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At least 1,171 records · Page 65

Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions

The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microorganisms. Quantitative measurements of these interactions are important for understanding and engineering ecosystem structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from the Drosophila melanogaster gut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by two Lactobacillus strains to an Acetobacter strain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair of Escherichia coli amino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells by demonstrating that, under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions.

3D printed device↗

Moiré metrology of energy landscapes in van der Waals heterostructures

The emerging field of twistronics, which harnesses the twist angle between two-dimensional materials, represents a promising route for the design of quantum materials, as the twist-angle-induced superlattices offer means to control topology and strong correlations. At the small twist limit, and particularly under strain, as atomic relaxation prevails, the emergent moiré superlattice encodes elusive insights into the local interlayer interaction. Here we introduce moiré metrology as a combined experiment-theory framework to probe the stacking energy landscape of bilayer structures at the 0.1 meV/atom scale, outperforming the gold-standard of quantum chemistry. Through studying the shapes of moiré domains with numerous nano-imaging techniques, and correlating with multi-scale modelling, we assess and refine first-principle models for the interlayer interaction. We document the prowess of moiré metrology for three representative twisted systems: bilayer graphene, double bilayer graphene and H-stacked MoSe 2 /WSe 2 . Moiré metrology establishes sought after experimental benchmarks for interlayer interaction, thus enabling accurate modelling of twisted multilayers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Vortex-sheet modeling of hydrodynamic instabilities produced by an oblique shock interacting with a perturbed interface in the HED regime

In this work, we consider hydrodynamic instabilities produced by the interaction of an oblique shock with a perturbed material interface under high-energy-density (HED) conditions. During this interaction, a baroclinic torque is generated along the interface due to the misalignment between the density and pressure gradients, thus leading to perturbation growth. Our objective is to understand the competition between the impulsive acceleration due to the normal component of the shock velocity, which drives the Richtmyer–Meshkov instability, and the shear flow across the interface due to the tangential component of the shock velocity, which drives the Kelvin–Helmholtz instability, as well as its relation to perturbation growth. Since the vorticity resulting from the shock-interface interaction is confined to the interface, we describe the perturbation growth using a two-dimensional vortex-sheet model. We demonstrate the ability of the vortex-sheet model to reproduce roll-up dynamics for non-zero Atwood numbers by comparing to past laser-driven HED experiments. We determine the dependence of the interface dynamics on the tilt angle and propose a time scaling for the perturbation growth at early time. Eventually, this scaling will serve as a platform for the design of future experiments. This study is the first attempt to incorporate into a vortex-sheet model the time-dependent interface decompression and the deceleration (as well as the corresponding Rayleigh–Taylor instability) arising from laser turn-off.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Towards Realistic Models of Heterogeneous Catalysis: Simulations of Oxidation Catalysis from First Principles

Among the most significant developments in heterogeneous catalysis in the last 20 years is the emergence of microkinetic models, often parameterized from density functional theory (DFT) calculations, used to quantify observed catalyst performance and to guide the discovery of new catalytic materials. While DFT directly reports binding energies and elementary step activation energies, the free energies that enter into microkinetic models must be computed from additional approximations. Frequently these free energy approximations assume ideal behavior—that adsorbates do not interact with one another, or that adsorbates are immobile or vibrate harmonically about a binding site. These assumptions can and do have an impact on predicted catalyst performance and potentially even on predicted trends. Our work relates to three categories of non-idealities, explored in the context of nitrogen oxidation and reduction catalysis on metal surfaces. One component relates to adsorbate translational free energy, the contribution least well described by conventional models, in which we develop modeling approaches that improve accuracy with limited increase in computational expense. A second component relates adsorbate-adsorbate interactions, in which we develop benchmark on-lattice interaction models and compare kinetic predictions with conventional mean-field models, in an effort to develop more robust coverage-dependent mean field modeling approaches. The last relates the most fundamental assumption of all—that of energy equipartition—in an effort to rationalize and guide plasma-enhanced catalysis.

99 GENERAL AND MISCELLANEOUS↗

First Estimation of Model Parameters for Neutrino-Induced Nucleon Knockout Using Simulation-Based Inference

To enable an accurate determination of oscillation parameters, accelerator-based neutrino experiments require detailed simulations of nuclear interaction physics in the GeV regime. While substantial effort from both theory and experiment is currently being invested to improve the fidelity of these simulations, their present deficiencies typically oblige experimental collaborations to resort to empirical tuning of simulation model parameters. As the precision requirements of the field continue to become more stringent, machine learning techniques may provide a powerful means of handling corresponding growth in the complexity of future neutrino interaction model tuning exercises. To study the suitability of simulation-based inference (SBI) for this physics application, in this paper we revisit a tuned configuration of the GENIE neutrino event generator that was originally developed by the MicroBooNE collaboration. Despite closely reproducing the adopted values of four physics parameters when confronted with the tuned cross-section predictions as input, we find that our trained SBI algorithm prefers modestly different values (within MicroBooNE's assigned uncertainties) and achieves slightly better goodness-of-fit when inference is run on the experimental data set originally used by MicroBooNE. We also find that our trained algorithm can create a fair approximation of an alternative neutrino scattering simulation, NuWro, that shares only a subset of its physics model parameters with GENIE.

Tame-Narvaez, Karla [Fermilab] (ORCID:000000022249↗

Neutrino-Argon Cross Sections in MicroBooNE: Measurements Spanning Multiple Interaction Channels, Final States, and Neutrino Fluxes

Neutrinos are one of the most elusive particles in the Standard Model of particle physics due to their tiny interaction cross section, which makes them challenging to detect and study. There are three known flavors of neutrinos, and any given neutrino probabilistically oscillates between them as a function of the particle's energy and propagation distance. Experimental characterization of these oscillations elucidates fundamental properties of the neutrino and the Standard Model. Meeting the precision goals of ongoing and future oscillation measurements requires detailed modeling of the way neutrinos interact with nuclear matter. Precision modeling of these interactions is a challenging theoretical problem, rich with intricate physics effects to explore, and requires input from equally precise measurements of neutrino-nucleus interaction cross sections spanning a broad range of scattering channels. To fill this need, there is an ongoing multi-experiment effort to measure these cross sections across energies, interaction channels, and nuclear targets. This thesis describes three analyses reporting neutrino-argon cross section measurements with data from the MicroBooNE liquid argon time projection chamber detector. These span multiple interaction channels, final state topologies, and neutrino fluxes. The first analysis is a set of inclusive charged current muon neutrino cross section measurements for final states with and without protons, which provides a unique view of the hadronic final state produced in these interactions. Second is a set of cross section measurements for neutral current neutral pion production, which provides a vital dataset on this under-characterized channel. Third is significant progress on measuring neutrinos produced by kaons decaying at rest, which represents a unique opportunity to measure cross sections with a mono-energetic flux of neutrinos. These measurements are accompanied by a modeling study in the GiBUU theory framework, which probes the sensitivity of the muon neutrino and pion production measurements to the modeling of nucleon-nucleon final state interactions in neutrino-nucleus scattering.

Bogart, Benjamin [Michigan U.]↗

Impact of Interaction Uncertainties on Neutrino-Nucleus Cross Section Measurements

Accelerator-based neutrino facilities represent forefront scientific endeavors, employing state-of-the-art techniques to investigate the properties of neutrinos and unveil signals of physics beyond the standard model. Neutrino-nucleus interactions constitute one of the biggest systematics in these experiments. As neutrino-nucleus cross section measurement statistics have started to surge in recent years, it's becoming vital to control systematics in these measurements. This presentation explores the pivotal role of neutrino interaction uncertainties, including nuclear effects and modeling approximations, in achieving precise neutrino cross-section measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Microbe-iron interactions control lignin decomposition in soil

Lignin decomposition is critically linked to terrestrial carbon (C) cycle due to the enormous C mass of lignin and its importance in controlling overall rates of litter decomposition. Interactions between lignin and iron (Fe) minerals have been increasingly recognized as key mediators of lignin decomposition in experimental studies. However, we still lack a quantitative understanding of how Fe minerals interact with microbes to control lignin decomposition. Here, we leveraged experimental results from an incubation of Fe-rich soil, in which lignin decomposition rates were measured at aerobic conditions after four levels of pre-treated O2 availability, to examine microbe-Fe (MiFe) interactions in lignin decomposition with a MiFe model. We quantified how Fe redox cycling interacted with microbial activities to control lignin decomposition via data-model integration. Our results showed that the MiFe model with time-dependent growth and mortality functions better represented CO2 release from lignin decomposition (R2 ranging from 0.96 to 0.97) than models assuming either first-order or Michaelis-Menten kinetics. Reduction of Fe(III) to Fe(II) after pre-treatments with lower O2 availability stimu-lated the Fenton reaction to break down macro-molecular lignin into small molecules available to microbes. The small molecules of lignin and necromass bounded with oxidized Fe and were protected from decomposition. After 1-year incubation, the model implied that most of C stabilized with Fe minerals was derived from small molecular lignin C. Our quantitative analysis of microbe-Fe interactions sheds new light on lignin decomposition and preservation and helps improve model prediction of soil C persistence under global change.

Liao, Cuijuan↗

Investigation of flow regimes in arc plasma–gas interactions using a two-temperature arc in crossflow model

The perpendicular impingement of a gas stream on an electric arc, a configuration known as the arc in crossflow, is of primary relevance in the study of plasma-gas interactions, as well as in industrial applications such as circuit breakers and wire-arc spraying. The flow dynamics in the arc in crossflow are the result of coupled fluid-thermal-electromagnetic phenomena accompanied by large property gradients, which can produce significant deviations from Local Thermodynamic Equilibrium (LTE) among electrons and gas species. These characteristics can lead to the establishment of distinct flow regimes depending on the relative values of the controlling parameters of the system, such as inflow velocity, arc current, and inter-electrode spacing. A two-temperature non-LTE (NLTE) model is used to investigate the arc dynamics and the establishment of flow regimes in the arc in crossflow. The plasma flow model is implemented within a nonlinear Variational Multiscale (VMS) numerical discretization approach that is less dissipative, and hence better suited to capture unstable behavior, than traditional VMS methods commonly used in computational fluid dynamics simulations. The Reynolds and the Enthalpy dimensionless numbers, characterizing the relative flow strength and arc strength, respectively, are chosen as the controlling parameters of the system. Simulation results reveal the onset of dynamic behavior and the establishment of steady, periodic, quasi-periodic, and chaotic or potentially turbulent, regimes, as identified by distinct spatiotemporal fluctuations. The computational findings reveal the role of increasing the relative arc strength on enhancing flow stability by delaying the growth of fluctuating and unstable flow behavior.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The roles of three-nucleon force and continuum coupling in mirror symmetry breaking of oxygen mass region

With both three-nucleon force and continuum coupling included, we have developed a self-consistent ab initio Gamow shell model within the Gamow Hartree-Fock (GHF) basis obtained by the realistic interaction itself. With the chiral two-nucleon N 3 LO and three-nucleon N 2 LO interactions, the Gamow shell model has been applied to the mirror systems of Z = 8 neutron-rich isotopes and N = 8 proton-rich isotones, giving good agreements with data in binding energies, dripline positions and excitation spectra. The GHF calculated that the 0 ds/2 , 1 S1/2 and 1 p3/2 orbitals are resonances. The resonance states and their interplay with nonresonant continua play a crucial role in the descriptions of nuclei around driplines. Excitation spectra and Thomas-Ehrman shifts observed can be better described when both three-nucleon force and continuum coupling are considered in calculations. The three-nucleon force and continuum coupling produce a combined effect on the Thomas-Ehrman shift, e.g., for the 1/2 + resonance level of 19Na. The calculations help the understandings of related nuclear astrophysical processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Numerical methods for nonlocal and fractional models

Partial differential equations (PDEs) are used with huge success to model phenomena across all scientific and engineering disciplines. However, across an equally wide swath, there exist situations in which PDEs fail to adequately model observed phenomena, or are not the best available model for that purpose. On the other hand, in many situations, nonlocal models that account for interaction occurring at a distance have been shown to more faithfully and effectively model observed phenomena that involve possible singularities and other anomalies. Here, we consider a generic nonlocal model, beginning with a short review of its definition, the properties of its solution, its mathematical analysis and of specific concrete examples. We then provide extensive discussions about numerical methods, including finite element, finite difference and spectral methods, for determining approximate solutions of the nonlocal models considered. In that discussion, we pay particular attention to a special class of nonlocal models that are the most widely studied in the literature, namely those involving fractional derivatives. The article ends with brief considerations of several modelling and algorithmic extensions, which serve to show the wide applicability of nonlocal modelling.

97 MATHEMATICS AND COMPUTING↗

Dark matter haloes in the multicomponent model. III. From dwarfs to galaxy clusters

A possibility of DM being multicomponent has a strong implication on resolving decades-long known cosmological problems on small scale. In addition to elastic scattering, the model allows for inelastic interactions, which can be characterized by a ‘velocity kick’ parameter. The simplest 2cDM model with cross-section 0.01 ≲ σ/m < 1cm 2 g -1 and the kick velocity V k ≃100kms -1 have been shown to robustly resolve the missing satellites, core-cusp, and too-big-to-fail problems in N-body cosmological simulations tested on Milky Way (MW)-like haloes of a virial mass ~5 × 10 11 M ⊙ (Papers I & II). With the aim of further constraining the parameter space available for the 2cDM model, we extend our analysis to dwarf and galaxy cluster haloes with their virial mass of ~10 7 -10 8 and ~10 13 -10 14 M ⊙ ⁠, respectively. We find that σ 0 /m ≳ 0.1 cm 2 g -1 is preferentially disfavoured for both dwarfs and galaxy cluster haloes in comparison with observations, while σ 0 /m = 0.001 cm 2 g -1 causes little perceptible difference from that of the CDM counterpart for most of the cross-section’s velocity dependence studied in this work. Our main result is that within the reasonable set of parameters, the 2cDM model can successfully explain the observational trends seen in dwarf galaxy and galaxy cluster haloes, and the model leaves us an open window for other possible alternative DM models.

79 ASTRONOMY AND ASTROPHYSICS↗

Analysis of mobility data to build contact networks for COVID-19

As social distancing policies and recommendations went into effect in response to COVID-19, people made rapid changes to the places they visit. These changes are clearly seen in mobility data, which records foot traffic using location trackers in cell phones. While mobility data is often used to extract the number of customers that visit a particular business or business type, it is the frequency and duration of concurrent occupancy at those sites that governs transmission. Understanding the way people interact at different locations can help target policies and inform contact tracing and prevention strategies. This paper outlines methods to extract interactions from mobility data and build networks that can be used in epidemiological models. Several measures of interaction are extracted: interactions between people, the cumulative interactions for a single person, and cumulative interactions that occur at particular businesses. Network metrics are computed to identify structural trends which show clear changes based on the timing of stay-at-home orders. Measures of interaction and structural trends in the resulting networks can be used to better understand potential spreading events, the percent of interactions that can be classified as close contacts, and the impact of policy choices to control transmission.

60 APPLIED LIFE SCIENCES↗

Numerical methods for nonlocal and fractional models

Partial differential equations (PDEs) are used, with huge success, to model phenomena arising across all scientific and engineering disciplines. However, across an equally wide swath, there exist situations in which PDE models fail to adequately model observed phenomena or are not the best available model for that purpose. On the other hand, in many situations, nonlocal models that account for interaction occurring at a distance have been shown to more faithfully and effectively model observed phenomena that involve possible singularities and other anomalies. In this article, we consider a generic nonlocal model, beginning with a short review of its definition, the properties of its solution, its mathematical analysis, and specific concrete examples. We then provide extensive discussions about numerical methods, including finite element, finite difference, and spectral methods, for determining approximate solutions of the nonlocal models considered. In that discussion, we pay particular attention to a special class of nonlocal models that are the most widely studied in the literature, namely those involving fractional derivatives. The article ends with brief considerations of several modeling and algorithmic extensions which serve to show the wide applicability of nonlocal modeling.

97 MATHEMATICS AND COMPUTING↗

SAGE Intrusion Detection System: Sensitivity Analysis Guided Explainability for Machine Learning.

This report details the results of a three-fold investigation of sensitivity analysis (SA) for machine learning (ML) explainability (MLE): (1) the mathematical assessment of the fidelity of an explanation with respect to a learned ML model, (2) quantifying the trustworthiness of a prediction, and (3) the impact of MLE on the efficiency of end-users through multiple users studies. We focused on the cybersecurity domain as the data is inherently non-intuitive. As ML is being using in an increasing number of domains, including domains where being wrong can elicit high consequences, MLE has been proposed as a means of generating trust in a learned ML models by end users. However, little analysis has been performed to determine if the explanations accurately represent the target model and they themselves should be trusted beyond subjective inspection. Current state-of-the-art MLE techniques only provide a list of important features based on heuristic measures and/or make certain assumptions about the data and the model which are not representative of the real-world data and models. Further, most are designed without considering the usefulness by an end-user in a broader context. To address these issues, we present a notion of explanation fidelity based on Shapley values from cooperative game theory. We find that all of the investigated MLE explainability methods produce explanations that are incongruent with the ML model that is being explained. This is because they make critical assumptions about feature independence and linear feature interactions for computational reasons. We also find that in deployed, explanations are rarely used due to a variety of reason including that there are several other tools which are trusted more than the explanations and there is little incentive to use the explanations. In the cases when the explanations are used, we found that there is the danger that explanations persuade the end users to wrongly accept false positives and false negatives. However, ML model developers and maintainers find the explanations more useful to help ensure that the ML model does not have obvious biases. In light of these findings, we suggest a number of future directions including developing MLE methods that directly model non-linear model interactions and including design principles that take into account the usefulness of explanations to the end user. We also augment explanations with a set of trustworthiness measures that measure geometric aspects of the data to determine if the model output should be trusted.

97 MATHEMATICS AND COMPUTING↗

Multiscale Control of Generic Second Order Traffic Models by Driver-Assist Vehicles

We study the derivation of generic high order macroscopic traffic models from a follow-the-leader particle description via a kinetic approach. First, we recover a third order traffic model as the hydrodynamic limit of an Enskog-type kinetic equation. Next, we introduce in the vehicle interactions a binary control modeling the automatic feedback provided by driver-assist vehicles and we upscale such a new particle description by means of another Enskog-based hydrodynamic limit. The resulting macroscopic model is now a generic second order model (GSOM), which contains in turn a control term inherited from the microscopic interactions. We show that such a control may be chosen so as to optimize global traffic trends, such as the vehicle flux or the road congestion, constrained by the GSOM dynamics. By means of numerical simulations, we investigate the effect of this control hierarchy in some specific case studies, which exemplify the multiscale path from the vehiclewise implementation of a driver-assist control to its optimal hydrodynamic design.

GSOM↗

Quantum simulation of an extended Dicke model with a magnetic solid

Abstract The Dicke model describes the cooperative interaction of an ensemble of two-level atoms with a single-mode photonic field and exhibits a quantum phase transition as a function of light–matter coupling strength. Extending this model by incorporating short-range atom–atom interactions makes the problem intractable but is expected to produce new physical phenomena and phases. Here, we simulate such an extended Dicke model using a crystal of ErFeO 3 , where the role of atoms (photons) is played by Er 3+ spins (Fe 3+ magnons). Through terahertz spectroscopy and magnetocaloric effect measurements as a function of temperature and magnetic field, we demonstrated the existence of a novel atomically ordered phase in addition to the superradiant and normal phases that are expected from the standard Dicke model. Further, we elucidated the nature of the phase boundaries in the temperature–magnetic-field phase diagram, identifying both first-order and second-order phase transitions. These results lay the foundation for studying multiatomic quantum optics models using well-characterized many-body solid-state systems.

Marquez Peraca, Nicolas↗

Signatures of Velocity-dependent Dark Matter Self-interactions in Milky Way-mass Halos

In this work, we explore the impact of elastic, anisotropic, velocity-dependent dark matter (DM) self-interactions on the host halo and subhalos of Milky Way (MW)--mass systems. We consider a generic self-interacting dark matter (SIDM) model parameterized by the masses of a light mediator and the DM particle. The ratio of these masses, w, sets the velocity scale above which momentum transfer due to DM self-interactions becomes inefficient. We perform high-resolution zoom-in simulations of an MW-mass halo for values of w that span scenarios in which self-interactions either between the host and its subhalos or only within subhalos efficiently transfer momentum, and we study the effects of self-interactions on the host halo and on the abundance, radial distribution, orbital dynamics, and density profiles of subhalos in each case. The abundance and properties of surviving subhalos are consistent with being determined primarily by subhalo--host halo interactions. In particular, subhalos on radial orbits in models with larger values of the cross section at the host halo velocity scale are more susceptible to tidal disruption owing to mass loss from ram pressure stripping caused by self-interactions with the host. This mechanism suppresses the abundance of surviving subhalos relative to collisionless DM simulations, with stronger suppression for larger values of w. Thus, probes of subhalo abundance around MW-mass hosts can be used to place upper limits on the self-interaction cross section at velocity scales of ~200 km s-1, and combining these measurements with the orbital properties and internal dynamics of subhalos may break degeneracies among velocity-dependent SIDM models.

79 ASTRONOMY AND ASTROPHYSICS↗