Distributed Model-Based Diffusion: Finite Horizon Contraction under Bounded Delay
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Mazumdar, Anirban [Sandia National Laboratories (S↗
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Sequential Infiltration Synthesis of Multinary Metal Oxides: The Role of Precursor Diffusion and Reactivity
Understanding volatile metal–organic precursor transport in polymer matrices during sequential infiltration synthesis (SIS) is critical to the design of hybrid materials of tailored composition and uniform structure. Here, we investigate the diffusion and reaction behavior of diethylzinc (DEZ) in poly(methyl methacrylate) (PMMA) matrices with variable indium and zinc incorporation. Unlike conventional SIS where precursors adduct or react directly with the polymer backbone, DEZ shows minimal interaction with PMMA. However, DEZ may interact strongly with In–OH or Zn–OH moieties that are previously incorporated into a PMMA thick film. Using spectroscopic ellipsometry, X-ray photoelectron spectroscopy depth profiling, and EDX line scans, we quantify Zn incorporation as a function of exposure time, polymer thickness, and previous infiltration steps. The Zn distribution evolves from surface-localized to deep within the ∼1 μm thick film with increasing DEZ exposures up to 30 min. A reaction-diffusion model incorporating a hindering factor to capture diffusivity decay due to product accumulation reproduces the Zn depth profile and yields physically meaningful parameters to guide future growth. Furthermore, this study provides a framework for interpreting metal–organic precursor infiltration behavior and highlights the utility of model-guided SIS process design.
diethylzinc↗
Flow matching meets biology and life science: a survey
Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions.
59 BASIC BIOLOGICAL SCIENCES↗
IoT-based retrofit information diffusion in future smart communities
Community-scale building retrofits are not merely scaled-up versions of single-building retrofits. They involve complex challenges, such as reconciling individual interests with collective goals and managing the dynamic interplay between buildings through mechanisms like power grids and social connections. Internet of Things (IoT) connectivity holds the potential to leverage these interplays to balance individual and collective interests effectively in smart communities. One critical aspect of this interplay is information diffusion, which shapes how retrofit decisions spread among neighbors, influencing individual choices and ultimately impacting community-level retrofit outcomes. In other words, IoT-based smart devices automatically push tailored retrofit notifications to homeowners, which completely changes the format of information diffusion in the future. To investigate this influence by such information diffusion, the study used CityBES to simulate energy performance for different retrofits and applied an information diffusion model to analyze how decisions spread in a networked community of 192 buildings. The diffusion process was modeled on a weighted, directed network, capturing the dynamics of information flow and decision-making across 16 scenarios. Individual retrofit benefits were evaluated through payback years, while community-level retrofit outcomes were assessed using greenhouse gas (GHG) emission reductions. The results demonstrate that easier information diffusion among neighbors encourages households to prioritize retrofit measures that align with the majority’s optimal choices, even at the expense of individual financial benefits. In this case, such collective prioritization enhanced community-level retrofit performance, increasing GHG emission reductions by up to 29.4 %. However, this improvement came with trade-offs, as the average payback period for households extended by approximately 1.74 years. These findings highlight the potential of IoT-based information diffusion in future smart communities to coordinate individual interests with collective goals, ultimately accelerating community-level building retrofits.
Shu, Lei↗
Measurement of atomic oxygen densities using TALIF on a dielectric barrier discharge: insights into the volume above a micro cavity plasma array
Dielectric barrier discharges, particularly micro cavity plasma arrays, offer significant potential for plasma-catalytic research due to their ability to ignite plasma in direct contact with a catalytic surface, enabling the observation of plasma-surface interactions. A key factor in their application is the generation of reactive species, such as atomic oxygen, within the cavities. These species can interact with both the surface (e.g. for activation or cleaning) and the gas being treated (e.g. for oxidation). Given the central role of oxygen atoms in plasma catalysis and their use as a model for more complex species, this work investigates the transport of these atoms out of the cavities. Two-photon absorption laser-induced fluorescence spectroscopy with picosecond laser excitation is performed in the volume above the cavities. The results are compared with a basic diffusion model. The reactor operates with a He/O 2 mixture at a flow rate of 1 slm and atmospheric pressure. Densities of up to 10 16 cm -3 are measured near the surface. Time-dependent measurements show that, at a distance of 350 µm from the surface, a density equilibrium is reached within less than 3 ms of reactor operation. Decay times due to ozone formation after the reactor is turned off are on a similar scale. Spatially resolved measurements show that the oxygen density decreases exponentially from the surface but remains detectable up to approximately 1 mm above the surface, indicating significant application potential. Variations in the O 2 admixture show a density maximum at 0.4%, confirming previous helium state enhanced actinometry measurements within the cavities.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Interpretable Deep Learning for Advancing Field-Enhanced Catalysis
This DOE Early Career project developed a physics-informed, interpretable AI-and-modeling framework to understand and exploit electric-field effects in heterogeneous catalysis, with ammonia cracking and synthesis as a representative pathway. The team built and validated methods to map local electric fields on metal surfaces and nanoparticles, showing that low-coordination features (tips/edges/corners) can concentrate fields by several-fold relative to flat facets. Using DFT-generated datasets, the project created physics-guided machine learning models that rapidly predict local electric fields and field-dependent adsorption energetics with near-DFT accuracy while reducing computational cost by orders of magnitude. These predictions were integrated with microkinetic modeling to quantify how field-dipole interactions reshape reaction energetics and mechanisms, enabling large increases in predicted catalytic rates and substantial reductions in operating temperature under favorable field conditions. To accelerate discovery of earth-abundant catalysts, the project combined interpretable ML screening (with electronic-structure descriptors identified as key drivers) with a generative inverse-design workflow based on diffusion models and physics constraints. The resulting closed-loop approach, linking simulation, mechanistic modeling, and AI, provides reusable tools and datasets for designing catalysts and operating conditions in field-enhanced catalysis, with broad relevance to electrostatic catalysis, plasma catalysis, electrocatalysis, and other energy-related chemical transformations.
30 DIRECT ENERGY CONVERSION↗
Thermal diffusion, exhaust gas recirculation and blending effects on lean premixed hydrogen flames
Thermodiffusively-unstable lean premixed hydrogen flames are investigated using two-dimensional direct numerical simulation employing finite-rate chemical kinetics. Three databases are generated focussing on the inclusion of the Soret effect, the recirculation of exhaust gas, and blending with methane. A simple rescaling of a classic thermal diffusion model is presented and shown to mimic multicomponent diffusion with very low computational cost and little-to-no loss in accuracy. It is also shown that a previously developed model for mean local flame speeds in lean premixed hydrogen flames can still be used provided Soret effects are taken into account in one-dimensional calculations. The addition of exhaust gas to the unburned mixture is found to enhance thermodiffusive instability; the primary mechanism for this was shown to be the highly-efficient third-body nature of water, with the reduction of adiabatic flame temperature a second-order effect. Again, the existing mean local flame speed model proved sufficient. Finally, blending with methane was found to reduce the thermodiffusive response of the flame, more so than the existing model suggests, despite adjustment of the fuel Lewis number; an adapted model is presented to account for this.
08 HYDROGEN↗
EvoDiffMol: evolutionary diffusion framework for 3D molecular design with optimized properties
Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a computational framework that integrates evolutionary algorithms with three-dimensional diffusion models for property-driven molecular generation. The method operates through adaptive evolutionary optimization, where population-based selection guides the generation process toward desired property landscapes. EvoDiffMol supports both unconstrained molecular design and scaffold-constrained generation that preserves fixed substructures while optimizing complementary regions. Comprehensive evaluation demonstrates exceptional performance, achieving the highest drug-likeness score (0.94) among all compared state-of-the-art methods while maintaining excellent validity, uniqueness, and novelty. Beyond single property optimization, the framework demonstrates flexible multi-property optimization capabilities, simultaneously controlling multiple molecular descriptors including synthetic accessibility, lipophilicity, topological polar surface area, and clinically relevant ADMET properties such as cardiotoxicity (hERG) and intestinal permeability (Caco-2). This adaptability spans from simple descriptors to practical pharmaceutical endpoints without requiring complete model retraining. The framework achieves precise control over target property values, generating molecules with properties closely matching specified targets for both single and multiple descriptors. Scaffold-constrained experiments preserve fixed molecular cores while maintaining effective property optimization. The three-dimensional representation offers advantages in maintaining structural validity during iterative optimization, with potential for geometry-aware applications in materials science and drug discovery.
3D molecular generation↗
GrainPaint: A multi-scale diffusion-based generative model for microstructure reconstruction of large-scale objects
Simulation-based approaches to microstructure generation can suffer from a variety of limitations, such as high memory usage, long computational times, and difficulties in generating complex geometries. Generative machine learning models present a way around these issues, but they have previously been limited by the fixed size of their generation area. Here, we present a new microstructure generation methodology leveraging advances in inpainting using denoising diffusion models to overcome this generation area limitation. We show that microstructures generated with the presented methodology are statistically similar to grain structures generated with a kinetic Monte Carlo simulator, SPPARKS.
36 MATERIALS SCIENCE↗
A semi-automated algorithm for designing stellarator divertor and limiter plates and application to HSX
We present a semi-automated algorithm for designing three-dimensional divertor or limiter plates targeting low heat loads. The algorithm designs the plates in two stages: firstly, the parallel heat flux distribution is caught on vertically-inclined plates at one or several toroidal locations. Secondly, the power per unit area is reduced by stretching, tilting and bending the plates toroidally. Heat transport is modelled using the EMC3-Lite code, which uses an anisotropic diffusion model. We apply this scheme to HSX, a medium-sized stellarator located at the University of Wisconsin–Madison. Starting from the current machine with an extended vessel wall, we construct plates which are able to effectively catch and spread the heat for three different magnetic configurations. The scheme has a computational cost in the order of tens of CPU-minutes, making it a powerful tool for semi-automated plasma-facing component design in three-dimensional environments.
anisotropic diffusion↗
AEOLUS: Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems
The AEOLUS Center is dedicated to developing a unified optimization-under-uncertainty framework for (1) learning predictive models from data and (2) optimizing experiments, processes, and designs governed by these models, all driven by complex, uncertain energy systems. AEOLUS addressed the critical need for principled, rigorous, scalable, and structure-exploiting capabilities for exploring parameter and decision spaces of complex forward simulation models---the so-called outer loop. This report summarizes the work done under DE-SC0021077 on (1) nonlocal models for solidification problems, (2) a multifidelity method for a nonlocal diffusion model, and (3) multifidelity Monte Carlo methods.
97 MATHEMATICS AND COMPUTING↗
Consistent solutions of the radiation diffusion equation in spherical and cylindrical geometries
We have extended the radiation diffusion model of Hammer and Rosen [Phys. Plasmas 10, 1829 (2003)] to diverging spherical and cylindrical geometries. The effect of curvilinear geometry on the supersonic, expanding wavefront increases as the internal radius of a spherical or cylindrical shell approaches zero. Small spherical geometries are important for modeling systems at the size scale of inertial confinement fusion capsules, at these scales existing quasi-analytic models for planar geometry significantly disagree with the results of simulation. With this method, the benefits of rapid iteration can be applied to common spherical systems at much smaller length scales. We present comparisons between numerical diffusion solutions and the analytic model to give ranges of applicability for the model.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Robustness of the Ensemble Score Filter to the Type of Assimilated Observation Networks
Recent advances in data assimilation (DA) have focused on developing more flexible approaches that can better accommodate nonlinearities in models and observations. However, it remains unclear how the performance of these advanced methods depends on the observation network characteristics. In this study, we present initial experiments with the surface quasi‐geostrophic model, in which we compare a recently developed ensemble filter using score‐based diffusion models with the standard Local Ensemble Transform Kalman Filter (LETKF). Our results show that the analysis solutions respond differently to the number, spatial distribution, and nonlinear fraction of assimilated observations. We also find notable changes in the multiscale characteristics of the analysis errors. Given that standard DA techniques will eventually be replaced by more advanced methods, we hope this study sets the ground for future efforts to reassess the value of Earth observing systems in the context of newly emerging algorithms.
97 MATHEMATICS AND COMPUTING↗
Conditional diffusion machine-learning framework for mapping valence electron distribution from convergent beam electron diffraction
Quantitative convergent beam electron diffraction (CBED) enables determination of aspherical valence electron distributions through refinement of low-order structure factors, which are highly sensitive to chemical bonding and charge density variations. However, conventional quantitative CBED (QCBED) requires solving a highly nonlinear inverse problem with many coupled parameters, and computationally intensive dynamical diffraction calculations, making it time-consuming and difficult to apply to complex systems. More broadly, reconstructing charge density and orbital electron distribution from diffraction data has long been a central challenge in both x-ray and electron crystallography. Here, in this study, we introduce an artificial-intelligence (AI)-based framework that replaces traditional refinement with a data-driven inverse solver. Using a large synthetic CBED dataset generated by Bloch-wave simulations, we train a conditional diffusion model to directly infer crystal structural parameters and multipole density formalism parameters, and hence valence electron distributions, from CBED patterns alone. By learning from forward simulations across realistic parameter space, the model effectively solves the inverse problem. Compared with direct regression approaches, the diffusion-based framework provides posterior parameter distributions for rigorous uncertainty quantification while preserving quantitative fidelity and reducing analysis time by orders of magnitude. By eliminating the need for external single-crystal x-ray diffraction data and complex nonlinear refinement, this approach enables practical, high-throughput, and in situ quantitative CBED, enabling real-time mapping of valence electron distributions and their correlation with functional responses in quantum and energy materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Exploring the energy landscape of RBMs: reciprocal space insights into bosons, hierarchical learning and symmetry breaking
Deep generative models have become ubiquitous due to their ability to learn and sample from complex distributions. Despite the proliferation of various frameworks, the relationships among these models remain largely unexplored, a gap that hinders the development of a unified theory of AI learning. In this work, we address two central challenges: clarifying the connections between different deep generative models and deepening our understanding of their learning mechanisms. We focus on Restricted Boltzmann Machines (RBMs), a class of generative models known for their universal approximation capabilities for discrete distributions. By introducing a reciprocal space formulation for RBMs, we reveal a connection between these models, diffusion processes, and systems of coupled bosons. Our analysis shows that at initialization, the RBM operates at a saddle point, where the local curvature is determined by the singular values of the weight matrix, whose distribution follows the Marc̆enko-Pastur law and exhibits rotational symmetry. During training, this rotational symmetry is broken due to hierarchical learning, where different degrees of freedom progressively capture features at multiple levels of abstraction. This leads to a symmetry breaking in the energy landscape, reminiscent of Landau’s theory. This symmetry breaking in the energy landscape is characterized by the singular values and the weight matrix eigenvector matrix. We derive the corresponding free energy in a mean-field approximation. We show that in the limit of infinite size RBM, the reciprocal variables are Gaussian distributed. Our findings indicate that in this regime, there will be some modes for which the diffusion process will not converge to the Boltzmann distribution. To illustrate our results, we trained replicas of RBMs with different hidden layer sizes using the MNIST dataset. Our findings not only bridge the gap between disparate generative frameworks but also shed light on the fundamental processes underpinning learning in deep generative models.
97 MATHEMATICS AND COMPUTING↗
Insights Into Seismicity Associated With Flexibly Operating Enhanced Geothermal System From Real‐Time Distributed Acoustic Sensing
Enhanced Geothermal Systems (EGS) have the capacity to broaden the accessible resource pool for geothermal power generation. Traditionally viewed as a “baseload” resource, their flexible operation might also enable dispatchable load‐following generation and long‐term energy storage, aligning them with the evolving landscape of decarbonized electricity systems. However, increasing permeability and extracting energy during EGS operations can induce microseismic events; for many prior EGS efforts, some associated seismicity has been observed. While energetically beneficial, the flexibility of EGS operations prompts our inquiry into whether new types of operations will yield previously unseen seismicity patterns. We demonstrate the use of distributed acoustic sensing (DAS) with real‐time edge computing to monitor seismicity during a pilot test of a cyclically operated EGS facility at the Blue Mountain geothermal field. Our focus lies in uncovering seismicity insights from the real‐time microseismic catalog, particularly during load‐following dispatchability tests simulating flexible EGS operation. Here, we find that variations in pore pressure consistently correlate with seismicity, and that controlling pressure cycles during flexible operations appears to constrain microseismic activity during subsequent cycles. The spatio‐temporal evolution of microseismic clouds recorded during cyclic injection cycles fits diffusive models over our available observation period. Additionally, seismicity elevation lags behind pore pressure increases, likely due to pressure diffusion to the fracture system boundary. Through real‐time monitoring, we offer novel insights into seismicity associated with flexibly operating EGS. Our findings suggest that leveraging DAS and edge computing can inform EGS operations and help mitigate induced seismicity.
Chamarczuk, Michal [Rice Univ., Houston, TX (Unite↗
Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics
To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.
Chemical structure↗
MoRE-Brain: Routed Mixture of Experts for Interpretable and Generalizable Cross-Subject fMRI Visual Decoding
Decoding visual experiences from fMRI offers a powerful avenue to understand human perception and develop advanced brain-computer interfaces. However, current progress often prioritizes maximizing reconstruction fidelity while overlooking interpretability, an essential aspect for deriving neuroscientific insight. To address this gap, we propose MoRE-Brain, a neuro-inspired framework designed for high-fidelity, adaptable, and interpretable visual reconstruction. MoRE-Brain uniquely employs a hierarchical Mixture-of-Experts architecture where distinct experts process fMRI signals from functionally related voxel groups, mimicking specialized brain networks. The experts are first trained to encode fMRI into the frozen CLIP space. A finetuned diffusion model then synthesizes images, guided by expert outputs through a novel dual-stage routing mechanism that dynamically weighs expert contributions across the diffusion process. MoRE-Brain offers three main advancements: First, it introduces a novel Mixture-of-Experts architecture grounded in brain network principles for neuro-decoding. Second, it achieves efficient cross-subject generalization by sharing core expert networks while adapting only subject-specific routers. Third, it provides enhanced mechanistic insight, as the explicit routing reveals precisely how different modeled brain regions shape the semantic and spatial attributes of the reconstructed image. Extensive experiments validate MoRE-Brain’s high reconstruction fidelity, with bottleneck analyses further demonstrating its effective utilization of fMRI signals, distinguishing genuine neural decoding from over-reliance on generative priors. Consequently, MoRE-Brain marks a substantial advance towards more generalizable and interpretable fMRI-based visual decoding.
Wei, Yuxiang [Georgia Institute of Technology]↗