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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET derived 3D segmented volumes as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the “dark complex,” modulate metabolic flux at a conserved regulatory node of the Calvin–Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.

Johnson, Connah G.↗
DOE OSTI2024

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando↗
DOE OSTI2022

A modified Susceptible-Infected-Recovered model for observed under-reported incidence data

Fitting Susceptible-Infected-Recovered (SIR) models to incidence data is problematic when not all infected individuals are reported. Assuming an underlying SIR model with general but known distribution for the time to recovery, this paper derives the implied differential-integral equations for observed incidence data when a fixed fraction of newly infected individuals are not observed. The parameters of the resulting system of differential equations are identifiable. Using these differential equations, we develop a stochastic model for the conditional distribution of current disease incidence given the entire past history of reported cases. We estimate the model parameters using Bayesian Markov Chain Monte-Carlo sampling of the posterior distribution. We use our model to estimate the transmission rate and fraction of asymptomatic individuals for the current Coronavirus 2019 outbreak in eight American Countries: the United States of America, Brazil, Mexico, Argentina, Chile, Colombia, Peru, and Panama, from January 2020 to May 2021. Our analysis reveals that the fraction of reported cases varies across all countries. For example, the reported incidence fraction for the United States of America varies from 0.3 to 0.6, while for Brazil it varies from 0.2 to 0.4.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Identifying Hydropower Operational Flexibilities in Presence of Streamflow and Net-load Uncertainty (Final Technical report)

In the existing operations, hydropower contributions to future system flexibility are generally modeled while maintaining traditional operating rules and constraints in supporting grid operation, such as the balancing of variable renewable energy production. Moreover, operation of large scale hydropower systems on major rivers has been investigated for decades, utilizing various systems engineering approaches, with the evolving electric grid, as the result of renewable resources integration, compounded by the changing climate (variability of river flows, intensification of hydrologic cycle resulting in more frequent extreme events) affecting water availability, the need for more advanced stochastic modeling and effective uncertainty analysis approaches have become necessary. The research results supported by this funding and presented in this report provide a new look at hydropower operational flexibility enforced by the changes identified above. Understanding how hydropower operates in response to the underlying uncertainties with respect to the system constraints is crucial in identifying its operational flexibility potentials. In this project, the flexibility of the operating hydropower facility is described by capturing uncertainties in both water and power system and formulating the operations as a multistage stochastic optimization problem. The proposed approach supports short- to seasonal-term operations and planning decision horizons.

13 HYDRO ENERGY↗
DOE OSTI2023

Predicting rare events using neural networks and short-trajectory data

Estimating the likelihood, timing, and nature of events is a major goal of modeling stochastic dynamical systems. When the event is rare in comparison with the timescales of simulation and/or measurement needed to resolve the elemental dynamics, accurate prediction from direct observations becomes challenging. In such cases a more effective approach is to cast statistics of interest as solutions to Feynman-Kac equations (partial differential equations). Here, we develop an approach to solve Feynman-Kac equations by training neural networks on short-trajectory data. Our approach is based on a Markov approximation but otherwise avoids assumptions about the underlying model and dynamics. This makes it applicable to treating complex computational models and observational data. Additionally, we illustrate the advantages of our method using a low-dimensional model that facilitates visualization, and this analysis motivates an adaptive sampling strategy that allows on-the-fly identification of and addition of data to regions important for predicting the statistics of interest. Finally, we demonstrate that we can compute accurate statistics for a 75-dimensional model of sudden stratospheric warming. This system provides a stringent test bed for our method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Methods to Evaluate Subcolumn Profiles Based on Two-Point Diagnostics

In atmospheric models, stochastic generation of subgrid-scale profiles or “subcolumns” has been used for a variety of purposes. Such subcolumns can be generated from subgrid probability density functions (PDFs) at different vertical levels, when such PDFs are available. To do so, the generator needs to decide how strongly points should be correlated in the vertical, that is, how much the values should be overlapped. This is sometimes called “PDF overlap.” To assess vertical correlation in a simplified, observable setting, here the vertical correlation of vertical velocity in subcloud layers is examined. Doppler lidar is used to evaluate the vertical profiles of vertical velocity produced by a large-eddy simulation (LES) model and the Subgrid Importance Latin Hypercube Sampler (SILHS) subcolumn generator. In order to diagnose unrealistic features in subcolumn profiles, various statistical diagnostics are examined here, including the bivariate PDF of vertical velocity at two separated points (i.e., altitudes), the two-point velocity correlation, the integral correlation length, the PDF of two-point velocity differences, and the skewness and kurtosis of two-point velocity differences. The profiles produced by LES match lidar well, except that they are too smooth at small scales. The profiles produced by SILHS exhibit sharp jumps from updraft to downdraft that are not observed in the lidar data. To reduce the generation of these unrealistically sharp jumps, the SILHS sampling method is revised. The diagnostics confirm that the revised sampling method reduces the overprediction of sharp jumps.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Stochastic scheduling of generating units with weekly energy storage: A hybrid decomposition approach

We propose a solution method for the large-scale stochastic unit commitment (SUC) problem with weekly-dispatched energy storage and significant weather-dependent stochastic generating capacity. Weekly storage facilities that mostly charge during weekends and discharge during weekdays require a weekly scheduling of generating units, which result in a large-scale optimization problem. This SUC problem is formulated as a two-stage stochastic model and we use the conditional value-at-risk as a risk measure. Using a Benders framework, the proposed solution method decomposes the problem into a mixed-integer linear master problem and linear and continuous subproblems. The master problem corresponds to the first-stage decisions throughout the week and includes all the commitment (binary) variables and their corresponding constraints. The subproblems correspond to the actual dispatch of the generating units on a weekly basis. Based on the success of column-and-constraint generation algorithms to solve robust optimization problems, we improve the low communication between the master problem and the subproblems in the standard Benders decomposition by adding primal variables and constraints from the subproblems to the master problem, which provides a better approximation of the recourse function. Furthermore, our computational experiments demonstrate the effectiveness of the proposed decomposition method using an instance of the South Carolina synthetic system with 90 generating units under 40 scenarios.

25 ENERGY STORAGE↗
DOE OSTI2026

Estimating value of information for heliostat washing operations at solar thermal plants

Concentrating solar power (CSP) plants depend on thousands of heliostats whose reflectance declines as dust accumulates. Operators routinely measure reflectance to estimate soiling and, in turn, inform cleaning schedules, but the value of collecting more frequent or more accurate data has not been formally quantified. This study introduces a Monte Carlo discrete event simulation framework that integrates stochastic models of soiling, weather, and measurement error with a dynamic cleaning dispatch policy to estimate annual energy production and operations costs. Applied to two representative central-receiver field configurations, the results show that both the frequency and accuracy of reflectance measurements can meaningfully impact plant performance. In both case studies, reducing measurement intervals yields significant returns, with the energy gains greatly exceeding the cost of more frequent data collection. The simulation framework serves as a decision-support tool for CSP operators, allowing them to input site-specific soiling conditions, measurement accuracy, and survey frequency to evaluate the tradeoffs between data collection cost and energy recovery, and to identify measurement strategies that maximize plant profit.

14 SOLAR ENERGY↗
DOE OSTI2025

A Bayesian framework to investigate radiation reaction in strong fields

Recent experiments aiming to measure phenomena predicted by strong-field quantum electrodynamics (SFQED) have done so by colliding relativistic electron beams and high-power lasers. In such experiments, measurements of collision parameters are not always feasible. However, precise knowledge of these parameters is required to accurately test SFQED. Here, we present a novel Bayesian inference procedure that infers collision parameters that could not be measured on-shot. This procedure is applicable to all-optical non-linear Compton scattering experiments investigating radiation reaction. The framework allows multiple diagnostics to be combined self-consistently and facilitates the inclusion of known information pertaining to the collision parameters. Using this Bayesian analysis, the relative validity of the classical, quantum-continuous and quantum-stochastic models of radiation reaction was compared for several test cases, which demonstrates the accuracy and model selection capability of the framework and highlight its robustness if the experimental values of fixed parameters differ from their values in the models.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Several Small or Single Large? Quantifying the Catchment-Wide Performance of On-Site Wastewater Treatment Plants with Inaccurate Sensors

On-site wastewater treatment plants (OSTs) often lack monitoring, resulting in unreliable treatment performance. They thus appear to be a stopgap solution despite their potential contribution to circular water management. Low-maintenance but inaccurate soft sensors are emerging that address this concern. However, how their inaccuracy impacts the catchment-wide treatment performance of a system of many OSTs has not been quantified. Here, we develop a stochastic model to estimate catchment-wide OST performances with a Monte Carlo simulation. In our study, soft sensors with a 70% accuracy improved the treatment performance from 66% of the time functional to 98%. Soft sensors optimized for specificity, indicating the true negative rate, improve the system performance, while sensors optimized for sensitivity, indicating the true positive rate, quantify the treatment performance more accurately. This new insight leads us to suggest programming two soft sensors in practical settings with the same hardware sensor data as input: one soft sensor geared to high specificity for maintenance scheduling and one geared to high sensitivity for performance quantification. Our findings suggest that a maintenance strategy combining inaccurate sensors with appropriate alarm management can vastly improve the mean catchment-wide treatment performance of a system of OSTs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Exploring single-cell biosynthetic noise and dynamics for enhanced betaxanthin production in Escherichia coli

Cell-to-cell variability often limits the efficiency of microbial bioproduction, yet how individual cells fluctuate over time and how these fluctuations shape population-level output remain unclear. To address this issue, we tracked a heterologous betaxanthin pathway in Escherichia coli using microfluidics-assisted time-lapse microscopy, allowing simultaneous measurement of fluctuations in betaxanthin, its biosynthetic enzyme DOD and growth across generations. Here we show that over 50% of high betaxanthin producers become medium or low producers after two divisions. Betaxanthin variation primarily originates from DOD noise, with a smaller contribution from growth rate fluctuations. We further develop a stochastic model to explore various control circuits and find that pathway enzyme or metabolite-based growth selection strategies are most effective in enhancing production. We experimentally validate the model by coupling enzyme expression to nutrient availability, which enriches high producers and boosts titer by 4.4-fold. Our results highlight key sources of metabolic heterogeneity and provide a framework for designing robust microbial processes.

Bacterial systems biology↗
DOE OSTI2026

Observation of quantum effects on radiation reaction in strong fields

Radiation reaction, the force experienced by an accelerated charge due to radiation emission, has long been the subject of extensive theoretical and experimental research. Experimental verification of a quantum, strong-field description of radiation reaction is fundamentally important, and has wide-ranging implications for astrophysics, laser-driven particle acceleration, next-generation particle colliders and inverse-Compton photon sources for medical and industrial applications. However, the difficulty of accessing regimes where strong field and quantum effects dominate inhibited previous efforts to observe quantum radiation reaction in charged particle dynamics with high significance. We report the first high significance (> 5σ) observation of strong-field radiation reaction on electron spectra where quantum effects are substantial. We obtain the first, quantitative, strong evidence favouring the quantum-continuous and quantum-stochastic models over the classical model; the quantum models perform comparably. The lower electron energy losses predicted by the quantum models accounts for their improved performance. Model comparison was performed using a novel Bayesian framework which has widespread utility for laser-particle collision experiments, including those utilising conventional accelerators, where some collision parameters cannot be measured directly.

Los, Eva E. [Imperial College London (United Kingd↗
DOE OSTI2023

Single-photon absorption and emission from a natural photosynthetic complex

Photosynthesis is generally assumed to be initiated by a single photon from the Sun, which, as a weak light source, delivers at most a few tens of photons per nanometre squared per second within a chlorophyll absorption band1. Yet much experimental and theoretical work over the past 40 years has explored the events during photosynthesis subsequent to absorption of light from intense, ultrashort laser pulses. Here, we use single photons to excite under ambient conditions the light-harvesting 2 (LH2) complex of the purple bacterium Rhodobacter sphaeroides, comprising B800 and B850 rings that contain 9 and 18 bacteriochlorophyll molecules, respectively. Excitation of the B800 ring leads to electronic energy transfer to the B850 ring in approximately 0.7 ps, followed by rapid B850-to-B850 energy transfer on an approximately 100-fs timescale and light emission at 850–875 nm. Using a heralded single photon source20,21 along with coincidence counting, we establish time correlation functions for B800 excitation and B850 fluorescence emission and demonstrate that both events involve single photons. We also find that the probability distribution of the number of heralds per detected fluorescence photon supports the view that a single photon can upon absorption drive the subsequent energy transfer and fluorescence emission and hence, by extension, the primary charge separation of photosynthesis. An analytical stochastic model and a Monte Carlo numerical model capture the data, further confirming that absorption of single photons is correlated with emission of single photons in a natural light-harvesting complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Counting generations in birth and death processes with competing Erlang and exponential waiting times

Lymphocyte populations, stimulated in vitro or in vivo, grow as cells divide. Stochastic models are appropriate because some cells undergo multiple rounds of division, some die, and others of the same type in the same conditions do not divide at all. If individual cells behave independently, then each cell can be imagined as sampling from a probability density of times to division and death. The exponential density is the most mathematically and computationally convenient choice. It has the advantage of satisfying the memoryless property, consistent with a Markov process, but it overestimates the probability of short division times. With the aim of preserving the advantages of a Markovian framework while improving the representation of experimentally-observed division times, we consider a multi-stage model of cellular division and death. We use Erlang-distributed (or, more generally, phase-type distributed) times to division, and exponentially distributed times to death. We classify cells into generations, using the rule that the daughters of cells in generation n are in generation n + 1. In some circumstances, our representation is equivalent to established models of lymphocyte dynamics. We find the growth rate of the cell population by calculating the proportions of cells by stage and generation. The exponent describing the late-time cell population growth, and the criterion for extinction of the population, differs from what would be expected if N steps with rate λ were equivalent to a single step of rate λ/N. We link with a published experimental dataset, where cell counts were reported after T cells were transferred to lymphopenic mice, using Approximate Bayesian Computation. In the comparison, the death rate is assumed to be proportional to the generation and the Erlang time to division for generation 0 is allowed to differ from that of subsequent generations. The multi-stage representation is preferred to a simple exponential in posterior distributions, and the mean time to first division is estimated to be longer than the mean time to subsequent divisions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Increasing extreme hourly precipitation risk for New York City after Hurricane Ida

The remnants of Hurricane Ida caused major damage and death in the United States on September 1st, 2021, and 11 people drowned in flooded basement apartments within New York City (NYC). It was catastrophic because the maximum hourly precipitation intensity, recorded as 3.47 inches (88.1 mm) per hour at Central Park, was unprecedentedly high for the NYC region. The stormwater infrastructure in NYC is built for 1.75 inches (44.5 mm) per hour, and so understanding the dynamic risk associated with Ida can inform city planning efforts for climate change’s impact on short duration extreme precipitation events. We contextualize this storm’s record-breaking hourly intensity within the historical record as well as project its risk in the near- to medium-term future using nonstationary stochastic models. These models are conditioned on average temperature (T avg ) and cooling degree day (CDD) projections from three climate models as a covariate, each with a SSP 126 and SSP 370 scenario. The likelihood of such a storm was slowly increasing even before Ida happened, but the projected aggregate reoccurrence risk of an event of Ida’s magnitude over time from the non-stationary models ranges from 4 to 52 times higher than the risk given by the stationary model. Using CDD as a covariate resulted in risks that were more than twice the magnitude than when using T avg . Presenting both covariates provides a broader envelope of uncertainty, which highlights the importance and nuances in the choice of a regionally appropriate covariate for non-stationary risk analysis.

Mossel, Carolien↗
DOE OSTI2023

Quantum computing for finance

Quantum computers are expected to surpass the computational capabilities of classical computers and have a transformative impact on numerous industry sectors. Here, we present a comprehensive summary of the state of the art of quantum computing for financial applications, with particular emphasis on stochastic modelling, optimization and machine learning. This Review is aimed at physicists, so it outlines the classical techniques used by the financial industry and discusses the potential advantages and limitations of quantum techniques. Finally, we look at the challenges that physicists could help tackle. Quantum computers are expected to surpass classical computers and transform industries. This Review focuses on quantum computing for financial applications and provides a summary for physicists on potential advantages and limitations of quantum techniques, as well as challenges that physicists could help tackle.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

The role of the droplet interface in controlling the multiphase oxidation of thiosulfate by ozone

Predicting reaction kinetics in aqueous microdroplets, including aerosols and cloud droplets, is challenging due to the probability that the underlying reaction mechanism can occur both at the surface and in the interior of the droplet. Additionally, few studies directly measure the surface activities of doubly charged anions, despite their prevalence in the atmosphere. Here, deep-UV second harmonic generation spectroscopy is used to probe surface affinities of the doubly charged anions thiosulfate, sulfate, and sulfite, key species in the thiosulfate ozonation reaction mechanism. Thiosulfate has an appreciable surface affinity with a measured Gibbs free energy of adsorption of -7.3 ± 2.5 kJ mol -1 in neutral solution, while sulfate and sulfite exhibit negligible surface propensity. The Gibbs free energy is combined with data from liquid flat jet ambient pressure X-ray photoelectron spectroscopy to constrain the concentration of thiosulfate at the surface in our model. Stochastic kinetic simulations leveraging these novel measurements show that the primary reaction between thiosulfate and ozone occurs at the interface and in the bulk, with the contribution of the interface decreasing from ~65% at pH 5 to ~45% at pH 13. Additionally, sulfate, the major product of thiosulfate ozonation and an important species in atmospheric processes, can be produced by two different pathways at pH 5, one with a contribution from the interface of >70% and the other occurring predominantly in the bulk (>98%). The observations in this work have implications for mining wastewater remediation, atmospheric chemistry, and understanding other complex reaction mechanisms in multiphase environments. Future interfacial or microdroplet/aerosol chemistry studies should carefully consider the role of both surface and bulk chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

CADIS and FW-CADIS Variance Reduction in Gamma Transport for Predicting Prompt Forensics Signatures

The goal of prompt nuclear forensics is to determine the characteristics of a nuclear detonation based on the signatures available almost immediately after the explosion. An important characteristic is the reaction time history (RTH), a measure of the device’s rate of neutron multiplication. The RTH can be estimated by observation of the gamma radiation emitted from the detonation, which can be detected directly or observed indirectly as Teller light. Gamma transport simulations used to predict these radiation fields are often modeled stochastically using the Monte Carlo N-Particle (MCNP) code, which can be a computationally demanding task due to the number of particle histories needed to achieve statistical convergence. In an attempt to improve the efficiency of these calculations, we evaluate two variance reduction techniques: Consistent Adjoint-Driven Importance Sampling (CADIS) and Forward-Weighted Consistent Adjoint-Driven Importance Sampling (FW-CADIS). These methods use a deterministically calculated adjoint flux to create weight windows and source biasing that guide MCNP sampling. We study the utility of CADIS and FW-CADIS for their use in MCNP gamma transport for nuclear forensics prediction simulations. Furthermore, the results demonstrate that both CADIS and FW-CADIS improve the accuracy for forensics-focused simulations, with CADIS being most beneficial in direct detection and FW-CADIS being ideal for computing a global Teller light source.

CADIS↗