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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Impacts of stochastic coalescence variability on warm rain initiation using Lagrangian microphysics in box and large-eddy simulations

Various coalescence methods for Lagrangian microphysics schemes are tested in box and large-eddy simulation (LES) models, including the stochastic all-or-nothing super-droplet method (SDM) and a version of SDM (dSDM) that applies a fractional approach similar to the average impact method. In LES, variabilities driven by microphysics and by flow realizations are separated using the “piggybacking” technique. Rain initiation averaged over many realizations of the box model is delayed and rain variability increases as the number of super-drops per collision volume ( N SD ) is decreased using SDM. In contrast, rain initiation time using SDM in LES is insensitive to N SD for 32 ≤ N SD ≤ 512. This is explained through the interaction between LES grid boxes, each acting as a separate collision volume. Variability across the ensemble of LES collision volumes using SDM results in rain quickly initiating in some of the LES grid cells at low N SD and leading to a similar overall timing of rain initiation from the cloud compared to simulations with high N SD . There is a ~20% decrease in the total rain mass and mean rain flux as N SD is increased from 32 to 256, with little additional change as N SD is increased from 256 to 512. The fractional coalescence approach in dSDM leads to reduced microphysical variability and a 15-18 min delay in rain initiation compared to SDM. Finally, an additional LES ensemble with microphysical variability feeding back to the dynamics shows that flow variability dominates the impact of microphysical variability on rain properties. Thus, flow variability must be constrained to isolate impacts of microphysical variability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Randomized Algorithms for Scientific Computing (RASC)

Randomized algorithms have propelled advances in artificial intelligence (AI) and represent a foundational research area in advancing AI for Science. Future advancements in DOE Office of Science priority areas such as climate science, astrophysics, fusion, advanced materials, combustion, and quantum computing all require randomized algorithms for surmounting challenges of complexity, robustness, and scalability. Advances in data collection and numerical simulation have changed the dynamics of scientific research and motivate the need for randomized algorithms. For instance, advances in imaging technologies such as X-ray ptychography, electron microscopy, electron energy loss spectroscopy, or adaptive optics lattice light-sheet microscopy collect hyperspectral imaging and scattering data in terabytes, at breakneck speed enabled by state-of-the-art detectors. The data collection is exceptionally fast compared with its analysis. Likewise, advances in high-performance architectures have made exascale computing a reality and changed the economies of scientific computing in the process. Floating-point operations that create data are essentially free in comparison with data movement. Thus far, most approaches have focused on creating faster hardware. Ironically, this faster hardware has exacerbated the problem by making data still easier to create. Under such an onslaught, scientists often resort to heuristic deterministic sampling schemes (e.g., low-precision arithmetic, sampling every nth element) and sacrifice potentially valuable accuracy. Dramatically better results can be achieved via randomized algorithms, reducing the data size as much as or more than naive deterministic subsampling can achieve, while retaining the high accuracy of computing on the full data set. By randomized algorithms we mean those algorithms that employ some form of randomness in internal algorithmic decisions to accelerate time to solution, increase scalability, or improve reliability. Examples include matrix sketching for solving large-scale least-squares problems (see Figure 1) and stochastic gradient descent for training machine learning models. We are not recommending heuristic methods but rather randomized algorithms that have certificates of correctness and probabilistic guarantees of optimality and near-optimality. Such approaches can be useful beyond acceleration, for example, in understanding how to avoid measure zero worst-case scenarios that plague methods such as QR matrix factorization.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

An efficient surrogate model of secondary electron formation and evolution

This work extends the adjoint-deep learning framework for runaway electron (RE) evolution, developed by McDevitt et al. [Phys. Plasmas 32, 042503 (2025)], to account for large-angle collisions. By incorporating large-angle collisions, the framework allows the avalanche of REs to be captured, an essential component of RE dynamics. This extension is accomplished by using a Rosenbluth–Putvinski approximation to estimate the distribution of secondary electrons generated by large-angle collisions. By evolving both the primary and multiple generations of secondary electrons, the present formulation can capture both the detailed temporal evolution of a RE population beginning from an arbitrary initial momentum space distribution, along with providing approximations to the saturated growth and decay rates of the RE population. Predictions of the adjoint-deep learning framework are verified against a traditional RE solver, with good agreement present across a broad range of parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Stochastic modal velocity field in rough-wall turbulence

Stochastically generated instantaneous velocity profiles are used to reproduce the outer region of rough-wall turbulent boundary layers in a range of Reynolds numbers extending from the wind tunnel to field conditions. Each profile consists in a sequence of steps, defined by the modal velocities and representing uniform momentum zones (UMZs), separated by velocity jumps representing the internal shear layers. Height-dependent UMZ is described by a minimal set of attributes: thickness, mid-height elevation, and streamwise (modal) and vertical velocities. These are informed by experimental observations and reproducing the statistical behaviour of rough-wall turbulence and attached eddy scaling, consistent with the corresponding experimental datasets. Sets of independently generated profiles are reorganized in the streamwise direction to form a spatially consistent modal velocity field, starting from any randomly selected profile. The operation allows one to stretch or compress the velocity field in space, increases the size of the domain and adjusts the size of the largest emerging structures to the Reynolds number of the simulated flow. By imposing the autocorrelation function of the modal velocity field to be anchored on the experimental measurements, we obtain a physically based spatial resolution, which is employed in the computation of the velocity spectrum, and second-order structure functions. The results reproduce the Kolmogorov inertial range extending from the UMZ and their attached-eddy vertical organization to the very-large-scale motions (VLSMs) introduced with the reordering process. The dynamic role of VLSM is confirmed in the –u'w' co-spectra and in their vertical derivative, representing a scale-dependent pressure gradient contribution.

42 ENGINEERING↗
DOE OSTI2022

Prediction of the energetic particle redistribution by an improved critical gradient model and analysis of the transport threshold

Based on the theory of critical gradient model (CGM) and following the simulation method proposed by Waltz et al., a combination of TGLFEP and EPtran code is employed to predict the energetic particle (EP) transport induced by Alfvén eigenmodes (AEs). To be consistent with the experiment, recent improvements to the simulation method include consideration of threshold evolution and orbit loss due to finite orbit width. The revised CGM is applied to simulate two DIII-D experimental discharges (#142111 and #153071). It well reproduces the experimental profiles with multiple unstable AEs and large-scale EP transport. Discharge #142111 had previously been simulated using a nonlinear MHD-kinetic code MEGA with a transport mechanism based on stochasticity induced by overlapping AE. By comparing the simulated EP profiles, we find that the AE transport threshold is approximated by both the MEGA nonlinear stability threshold and the proposed CGM threshold (error <5% for single n and <17% for multiple n simulation). Both of them are larger than the linear stability threshold of the most unstable AE mode by a quantity of the order of the flux needed to sustain EP transport by the background turbulence. Additionally, we have also applied the improved CGM to simulate the α particle redistribution for a China Fusion Engineering Test Reactor steady state scenario. Because of the clear separation between the AE unstable region and the loss cone, only a moderate α particle loss of ~9.6% is predicted.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

A quantitative model of charge injection by ruthenium chromophores connecting femtosecond to continuous irradiance conditions

A kinetic framework for the ultrafast photophysics of tris(2,2-bipyridine)ruthenium(II) phosphonated and methyl-phosphonated derivatives is used as a basis for modeling charge injection by ruthenium dyes into a semiconductor substrate. By including the effects of light scattering, dye diffusion, and adsorption kinetics during sample preparation and the optical response of oxidized dyes, quantitative agreement with multiple transient absorption datasets is achieved on timescales spanning femtoseconds to nanoseconds. In particular, quantitative agreement with important spectroscopic handles—the decay of an excited state absorption signal component associated with charge injection in the UV region of the spectrum and the dynamical redshift of a ~500 nm isosbestic point—validates our kinetic model. Pseudo-first-order rate coefficients for charge injection are estimated in this work, with an order of magnitude ranging from 10 11 to 10 12 s –1 . The model makes the minimalist assumption that all excited states of a particular dye have the same charge injection coefficient, an assumption that would benefit from additional theoretical and experimental exploration. Here, we have adapted this kinetic model to predict charge injection under continuous solar irradiation and find that as many as 68 electron transfer events per dye per second take place, significantly more than prior estimates in the literature.

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

Strong Red Noise Ocean Forcing on Atlantic Multidecadal Variability Assessed from Surface Heat Flux: Theory and Application

The role of ocean forcing on Atlantic multidecadal variability (AMV) is assessed from the (downward) heat flux–SST relation in the framework of a new stochastic climate theory forced by red noise ocean forcing. Previous studies suggested that atmospheric forcing drives SST variability from monthly to interannual time scales, with a positive heat flux–SST correlation, while heat flux induced by ocean processes can drive SST variability at decadal and longer time scales, with a negative heat flux–SST correlation. Here, first, we develop a theory to show how the sign of heat flux–SST correlation is affected by atmospheric and oceanic forcing with time scale. In particular, a red noise ocean forcing is necessary for the sign reversal of heat flux–SST correlation. Furthermore, this sign reversal can be detected equivalently in three approaches: the low-pass correlation at lag zero, the unfiltered correlation at long (heat flux) lead, and the real part of the heat flux–SST coherence. Second, we develop a new scheme in combination with the theory to assess the magnitude and time scale of the red noise ocean forcing for AMV in the GFDL SPEAR model (Seamless System for Prediction and Earth System Research) and observations. In both the model and observations, the ocean forcing on AMV is in general comparable with the atmospheric forcing, with a 90% probability greater than the atmospheric forcing in observations. In contrast to the white noise atmospheric forcing, the ocean forcing has a persistence time comparable or longer than a year, much longer than the SST persistence of ~3 months. This slow ocean forcing is associated implicitly with slow subsurface ocean dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Insights into Methodologies and Stochastic Optimization of Thermal Energy Storage-Coupled Advanced Reactor Systems: A Comparison of Methods for Accessing Long-Term Sub-System Sizing Adequacy

This paper investigates the potential of coupling Thermal Energy Storage (TES) with Advanced Reactors (ARs) to address uncertainties posed by climate change in deep decarbonized power systems. The TES Use-case Team at Idaho National Laboratory (INL) has examined the potential of storing thermal energy from ARs during low demand periods and optimizing discharge during peak-priced hours, in both steady-state and transient conditions. Building on this groundwork, this study bridges the gaps in optimal sizing of the sub-system of TES-coupled AR systems using Risk Analysis Virtual Environment (RAVEN) and Holistic Energy Resource Optimization Network (HERON), INL?s framework for grid optimization. By applying this framework, we present statistically-robust optimal charge, discharge including balance of plant (BOP), and storage sizing for the High-Temperature Gas-Cooled Reactor (HTGR) with 203 MWth output. To this end, we generated synthetic price samples for 30 years using 2018 ? 2021 real-time market data from ERCOT, PJM and MISO. Our results reveals that the TES-coupled HTGR system is highly effective in maximizing revenue from electricity sales. We observed a substantial increase of 40 % in ERCOT and a noteworthy 15 % increase in PJM and MISO when compared to the conventional BOP without TES. This improvement is achieved through regionally-tailored sub-system sizing, which ranges from 398 to 416 MWth for the discharge system and 610 to 1029 MWth for the TES. We find that the average electricity price directly impacts the overall economics, while price volatility influences storage size. Additional sensitivity analyses were performed to access the impact of key assumptions on system economics and sizing, differentiating the optimization window (i.e., 24 ? 219 hours of chronological observations) and by imposing storage continuity condition in tracking TES cycles. We observed that at the 120-hour of the optimization window, a reasonable balance between computation time and accuracy was achieved. Our analysis also highlights the significance of conducting multi-day cycle analysis (> 120-hour) for TES to capture interaction between electricity prices and storage dynamics, providing a comprehensive understanding of TES behavior that AR developers should integrate into their plant designs.

25 ENERGY STORAGE↗
DOE OSTI2024

An open-source framework for balancing computational speed and fidelity in production cost models

Studies of bulk power system operations need to incorporate uncertainty and sensitivity analyses, especially around exposure to weather and climate variability and extremes, but this remains a computational modeling challenge. Commercial production cost models (PCMs) have shorter runtimes, but also important limitations (opacity, license restrictions) that do not fully support stochastic simulation. Open-source PCMs represent a potential solution. They allow for multiple, simultaneous runs in high-performance computing environments and offer flexibility in model parameterization. Yet, developers must balance computational speed (i.e. runtime) with model fidelity (i.e. accuracy). In this paper, we present Grid Operations (GO), a framework for instantiating open-source, scale-adaptive PCMs. GO allows users to search across parameter spaces to identify model versions that appropriately balance computational speed and fidelity based on experimental needs and resource limits. Results provide generalizable insights on how to navigate the fidelity and computational speed tradeoff through parameter selection. We show that models with coarser network topologies can accurately mimic market operations, sometimes better than higher-resolution models. It is thus possible to conduct large simulation experiments that characterize operational risks related to climate and weather extremes while maintaining sufficient model accuracy.

42 ENGINEERING↗
DOE OSTI2022

Flame acceleration and transition to detonation in a pre-/main-chamber combustion system

Numerical simulations are performed to study the mechanism of deflagration to detonation transition (DDT) in a pre-/main-chamber combustion system with a stoichiometric ethylene–oxygen mixture. A Godunov algorithm, fifth-order in space, and third-order in time, is used to solve the fully compressible Navier–Stokes equations on a dynamically adapting mesh. A single-step, calibrated chemical diffusive model described by Arrhenius kinetics is used for energy release and conservation between the fuel and the product. The two-dimensional simulation shows that a laminar flame grows in the pre-chamber and then develops into a jet flame as it passes through the orifice. A strong shock forms immediately ahead of the flame, reflecting off the walls and interacting with the flame front. The shock–flame interactions are crucial for the development of flame instabilities, which trigger the subsequent flame development. The DDT arises due to a shock-focusing mechanism, where multiple shocks collide at the flame front. A chemical explosive mode analysis (CEMA) criterion is developed to study the DDT ignition mode. Preliminary one-dimensional computations for a laminar propagating flame, a fast flame deflagration, and a Chapman–Jouguet detonation are conducted to demonstrate the validity of CEMA on the chemical-diffusive model, as well as to determine the proper conditioning value for CEMA diagnostic. The two-dimensional analysis with CEMA indicates that the DDT initiated by the shock-focusing mechanism can form a strong thermal expansion region at the flame front that features large positive eigenvalues for the chemical explosive mode and dominance of the local autoignition mode. Thus, the CEMA criterion proposed in this study provides a robust diagnostic for identifying autoignition-supported DDT, of which the emergence of excessive local autoignition mode is found to be a precursor. The effect of grid size, initial temperature, and orifice size are then evaluated, and results show that although the close-chamber DDT is highly stochastic, the detonation initiation mechanism remains robust.

42 ENGINEERING↗
DOE OSTI2020

Characterization of Partially Observed Epidemics - Application to COVID-19

This report documents a statistical method for the "real-time" characterization of partially observed epidemics. Observations consist of daily counts of symptomatic patients, diagnosed with the disease. Characterization, in this context, refers to estimation of epidemiological parameters that can be used to provide short-term forecasts of the ongoing epidemic, as well as to provide gross information for the time-dependent infection rate. The characterization problem is formulated as a Bayesian inverse problem, and is predicated on a model for the distribution of the incubation period. The model parameters are estimated as distributions using a Markov Chain Monte Carlo (MCMC) method, thus quantifying the uncertainty in the estimates. The method is applied to the COVID-19 pandemic of 2020, using data at the country, provincial (e.g., states) and regional (e.g. county) levels. The epidemiological model includes a stochastic component due to uncertainties in the incubation period. This model-form uncertainty is accommodated by a pseudo-marginal Metropolis-Hastings MCMC sampler, which produces posterior distributions that reflect this uncertainty. We approximate the discrepancy between the data and the epidemiological model using Gaussian and negative binomial error models; the latter was motivated by the over-dispersed count data. For small daily counts we find the performance of the calibrated models to be similar for the two error models. For large daily counts the negative-binomial approximation is numerically unstable unlike the Gaussian error model. Application of the model at the country level (for the United States, Germany, Italy, etc.) generally provided accurate forecasts, as the data consisted of large counts which suppressed the day-to-day variations in the observations. Further, the bulk of the data is sourced over the duration before the relaxation of the curbs on population mixing, and is not confounded by any discernible country-wide second wave of infections. At the state-level, where reporting was poor or which evinced few infections (e.g., New Mexico), the variance in the data posed some, though not insurmountable, difficulties, and forecasts were able to capture the data with large uncertainty bounds. The method was found to be sufficiently sensitive to discern the flattening of the infection and epidemic curve due to shelter-in-place orders after around 90% quantile for the incubation distribution (about 10 days for COVID-19). The proposed model was also used at a regional level to compare the forecasts for the central and north-west regions of New Mexico. Modeling the data for these regions illustrated different disease spread dynamics captured by the model. While in the central region the daily counts peaked in the late April, in the north-west region the ramp-up continued for approximately three more weeks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

On the molecular correlations that result in field-dependent conductivities in electrolyte solutions

Employing recent advances in response theory and nonequilibrium ensemble reweighting, we study the dynamic and static correlations that give rise to an electric field-dependent ionic conductivity in electrolyte solutions. We consider solutions modeled with both implicit and explicit solvents, with different dielectric properties, and at multiple concentrations. Implicit solvent models at low concentrations and small dielectric constants exhibit strongly field-dependent conductivities. We compare these results to Onsager-Wilson theory of the Wien effect, which provides a qualitatively consistent prediction at low concentrations and high static dielectric constants but is inconsistent away from these regimes. The origin of the discrepancy is found to be increased ion correlations under these conditions. Explicit solvent effects act to suppress nonlinear responses, yielding a weakly field-dependent conductivity over the range of physically realizable field strengths. By decomposing the relevant time correlation functions, we find that the insensitivity of the conductivity to the field results from the persistent frictional forces on the ions from the solvent. Our findings illustrate the utility of nonequilibrium response theory in rationalizing nonlinear transport behavior.

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

Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules

Abstract Graph Convolutional Neural Network (GCNN) is a popular class of deep learning (DL) models in material science to predict material properties from the graph representation of molecular structures. Training an accurate and comprehensive GCNN surrogate for molecular design requires large-scale graph datasets and is usually a time-consuming process. Recent advances in GPUs and distributed computing open a path to reduce the computational cost for GCNN training effectively. However, efficient utilization of high performance computing (HPC) resources for training requires simultaneously optimizing large-scale data management and scalable stochastic batched optimization techniques. In this work, we focus on building GCNN models on HPC systems to predict material properties of millions of molecules. We use HydraGNN, our in-house library for large-scale GCNN training, leveraging distributed data parallelism in PyTorch. We use ADIOS, a high-performance data management framework for efficient storage and reading of large molecular graph data. We perform parallel training on two open-source large-scale graph datasets to build a GCNN predictor for an important quantum property known as the HOMO-LUMO gap. We measure the scalability, accuracy, and convergence of our approach on two DOE supercomputers: the Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF) and the Perlmutter system at the National Energy Research Scientific Computing Center (NERSC). We present our experimental results with HydraGNN showing (i) reduction of data loading time up to 4.2 times compared with a conventional method and (ii) linear scaling performance for training up to 1024 GPUs on both Summit and Perlmutter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Demand Driven Cycamore Archetypes

Future nuclear fuel cycle options may present advantages over today’s once-through fuel cycle. Nuclear fuel cycle simulation tools assess the performance of those fuel cycles as well as the dynamics of long-term technology transitions. In many nuclear fuel cycle simulation tools, it has historically been the responsibility of the user to manually define facility deployment schemes and all facility parameters. While this is straightforward in simple fuel cycles, transitions from one fuel cycle to another can be more complex. In particular, deployment schemes for supportive fuel cycle facilities beyond the reactor become complex if the analyst desires to avoid gaps in the nuclear fuel and power supply chain during those transition scenarios. As nuclear fuel cycle analysis approaches questions regarding the feasibility and performance of the deployment schemes and technology choices during technology transition, automation of this historically manual process is necessary. The main objective of this work was to develop and demonstrate Cyclus automation capabilities toward key nuclear fuel cycle transition scenarios. While deploying reactors to meet power demand is trivial, and existed in the earliest versions of CYCLUS, automated, predictive deployment and decommissioning of other facilities is more complex. These include mining, milling, enrichment, fuel fabrication, reprocessing, and others. For example, a balanced closed fuel cycle may require ensuring that there is enough fast reactor fuel for their operation and may drive deployment of a fleet of light water reactors. This concern comprises the main challenge that drove the project effort. The Demand-Driven Cycamore Archetype project (NEUP-FY16-10512) aimed to develop CYCAMORE demand-driven deployment capabilities and thereby automate transition scenario definition. The developed software package, d3ploy, in the form of a CYCLUS Institution agent, deploys Facilities to meet the front-end and back-end demands of the fuel cycle. The University of South Carolina and the University of Illinois applied multiple algorithmic approaches to this challenge. This project developed an in situ demand-driven development schedule calculation through non-optimizing, deterministic-optimizing, and stochastic-optimizing algorithms as CYCLUS archetypes and demonstrated these new archetypes in program-supporting fuel cycle transition scenarios. Both objectives were achieved. This report documents the results and deliverables obtained toward these achievements in detail.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Persistent Elevated Soot Emissions Induced by Clustered Stochastic Preignition Events

Stochastic Preignition (SPI) is an abnormal combustion phenomenon that can occur in spark-ignition engines particularly under high-load operation. SPI is characterized by uncontrolled initiation of combustion prior to spark discharge, an abnormal combustion process that can lead to severe knock events and significant engine damage. SPI has been associated with fuel properties, lubricant composition, and engine design and operation. Here, in this work, a single-cylinder test engine with a dry-sump oil system was utilized to study the SPI response of E10 and E25 fuels with a range of Reid Vapor Pressure (RVP). An automated test procedure was employed, consisting of ten square-waved load profile segments, with each segment composed of 5 min of low-load operation followed by 25 min of sustained high-load operation. These tests were replicated across multiple days of testing including a lubricant triple flush between tests, and an online Fuel in Oil diagnostic measurement. Exhaust particulate emissions were continuously measured by an AVL microsoot sensor (MSS). Elevated particulate matter emissions were observed to occur concurrently with SPI events as blooms of soot. Particularly after clustered events (i.e., multiple SPI cycles occurring within 10 consecutive engine cycles), high soot emissions were observed to persist over several days of sequential operation despite daily lubricant changes, a complete warm-up procedure, and sustained low-load operation between test segments. This result implies that the particulate emissions trends may be dominated by deposit-based effects, where higher load operation is needed to alter deposition and formation processes. The observed soot blooms were also found to correspond to a reduction in the engine fueling and the fuel engine oil dilution rate despite the engine exhaust remaining at stoichiometric exhaust operation. These observations suggest that post-SPI events, pathways for lubricant migration and consumption into the combustion chamber may occur until these pathways are closed from deposit formation or ring dynamics during extended operation. These observed sooting propensity persisted with all fuels tests, but a linear correlation was observed between the summation of soot and particulate matter index (PMI) value for each fuel as well as SPI events, proving that PMI is a crucial fuel property for reducing SPI.

Splitter, Derek [Oak Ridge National Laboratory (OR↗
DOE OSTI2023

Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments

mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Our simulation results show that with careful application this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. We conclude that the proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell Signaling applications requiring simultaneous study of multiple mRNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Universal energy-speed-accuracy trade-offs in driven nonequilibrium systems

The connection between measure theoretic optimal transport and dissipative nonequilibrium dynamics provides a language for quantifying nonequilibrium control costs, leading to a collection of thermodynamic speed limits, which rely on the assumption that the target probability distribution is perfectly realized. This is almost never the case in experiments or numerical simulations, so here we address the situation in which the external controller is imperfect. We obtain a lower bound for the dissipated work in generic nonequilibrium control problems that (1) is asymptotically tight and (2) matches the thermodynamic speed limit in the case of optimal driving. Along with analytically solvable examples, we refine this imperfect driving notion to systems in which the controlled degrees of freedom are slow relative to the nonequilibrium relaxation rate, and identify independent energy contributions from fast and slow degrees of freedom. Furthermore, we develop a strategy for optimizing minimally dissipative protocols based on optimal transport flow matching, a generative machine learning technique. Furthermore, this latter approach ensures the scalability of both the theoretical and computational framework we put forth. Crucially, we demonstrate that we can compute the terms in our bound numerically using efficient algorithms from the computational optimal transport literature and that the protocols we learn saturate the bound.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Generalized master equation for particle transport in binary random media with renewal statistics

Particle transport in binary stochastic mixtures is classically modeled assuming Markovian or exponential mixing statistics but in many applications material memory invalidates the Markov assumption. For non-Markovian mixing characterized by alternating renewal processes, a transport-theoretic framework is presented that provides an exact description of transport in nonscattering random binary media with general non-exponential statistics. Our approach is to Markovianize the problem by augmenting the {material type, particle flux} state space with the age or distance from the last interface. A Chapman-Kolmogorov equation is formulated for the joint probability density of the material type, particle flux, and age, and subsequently reduced to a generalized Master equation (GME) in differential form. This constitutes the primary result of this work. A state-updating Monte Carlo algorithm consistent with the GME is developed and benchmarked against analytical solutions for multiple chord-length laws. For purely absorbing renewal statistical media, the GME reproduces analytical benchmarks for the equilibrium age distribution, interior mean/variance of material-conditioned fluxes, and boundary transmittance. Simulations further demonstrate that a Markov (exponential) approximation of non-exponential statistics can introduce large errors in transmittance and interior flux profiles. Lastly, the reintroduction of memory due to scattering is briefly addressed through heuristic considerations.

Fluctuations & noise↗