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At least 1,153 records · Page 64

Securing Grid-interactive Efficient Buildings (GEB) through Cyber Defense and Resilient System (CYDRES)

The DOE CYDRES project is driven by the urgent need to address critical research gaps in the domain of cyber-physical security of smart buildings, including Grid-interactive Efficient Buildings (GEBs). CYDRES, a real-time advanced building resilient platform, aims to enhance the cyber-attack-immune capabilities of buildings through multi-layered prevention, detection, and adaptation mechanisms. CYDRES consists of five key modules: a multi-layer network analyzer, an Automatic Fault Detection, Diagnosis, and Prognosis (AFDDP) framework, an intelligent mode selector, a cyber-resilient control framework, and a situation awareness platform. The Network Analyzer employs a data-driven framework that includes a protocol state learning tool and a CRF (Conditional Random Field) command validator. In Hardware-In-the-Loop (HIL) testbeds, it achieved 100% detection accuracy with a false alarm rate of 3%, validating its efficacy in identifying selected cyber-attacks. The AFDDP framework leverages pattern matching, PCA (Principal Component Analysis)-based strategies, and a DBN (Dynamic Bayesian Network)-based fault diagnosis approach to pinpoint the causes of physical system abnormalities using Building Automation System (BAS) data. In HIL experiments, the AFDDP module attained a detection accuracy of over 95% with a false alarm rate below 7%. Additionally, the fault detector utilized machine learning (Random Forest) and deep learning (Multi-Layer Perceptron) methods with acoustic sensor data to achieve a 100% fault detection accuracy in Heating, Ventilation, and Air-Conditioning (HVAC) equipment. The Mode Selector offered real-time impact analysis, allowing immediate actions to protect BASs in the face of emerging threats. The cyber-resilient control framework included an adaptive Model Predictive Control (MPC) and a measurement compensator, reducing temperature violations by up to 94% and improving the total demand flexibility by up to 70% in HIL experiments. Such HIL experiments covered a cyber-attack case and a physical fault case, showcasing CYDRES’ efficiency in maintaining operational continuity during threats. The situation awareness platform in Grafana enhanced real-time threat detection and response visualization, augmenting the operational awareness for building operators. CYDRES demonstrated high technical effectiveness in various test scenarios, particularly in HIL environments. The project's phased development approach ensured efficient use of resources, highlighting its practical feasibility and readiness for commercialization. By enhancing the security and resilience of building operations, CYDRES represents a significant advance in mitigating risks associated with cyber-physical systems, thereby enhancing public confidence in the safety of modern building infrastructure. Future directions for the project include expanding testing protocols, refining AFDDP methodologies, exploring more comprehensive resilient control strategies, and testing in real commercial buildings.

42 ENGINEERING↗

Bayesian optimization with active learning of design constraints using an entropy-based approach

Abstract The design of alloys for use in gas turbine engine blades is a complex task that involves balancing multiple objectives and constraints. Candidate alloys must be ductile at room temperature and retain their yield strength at high temperatures, as well as possess low density, high thermal conductivity, narrow solidification range, high solidus temperature, and a small linear thermal expansion coefficient. Traditional Integrated Computational Materials Engineering (ICME) methods are not sufficient for exploring combinatorially-vast alloy design spaces, optimizing for multiple objectives, nor ensuring that multiple constraints are met. In this work, we propose an approach for solving a constrained multi-objective materials design problem over a large composition space, specifically focusing on the Mo-Nb-Ti-V-W system as a representative Multi-Principal Element Alloy (MPEA) for potential use in next-generation gas turbine blades. Our approach is able to learn and adapt to unknown constraints in the design space, making decisions about the best course of action at each stage of the process. As a result, we identify 21 Pareto-optimal alloys that satisfy all constraints. Our proposed framework is significantly more efficient and faster than a brute force approach.

36 MATERIALS SCIENCE↗

Bayes_Opt-SWMM: A Gaussian process-based Bayesian optimization tool for real-time flood modeling with SWMM

Real-time flood model plays a pivotal role in averting urban flood damage, particularly when there is minimal lead time for preparatory measures. However, urban flood modeling in real-time often contends with inherent uncertainties arising from input data uncertainty and parameter ambiguities. Here this study introduces a real-time calibration (RTC) tool called Bayes_Opt-SWMM, specifically tailored for real-time urban flood modeling and uncertainty optimization. This tool leverages the Gaussian process-based Bayesian optimization algorithm and interfaces seamlessly with the Stormwater Management Model (SWMM). It integrates real-time model forcing data and flood monitoring collected through sensors and gauges which are strategically placed within critical locations of urban drainage systems. Our approach hinges on the Surrogate Model based Uncertainty Optimization (SMUO) concept, providing an avenue for enhancing real-time flood modeling. Bayes_Opt-SWMM runs the optimization process using a surrogate model called Gaussian Process emulator with two inference methods: (1) the Gaussian Process (GP) model and (2) Markov Chain Monte Carlo (MCMC) algorithm in GP model (GP_MCMC). Furthermore, three acquisition functions, namely Expected Improvement (EI), Maximum Probability of Improvement (MPI), and Lower Confidence Bound (LCB), facilitate optimal parameter fitting within the surrogate models. The efficiency of GP-based surrogate models in learning SWMM model parameters, leads to an improved uncertainty quantification and accelerated real-time flood modeling in urban areas. Overall, Bayes_Opt-SWMM emerges as a cost-effective and valuable tool for real-time flood modeling and monitoring, with significant potential for managing intelligent storm water systems in urban environments.

54 ENVIRONMENTAL SCIENCES↗

MultiPEM Toolbox: User Manual [Rev. 2]

This document explains use of the Multi-Phenomenology Explosion Monitoring (Multi PEM) Toolbox, a collection of R scripts for estimating the unknown device parameters of a new event with uncertainty quantification. The methodology and application used for illustration in this user manual are fully documented in a Los Alamos National Laboratory technical report hereafter designated “WPA” for reference. Additional details on the application are found in a recent journal article. Two assessment types are available: rapid and complete. Rapid assessments are conducted in two stages, as described in Section 2. In the first stage, calibration data are used to estimate forward and error model parameters (WPA, §5.1) and (if relevant) errors-in-variables yield values for calibration sources (WPA, §3, Equation (3)). In the second stage, new event data are used to estimate the unknown new event device parameters (WPA, §5.2) with uncertainty quantification. Two options for treating the inferred first stage parameters in second stage Bayesian analysis are available: fixing them at their maximum likelihood estimate (default), or multiple imputation. Multiple imputation involves utilizing several posterior samples (imputations) of the first stage parameters as fixed values in the second stage posterior sampling of the new event device parameters. Second stage sampling is conducted across imputations in parallel to improve computational efficiency. This method produces improved uncertainty quantification of the new event device parameters compared with the default treatment of the first stage parameters, at the expense of additional computation. Complete assessments are conducted in a single stage, as described in Section 3. Calibration and (if relevant) new event data are used simultaneously to estimate all forward model, error model, and (if relevant) new event device parameters with uncertainty quantification on the latter. As the name suggests, rapid assessments generally run substantially faster than complete assessments (even with multiple imputation), because the results of first stage analysis can be stored and incorporated into estimating a relatively low-dimensional space of new event device parameters whenever relevant new event data becomes available. On the other hand, complete assessments must be run on the full set of model and device parameters with calibration and new event data every time the latter becomes available.

97 MATHEMATICS AND COMPUTING↗

Kriging-Based Inverse Uncertainty Quantification of BISON Fission Gas Release Model

Nuclear reactor fuel performance analysis studies the thermo-mechanical behavior of fuel rods and verify their compliance with safety criteria under both normal operation and accidental conditions. One of the major concerns in fuel performance analysis is the behavior of the fission gases xenon and krypton in uranium dioxide fuel, which significantly affect the thermo-mechanical performance of the nuclear fuel rods employed in current LWRs. Previously, the modeling of fission gas release (FGR) in nuclear fuel performance codes have been relying on empirical models which are not applicable beyond their range of calibration. Recently a more efficient and flexible physics-based FGR and swelling model that can describe a wider range of reactor operation conditions have been implemented in fuel performance code BISON. In this work, we performed Bayesian calibration to inversely quantify the uncertainties associated with the 5 tuning parameters in BISON FGR model, based on the time-dependent FGR measurement data from Riso-AN3 benchmark. It takes around 1 hour and 40 minutes for BISON to simulate the Riso-AN3 benchmark with a moderate mesh size using 32 processors. As hundreds of thousands of BISON simulations are needed during Markov Chain Monte Carlo (MCMC) sampling, running BISON directly is not a viable solution. Therefore we propose to use Kriging-based metamodels to replace BISON during MCMC sampling. Surrogate model is an approximation of the input/output relation of a computer code/model. It is also called metamodel, response surface, emulator. Surrogate models usually take much less computational time than the original model (like BISON) while maintaining the input/output relation of the original model to a desirable accuracy. Constructing the metamodels normally requires small number of executions of the original model. Once validated, metamodels can be used to perform uncertainty and sensitivity analysis, Bayesian calibration, optimization, etc.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Targeted materials discovery using Bayesian algorithm execution

Rapid discovery and synthesis of future materials requires intelligent data acquisition strategies to navigate large design spaces. A popular strategy is Bayesian optimization, which aims to find candidates that maximize material properties; however, materials design often requires finding specific subsets of the design space which meet more complex or specialized goals. We present a framework that captures experimental goals through straightforward user-defined filtering algorithms. These algorithms are automatically translated into one of three intelligent, parameter-free, sequential data collection strategies (SwitchBAX, InfoBAX, and MeanBAX), bypassing the time-consuming and difficult process of task-specific acquisition function design. Our framework is tailored for typical discrete search spaces involving multiple measured physical properties and short time-horizon decision making. We demonstrate this approach on datasets for TiO 2 nanoparticle synthesis and magnetic materials characterization, and show that our methods are significantly more efficient than state-of-the-art approaches. Overall, our framework provides a practical solution for navigating the complexities of materials design, and helps lay groundwork for the accelerated development of advanced materials.

42 ENGINEERING↗

Explainable multi-fidelity Bayesian neural network for distribution system state estimation

Distribution System State Estimation (DSSE) is frequently constrained by limited real-time measurements, the uncertainties introduced by distributed energy resources, and the presence of bad data. To address them, this paper proposes an enhanced Multi-Fidelity Bayesian Neural Network (MFBNN) DSSE approach. A low-fidelity layer based on a Deep Neural Network (DNN) is first pre-trained on pseudo-measurement data to learn fundamental state features. Subsequently, a high-fidelity Bayesian Neural Network (BNN) layer leverages limited but high-quality real-time measurements to refine these features, thereby achieving accurate DSSE. Additionally, the deep SHapley Additive exPlanation (SHAP) is developed to quantify the influence of measurement data on DSSE through dual perspectives of global feature importance and local nodal contributions, establishing a hierarchical explainability framework for machine learning-based DSSE. Comparative studies conducted on the IEEE 13-bus system and a real-world 2135-node system from Dominion Energy demonstrate that the proposed method excels in estimation accuracy, even under situations of high noise levels, bad data, and missing data. Further comparisons with Weighted Least Squares (WLS) and other machine learning-based DSSE approaches verify that the proposed framework offers higher accuracy, improved interpretability, and enhanced robustness.

Bad data↗

A score-based diffusion model approach for adaptive learning of stochastic partial differential equation solutions

In this paper, we propose a novel framework for adaptively learning the time-evolving solutions of stochastic partial differential equations (SPDEs) using score-based diffusion models within a recursive Bayesian inference setting. SPDEs play a central role in modeling complex physical systems under uncertainty, but their numerical solutions often suffer from model errors and reduced accuracy due to incomplete physical knowledge and environmental variability. To address these challenges, we encode the governing physics into the score function of a diffusion model using simulation data and incorporate observational information via a likelihood-based correction in a reverse-time stochastic differential equation. This enables adaptive learning through iterative refinement of the solution as new data becomes available. To improve computational efficiency in high-dimensional settings, we introduce the ensemble score filter, a training-free approximation of the score function designed for real-time inference. Numerical experiments on benchmark SPDEs demonstrate the accuracy and robustness of the proposed method under sparse and noisy observations.

97 MATHEMATICS AND COMPUTING↗

Applying Bayesian inference and deterministic anisotropy to retrieve the molecular structure ∣Ψ(R)∣2 distribution from gas-phase diffraction experiments

Abstract Currently, our general approach to retrieving molecular structures from ultrafast gas-phase diffraction heavily relies on complex ab initio electronic or vibrational excited state simulations to make conclusive interpretations. Without such simulations, inverting this measurement for the structural probability distribution is typically intractable. This creates a so-called inverse problem. Here we address this inverse problem by developing a broadly applicable method that approximates the molecular frame structure ∣Ψ( R , t )∣ 2 distribution independent of these complex simulations. We retrieve the vibronic ground state ∣Ψ( R )∣ 2 for both simulated stretched NO 2 and measured N 2 O. From measured N 2 O, we observe 40 mÅ coordinate-space resolution from 3.75 Å −1 reciprocal space range and poor signal-to-noise, a 50X improvement over traditional Fourier transform methods. In simulated NO 2 diffraction experiments, typical to high signal-to-noise levels predict 100–1000X resolution improvements, down to 0.1 mÅ. By directly measuring the width of ∣Ψ( R )∣ 2 , we open ultrafast gas-phase diffraction capabilities to measurements beyond current analysis approaches. This method has the potential to effectively turn gas-phase ultrafast diffraction into a discovery-oriented technique to probe systems that are prohibitively difficult to simulate.

74 ATOMIC AND MOLECULAR PHYSICS↗

Identifying microbial drivers in biological phenotypes with a Bayesian network regression model

Abstract In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions in the brain that are associated with specific human traits, yet their potential to elucidate microbial drivers in biological phenotypes for microbiome research remains unknown. In particular, microbial networks are challenging due to their high dimension and high sparsity compared to brain networks. Furthermore, unlike in brain connectome research, in microbiome research, it is usually expected that the presence of microbes has an effect on the response (main effects), not just the interactions. Here, we develop the first thorough investigation of whether Bayesian Network Regression models are suitable for microbial datasets on a variety of synthetic and real data under diverse biological scenarios. We test whether the Bayesian Network Regression model that accounts only for interaction effects (edges in the network) is able to identify key drivers (microbes) in phenotypic variability. We show that this model is indeed able to identify influential nodes and edges in the microbial networks that drive changes in the phenotype for most biological settings, but we also identify scenarios where this method performs poorly which allows us to provide practical advice for domain scientists aiming to apply these tools to their datasets. BNR models provide a framework for microbiome researchers to identify connections between microbes and measured phenotypes. We allow the use of this statistical model by providing an easy‐to‐use implementation which is publicly available Julia package at https://github.com/solislemuslab/BayesianNetworkRegression.jl .

59 BASIC BIOLOGICAL SCIENCES↗

Decision-Making Under Uncertainty for a Digital Thread-Enabled Design Process

Abstract Digital thread is a data-driven architecture that links together information from all stages of the product lifecycle. Despite increasing application in manufacturing, maintenance/operations, and design related tasks, a principled formulation of analyzing the decision-making problem under uncertainty for the digital thread remains absent. The contribution of this article is to present a formulation using Bayesian statistics and decision theory. First, we address how uncertainty propagates in the product lifecycle and how the digital thread evolves based on the decisions we make and the data we collect. By using these mechanics, we explore designing over multiple product generations or iterations and provide an algorithm to solve the underlying multistage decision problem. We illustrate our method on an example structural design problem where our method can quantify and optimize different types and sequences of decisions, ranging from experimentation, manufacturing, and sensor placement/selection, to minimize total accrued costs.

Engineering↗

Near-IR Transmission Spectrum of HAT-P-32b using HST/WFC3

We report here the analysis of the near-infrared transit spectrum of the hot Jupiter HAT-P-32b, which was recorded with the Wide Field Camera 3 (WFC3) on board the Hubble Space Telescope. HAT-P-32b is one of the most inflated exoplanets discovered, making it an excellent candidate for transit spectroscopic measurements. To obtain the transit spectrum, we have adopted different analysis methods, both parametric and non-parametric (Independent Component Analysis, ICA), and compared the results. The final spectra are all consistent within 0.5σ. The uncertainties obtained with ICA are larger than those obtained with the parametric method by a factor of ∼1.6–1.8. This difference is the trade-off for higher objectivity due to the lack of any assumption about the instrument systematics compared to the parametric approach. The ICA error bars are therefore worst-case estimates. To interpret the spectrum of HAT-P-32b we used T-REx, our fully Bayesian spectral retrieval code. As for other hot Jupiters, the results are consistent with the presence of water vapor (logH{sub 2}O=−3.45{sub −1.65}{sup +1.83}), clouds (top pressure between 5.16 and 1.73 bar). Spectroscopic data over a broader wavelength range are needed to de-correlate the mixing ratio of water vapor from clouds and identify other possible molecular species in the atmosphere of HAT-P-32b.

79 ASTRONOMY AND ASTROPHYSICS↗

Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET

Abstract. The ability to monitor, understand, and predict the dynamics of the terrestrial carbon cycle requires the capacity to robustly and coherently synthesize multiple streams of information that each provide partial information about different pools and fluxes. In this study, we introduce a new terrestrial carbon cycle data assimilation system, built on the PEcAn model–data eco-informatics system, and its application for the development of a proof-of-concept carbon “reanalysis” product that harmonizes carbon pools (leaf, wood, soil) and fluxes (GPP, Ra, Rh, NEE) across the contiguous United States from 1986–2019. We first calibrated this system against plant trait and flux tower net ecosystem exchange (NEE) using a novel emulated hierarchical Bayesian approach. Next, we extended the Tobit–Wishart ensemble filter (TWEnF) state data assimilation (SDA) framework, a generalization of the common ensemble Kalman filter which accounts for censored data and provides a fully Bayesian estimate of model process error, to a regional-scale system with a calibrated localization. Combined with additional workflows for propagating parameter, initial condition, and driver uncertainty, this represents the most complete and robust uncertainty accounting available for terrestrial carbon models. Our initial reanalysis was run on an irregular grid of ∼ 500 points selected using a stratified sampling method to efficiently capture environmental heterogeneity. Remotely sensed observations of aboveground biomass (Landsat LandTrendr) and leaf area index (LAI) (MODIS MOD15) were sequentially assimilated into the SIPNET model. Reanalysis soil carbon, which was indirectly constrained based on modeled covariances, showed general agreement with SoilGrids, an independent soil carbon data product. Reanalysis NEE, which was constrained based on posterior ensemble weights, also showed good agreement with eddy flux tower NEE and reduced root mean square error (RMSE) compared to the calibrated forecast. Ultimately, PEcAn's new open-source regional data assimilation framework provides a scalable workflow for harmonizing multiple data constraints and providing a uniform synthetic platform for carbon monitoring, reporting, and verification (MRV) as well as accelerating terrestrial carbon cycle research.

54 ENVIRONMENTAL SCIENCES↗

Optimal Experimental Design for Inverse Problems in the Presence of Observation Correlations

Optimal experimental design (OED) is the general formalism of sensor placement and decisions on the data collection strategy for engineered or natural experiments. This problem is prevalent in many critical fields such as battery design, numerical weather prediction, geosciences, environmental and urban studies. State-of-the-art computational methods for experimental design do not accommodate correlation structure in observational errors produced by many expensive-to-operate devices such as X-ray machines, radars, and satellites. Discarding evident data correlations leads to biased results, higher expenses, and waste of valuable resources. We present a general formulation of the OED formalism for model-constrained large-scale Bayesian linear inverse problems, where measurement errors are generally correlated. The proposed approach utilizes the Hadamard product of matrices to formulate the weighted-likelihood, and is valid for both finite as well as infinite-dimensional Bayesian inverse problems. Extensive numerical experiments are carried out for empirical verification of the proposed approach using an advection-diffusion model, where the objective is to optimally place a small set of sensors, under a limited budget, to predict the concentration of a contaminant in a closed and bounded domain.

Correlated observations↗

PINN surrogate of Li-ion battery models for parameter inference, Part II: Regularization and application of the pseudo-2D model

Bayesian parameter inference is useful to improve Li-ion battery diagnostics and can help formulate battery aging models. However, it is computationally intensive and cannot be easily repeated for multiple cycles, multiple operating conditions, or multiple replicate cells. To reduce the computational cost of Bayesian calibration, numerical solvers for physics-based models can be replaced with faster surrogates. A physics-informed neural network (PINN) is developed as a surrogate for the pseudo-2D (P2D) battery model calibration. For the P2D surrogate, additional training regularization was needed as compared to the PINN single-particle model (SPM) developed in Part I. Both the PINN SPM and P2D surrogate models are exercised for parameter inference and compared to data obtained from a direct numerical solution of the governing equations. A parameter inference study highlights the ability to use these PINNs to calibrate scaling parameters for the cathode Li diffusion and the anode exchange current density. By realizing computational speed-ups of ~2250x for the P2D model, as compared to using standard integrating methods, the PINN surrogates enable rapid state-of-health diagnostics. Finally, in the low-data availability scenario, the testing error was estimated to ~2 mV for the SPM surrogate and ~10 mV for the P2D surrogate which could be mitigated with additional data.

25 ENERGY STORAGE↗

Maternal exposure to ozone and PM{sub 2.5} and the prevalence of orofacial clefts in four U.S. states

Background: While there is some evidence that maternal exposure to ambient air pollution is associated with orofacial clefts in offspring, the epidemiologic studies have been largely equivocal. We evaluated whether maternal exposure to elevated county-level ambient fine particulate matter with aerodynamic diameter ≤2.5 µm (PM{sub 2.5}) and ozone during early gestation was associated with a higher prevalence of orofacial clefts. Methods: Birth data consisting of 4.7 million births from 2001 to 2007 were obtained from National Birth Defects Prevention Network for four states — Arizona, Florida, New York (excluding New York City), and Texas. The air pollution exposure assessment for gestational weeks 5–10 was based on county-level average concentrations of PM{sub 2.5} and ozone data generated using a Bayesian fusion model available through CDC's Environmental Public Health Tracking Network. Two outcomes were analyzed separately: cleft lip with or without cleft palate, cleft palate alone. In logistic regression analyses, we adjusted for factors that were suspected confounders or modifiers of the association between the prevalence of orofacial clefts and air pollution, i.e., infant sex, race-ethnicity, maternal education, smoking status during pregnancy, whether this was mother's first baby, maternal age. Results: Each 10 µg/m{sup 3} increase in PM{sub 2.5} concentration was significantly associated with cleft palate alone (OR =1.43, 95% CI: 1.11–1.86). There was no significant association between PM{sub 2.5} concentration and cleft lip with or without cleft palate. No associations were observed between ozone exposure and the two outcomes of orofacial clefts. Conclusions: Our study suggests that PM{sub 2.5} significantly increased the risk of cleft palate alone, but did not change the incidence of cleft lip with or without palate. Ozone levels did not correlate with incidence of orofacial clefts. - Highlights: • This is a large study with about 4.7 million births and 7000 orofacial cleft cases. • PM{sub 2.5} significantly increased the risk of cleft palate alone. • PM{sub 2.5} did not change the incidence of cleft lip with or without palate. • Ozone levels did not correlate with incidence of orofacial clefts.

54 ENVIRONMENTAL SCIENCES↗

Play fairway analysis of geothermal resources across the state of Hawaii: 2. Resource probability mapping

We develop a new geostatistical method to combine evidence provided by diverse geological data sets and produce maps of geothermal resource probability. The application is to the State of Hawaii, and the data sets include the locations and ages of mapped volcanic centers, gravity and magnetotelluric measurements, groundwater temperature and geochemistry, ground surface deformation, seismicity, water table elevation, and groundwater recharge. Using the basic principles of Bayesian statistics, these data and expert knowledge about the effects and importance of the data are used to compute the probabilities of the primary resource qualities of elevated subsurface heat, reservoir permeability, and reservoir fluid content. The product of these marginal probabilities estimates the joint probability of all three qualities and hence the probability of a successful geothermal prospect at each map point. An analogous set of algorithms is used to quantify the confidence in the probability at each point. Not surprisingly, we find that successful geothermal prospects are most probable on the active volcanoes of Hawaii Island, including the area of Hawaii’s single geothermal energy plant. Probability decreases primarily with shield volcano age, being relatively moderate in select locations on Maui and Lanai, relatively low on Oahu, and minimal on Kauai. Future exploration efforts should consider these results as well as the practical, societal, and economic conditions that influence development viability. Here, the difficulties of interisland power transmission mean that even areas with moderate to low probabilities are worth investigating on islands with population centers.

15 GEOTHERMAL ENERGY↗

Finding Our Way in the Dark Proteome

The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. In conclusion, we envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗