchers to prototype new imaging models, integrate machine learning approaches, or build entirely new workflows on top of its core components. We demonstrate Pty-Chi's capabilities through challenging case studies that involve limited coherence, low overlap, and unstable illumination during scanning, which highlight its accuracy, versatility, and extensibility. With community-driven development and open contribution, Pty-Chi offers a modern, maintainable platform for advancing computational ptychography and for enabling innovative imaging algorithms at synchrotron facilities and beyond.

physics.optics↗

arXiv2024

Homomorphic data compression for real time photon correlation analysis

The construction of highly coherent x-ray sources has enabled new research opportunities across the scientific landscape. The maximum raw data rate per beamline now exceeds 40 GB/s, posing unprecedented challenges for the online processing and offline storage of the big data. Such challenge is particularly prominent for x-ray photon correlation spectroscopy (XPCS), where real time analyses require simultaneous calculation on all the previously acquired data in the time series. We present a homomorphic compression scheme to effectively reduce the computational time and memory space required for XPCS analysis. Leveraging similarities in the mathematical expression between a matrix-based compression algorithm and the correlation calculation, our approach allows direct operation on the compressed data without their decompression. The lossy compression reduces the computational time by a factor of 10,000, enabling real time calculation of the correlation functions at kHz framerate. Our demonstration of a homomorphic compression of scientific data provides an effective solution to the big data challenge at coherent light sources. Beyond the example shown in this work, the framework can be extended to facilitate real-time operations directly on a compressed data stream for other techniques.

math.NA↗

arXiv2024

Optical Control of Adaptive Nanoscale Domain Networks

Adaptive networks can sense and adjust to dynamic environments to optimize their performance. Understanding their nanoscale responses to external stimuli is essential for applications in nanodevices and neuromorphic computing. However, it is challenging to image such responses on the nanoscale with crystallographic sensitivity. Here, the evolution of nanodomain networks in (PbTiO3)n/(SrTiO3)n superlattices was directly visualized in real space as the system adapts to ultrafast repetitive optical excitations that emulate controlled neural inputs. The adaptive response allows the system to explore a wealth of metastable states that were previously inaccessible. Their reconfiguration and competition were quantitatively measured by scanning x-ray nanodiffraction as a function of the number of applied pulses, in which crystallographic characteristics were quantitatively assessed by assorted diffraction patterns using unsupervised machine-learning methods. The corresponding domain boundaries and their connectivity were drastically altered by light, holding promise for light-programmable nanocircuits in analogy to neuroplasticity. Phase-field simulations elucidate that the reconfiguration of the domain networks is a result of the interplay between photocarriers and transient lattice temperature. The demonstrated optical control scheme and the uncovered nanoscopic insights open opportunities for remote control of adaptive nanoscale domain networks.

cond-mat.mes-hall↗

arXiv2023

Demonstration of an AI-driven workflow for autonomous high-resolution scanning microscopy

With the continuing advances in scientific instrumentation, scanning microscopes are now able to image physical systems with up to sub-atomic-level spatial resolutions and sub-picosecond time resolutions. Commensurately, they are generating ever-increasing volumes of data, storing and analysis of which is becoming an increasingly difficult prospect. One approach to address this challenge is through self-driving experimentation techniques that can actively analyze the data being collected and use this information to make on-the-fly measurement choices, such that the data collected is sparse but representative of the sample and sufficiently informative. Here, we report the Fast Autonomous Scanning Toolkit (FAST) that combines a trained neural network, a route optimization technique, and efficient hardware control methods to enable a self-driving scanning microscopy experiment. The key features of our method are that: it does not require any prior information about the sample, it has a very low computational cost, and that it uses generic hardware controls with minimal experiment-specific wrapping. We test this toolkit in numerical experiments and a scanning dark-field x-ray microscopy experiment of a $WSe_2$ thin film, where our experiments show that a FAST scan of <25% of the sample is sufficient to produce both a high-fidelity image and a quantitative analysis of the surface distortions in the sample. We show that FAST can autonomously identify all features of interest in the sample while significantly reducing the scan time, the volume of data acquired, and dose on the sample. The FAST toolkit is easy to apply for any scanning microscopy modalities and we anticipate adoption of this technique will empower broader multi-level studies of the evolution of physical phenomena with respect to time, temperature, or other experimental parameters.

physics.app-ph↗

arXiv2023

X-ray Nano-imaging of Defects in Thin Film Catalysts via Cluster Analysis

Functional properties of transition-metal oxides strongly depend on crystallographic defects. In transition-metal-oxide electrocatalysts such as SrIrO3 (SIO), crystallographic lattice deviations can affect ionic diffusion and adsorbate binding energies. Scanning x-ray nanodiffraction enables imaging of local structural distortions across an extended spatial region of thin samples. Line defects remain challenging to detect and localize using nanodiffraction, due to their weak diffuse scattering. Here we apply an unsupervised machine learning clustering algorithm to isolate the low-intensity diffuse scattering in as-grown and alkaline-treated thin epitaxially strained SIO films. We pinpoint the defect locations, find additional strain variation in the morphology of electrochemically cycled SIO, and interpret the defect type by analyzing the diffraction profile through clustering. Our findings demonstrate the use of a machine learning clustering algorithm for identifying and characterizing hard-to-find crystallographic defects in thin films of electrocatalysts and highlight the potential to study electrochemical reactions at defect sites in operando experiments.

cond-mat.mtrl-sci↗

arXiv2022

CEGANN: Crystal Edge Graph Attention Neural Network for multiscale classification of materials environment

Machine learning models and applications in materials design and discovery typically involve the use of feature representations or "descriptors" followed by a learning algorithm that maps them to a user-desired property of interest. Most popular mathematical formulation-based descriptors are not unique across atomic environments or suffer from transferability issues across different application domains and/or material classes. In this work, we introduce the Crystal Edge Graph Attention Neural Network (CEGANN) workflow that uses graph attention-based architecture to learn unique feature representations and perform classification of materials across multiple scales (from atomic to mesoscale) and diverse classes ranging from metals, oxides, non-metals and even hierarchical materials such as zeolites and semi ordered materials such as mesophases. We first demonstrate a case study where the classification is based on a global, structure-level representation such as space group and structural dimensionality (e.g., bulk, 2D, clusters etc.). Using representative materials such as polycrystals and zeolites, we next demonstrate the transferability of our network in successfully performing local atom-level classification tasks, such as grain boundary identification and other heterointerfaces. We also demonstrate classification in (thermal) noisy dynamical environments using a representative example of crystal nucleation and growth of a zeolite polymorph from an amorphous synthesis mixture. Finally, we characterize the formation of a binary mesophase and its phase transitions and the growth of ice, demonstrating the performance of CEGANN in systems with thermal noise and compositional diversity. Overall, our approach is agnostic to the material type and allows for multiscale classification of features ranging from atomic-scale crystal structures to heterointerfaces to microscale grain boundaries.

cond-mat.mtrl-sci↗

arXiv2021

Learning with Delayed Rewards -- A case study on inverse defect design in 2D materials

Defect dynamics in materials are of central importance to a broad range of technologies from catalysis to energy storage systems to microelectronics. Material functionality depends strongly on the nature and organization of defects, their arrangements often involve intermediate or transient states that present a high barrier for transformation. The lack of knowledge of these intermediate states and the presence of this energy barrier presents a serious challenge for inverse defect design, especially for gradient-based approaches. Here, we present a reinforcement learning (Monte Carlo Tree Search) based on delayed rewards that allow for efficient search of the defect configurational space and allows us to identify optimal defect arrangements in low dimensional materials. Using a representative case of 2D MoS2, we demonstrate that the use of delayed rewards allows us to efficiently sample the defect configurational space and overcome the energy barrier for a wide range of defect concentrations (from 1.5% to 8% S vacancies), the system evolves from an initial randomly distributed S vacancies to one with extended S line defects consistent with previous experimental studies. Detailed analysis in the feature space allows us to identify the optimal pathways for this defect transformation and arrangement. Comparison with other global optimization schemes like genetic algorithms suggests that the MCTS with delayed rewards takes fewer evaluations and arrives at a better quality of the solution. The implications of the various sampled defect configurations on the 2H to 1T phase transitions in MoS2 are discussed. Overall, we introduce a Reinforcement Learning (RL) strategy employing delayed rewards that can accelerate the inverse design of defects in materials for achieving targeted functionality.

cond-mat.mtrl-sci↗

arXiv2020

High resolution functional imaging through Lorentz transmission electron microscopy and differentiable programming

Lorentz transmission electron microscopy is a unique characterization technique that enables the simultaneous imaging of both the microstructure and functional properties of materials at high spatial resolution. The quantitative information such as magnetization and electric potentials is carried by the phase of the electron wave, and is lost during imaging. In order to understand the local interactions and develop structure-property relationships, it is necessary to retrieve the complete wavefunction of the electron wave, which requires solving for the phase shift of the electrons (phase retrieval). Here we have developed a method based on differentiable programming to solve the inverse problem of phase retrieval, using a series of defocused microscope images. We show that our method is robust and can outperform widely used \textit{transport of intensity equation} in terms of spatial resolution and accuracy of the retrieved phase under same electron dose conditions. Furthermore, our method shares the same basic structure as advanced machine learning algorithms, and is easily adaptable to various other forms of phase retrieval in electron microscopy.

cond-mat.mtrl-sci↗

arXiv2020

BLAST: Bridging Length/time scales via Atomistic Simulation Toolkit

The ever-increasing power of supercomputers coupled with highly scalable simulation codes have made molecular dynamics an indispensable tool in applications ranging from predictive modeling of materials to computational design and discovery of new materials for a broad range of applications. Multi-fidelity scale bridging between the various flavors of molecular dynamics i.e. ab-initio, classical and coarse-grained models has remained a long-standing challenge. Here, we introduce our framework BLAST (Bridging Length/time scales via Atomistic Simulation Toolkit) that leverages machine learning principles to address this challenge. BLAST is a multi-fidelity scale bridging framework that provide users with the capabilities to train and develop their own classical atomistic and coarse-grained interatomic potentials (force fields) for molecular simulations. BLAST is designed to address several long-standing problems in the molecular simulations community, such as unintended misuse of existing force fields due to knowledge gap between developers and users, bottlenecks in traditional force field development approaches, and other issues relating to the accuracy, efficiency, and transferability of force fields. Here, we discuss several important aspects in force field development and highlight features in BLAST that enable its functionalities and ease of use.

cs.CE↗

arXiv2019

Active Learning the Coarse-Grained Energy Landscape For Water Clusters From Sparse Training Data

ANNs are currently trained by generating large quantities (On the order of $10^{4}$ or greater) of structural data in hopes that the ANN has adequately sampled the energy landscape both near and far-from-equilibrium. This can, however, be a bit prohibitive when it comes to more accurate levels of quantum theory. As such it is desirable to train a model using the absolute minimal data set possible, especially when costs of high-fidelity calculations such as CCSD and QMC are high. Here, we present an Active Learning approach that iteratively trains an ANN model to faithfully replicate the coarse-grained energy surface of water clusters using only 426 total structures in its training data. Our active learning workflow starts with a sparse training dataset which is continually updated via a Monte Carlo scheme that sparsely queries the energy landscape and tests the network performance. Next, the network is retrained with an updated training set that includes failed configurations/energies from previous iteration until convergence is attained. Once trained, we generate an extensive test set of ~100,000 configurations sampled across clusters ranging from 1 to 200 molecules and demonstrate that the trained network adequately reproduces the energies (within mean absolute error (MAE) of ~ 2 meV/molecule) and forces (MAE ~ 40 meV/{Å}) compared to the reference model. More importantly, the trained ANN model also accurately captures both the structure as well as the free energy as a function of the various cluster sizes. Overall, this study reports a new active learning scheme with promising strategy to develop accurate force-fields for molecular simulations using extremely sparse training data sets.

physics.comp-ph↗

arXiv2017

Evolutionary optimization of a charge transfer ionic potential model for Ta/Ta-oxide hetero-interfaces

Tantalum, tantalum oxide and their hetero-interfaces are of tremendous technological interest in several applications spanning electronics, thermal management, catalysis and biochemistry. For example, local oxygen stoichiometry variation in TaOx memristors comprising of metallic (Ta) and insulating oxide (Ta2O5) have been shown to result in fast switching on the sub-nanosecond timescale over a billion cycles, relevant to neuromorphic computation. Despite its broad importance, an atomistic scale understanding of oxygen stoichiometry variation across Ta/TaOx hetero-interfaces, such as during early stages of oxidation and oxide growth, is not well understood. This is mainly due to the lack of a variable charge interatomic potential model for tantalum oxides that can accurately describe the ionic interactions in the metallic (Ta) and oxide (TaOx) environment as well as at their interfaces. To address this challenge, we introduce a charge transfer ionic potential (CTIP) model for Ta/Ta-oxide system by training against lattice parameters, cohesive energies, equations of state, and elastic properties of various experimentally observed Ta2O5 polymorphs. The best set of CTIP parameters are determined by employing a single-objective global optimization scheme driven by genetic algorithms followed by local Simplex optimization. Our newly developed CTIP potential accurately predicts structure, thermodynamics, energetic ordering of polymorphs, as well as elastic and surface properties of both Ta and Ta2O5, in excellent agreement with DFT calculations and experiments. We employ our newly parameterized CTIP potential to investigate the early stages of oxidation of Ta at different temperatures and atomic/molecular nature of the oxidizing species.

cond-mat.mtrl-sci↗

arXiv2017

Perovskite Quantum Organismoids

A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making1-3. This behavior, known as habituation, is universal among forms of life with a central nervous system, and interestingly observed even in single cellular organisms that do not possess a brain4-5. Here, we report the discovery of habituation based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization via reversible dopant incorporation. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by a combination of first-principles theory, synchrotron investigations, ab-initio dynamical simulations and in-situ environmental breathing studies. We implement a new learning algorithm inspired from the conductance relaxation behavior of perovskites that naturally incorporates habituation and demonstrate "learning to forget": a key feature of animal and human brains6. Most surprisingly, our results show that incorporating this elementary skill in learning dramatically boosts the capability of artificial cognitive systems.

cond-mat.mtrl-sci↗