arXiv subjects

Subramanian Sankaranarayanan

Publications and source records attributed to Subramanian Sankaranarayanan.

17 recordsLinked to original sources

arXiv2026

AutoMOOSE: Use Case and Logical Views of Agentic Phase-Field Simulation Software

AutoMOOSE is an agentic software framework that converts a natural-language request into an executed, screened, and interpreted MOOSE phase-field simulation. Here, we deploy AutoMOOSE as a agentic software, complementing our prior work which focused on development of the agentic tool. We describe our software framework and architecture through Use Case and logical views of the 1+5 architectural-views model, covering its user roles, component structure, six-agent pipeline, physics plugin layer, Model Context Protocol interface, and screening/falsification/recovery loop. Our architecture separates physical falsification from automatic repair, so corrected simulations remain inspectable and must be re-admitted before acceptance. We focus on software design, extensibility, interoperability, and reuse of the AutoMoose framework for broad utilization in multiphysics materials design problems.

cond-mat.mtrl-sci↗

arXiv2026

From Stacking Disorder to Cubic Order: Ice Crystallization from Deeply Supercooled Water

Crystallization far from equilibrium can generate morphologies that defy classical crystal habits, yet the microscopic mechanisms linking atomic-scale disorder to emergent macroscopic order remain elusive. Here we use in situ cryogenic transmission electron microscopy with a membrane-encapsulated microdroplet platform to directly visualize the freezing of deeply supercooled water at molecular resolution. We show that homogeneous nucleation produces stacking-disordered ice composed of mixed hexagonal and cubic sequences, in which cubic ice initially exists only as isolated monolayers. The gradual thickening of these cubic layers constitutes the key kinetic mechanism that governs the entire crystallization pathway. As thickening proceeds, nanoscale, defect-free cubic ice germs nucleate on the basal planes of the disordered lattice. These faceted cubic germs act as facet-registered kinetic seeds that enforce cubic twinning and sequentially multiply growth branches. This kinetic pathway reproducibly generates robust eight-branched dendrites with global cubic (octahedral) symmetry, even though each branch remains highly stacking-disordered. At later stages, latent heat release drives a crossover to the thermodynamically favored hexagonal phase; remarkably, the pre-established global cubic symmetry is retained. These results reveal how strong kinetic driving forces convert microscopic disorder into emergent macroscopic symmetry, providing a general framework for understanding and controlling rapid crystallization far from equilibrium.

cond-mat.mtrl-sci↗

arXiv2026

Physics-Informed Tree Search for High-Dimensional Computational Design

High-dimensional design spaces underpin a wide range of physics-based modeling and computational design tasks in science and engineering. These problems are commonly formulated as constrained black-box searches over rugged objective landscapes, where function evaluations are expensive, and gradients are unavailable or unreliable. Conventional global search engines and optimizers struggle in such settings due to the exponential scaling of design spaces, the presence of multiple local basins, and the absence of physical guidance in sampling. We present a physics-informed Monte Carlo Tree Search (MCTS) framework that extends policy-driven tree-based reinforcement concepts to continuous, high-dimensional scientific optimization. Our method integrates population-level decision trees with surrogate-guided directional sampling, reward shaping, and hierarchical switching between global exploration and local exploitation. These ingredients allow efficient traversal of non-convex, multimodal landscapes where physically meaningful optima are sparse. We benchmark our approach against standard global optimization baselines on a suite of canonical test functions, demonstrating superior or comparable performance in terms of convergence, robustness, and generalization. Beyond synthetic tests, we demonstrate physics-consistent applicability to (i) crystal structure optimization from clusters to bulk, (ii) fitting of classical interatomic potentials, and (iii) constrained engineering design problems. Across all cases, the method converges with high fidelity and evaluation efficiency while preserving physical constraints. Overall, our work establishes physics-informed tree search as a scalable and interpretable paradigm for computational design and high-dimensional scientific optimization, bridging discrete decision-making frameworks with continuous search in scientific design workflows.

cs.LG↗

arXiv2025

Temporally staggered cropping co-benefits beneficial insects and pest control globally

Reconciling increasing food production with biodiversity conservation is critical yet challenging, particularly given global declines in beneficial insects driven by monoculture intensification. Intercropping, the simultaneous or sequential cultivation of multiple crops, has been proposed as a viable strategy to enhance beneficial insect services and suppress pests, yet global evidence regarding optimal spatiotemporal intercropping configurations remains fragmented. Here, we synthesize results from 7,584 field experiments spanning six continents and 22 Koppen climate regions, evaluating effects of spatial (row, strip, mixed, agroforestry) and temporal (additive, replacement, relay) intercropping configuations on beneficial insect (predators, parasitoids, pollinators) abundance and pest suppression using the Management Efficiency Ratio (MER; log ratio of abundance in intercropping versus monoculture). Relay intercropping, characterized by temporally staggered planting, emerged as the universally optimal temporal configuration, substantially increasing predator (MER = 0.473) and parasitoid populations (MER = 0.512) and effectively suppressing pests (MER = -0.611) globally. At regional scales, identical spatiotemporal configurations simultaneously optimized beneficial insect predator abundance and pest suppression in 57% of regions, while other regions required distinct, insect-specific approaches. Our findings highlight relay intercropping as a globally generalizable solution, but underscore regional variation that calls for targeted policies to simultaneously secure food production and biodiversity conservation.

q-bio.PE↗

arXiv2025

COT-AD: Cotton Analysis Dataset

This paper presents COT-AD, a comprehensive Dataset designed to enhance cotton crop analysis through computer vision. Comprising over 25,000 images captured throughout the cotton growth cycle, with 5,000 annotated images, COT-AD includes aerial imagery for field-scale detection and segmentation and high-resolution DSLR images documenting key diseases. The annotations cover pest and disease recognition, vegetation, and weed analysis, addressing a critical gap in cotton-specific agricultural datasets. COT-AD supports tasks such as classification, segmentation, image restoration, enhancement, deep generative model-based cotton crop synthesis, and early disease management, advancing data-driven crop management

cs.CV↗

arXiv2023

Infrared Nanoimaging of Hydrogenated Perovskite Nickelate Synaptic Devices

Solid-state devices made from correlated oxides such as perovskite nickelates are promising for neuromorphic computing by mimicking biological synaptic function. However, comprehending dopant action at the nanoscale poses a formidable challenge to understanding the elementary mechanisms involved. Here, we perform operando infrared nanoimaging of hydrogen-doped correlated perovskite, neodymium nickel oxide (H-NdNiO3) devices and reveal how an applied field perturbs dopant distribution at the nanoscale. This perturbation leads to stripe phases of varying conductivity perpendicular to the applied field, which define the macroscale electrical characteristics of the devices. Hyperspectral nano-FTIR imaging in conjunction with density functional theory calculations unveil a real-space map of multiple vibrational states of H-NNO associated with OH stretching modes and their dependence on the dopant concentration. Moreover, the localization of excess charges induces an out-of-plane lattice expansion in NNO which was confirmed by in-situ - x-ray diffraction and creates a strain that acts as a barrier against further diffusion. Our results and the techniques presented here hold great potential to the rapidly growing field of memristors and neuromorphic devices wherein nanoscale ion motion is fundamentally responsible for function.

physics.app-ph↗

arXiv2023

MLExchange: A web-based platform enabling exchangeable machine learning workflows for scientific studies

Machine learning (ML) algorithms are showing a growing trend in helping the scientific communities across different disciplines and institutions to address large and diverse data problems. However, many available ML tools are programmatically demanding and computationally costly. The MLExchange project aims to build a collaborative platform equipped with enabling tools that allow scientists and facility users who do not have a profound ML background to use ML and computational resources in scientific discovery. At the high level, we are targeting a full user experience where managing and exchanging ML algorithms, workflows, and data are readily available through web applications. Since each component is an independent container, the whole platform or its individual service(s) can be easily deployed at servers of different scales, ranging from a personal device (laptop, smart phone, etc.) to high performance clusters (HPC) accessed (simultaneously) by many users. Thus, MLExchange renders flexible using scenarios -- users could either access the services and resources from a remote server or run the whole platform or its individual service(s) within their local network.

cs.LG↗

arXiv2022

AutoPhaseNN: Unsupervised Physics-aware Deep Learning of 3D Nanoscale Bragg Coherent Diffraction Imaging

The problem of phase retrieval, or the algorithmic recovery of lost phase information from measured intensity alone, underlies various imaging methods from astronomy to nanoscale imaging. Traditional methods of phase retrieval are iterative in nature, and are therefore computationally expensive and time consuming. More recently, deep learning (DL) models have been developed to either provide learned priors to iterative phase retrieval or in some cases completely replace phase retrieval with networks that learn to recover the lost phase information from measured intensity alone. However, such models require vast amounts of labeled data, which can only be obtained through simulation or performing computationally prohibitive phase retrieval on hundreds of or even thousands of experimental datasets. Using a 3D nanoscale X-ray imaging modality (Bragg Coherent Diffraction Imaging or BCDI) as a representative technique, we demonstrate AutoPhaseNN, a DL-based approach which learns to solve the phase problem without labeled data. By incorporating the physics of the imaging technique into the DL model during training, AutoPhaseNN learns to invert 3D BCDI data from reciprocal space to real space in a single shot without ever being shown real space images. Once trained, AutoPhaseNN is about one hundred times faster than traditional iterative phase retrieval methods while providing comparable image quality.

physics.app-ph↗

arXiv2021

Machine Learning the Metastable Phase Diagram of Materials

Phase diagrams are an invaluable tool for material synthesis and provide information on the phases of the material at any given thermodynamic condition. Conventional phase diagram generation involves experimentation to provide an initial estimate of thermodynamically accessible phases, followed by use of phenomenological models to interpolate between the available experimental data points and extrapolate to inaccessible regions. Such an approach, combined with first-principles calculations and data-mining techniques, has led to exhaustive thermodynamic databases albeit at distinct thermodynamic equilibria. In contrast, materials during their synthesis, operation, or processing, may not reach their thermodynamic equilibrium state but, instead, remain trapped in a local free energy minimum, that may exhibit desirable properties. Mapping these metastable phases and their thermodynamic behavior is highly desirable but currently lacking. Here, we introduce an automated workflow that integrates first principles physics and atomistic simulations with machine learning (ML), and high-performance computing to allow rapid exploration of the metastable phases of a given elemental composition. Using a representative material, carbon, with a vast number of metastable phases without parent in equilibrium, we demonstrate automatic mapping of hundreds of metastable states ranging from near equilibrium to those far-from-equilibrium. Moreover, we incorporate the free energy calculations into a neural-network-based learning of the equations of state that allows for construction of metastable phase diagrams. High temperature high pressure experiments using a diamond anvil cell on graphite sample coupled with high-resolution transmission electron microscopy are used to validate our metastable phase predictions. Our introduced approach is general and broadly applicable to single and multi-component systems.

cond-mat.mtrl-sci↗

arXiv2021

Atomistic Evidence of Nucleation Mechanism for the Direct Graphite-to-Diamond Transformation

The direct graphite-to-diamond transformation mechanism has been a subject of intense study and remains debated concerning the initial stages of the conversion, the intermediate phases, and their transformation pathways. Here, we successfully recover samples at early conversion stage by tuning high-pressure/high-temperature conditions and reveal direct evidence supporting the nucleation-growth mechanism. Atomistic observations show that intermediate orthorhombic graphite phase mediates the growth of diamond nuclei. Furthermore, we observe that quenchable orthorhombic and rhombohedra graphite are stabilized in buckled graphite at lower temperatures. These intermediate phases are further converted into hexagonal and cubic diamond at higher temperatures following energetically favorable pathways in the order: graphite -> orthorhombic graphite -> hexagonal diamond, graphite -> orthorhombic graphite -> cubic diamond, graphite -> rhombohedra graphite -> cubic diamond. These results significantly improve our understanding of the transformation mechanism, enabling the synthesis of different high-quality forms of diamond from graphite.

cond-mat.mtrl-sci↗

arXiv2021

Lonsdaleite: The diamond with optimized bond lengths and enhanced hardness

Diamond is known as the hardest substance due to its ultra-strong tetrahedral sp3 carbon bonding framework. The only weak link is its cubic cleavage planes between (111) buckled honeycomb layers. Compressing graphite single crystals and heating to moderate temperatures, we synthesized a bulk, pure, hexagonal diamond (lonsdaleite) with distorted carbon tetrahedrons that shorten the bond between its hexagonal (001) buckled honeycomb layers, thus strengthening their linkage. We observed direct transformation of graphite (100) to lonsdaleite (002) and graphite (002) to lonsdaleite (100). We find the bulk lonsdaleite has superior mechanical properties of Vicker hardnesses HV = 164+/-11 GPa and 124+/-13 GPa, measured on the surface corresponding to the original graphite (001) and (100) surfaces, respectively. Properties of lonsdaleite as the supreme material can be further enhanced by purifying the starting material graphite carbon and fine-tuning the high pressure-temperature synthesis conditions.

cond-mat.mtrl-sci↗

arXiv2020

Combinatorial Black-Box Optimization with Expert Advice

We consider the problem of black-box function optimization over the boolean hypercube. Despite the vast literature on black-box function optimization over continuous domains, not much attention has been paid to learning models for optimization over combinatorial domains until recently. However, the computational complexity of the recently devised algorithms are prohibitive even for moderate numbers of variables; drawing one sample using the existing algorithms is more expensive than a function evaluation for many black-box functions of interest. To address this problem, we propose a computationally efficient model learning algorithm based on multilinear polynomials and exponential weight updates. In the proposed algorithm, we alternate between simulated annealing with respect to the current polynomial representation and updating the weights using monomial experts' advice. Numerical experiments on various datasets in both unconstrained and sum-constrained boolean optimization indicate the competitive performance of the proposed algorithm, while improving the computational time up to several orders of magnitude compared to state-of-the-art algorithms in the literature.

cs.LG↗

arXiv2020

Real-time 3D Nanoscale Coherent Imaging via Physics-aware Deep Learning

Phase retrieval, the problem of recovering lost phase information from measured intensity alone, is an inverse problem that is widely faced in various imaging modalities ranging from astronomy to nanoscale imaging. The current process of phase recovery is iterative in nature. As a result, the image formation is time-consuming and computationally expensive, precluding real-time imaging. Here, we use 3D nanoscale X-ray imaging as a representative example to develop a deep learning model to address this phase retrieval problem. We introduce 3D-CDI-NN, a deep convolutional neural network and differential programming framework trained to predict 3D structure and strain solely from input 3D X-ray coherent scattering data. Our networks are designed to be "physics-aware" in multiple aspects; in that the physics of x-ray scattering process is explicitly enforced in the training of the network, and the training data are drawn from atomistic simulations that are representative of the physics of the material. We further refine the neural network prediction through a physics-based optimization procedure to enable maximum accuracy at lowest computational cost. 3D-CDI-NN can invert a 3D coherent diffraction pattern to real-space structure and strain hundreds of times faster than traditional iterative phase retrieval methods, with negligible loss in accuracy. Our integrated machine learning and differential programming solution to the phase retrieval problem is broadly applicable across inverse problems in other application areas.

eess.IV↗

arXiv2020

Active Learning A Neural Network Model For Gold Clusters \& Bulk From Sparse First Principles Training Data

Small metal clusters are of fundamental scientific interest and of tremendous significance in catalysis. These nanoscale clusters display diverse geometries and structural motifs depending on the cluster size; a knowledge of this size-dependent structural motifs and their dynamical evolution has been of longstanding interest. Classical MD typically employ predefined functional forms which limits their ability to capture such complex size-dependent structural and dynamical transformation. Neural Network (NN) based potentials represent flexible alternatives and in principle, well-trained NN potentials can provide high level of flexibility, transferability and accuracy on-par with the reference model used for training. A major challenge, however, is that NN models are interpolative and requires large quantities of training data to ensure that the model adequately samples the energy landscape both near and far-from-equilibrium. Here, we introduce an active learning (AL) scheme that trains a NN model on-the-fly with minimal amount of first-principles based training data. Our AL workflow is initiated with a sparse training dataset (1 to 5 data points) and is updated on-the-fly via a Nested Ensemble Monte Carlo scheme that iteratively queries the energy landscape in regions of failure and updates the training pool to improve the network performance. Using a representative system of gold clusters, we demonstrate that our AL workflow can train a NN with ~500 total reference calculations. Our NN predictions are within 30 meV/atom and 40 meV/Åof the reference DFT calculations. Moreover, our AL-NN model also adequately captures the various size-dependent structural and dynamical properties of gold clusters in excellent agreement with DFT calculations and available experiments.

physics.comp-ph↗

arXiv2020

Screening of Therapeutic Agents for COVID-19 using Machine Learning and Ensemble Docking Simulations

The world has witnessed unprecedented human and economic loss from the COVID-19 disease, caused by the novel coronavirus SARS-CoV-2. Extensive research is being conducted across the globe to identify therapeutic agents against the SARS-CoV-2. Here, we use a powerful and efficient computational strategy by combining machine learning (ML) based models and high-fidelity ensemble docking simulations to enable rapid screening of possible therapeutic molecules (or ligands). Our screening is based on the binding affinity to either the isolated SARS-CoV-2 S-protein at its host receptor region or to the Sprotein-human ACE2 interface complex, thereby potentially limiting and/or disrupting the host-virus interactions. We first apply our screening strategy to two drug datasets (CureFFI and DrugCentral) to identify hundreds of ligands that bind strongly to the aforementioned two systems. Candidate ligands were then validated by all atom docking simulations. The validated ML models were subsequently used to screen a large bio-molecule dataset (with nearly a million entries) to provide a rank-ordered list of ~19,000 potentially useful compounds for further validation. Overall, this work not only expands our knowledge of small-molecule treatment against COVID-19, but also provides an efficient pathway to perform high-throughput computational drug screening by combining quick ML surrogate models with expensive high-fidelity simulations, for accelerating the therapeutic cure of diseases.

q-bio.BM↗

arXiv2020

Machine Learning for Multi-fidelity Scale Bridging and Dynamical Simulations of Materials

Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive ab-initio MD to relatively lower fidelity but much more efficient classical MD such as atomistic and coarse-grained models. Each of these different flavors of MD have been independently used by materials scientists to bring about breakthroughs in materials discovery and design. A significant gulf exists between the various MD flavors, each having varying levels of fidelity. The accuracy of DFT or ab-initio MD is generally much higher than that of classical atomistic simulations which is higher than that of coarse-grained models. Multi-fidelity scale bridging to combine the accuracy and flexibility of ab-initio MD with efficiency classical MD has been a longstanding goal. The advent of big-data analytics has brought to the forefront powerful machine learning methods that can be deployed to achieve this goal. Here, we provide our perspective on the challenges in multi-fidelity scale bridging and trace the developments leading up to the use of machine learning algorithms and data-science towards addressing this grand challenge.

physics.comp-ph↗

arXiv2016

Methodology of Parameterization of Molecular Mechanics Force Field From Quantum Chemistry Calculations using Genetic Algorithm: A case study of methanol

In molecular dynamics (MD) simulation, force field determines the capability of an individual model in capturing physical and chemistry properties. The method for generating proper parameters of the force field form is the key component for computational research in chemistry, biochemistry, and condensed-phase physics. Our study showed that the feasibility to predict experimental condensed phase properties (i.e., density and heat of vaporization) of methanol through problem specific force field from only quantum chemistry information. To acquire the satisfying parameter sets of the force field, the genetic algorithm (GA) is the main optimization method. For electrostatic potential energy, we optimized both the electrostatic parameters of methanol using the GA method, which leads to low deviations of between the quantum mechanics (QM) calculations and the GA optimized parameters. We optimized the van der Waals (vdW) parameters both using GA and guided GA methods by calibrating interaction energy of various methanol homo-clusters, such as nonamers, undecamers, or tridecamers. Excellent agreement between the training dataset from QM calculations (i.e., MP2) and GA optimized parameters can be achieved. However, only the guided GA method, which eliminates the overestimation of interaction energy from MP2 calculations in the optimization process, provides proper vdW parameters for MD simulation to get the condensed phase properties (i.e., density and heat of vaporization) of methanol. Throughout the whole optimization process, the experimental value were not involved in the objective functions, but were only used for the purpose of justifying models (i.e., nonamers, undecamers, or tridecamers) and validating methods (i.e., GA or guided GA). Our method shows the possibility of developing descriptive polarizable force field using only QM calculations.

physics.atm-clus↗