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At least 37 records · Page 2

FunDiff: diffusion models over function spaces for physics-informed generative modeling

Recent advances in generative modeling-particularly diffusion models and flow matching-have been widely used for synthesizing discrete data such as images and videos. However, adapting these models to physical applications remains challenging, as the quantities of interest are continuous functions governed by complex physical laws. To address this, we introduce FunDiff, an efficient and robust framework for generative modeling in function spaces. FunDiff combines a latent diffusion process with a function autoencoder architecture to handle input functions with varying discretizations, generates continuous functions that can be evaluated at arbitrary locations, and seamlessly incorporate physical priors. These priors are enforced through architectural constraints or physics-informed loss functions, ensuring that generated samples satisfy fundamental physical laws. We theoretically establish minimax optimality guarantees for density estimation in function spaces, demonstrating that diffusion-based estimators achieve optimal convergence rates under suitable regularity conditions. We further demonstrate the practical effectiveness of FunDiff across diverse applications in fluid dynamics and solid mechanics. Empirical results indicate that our method can generate physically consistent samples with high fidelity to the target distribution, and exhibit robustness to noisy and low-resolution data.

Wang, Sifan [Yale University, New Haven, CT (Unite↗

Machine‐learning‐based construction of barrier functions and models for safe model predictive control

Abstract In this paper, we propose a control Lyapunov‐barrier function‐based model predictive control method utilizing a feed‐forward neural network specified control barrier function (CBF) and a recurrent neural network (RNN) predictive model to stabilize nonlinear processes with input constraints, and to guarantee that safety requirements are met for all times. The nonlinear system is first modeled using RNN techniques, and a CBF is characterized by constructing a feed‐forward neural network (FNN) model with unique structures and properties. The FNN model for the CBF is trained based on data samples collected from safe and unsafe operating regions, and the resulting FNN model is verified to demonstrate that the safety properties of the CBF are satisfied. Given sufficiently small bounded modeling errors for both the FNN and the RNN models, the proposed control system is able to guarantee closed‐loop stability while preventing the closed‐loop states from entering unsafe regions in state‐space under sample‐and‐hold control action implementation. We provide the theoretical analysis for bounded unsafe sets in state‐space, and demonstrate the effectiveness of the proposed control strategy using a nonlinear chemical process example with a bounded unsafe region.

Chen, Scarlett↗

Least H 2 norm updating of quadratic interpolation models for derivative-free trust-region algorithms

One particular class of derivative-free optimization algorithms is trust-region algorithms based on quadratic models given by the under-determined interpolation. Different techniques in updating the quadratic model from iteration to iteration will give different interpolation models. We propose a new way to update the quadratic model by minimizing the $H^{2}$ norm of the difference between neighboring quadratic models. The motivation for applying the $H^{2}$ norm is given. The theoretical properties of our new updating technique are also presented. We propose the projection in the sense of $H^{2}$ norm and the interpolation error analysis of our model function. We obtain the coefficients of the quadratic model function using the Karush–Kuhn–Tucker (KKT) conditions. Numerical results show the advantages of our model on the test set considered, and the derivative-free algorithms based on our least $H^{2}$ norm updating quadratic model functions can solve test problems with fewer function evaluations than the algorithm based on the least Frobenius norm updating model and the other compared methods.

derivative-free optimization↗

Multiobjective Optimal Controlled Variable Selection for a Gas Turbine–Solid Oxide Fuel Cell System Using a Multiagent Optimization Platform

Hybrid gas turbine–fuel cell systems have immense potential for high efficiency in electrical power generation with cleaner emissions compared with fossil-fueled power generation. We report a systematic controlled variable (CV) selection method is deployed for a hybrid gas turbine–fuel cell system in the HyPer (hybrid performance) facility at the U.S. Department of Energy’s National Energy Technology Laboratory (NETL) for maximizing its economic and control performance. A three-stage approach is used for the CV selection comprising a priori analysis, multiobjective optimization, and a posteriori analysis. The a priori analysis helps to screen off several candidate CVs, thus reducing the size of the combinatorial optimization problem for multiobjective CV selection. For optimal CV selection, a transfer function model of the HyPer facility is identified. By considering several candidate models, the final transfer function model is selected using Akaike’s Final Prediction Error criterion. Experimental data from the HyPer facility are used to estimate the noise in the measurement data. For solving the combinatorial multiobjective optimization problem for CV selection, a multiagent optimization platform comprising simulated annealing, genetic algorithm, and efficient ant colony optimization algorithms is used. Pareto-optimal CV sets exhibit a high trade-off between the economic and control objective. The a posteriori analysis is undertaken for several top Pareto-optimal CV sets. An optimal CV set is selected that shows the best compromise between process economics and controllability under both nominal and off-design conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Significance of Aggregation Methods in Functional Group Modeling

The growth of forests and the feedbacks between forests and environmental changes are central issues in the planetary carbon cycle, global climate change, and basic plant ecology. A challenge to understanding both growth and feedbacks from local to global scales is that many critical metabolic processes vary among species. An innovation in solving this challenge is the recognition that species can be lumped into “functional groups” based on metabolic similarity, and these functional groups can then be studied in computational models that simulate ecosystem function. Despite the vast resources devoted to functional group studies and the progress made by them, an important logical and biological question has not been formally addressed, “How do the groupings alter the results of modeling studies?” To what extent do modeling results depend on the choices made in aggregating taxa into functional groups. Here, we consider the effects of using different aggregation strategies in simulating the carbon dynamics of a deciduous forest. Understanding the impacts that aggregation strategy has on efforts to simulate regional-to-global-scale forest dynamics offers insights into both ecosystem regulation and model function and addresses this central problem in the study of carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗

RootSlice —A novel functional-structural model for root anatomical phenotypes

Root anatomy is an important determinant of root metabolic costs, soil exploration, and soil resource capture. Root anatomy varies substantially within and among plant species. RootSlice is a multicellular functional-structural model of root anatomy developed to facilitate the analysis and understanding of root anatomical phenotypes. RootSlice can capture phenotypically accurate root anatomy in three dimensions of different root classes and developmental zones, of both monocotyledonous and dicotyledonous species. Several case studies are presented illustrating the capabilities of the model. For maize nodal roots, the model illustrated the role of vacuole expansion in cell elongation; and confirmed the individual and synergistic role of increasing root cortical aerenchyma and reducing the number of cortical cell files in reducing root metabolic costs. Integration of RootSlice for different root zones as the temporal properties of the nodal roots in the whole-plant and soil model OpenSimRoot/maize enabled the multiscale evaluation of root anatomical phenotypes, highlighting the role of aerenchyma formation in enhancing the utility of cortical cell files for improving plant performance over varying soil nitrogen supply. Such integrative in silico approaches present avenues for exploring the fitness landscape of root anatomical phenotypes.

59 BASIC BIOLOGICAL SCIENCES↗

Defect Thermodynamics and Transport Properties of Proton Conducting Perovskite Electrode and Electrolyte Materials Evaluated Based on Density Functional Theory Modeling

Both electron-rich and electron-poor perovskite oxides have been used in solid oxide cell applications as electrode and electrolyte materials. The rich oxygen defect chemistry and its coupling to temperature, hydrogen-steam or oxygen-steam gas pressure, or to the applied potentials creates enormous complexities for modeling performance and degradation of the materials. Herein, density functional theory-based thermodynamic modeling was carried out to describe the defect chemistry and transport properties of the proton-conducting electrolyte BaZr1-xYxO3-δ (x≤0.1) and of the triple-conducting perovskite (La,Ba)(Fe,M)O3-δ (M=Y and Zr). The defect thermodynamics of intrinsic point defects and the hydrogen-related defect reactions were solved in integrated defect models and further used to predict the Brouwer diagram and the transport properties of the functional perovskites. For the electron-poor electrolytes BaZr0.9Y0.1O3-δ, the developed model has been used to describe the experimental transport properties in the SOC operating conditions. Specifically, the roles played by the acceptor-bound holes and the intrinsic and hydrogen point defects upon the conductivities of holes, protons, and oxygen vacancies under the hydrogen-rich and oxygen-rich conditions at various humidity levels were demonstrated. A defect modeling tool was also developed for the triple-conducting perovskite (La,Ba)(Fe,M)O3-δ (M=Y and Zr) to examine magnetic effects and hydride defects in defect equilibria.

defect thermodynamics↗

Large language models generate functional protein sequences across diverse families

Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here, in this paper, we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.

59 BASIC BIOLOGICAL SCIENCES↗

Landmark-Warped Emulators for Models with Misaligned Functional Response

Many computer models output functional data, and in some cases, these functional data have similar, but misaligned, shape characteristics. In this paper, we introduce a general approach for building emulators for computer models that output misaligned functional data when key values in the functional response (landmarks) can be easily identified. This approach has two main parts: modeling the aligned (using the landmarks) functional data, and modeling the functions that map the misaligned data to the aligned space (warping functions). As the warping functions are required to be monotonic, we give special attention to modeling monotonic functional response data. We discuss how our approach can be easily applied for a variety of typical emulators, such as Gaussian processes, Bayesian multivariate adaptive regression splines, and Bayesian additive regression trees, and how sensitivity analysis can be performed. We demonstrate our approach by building emulators for two applications: (1) a high-energy-density physics computer model used to simulate inertial confinement fusion ignition experiments, where model outputs are highly misaligned, and (2) a multiphysics continuum hydrocode used to simulate high-velocity impact experiments, where model outputs are only slightly misaligned. In case (1) traditional methods cannot be applied, while in (2) they can be applied, but the proposed method performs significantly better.

97 MATHEMATICS AND COMPUTING↗

Landmark-embedded Gaussian process with applications for functional data modeling

In practice, we often need to infer the value of a target variable from functional observation data. A challenge in this task is that the relationship between the functional data and the target variable is very complex: the target variable not only influences the shape but also the location of the functional data. In addition, due to the uncertainties in the environment, the relationship is probabilistic, that is, for a given fixed target variable value, we still see variations in the shape and location of the functional data. To address this challenge, we present a landmark-embedded Gaussian process model that describes the relationship between the functional data and the target variable. A unique feature of the model is that landmark information is embedded in the Gaussian process model so that both the shape and location information of the functional data are considered simultaneously in a unified manner. Gibbs-Metropolis-Hasting algorithm is used for model parameters estimation and target variable inference. The performance of the proposed framework is evaluated by extensive numerical studies and a case study of nano-sensor calibration.

42 ENGINEERING↗

Dynamic Rupture Modeling of the 1999 Chi-Chi, Taiwan Earthquake Using 3DFinite Element Method. Sensitivity Analysis of Slip Rate Function to Model Parameters of Crustal Weak-Zone

The main objective of this study was the dynamic rupture modeling of the M7.3 1999 Chi-Chi, Taiwan earthquake. The purpose of the numerical modeling was two folded. First, using models of rupture dynamics, derive kinematic rupture characteristics, including spatial and temporal variations of the slip rate time history and rupture speed, in the long-period ground motion generation area (LMGA), strong motion generation areas (SMGAs) and background fault area for a thrust shallow rupture. Second, investigate the sensitivity of source time function characteristics in the LMGA and SMGA areas to model parameterization of low-velocity weak zone, such as thickness and shear wave velocity.

58 GEOSCIENCES↗

Can Cooling and Heating Functions Be Modeled with Homogeneous Radiation Fields?

Abstract Cooling and heating functions describe how radiative processes impact the thermal state of a gas as a function of its temperature and other physical properties. In a most general case the functions depend on the detailed distributions of ionic species and on the radiation spectrum. Hence, these functions may vary on a very wide range of spatial and temporal scales. In this paper, we explore cooling and heating functions between 5 ≤ z ≤ 10 in simulated galaxies from the Cosmic Reionization On Computers project. We compare three functions: (1) the actual cooling and heating rates of hydrodynamic cells as a function of cell temperature, (2) the median cooling and heating functions computed using median interstellar medium (ISM) properties (median ISM), and (3) the median of the cooling and heating functions of all gas cells (instantaneous). We find that the median ISM and instantaneous approaches to finding a median cooling and heating function give identical results within the spread due to cell-to-cell variation. However, the actual cooling (heating) rates experienced by the gas at different temperatures in the simulations do not correspond to either summarized cooling (heating) functions. In other words, the thermodynamics of the gas in the simulations cannot be described by a single set of a cooling plus a heating function with a spatially constant radiation field that could be computed with common tools, such as CLOUDY.

79 ASTRONOMY AND ASTROPHYSICS↗

EPR and 31 P ENDOR Characterization of Pseudo-Jahn–Teller Dynamics and N 2 Activation in Functional Nitrogenase Models, P 3 E M(N 2 ) (M = Fe, Co; E = Si, B, C)

Here, the nominally trigonal, pseudo-Jahn-Teller (PJT)-active, S = ½ N 2 -bound transition-metal complexes, P 3 E M(N 2 ), M = Fe, Co, with three in-plane phosphine-ligands and axial donors, E = Si, B, C, include functional nitrogenase models that catalyze reduction of N 2 to NH 3 . We applied EPR, 31 P ENDOR spectroscopy and DFT computations to characterize the PJT-induced distortions of four selected P 3 E M(N 2 ), revealing how the metal-ion and axial ligand E together tune both PJT dynamics and N 2 activation for reduction. Comparisons reveal an unrecognized correlation between PJT distortion, M-E bond elasticity, and N 2 activation, providing guidelines for designing bioinspired N 2 -reduction catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scalable Volume Visualization for Big Scientific Data Modeled by Functional Approximation

Considering the challenges posed by the space and time complexities in handling extensive scientific volumetric data, various data representations have been developed for the analysis of large-scale scientific data. Multivariate functional approximation (MFA) is an innovative data model designed to tackle substantial challenges in scientific data analysis. It computes values and derivatives with high-order accuracy throughout the spatial domain, mitigating artifacts associated with zero- or first-order interpolation. However, the slow query time through MFA makes it less suitable for interactively visualizing a large MFA model. In this work, we develop the first scalable interactive volume visualization pipeline, MFA-DVV, for the MFA model encoded from large-scale datasets. Our method achieves low input latency through distributed architecture, and its performance can be further enhanced by utilizing a compressed MFA model while still maintaining a high-quality rendering result for scientific datasets. We conduct comprehensive experiments to show that MFA-DVV can decrease the input latency and achieve superior visualization results for big scientific data compared with existing approaches.

big scientific dataset↗

Structural models and functional annotations for the Sphagnum divinum proteome

This dataset contains the structural models for the primary transcripts of the Sphagnum divinum proteome. Additionally, for a subset of these proteins, sequence and structural alignment results are provided. This dataset represents the most thorough structural study of a Sphagnum species, also known as peat mosses, by providing three-dimensional atomic resolution structures of the majority of the encoded proteins as well as structural alignment results used in the application of annotating the proteome. References (DOI) AlphaFold v2 Monomer: https://doi.org/10.1038/s41586-021-03819-2. References (DOI) US-align2: https://doi.org/10.1038/s41592-022-01585-1

59 BASIC BIOLOGICAL SCIENCES↗

Atomic-Layer-Deposited Aluminum Oxide Thin Films Probed with X-ray Scattering and Compared to Molecular Dynamics and Density Functional Theory Models

A better understanding of amorphous aluminum oxide’s structure and electronic properties is obtained through combined experimental and computational approaches. Grazing incidence X-ray scattering measurements were carried out on aluminum oxide thin films grown using thermal atomic layer deposition. The corresponding pair distribution functions (PDFs) showed structures similar to previously reported PDFs of solid-state amorphous alumina and molten alumina. Structural models based on crystalline alumina polymorphs (PDFgui) and amorphous alumina (molecular dynamics, MD) were examined for structural comparisons to the experimental PDF data. Smaller MD models were optimized and verified against larger models to allow for quantum chemical electronic structure calculations. The electronic structure of the amorphous alumina models yields additional insight into the band structure and electronic defects present in amorphous alumina that are not present in crystalline samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗