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DOE OSTI2020

Pattern formation in a coupled membrane-bulk reaction-diffusion model for intracellular polarization and oscillations

Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity molecules. Here we study the distribution of the polarity protein Cdc42 in a mass-conserved membrane-bulk model, and explore the effects of diffusion and spatial dimensionality on spatio-temporal pattern formation. We first analyze a one-dimensional (1-D) model for Cdc42 oscillations in fission yeast, consisting of two diffusion equations in the bulk domain coupled to nonlinear ODEs for binding kinetics at each end of the cell. In 1-D, our analysis reveals the existence of symmetric and asymmetric steady states, as well as anti-phase relaxation oscillations typical of slow-fast systems. We then extend our analysis to a two-dimensional (2-D) model with circular bulk geometry, for which species can either diffuse inside the cell or become bound to the membrane and undergo a nonlinear reaction-diffusion process. We also consider a nonlocal system of PDEs approximating the dynamics of the 2-D membrane-bulk model in the limit of fast bulk diffusion. In all three model variants we find that mass conservation selects perturbations of spatial modes that simply redistribute mass. In 1-D, only anti-phase oscillations between the two ends of the cell can occur, and in-phase oscillations are excluded. In higher dimensions, no radially symmetric oscillations are observed. Instead, the only instabilities are symmetry-breaking, either corresponding to stationary Turing instabilities, leading to the formation of stationary patterns, or to oscillatory Turing instabilities, leading to traveling and standing waves. Codimension-two Bogdanov—Takens bifurcations occur when the two distinct instabilities coincide, causing traveling waves to slow down and to eventually become stationary patterns. Our work clarifies the effect of geometry and dimensionality on behaviors observed in ma.ss-conserved cell polarity models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Experimental and numerical study of the shielding effect of two tandem rough cylinders in flow-induce oscillation

The shielding effect of the downstream cylinder in flow induced oscillation (FIO) of two cylinders arranged in tandem is studied experimentally and numerically at Reynolds number 30,000 to 120,000. Both cylinders are in one degree-of-freedom, transverse-oscillations, and have turbulence stimulation in the form of selective surface roughness to expand FIO beyond vortex-induced vibration (VIV) into galloping. Shielding of the downstream cylinder has a negative effect on harnessing hydrokinetic energy. Further, to study its effect and mechanics, selective cases are studied both numerically and experimentally and discussed to demonstrate the shielding effect on the downstream cylinder and understand its cause. The main conclusions are: (1) The shielding effect for the downstream cylinder shows a strong relation to the damping ratio. As the damping ratio increases, the shielding effect is mitigated. Additionally, the oscillation of the rear cylinder becomes stable and shows stable frequency. (2) In the VIV region, as the stiffness and natural frequency increase, the shielding effect decreases substantially. (3) In the VIV region, the vorticity of the vortices shedding from both the upper and the lower sides of the downstream cylinder does not accumulate enough due to the attraction by the vortices shed from the upstream cylinder, thus resulting in partial suppression of the oscillation on the downstream cylinder. (4) In the galloping region, the shielding effect for the downstream cylinder depends on whether the vorticity near the downstream cylinder is strengthened by the vortices generated by the shear layers of the upstream cylinder or weakened.

42 ENGINEERING↗

DOE OSTI2023

Learning effective stochastic differential equations from microscopic simulations: Linking stochastic numerics to deep learning

We identify effective stochastic differential equations (SDEs) for coarse observables of fine-grained particle- or agent-based simulations; these SDEs then provide useful coarse surrogate models of the fine scale dynamics. We approximate the drift and diffusivity functions in these effective SDEs through neural networks, which can be thought of as effective stochastic ResNets. The loss function is inspired by, and embodies, the structure of established stochastic numerical integrators (here, Euler–Maruyama and Milstein); our approximations can thus benefit from backward error analysis of these underlying numerical schemes. They also lend themselves naturally to “physics-informed” gray-box identification when approximate coarse models, such as mean field equations, are available. Existing numerical integration schemes for Langevin-type equations and for stochastic partial differential equations can also be used for training; we demonstrate this on a stochastically forced oscillator and the stochastic wave equation. Our approach does not require long trajectories, works on scattered snapshot data, and is designed to naturally handle different time steps per snapshot. We consider both the case where the coarse collective observables are known in advance, as well as the case where they must be found in a data-driven manner.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

First Sterile Neutrino Search at NOvA Experiment Using both Neutrino and Anti-Neutrino Data

Neutrinos are among the most abundant fundamental particles in the universe, and yet they are so elusive that they pass through almost everything without leaving a trace. For decades, researchers have measured neutrino oscillations in great detail, refining our understanding of the theories. Yet, once again, neutrino shows their incredibly surprising nature through some recent experimental results, suggesting that our current understanding might be incomplete. Several experiments have observed an unexpected difference in the observed neutrino behaviour from what the Standard Model predicts, showing an excess in some cases (e.g. LSND, MiniBooNE) and a deficit of neutrino events in others (e.g. SAGE, GALLEX). These anomalies challenge our conventional theories of standard three neutrino flavors and phenomenologically motivate the sterile neutrino hypothesis, which does not interact through the usual weak force. While some results appear consistent with this idea, others have found no supporting evidence (e.g. MicroBooNE), leaving the question unanswered. NOvA is one such long-baseline neutrino experiment with its Near Detector (ND) at Fermilab and a Far Detector (FD) at 810 km in Minnesota. It uses the NuMI beam as its primary source of neutrinos for oscillation studies. Its two-detector setup, extended baseline, and ability to conduct combined $\nu$-$\bar\nu$ analyses position it to explore these phenomena in new ways. We use the joint $\nu_{\mu}$ and neutral current (NC) disappearance channels to probe active-sterile mixing in the 3+1 model. This analysis utilizes a data sample of 27$\times$10$^{20}$ protons on target (POT) in neutrino mode and 12.5$\times$10$^{20}$ protons on target (POT) in antineutrino mode. We found no evidence of sterile neutrino at 90$\%$ C.L. We present the limits in $\sin^{2}\theta_{24}$ vs $\Delta m^{2}_{41}$, $\sin^{2}\theta_{34}$ vs $\Delta m^{2}_{41}$, and $\sin^{2}2\theta_{\mu\tau}$ vs $\Delta m^{2}_{41}$ parameter spaces. The limits provided by this analysis are world leading in most of the parameter spaces.

Chaudhary, Shivam [Indian Inst. of Info. Tech. Guw↗

DOE OSTI2020

Single-atom heat engine as a sensitive thermal probe

We propose employing a quantum heat engine as a sensitive probe for thermal baths. In particular, we study a single-atom Otto engine operating in an open thermodynamic cycle. Owing to its cyclic nature, the engine is capable of translating small temperature differences between two baths into a macroscopic oscillation in a flywheel. We present analytical and numerical modeling of the quantum dynamics of the engine and estimate it to be capable of detecting temperature differences as small as 2 μK. This sensitivity can be further improved by utilizing quantum resources such as squeezing of the ion motion. The proposed scheme does not require quantum state initialization and is able to detect small temperature differences in a wide range of base temperatures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Dark Matter Search in the Muon g-2 experiment at Fermilab

Dark matter is one of the most interesting research topics in physics. Many particle physicists are trying to identify it because we know that dark matter could be a major component of a complete fundamental description of nature. The Muon g-2 Experiment at Fermilab measures the anomalous precession frequency of the muon. Oscillations of this precession frequency could be produced by dark matter coupling to muons. This talk will describe how we could observe DM signals in the Muon g-2 data. I will explain how we determine the Muon g-2 DM mass range sensitivity, and analysis strategies throughout the mass range. Finally, I will present the expected Muon g-2 experiment discovery/exclusion reach in selected DM model-dependent scenarios.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Characterization of ELM pacing via vertical jogs on DIII-D

Edge localized mode (ELM) pacing via vertical plasma oscillations or jogging has been successfully demonstrated on DIII-D. Rapid vertical movement of the plasma toward the X-point has been shown to effectively trigger ELMs. By vertically oscillating the plasma at a rate of 10 Hz, the ELM frequency increased from ~5 Hz, the natural ELM frequency in similar DIII-D discharges, to 20 Hz. Downward jogs have been observed to trigger multiple ELMs in one cycle. ELMs triggered at higher than natural frequencies lead to smaller decreases in stored energy, from 8% to as little as below 1%. As a consequence, the peak heat flux to the divertor has been observed to be reduced by a factor of ~2. In addition, a reduction in the carbon impurity concentration has been observed. During downward jogs in the lower single null (LSN) configuration, the X-point movement is slower and smaller than the top of the plasma. As a result, a reduction in the plasma cross-section and hence volume has been observed. To understand the mechanism of ELM triggering by jogging, a toy model of the edge toroidal current has been built and tested with DIII-D experiment data. The experimental data and model suggest that when the plasma moves down toward the X-point, a net positive toroidal current is locally induced in the edge region. ELITE stability analysis suggests that this current pushes the plasma state across the peeling side of the peeling–ballooning stability boundary into the unstable region triggering ELMs.

ELM pacing↗

DOE OSTI2023

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Background: Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013–2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. Results: Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. Conclusions: This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

16S rRNA gene sequencing↗

DOE OSTI2023

Theoretical tools for neutrino scattering: interplay between lattice QCD, EFTs, nuclear physics, phenomenology, and neutrino event generators

Neutrino physics is entering a precision era in which measurements of neutrino oscillations, astrophysical neutrinos from supernovae and other sources, and coherent neutrino scattering will provide insight on the nature of neutrino masses, the presence of CP violation, and perhaps more exotic new physics in the neutrino sector. Maximizing the discovery potential of increasingly precise neutrino experiments will require an improved theoretical understanding of neutrino-nucleus cross sections over a wide range of energies that uses a combination of lattice QCD, nuclear effective theories, phenomenological models, and neutrino event generators to make reliable theory predictions for experimentally relevant nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Inclusive and exclusive electron scattering data analysis from Jefferson Lab experiment E12-14-012

Since the first observations of neutrino oscillation, neutrino experiments have come a long way toward precise measurements of the neutrino oscillation parameters, but some obstacles still remain. The next generation of oscillation experiments, including the Deep Underground Neutrino Experiment (DUNE), will be using the Liquid Argon Time Projection Chambers (LArTPCs) with natural argon as the neutrino target material. A precise model of the neutrino cross section on argon does not exist, which is a source of significant uncertainty in such experiments. The E12-14-012 experiment at Jefferson Lab seeks to help remedy this via electron scattering measurements on argon and titanium targets. The experiment collected both inclusive (e,e') and exclusive (e,e'p) data at a wide range of kinematics with the intent to measure the electron-nucleus cross section and thus derive a spectral function for argon that can be used with neutrino experiments. The use of titanium in this experiment stems from the equivalent shell structure that its protons share with the neutrons in argon, which will be crucial in oscillation experiments but cannot be measured directly in electron scattering. This thesis collects several papers which present results from the E12-14-012 experiment. These results include the inclusive (e,e') cross sections for carbon, titanium, argon, and aluminum at a beam energy of 2.22 GeV and a scattering angle of 15.54 deg with uncertainty of less than 5%. Also included are the first results of the exclusive (e,e'p) cross section on argon and titanium.

Murphy, Matthew D.↗

DOE OSTI2022

Natural orbitals for the ab initio no-core configuration interaction approach

Ab initio no-core configuration interaction (NCCI) calculations for the nuclear many-body problem have traditionally relied upon an antisymmetrized product (Slater determinant) basis built from harmonic oscillator orbitals. The accuracy of such calculations is limited by the finite dimensions which are computationally feasible for the truncated many-body space. We therefore seek to improve the accuracy obtained for a given basis size by optimizing the choice of single-particle orbitals. Natural orbitals, which diagonalize the one-body density matrix, provide a basis which maximizes the occupation of low-lying orbitals, thus accelerating convergence in a configuration-interaction basis, while also possibly providing physical insight into the single-particle structure of the many-body wave function. We describe the implementation of natural orbitals in the NCCI framework and examine the nature of the natural orbitals thus obtained, the properties of the resulting many-body wave functions, and the convergence of observables. After taking 3 He as an illustrative testbed, we explore aspects of NCCI calculations with natural orbitals for the ground state of the p-shell neutron halo nucleus 6 He .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

A Computational Framework for Simulations of Dissipative Nonadiabatic Dynamics on Hybrid Oscillator-Qubit Quantum Devices

Here, we introduce a computational framework for simulating nonadiabatic vibronic dynamics on circuit quantum electrodynamics (cQED) platforms. Our approach leverages hybrid oscillator-qubit quantum hardware with midcircuit measurements and resets, enabling the incorporation of environmental effects such as dissipation and dephasing. To demonstrate its capabilities, we simulate energy transfer dynamics in a triad model of photosynthetic chromophores inspired by natural antenna systems. We specifically investigate the role of dissipation during the relaxation dynamics following photoexcitation, where electronic transitions are coupled to the evolution of quantum vibrational modes. Our results indicate that hybrid oscillator-qubit devices, operating with noise levels below the intrinsic dissipation rates of typical molecular antenna systems, can achieve the simulation fidelity required for practical computations on near-term and early fault-tolerant quantum computing platforms.

Hamiltonians↗

DOE OSTI2023

A subdivision-stabilized B-spline mixed material point method

Subjected to external loadings, polymeric materials, e.g., biological tissues, hydrogels, and elastomers, may undergo extreme, nearly incompressible, (self-)contact deformations. For numerical modeling employing mesh-based techniques such as the finite element method (FEM), these deformations pose significant challenges due to large distortions in the deformed geometry, accuracy issues stemming from volumetric locking effects, and increased computational cost from complex contact searches. As an alternative to mesh-based methods, the material point method (MPM), a continuum-based particle technique, is gaining attention for its ability to handle extreme distortions and capture no-slip contact without added cost. For nearly incompressible material behaviors, while mixed formulations can address locking effects by treating displacements and pressure as independent fields, they can suffer from numerical instabilities close to the incompressibility limit due to the violation of the inf-sup condition, leading to inaccurate nodal pressure solutions. Here we propose an efficient and stable mixed B-spline material point method with highest achievable regularity for quasi-compressible polymeric materials. Using the two-scale relation of B-splines, we introduce a subdivision-stabilization for the two-field mixed MPM and obtain numerically stable, oscillation-free nodal solutions with equal-order interpolations with optimal regularity. Building on the Eulerian-Lagrangian nature of MPM, a previously-converged solution framework is adopted to mitigate issues related to cell-crossing and numerical fracture artifact present in standard MPM. We assess the stability and accuracy of the developed mixed MPM at large deformations for soft materials through the benchmark Cook’s membrane problem. Additionally, we test the robustness of the proposed MPM by modeling several examples, including the compression and indentation of a circular block into a quasi-compressible substrate and the twisting deformation of a rectangular block. The findings demonstrate the MPM’s capabilities for modeling practical soft material applications.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Molecular-Level Insights into the NMR Relaxivity of Gadobutrol Using Quantum and Classical Molecular Simulations

MRI is an indispensable diagnostic tool in modern medicine; however, understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge, hindering the molecular-guided development of more effective contrast agents. By using quantum-based polarizable force fields, the first-of-its-kind molecular dynamics (MD) simulations of Gadobutrol are reported where the 1 H NMR longitudinal relaxivity r 1 of the aqueous phase is determined without any adjustable parameters. The MD simulations of r 1 dispersion (i.e., frequency dependence) show good agreement with measurements at frequencies of interest in clinical MRI. Importantly, the simulations reveal key insights into the molecular level processes leading to r 1 dispersion by decomposing the NMR dipole–dipole autocorrelation function G(t) into a discrete set of molecular modes, analogous to the eigenmodes of a quantum harmonic oscillator. The molecular modes reveal important aspects of the underlying mechanisms governing r 1 , such as its multiexponential nature and the importance of the second eigenmodal decay. By simply analyzing the MD trajectories on a parameter-free approach, the Gadobutrol simulations show that the outer-shell water contributes ∼50% of the total relaxivity r 1 compared to the inner-shell water, in contrast to simulations of (nonchelated) gadolinium-aqua where the outer shell contributes only ∼15% of r 1 . The deviation between simulations and measurements of r 1 below clinical MRI frequencies is used to determine the low-frequency electron-spin relaxation time for Gadobutrol, in good agreement with independent studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

The essential character of the neutrino mechanism of core-collapse supernova explosions

Abstract Calibrating with detailed 2D core-collapse supernova (CCSN) simulations, we derive a simple CCSN explosion condition based solely upon the terminal density profiles of state-of-the-art stellar evolution calculations of the progenitor massive stars. This condition captures the vast majority of the behaviour of the one hundred 2D state-of-the-art models we performed to gauge its usefulness. The goal is to predict, without resort to detailed simulation, the explodability of a given massive star. We find that the simple maximum fractional ram pressure jump discriminant we define works well ∼90 per cent of the time and we speculate on the origin of the few false positives and false negatives we witness. The maximum ram pressure jump generally occurs at the time of accretion of the silicon/oxygen interface, but not always. Our results depend upon the fidelity with which the current implementation of our code F ornax adheres to Nature and issues concerning the neutrino–matter interaction, the nuclear equation of state, the possible effects of neutrino oscillations, grid resolution, the possible role of rotation and magnetic fields, and the accuracy of the numerical algorithms employed remain to be resolved. Nevertheless, the explodability condition we obtain is simple to implement, shows promise that it might be further generalized while still employing data from only the unstable Chandrasekhar progenitors, and is a more credible and robust simple explosion predictor than can currently be found in the literature.

Astronomy & Astrophysics↗

DOE OSTI2021

Effect of Hydrogen on Steady-State and Transient Combustion Instability Characteristics

This paper examines the effects of steady-state and transient hydrogen enrichment on thermoacoustic instability in a model gas turbine combustor. Combustion instability, a feedback loop between flame heat release rate oscillations and combustor acoustics, is characterized in a swirl-stabilized flame operated at a range of hydrogen–natural gas fuel blends and heat rates. Measurements of combustor chamber pressure fluctuations and CH* chemiluminescence imaging are used to characterize instability at a range of operating conditions. Steady-state tests show that both mixture heat rate and hydrogen content affect system stability. At a given heat rate, higher levels of hydrogen result in unstable combustion. As heat rate increases, instability occurs at lower concentrations of hydrogen in the fuel. Transient operation was tested in two directions—instability onset and decay—and two hydrogen-addition times—a short time of 1 ms and a longer time of 4 s. Results show that instability onset processes, through the transient addition of hydrogen, are highly repeatable regardless of the timescale of hydrogen addition. Certain instability decay processes are less repeatable, resulting in cases that do not fully transition from unstable to stable combustion despite similar changes in hydrogen fuel flow rate. Flame behavior before, during, and after the transient is characterized using high-speed CH* chemiluminescence imaging. Analysis of the high-speed images shows changes in flame stabilization and dynamics during the onset and decay processes. Finally, the results of this study can have implications for systems that experience variations in fuel composition, particularly in light of growing interest in hydrogen as a renewable fuel.

42 ENGINEERING↗

DOE OSTI2024

Searches for Heavy Neutral Leptons (HNL) in CMS

The smallness of neutrino masses in conjunction with the observed flavor oscillations in the neutrino sector can be hinting to physics beyond the standard model. These observations can be naturally accommodated by the so-called "seesaw" mechanism, in which new Heavy Neutral Leptons (HNL) are postulated. Additionally, several HNL models provide a DM candidate or include a possible explanation for the observed baryon asymmetry. This talk presents an comprehensive overview of the CMS HNL program with a focus on the new experimental results as shown in a recently published review paper by CMS.The talk will highlight several novel and complementary approaches using both prompt and long-lived signatures using the full Run-II data-set collected at the LHC.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Data assimilation in operator algebras

We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a nonabelian operator algebra, which provides a representation of observables by multiplication operators and probability densities by density operators (quantum states). In the algebraic approach, the forecast step of data assimilation is represented by a quantum operation induced by the Koopman operator of the dynamical system. Moreover, the analysis step is described by a quantum effect, which generalizes the Bayesian observational update rule. Projecting this formulation to finite-dimensional matrix algebras leads to computational schemes that are i) automatically positivity-preserving and ii) amenable to consistent data-driven approximation using kernel methods for machine learning. Moreover, these methods are natural candidates for implementation on quantum computers. Applications to the Lorenz 96 multiscale system and the El Niño Southern Oscillation in a climate model show promising results in terms of forecast skill and uncertainty quantification.

97 MATHEMATICS AND COMPUTING↗