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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Stochastic journeys of cell progenies through compartments and the role of self-renewal, symmetric and asymmetric division

Abstract Division and differentiation events by which cell populations with specific functions are generated often take place as part of a developmental programme, which can be represented by a sequence of compartments. A compartment is the set of cells with common characteristics; sharing, for instance, a spatial location or a phenotype. Differentiation events are transitions from one compartment to the next. Cells may also die or divide. We consider three different types of division events: (i) where both daughter cells inherit the mother’s phenotype (self-renewal), (ii) where only one of the daughters changes phenotype (asymmetric division), and (iii) where both daughters change phenotype (symmetric division). The self-renewal probability in each compartment determines whether the progeny of a single cell, moving through the sequence of compartments, is finite or grows without bound. We analyse the progeny stochastic dynamics with probability generating functions. In the case of self-renewal, by following one of the daughters after any division event, we may construct lifelines containing only one cell at any time. We analyse the number of divisions along such lines, and the compartment where lines terminate with a death event. Analysis and numerical simulations are applied to a five-compartment model of the gradual differentiation of hematopoietic stem cells and to a model of thymocyte development: from pre-double positive to single positive (SP) cells with a bifurcation to either SP4 or SP8 in the last compartment of the sequence.

Science & Technology - Other Topics↗
DOE OSTI2024

Probing scrambling and operator size distributions using random mixed states and local measurements

The dynamical spreading of quantum information through a many-body system, typically called scrambling, is a complex process that has proven to be essential to describe many properties of out-of-equilibrium quantum systems. Scrambling can, in principle, be fully characterized via the use of out-of-time-ordered correlation functions, which are notoriously hard to access experimentally. In this work, we put forward an alternative toolbox of measurement protocols to experimentally probe scrambling by accessing properties of the operator size probability distribution, which tracks the size of the support of observables in a many-body system over time. Our measurement protocols require the preparation of separable mixed states together with local operations and measurements, and combine the tools of randomized operations, a modern development of near-term quantum algorithms, with the use of mixed states, a standard tool in NMR experiments. We demonstrate how to efficiently probe the probability-generating function of the operator distribution and discuss the challenges associated with obtaining the moments of the operator distribution. We further show that manipulating the initial state of the protocol allows us to directly obtain the individual elements of the distribution for small system sizes. Published by the American Physical Society 2024

Blocher, Philip Daniel (ORCID:0000000163027567)↗
DOE OSTI2022

Why are cell populations maintained via multiple compartments?

We consider the maintenance of ‘product’ cell populations from ‘progenitor’ cells via a sequence of one or more cell types, or compartments, where each cell’s fate is chosen stochastically. If there is only one compartment then large amplification, that is, a large ratio of product cells to progenitors comes with disadvantages. The product cell population is dominated by large families (cells descended from the same progenitor) and many generations separate, on average, product cells from progenitors. These disadvantages are avoided using suitably constructed sequences of compartments: the amplification factor of a sequence is the product of the amplification factors of each compartment, while the average number of generations is a sum over contributions from each compartment. Passing through multiple compartments is, in fact, an efficient way to maintain a product cell population from a small flux of progenitors, avoiding excessive clonality and minimizing the number of rounds of division en route. We use division, exit and death rates, estimated from measurements of single-positive thymocytes, to choose illustrative parameter values in the single-compartment case. We also consider a five-compartment model of thymocyte differentiation, from double-negative precursors to single-positive product cells.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

Statistical Treatment of Convolutional Neural Network Superresolution of Inland Surface Wind for Subgrid-Scale Variability Quantification

Abstract Machine learning models have been employed to perform either physics-free data-driven or hybrid dynamical downscaling of climate data. Most of these implementations operate over relatively small downscaling factors because of the challenge of recovering fine-scale information from coarse data. This limits their compatibility with many global climate model outputs, often available between ∼50- and 100-km resolution, to scales of interest such as cloud resolving or urban scales. This study systematically examines the capability of a type of superresolving convolutional neural network (SR-CNNs) to downscale surface wind speed data over land from different coarse resolutions (25-, 48-, and 100-km resolution) to 3 km. For each downscaling factor, we consider three convolutional neural network (CNN) configurations that generate superresolved predictions of fine-scale wind speed, which take between one and three input fields: coarse wind speed, fine-scale topography, and diurnal cycle. In addition to fine-scale wind speeds, probability density function parameters are generated through which sample wind speeds can be generated, accounting for the intrinsic stochasticity of wind speed. For assessing generalization to new data, CNN models are tested on regions with different topography and climate that are unseen during training. The evaluation of superresolved predictions focuses on subgrid-scale variability and the recovery of extremes. Models with coarse wind and fine topography as inputs exhibit the best performance when compared with other model configurations, operating across the same downscaling factor. Our diurnal cycle encoding results in lower out-of-sample generalizability when compared with other input configurations.

17 WIND ENERGY↗
DOE OSTI2025

Turbulence statistical analysis of the L-H transition and RMPs in KSTAR

Here, we investigate the turbulence statistics associated with low-to-high confinement (L-H) transitions and externally applied resonant magnetic perturbations (RMPs) in KSTAR. Time-series fluctuations of electron density n e , electron temperature T e , and the time derivative of the poloidal magnetic field dB θ /dt (Mirnov coils) are analysed using information-geometric measures (information rate Γ and information length $\mathcal{L}$ = ∫ Γ dt), together with kurtosis κ and variance σ 2 . In low-density upper single-null plasmas (n e ~ 1.2 x 10 19 m -3 ), a ~80 kHz magnetic mode coupling n e , T e , dB θ /dt and emerges prior to the L-H transition and persists into the edge-localised modes H-mode. Edge-localised RMPs (ERMPs) suppress this coherent mode but enhance intermittency, producing frequent bursts that abruptly reshape the time-dependent probability density functions (PDFs) and generate large spikes in Γ (with smaller changes in κ), signalling ERMP-driven departures from quasi-stationarity. The impact of ERMPs on background fluctuation levels depends on density, radial location, and the fluctuating variable itself ($\tilde{n}$, $\tilde{T}$, $\dot{B}$ θ ), whereas $\mathcal{L}$ provides a robust, regime-agnostic measure of cumulative statistical reorganisation and spatial decorrelation. In particular, at low density we observe weaker coupling between $\tilde{n}$ and $\tilde{T}$, along with a tendency toward decreased radial correlation-most clearly for $\tilde{T}$-under ERMPs. Overall, information geometry cleanly captures intermittent events, quantifies non-equilibrium PDF evolution, and offers a compact, cross-diagnostic metric for assessing resonant magnetic perturbation effects on edge transport and correlation across densities, radial locations, and confinement states.

Kim, Eun-jin [Coventry Univ. (United Kingdom); Seo↗
DOE OSTI2025

Conditional Pseudo-Reversible Normalizing Flow for Surrogate Modeling in Quantifying Uncertainty Propagation

We introduce a conditional pseudo-reversible normalizing flow (PR-NF) that directly learns conditional probability distributions from noisy physical models to efficiently quantify both forward and inverse uncertainty propagation. Traditional surrogate modeling approaches approximate only the deterministic component of physical models, requiring separate noise characterization and computationally expensive sampling methods for inverse problems. Here, in this work, we develop the conditional PR-NF model to directly learn and efficiently generate samples from the conditional probability density functions (PDFs). The training process utilizes dataset consisting of input-output pairs without requiring prior knowledge about the noise and the function. Once trained, our model efficiently generates samples from conditional PDFs for any input within the training domain. Moreover, the pseudo-reversibility feature allows for the use of fully connected neural network architectures, which simplifies the implementation and enables theoretical analysis. We provide a rigorous convergence analysis of the conditional PR-NF model, showing its ability to converge to the target conditional PDF using the Kullback−Leibler divergence. To demonstrate the effectiveness of our method, we apply it to several benchmark tests and a real-world geologic carbon storage problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A reaction mechanism for plasma electrolysis of AgNO 3 forming silver nanoclusters and nanoparticles

In plasma-driven solution electrolysis (PDSE), gas-phase plasma-produced species interact with an electrolytic solution to produce, for example, nanoparticles. An atmospheric pressure plasma jet (APPJ) directed onto a liquid solution containing a metallic salt will promote reduction of metallic ions in solution, generating metallic clusters that nucleate to form nanoparticles. In this article, results from a computational investigation are discussed of a PDSE process in which a radio-frequency APPJ sustained in helium impinges on a silver nitrate solution, resulting in growth of silver nanoparticles. A reaction mechanism was developed and implemented in a global plasma chemistry model to predict nanoparticle growth. To develop the reaction mechanism, density functional theory was used to generate probable silver growth pathways up to Ag 9 . Neutral clusters larger than Ag 9 were classified as nanoparticles. Kinetic reaction rate coefficients for thermodynamically favorable growth pathways were estimated based on an existing, empirically determined base reaction mechanism for smaller Ag particle interactions. These rates were used in conjunction with diffusion-controlled reaction rate coefficients that were calculated for other Ag species. The role of anions in reduction of Agn ions in forming nanoparticles is also discussed. Oxygen containing impurities or admixtures to the helium, air entrainment into the APPJ, and dissociation of saturated water vapor above the solution can produce additional reactive oxygen species in solution, resulting in the production of anions and O 2 – in particular. For a given molarity, delivering a sufficient fluence of reducing species will produce similar nanoparticle densities and sizes for all applied power levels. In conclusion, comparisons are made to alternate models for nanoparticle formation, including charged nanoparticles and use of direct current plasmas.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Data-driven Vulnerability Analysis of Networked Pipeline System

This paper introduces an attack generation framework for evaluating the vulnerability of nonlinear networked pipeline systems. The vulnerability analysis is formulated as determining the presence of feasible attack sets, defined by boundary functions representing the effectiveness and stealthiness of attack signals with respect to the objective and attack detection module. The framework utilizes three data-driven models, including two discriminative models that learn the boundary functions and a generative model that produces elements of the feasible attack set. A new loss function ensures successful attack generation with high probability.

03 NATURAL GAS↗
DOE OSTI2022

Database-wide hazard modelling of the onset of DIII-D tearing modes with field features

The rate of onset (hazard) of tearing modes is modelled probabilistically using statistical learning algorithms. Axisymmetric energy-density equilibrium fields are taken as raw high-dimensional input features which are reduced with principal component analysis. Signal processing of non-axisymmetric magnetics fluctuation array data provides the target information from which to learn. Model selection, visualization and calibration assessment procedures are detailed. Here, the analysis is deployed at large scale across the DIII-D tokamak database. Standard model selection criteria suggest that the energy-density post-processed feature is a better choice for modelling the onset rate compared to the non-processed equilibrium reconstruction solution. Two example applications of the learned rate function are demonstrated: (i) proximity-to-onset discharge monitoring and (ii) database analysis showing an (expected) observational global trend that the general hazard increases as a plasma performance metric increases. An important connection between the hazard function and its use as a conditional probability generator is reviewed in the Appendix.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Stochastic Framework for Optimal Control of Planetary Reentry Trajectories Under Multilevel Uncertainties

We present a novel stochastic optimal control framework that accounts for various types of uncertainties, with application to reentry trajectory planning. The formulation of the optimal trajectory control problem is presented in the context of an indirect method where a functional objective associated with the terminal vehicle speed is to be minimized. Uncertain input parameters in the optimal trajectory control model, including aerodynamic parameters and initial and terminal conditions, are modeled as aleatory random variables, while the statistical parameters of these aleatory distributions are themselves random variables. The parametric and model uncertainties are simultaneously propagated through an extended polynomial chaos expansion (EPCE) formalism. Several metrics are described to evaluate response statistics and presented as insightful tools for robust decision making. Specifically, the response probability density function (PDF) reflecting influence of both epistemic and aleatory uncertainties is obtained. By sampling over the random variables representing model error, an ensemble of response PDFs is generated and the associated failure probability is estimated as a random variable with its own polynomial chaos expansion. Besides, the sensitivity index functions of response PDF with respect to the statistical parameters are evaluated. Coupling parametric and model uncertainties within the EPCE framework leads to a robust and efficient paradigm for multilevel uncertainty propagation and PDF characterization in general optimal control problems.

Engineering↗
DOE OSTI2024

Computing the QRPA level density with the finite amplitude method

Here, we describe a new algorithm to calculate the vibrational nuclear level density of an atomic nucleus. Fictitious perturbation operators that probe the response of the system are generated by drawing their matrix elements from some probability distribution function. We use the Finite Amplitude Method to explicitly compute the response for each such sample. With the help of the Kernel Polynomial Method, we build an estimator of the vibrational level density and provide the upper bound of the relative error in the limit of infinitely many random samples. The new algorithm can give accurate estimates of the vibrational level density. Since it is based on drawing multiple samples of perturbation operators, its computational implementation is naturally parallel and scales like the number of available processing units.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Distributions of Particles Accelerated by Strong Alfvénic Turbulence

This work presents a model for generating nonthermal power-law tails of particles’ energy probability density functions in turbulent collisionless plasmas, applicable to both nonrelativistic and relativistic scenarios. We propose that strong Alfvénic turbulence energizes plasma particles through curvature acceleration, particularly for particles with Larmor radii comparable to the scales of turbulence. When the energy density of the energized particles increases, the efficiency of the energy exchange process diminishes. As a result, the acceleration process saturates, leading to power-law distributions of particle momentum and energy. In the nonrelativistic case, the momentum probability density function scales as f(p)dp ∝ p −3 dp, while in the ultrarelativistic case, the energy probability density function scales as f(γ)dγ ∝ γ −3 dγ, where γ is the Lorentz factor. This model provides a unified framework for understanding particle acceleration in both energy regimes, complementing existing analytical approaches. The predicted scalings are consistent with available observations of energetic ion distributions in the heliosphere and with the findings from numerical simulations of ultrarelativistic particle acceleration in magnetically dominated plasma turbulence.

Alfven waves↗
DOE OSTI2024

Breakup dynamics in a pressure-swirl injector for urea-water solution applications: A computational study

The co-optimization of in-cylinder combustion and after-treatment technology has become a major aspect in engine design and development, with the goal of meeting the increasingly restrictive emission regulations in the transportation industry. Selective Catalytic Reduction is a robust technology to control the emission of NO x , and the injection of urea in water solution is the exhaust tailpipe is a key aspect of its operation. The proposed work uses high-fidelity Computational Fluid Dynamics to characterize the atomization dynamics of the liquid jet in relevant cross-flow conditions. The study focuses on a commercial low-pressure (9 bar) pressure-swirl injector which is characterized in its internal geometry through high-resolution X-ray micro-computational tomography. The internal two-phase flow has been modeled according to the volume-of-fluid approach in a large eddy simulation framework and validated against near-nozzle X-ray radiography measurement. Moreover, characterizing the breakup dynamics for the swirling hollow cone formation, and assessing the influence of the cross-flow in the breakup dynamics was completed. The results have been reported proposing Re-Oh maps and probability density functions of the spray kinematics. Higher cross-flow momentum generates an increase in the jet intact length and a reduction of the liquid droplet diameters. The axial momentum of the jet is affected by the cross-flow already in the near-nozzle region, determining a relevant deviation of the spray velocities. In conclusion, this work aims to inform the initialization of Eulerian-Lagrangian spray models through the assignment of droplet kinematics and static one-way coupling between volume-of-fluid results and Lagrangian spray parcels, to be used for system-size domain simulations.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

Efficient 3D Molecular Design with an E(3) Invariant Transformer VAE

This work introduces a three-dimensional (3D) invariant graph-to-string transformer variational autoencoders (VAE) (Vagrant) for generating molecules with accurate density functional theory (DFT)-level properties. Vagrant learns to model the joint probability distribution of a 3D molecular structure and its properties by encoding molecular structures into a 3D-aware latent space. Directed navigation through this latent space implicitly optimizes the 3D structure of a molecule, and the latent embedding can be used to condition a generative transformer to predict the candidate structure as a one-dimensional (1D) sequence. Additionally, we introduce two novel sampling methods that exploit the latent characteristics of a VAE to improve performance. Here, we show that our method outperforms comparable 3D autoregressive and diffusion methods for predicting quantum chemical property values of novel molecules in terms of both sample quality and computational efficiency.

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

Development of nuclear data processing code FRENDY version 2

Nuclear data processing is an important interface between an evaluated nuclear data library and neutronics calculation codes. JAEA has been developed the new nuclear data processing code FRENDY from 2013. FRENDY version 1 generates the ACE files used for the continuous-energy Monte Carlo codes including PHITS, Solomon, Serpent,and MCNP and it was released as the open-source software under the 2-clause BSD license in 2019.After we released FRENDY version 1, many functions, e.g., the multi-group neutron cross-section library generation, the statistical uncertainty quantification of the probability tables for unresolved resonance cross-section, the 'perturbation' of the ACE file for uncertainty quantification, and the modification of the ENDF-6 formatted nuclear data file, have been developed. We released FRENDY version 2 including these functions. The present paper gives an overview of FRENDY and presents features of new functions implemented in FRENDY version 2. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

A Corrected Score Function Framework for Modelling Circadian Gene Expression

Many biological processes display oscillatory behaviour based on an approximately 24 h internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic studies have identified associations between gene expression during a 24 h period and an individual's health. A challenge with analysing data from these studies is that each individual's internal timing system is offset relative to the 24 h day-night cycle, where day–night cycle time is recorded for each collected sample. Laboratory procedures can accurately determine each individual's offset and determine the internal time of sample collection. However, these laboratory procedures are labour-intensive and expensive. Here, in this paper, we propose a corrected score function framework to obtain a regression model of gene expression given internal time when the offset of each individual is too burdensome to determine. A feature of this framework is that it does not require the probability distribution generating offsets to be symmetric with a mean of zero. Simulation studies validate the use of this corrected score function framework for cosinor regression, which is prevalent in circadian transcriptomic studies. Illustrations with data from three circadian transcriptomic studies further demonstrate that the proposed framework consistently mitigates bias relative to using a score function that does not account for this offset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

2D k -th nearest neighbour statistics: a highly informative probe of galaxy clustering

ABSTRACT Beyond standard summary statistics are necessary to summarize the rich information on non-linear scales in the era of precision galaxy clustering measurements. For the first time, we introduce the 2D k-th nearest neighbour (kNN) statistics as a summary statistic for discrete galaxy fields. This is a direct generalization of the standard 1D kNN by disentangling the projected galaxy distribution from the redshift-space distortion signature along the line-of-sight. We further introduce two different flavours of 2D kNNs that trace different aspects of the galaxy field: the standard flavour which tabulates the distances between galaxies and random query points, and a ‘DD’ flavour that tabulates the distances between galaxies and galaxies. We showcase the 2D kNNs’ strong constraining power both through theoretical arguments and by testing on realistic galaxy mocks. Theoretically, we show that 2D kNNs are computationally efficient and directly generate other statistics such as the popular two-point correlation function (2PCF), voids probability function, and counts-in-cell statistics. In a more practical test, we apply the 2D kNN statistics to simulated galaxy mocks that fold in a large range of observational realism and recover parameters of the underlying extended halo occupation distribution (HOD) model that includes velocity bias and galaxy assembly bias. We find unbiased and significantly tighter constraints on all aspects of the HOD model with the 2D kNNs, both compared to the standard 1D kNN, and the classical redshift-space 2PCF.

79 ASTRONOMY AND ASTROPHYSICS↗