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Open Access Policy Deposits

This series is automatically populated with publications deposited by UC San Diego Department of Physics researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.

Electrode biasing maintains the edge shear layer at high density in the J-TEXT tokamak

(2022)

Abstract Collapse of the edge flow shear as the line-averaged density approaches the Greenwald density limit has been observed as a precursor to the enhanced edge particle flux characteristic of proximity to the density limit regime. Here, we report the use of a biased electrode to sustain the edge shear layer in high density discharges, in which the shear layer would otherwise collapse. A stable increase in line-averaged density is observed along with a strong increase in edge density. These experiments were carried out on the J-TEXT tokamak. The Reynolds stress at the edge is enhanced, and the zonal flow sustained, while density perturbation levels, the flux of turbulence internal energy (i.e., turbulence spreading), and particle and heat flux all decrease significantly. Electron adiabaticity increases, and bias voltage modulation experiments show that an increase in the edge shear leads the increase in adiabaticity. These results suggest that external edge E × B flow shear drive may be of interest for sustaining edge plasma states at high density, and support the hypothesis that collapse of the edge shear layer triggers the onset of the strong transport and turbulence characteristic of the density limit regime.

SOL width broadening by spreading of pedestal turbulence

(2022)

Abstract The pedestal turbulence intensity required to convert the thin, laminar H-mode scrape-off layer (SOL) to a broad turbulent SOL is calculated using the theory of turbulence spreading. A lower bound on the pedestal turbulence level to exceed the neoclassical heuristic drift (HD) width is derived. A reduced model of SOL turbulence spreading is used to determine the SOL width as a function of intensity flux from the pedestal to the SOL. The cross-over value for exceeding the HD model width is then calculated. We determine the pedestal turbulence levels—and the critical scalings thereof—required to achieve this level of broadening. Both drift wave and ballooning mode turbulence are considered. A sensitivity analysis reveals that the key competition is that between spreading and linear E × B shear damping. The required pedestal turbulence levels scale with ρ/R.

Instability and turbulent relaxation in a stochastic magnetic field

(2022)

Abstract An analysis of instability dynamics in a stochastic magnetic field is presented for the tractable case of the resistive interchange. Externally prescribed static magnetic perturbations convert the eigenmode problem to a stochastic differential equation, which is solved by the method of averaging. The dynamics are rendered multi-scale, due to the size disparity between the test mode and magnetic perturbations. Maintaining quasi-neutrality at all orders requires that small-scale convective cell turbulence be driven by disparate scale interaction. The cells in turn produce turbulent mixing of vorticity and pressure, which is calculated by fluctuation-dissipation type analyses, and are relevant to pump-out phenomena. The development of correlation between the ambient magnetic perturbations and the cells is demonstrated, showing that turbulence will ‘lock on’ to ambient stochasticity. Magnetic perturbations are shown to produce a magnetic braking effect on vorticity generation at large scale. Detailed testable predictions are presented. The relations of these findings to the results of available simulations and recent experiments are discussed.

Ion heat and parallel momentum transport by stochastic magnetic fields and turbulence

(2022)

Abstract The theory of turbulent transport of parallel momentum and ion heat by the interaction of stochastic magnetic fields and turbulence is presented. Attention is focused on determining the kinetic stress and the compressive energy flux. A critical parameter is identified as the ratio of the turbulent scattering rate to the rate of parallel acoustic dispersion. For the parameter large, the kinetic stress takes the form of a viscous stress. For the parameter small, the quasilinear residual stress is recovered. In practice, the viscous stress is the relevant form, and the quasilinear limit is not observable. This is the principal prediction of this paper. A simple physical picture is developed and shown to recover the results of the detailed analysis.

Cover page of The LHC Olympics 2020 a community challenge for anomaly detection in high energy physics.

The LHC Olympics 2020 a community challenge for anomaly detection in high energy physics.

(2021)

A new paradigm for data-driven, model-agnostic new physics searches at colliders is emerging, and aims to leverage recent breakthroughs in anomaly detection and machine learning. In order to develop and benchmark new anomaly detection methods within this framework, it is essential to have standard datasets. To this end, we have created the LHC Olympics 2020, a community challenge accompanied by a set of simulated collider events. Participants in these Olympics have developed their methods using an R&D dataset and then tested them on black boxes: datasets with an unknown anomaly (or not). Methods made use of modern machine learning tools and were based on unsupervised learning (autoencoders, generative adversarial networks, normalizing flows), weakly supervised learning, and semi-supervised learning. This paper will review the LHC Olympics 2020 challenge, including an overview of the competition, a description of methods deployed in the competition, lessons learned from the experience, and implications for data analyses with future datasets as well as future colliders.

Enhanced particle transport events approaching the density limit of the J-TEXT tokamak

(2021)

Enhanced particle transport events are discovered and analyzed as the density limit of the J-TEXT tokamak is approached. Edge shear layer collapse is observed and the ratio of Reynolds power to turbulence production decreases. Simultaneously, the divergence of turbulence internal energy flux (i.e. turbulence spreading) increases, indicating that shear layer collapse triggers an outward spreading event. Studies of correlations show that the enhanced particle transport events are quasi-coherent, and manifested primarily in density fluctuations which exhibit positive skewness. Electron adiabaticity emerges as the critical parameter which signals transport event onset. For α < 0.35 as density approaches the Greenwald density, both turbulence spreading and density fluctuations rise rapidly. Taken together, these results elucidate the connections between edge shear layer, density fluctuations, particle transport events, turbulence spreading and plasma edge cooling as the density limit is approached.

Suboptimal resource allocation in changing environments constrains response and growth in bacteria.

(2021)

To respond to fluctuating conditions, microbes typically need to synthesize novel proteins. As this synthesis relies on sufficient biosynthetic precursors, microbes must devise effective response strategies to manage depleting precursors. To better understand these strategies, we investigate the active response of Escherichia coli to changes in nutrient conditions, connecting transient gene expression to growth phenotypes. By synthetically modifying gene expression during changing conditions, we show how the competition by genes for the limited protein synthesis capacity constrains cellular response. Despite this constraint cells substantially express genes that are not required, trapping them in states where precursor levels are low and the genes needed to replenish the precursors are outcompeted. Contrary to common modeling assumptions, our findings highlight that cells do not optimize growth under changing environments but rather exhibit hardwired response strategies that may have evolved to promote fitness in their native environment. The constraint and the suboptimality of the cellular response uncovered provide a conceptual framework relevant for many research applications, from the prediction of evolution to the improvement of gene circuits in biotechnology.

Cover page of Let it rip: the mechanics of self-bisection in asexual planarians determines their population reproductive strategies.

Let it rip: the mechanics of self-bisection in asexual planarians determines their population reproductive strategies.

(2021)

Asexual freshwater planarians reproduce by transverse bisection (binary fission) into two pieces. This process produces a head and a tail, which fully regenerate within 1-2 weeks. How planarians split into two offspring-using only their musculature and substrate traction-is a challenging biomechanics problem. We found that three different species,Dugesia japonica,Girardia tigrinaandSchmidtea mediterranea, have evolved three different mechanical solutions to self-bisect. Using time lapse imaging of the fission process, we quantitatively characterize the main steps of division in the three species and extract the distinct and shared key features. Across the three species, planarians actively alter their body shape, regulate substrate traction, and use their muscles to generate tensile stresses large enough to overcome the ultimate tensile strength of the tissue. Moreover, we show thathoweach planarian species divides dictates how resources are split among its offspring. This ultimately determines offspring survival and reproductive success. Thus, heterospecific differences in the mechanics of self-bisection of individual worms explain the observed differences in the population reproductive strategies of different planarian species.

A traveling-wave solution for bacterial chemotaxis with growth.

(2021)

Bacterial cells navigate their environment by directing their movement along chemical gradients. This process, known as chemotaxis, can promote the rapid expansion of bacterial populations into previously unoccupied territories. However, despite numerous experimental and theoretical studies on this classical topic, chemotaxis-driven population expansion is not understood in quantitative terms. Building on recent experimental progress, we here present a detailed analytical study that provides a quantitative understanding of how chemotaxis and cell growth lead to rapid and stable expansion of bacterial populations. We provide analytical relations that accurately describe the dependence of the expansion speed and density profile of the expanding population on important molecular, cellular, and environmental parameters. In particular, expansion speeds can be boosted by orders of magnitude when the environmental availability of chemicals relative to the cellular limits of chemical sensing is high. Analytical understanding of such complex spatiotemporal dynamic processes is rare. Our analytical results and the methods employed to attain them provide a mathematical framework for investigations of the roles of taxis in diverse ecological contexts across broad parameter regimes.

On the optimality of the enzyme-substrate relationship in bacteria.

(2021)

Much recent progress has been made to understand the impact of proteome allocation on bacterial growth; much less is known about the relationship between the abundances of the enzymes and their substrates, which jointly determine metabolic fluxes. Here, we report a correlation between the concentrations of enzymes and their substrates in Escherichia coli. We suggest this relationship to be a consequence of optimal resource allocation, subject to an overall constraint on the biomass density: For a cellular reaction network composed of effectively irreversible reactions, maximal reaction flux is achieved when the dry mass allocated to each substrate is equal to the dry mass of the unsaturated (or "free") enzymes waiting to consume it. Calculations based on this optimality principle successfully predict the quantitative relationship between the observed enzyme and metabolite abundances, parameterized only by molecular masses and enzyme-substrate dissociation constants (Km). The corresponding organizing principle provides a fundamental rationale for cellular investment into different types of molecules, which may aid in the design of more efficient synthetic cellular systems.