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Open Access Publications from the University of California

Department of Physics

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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.

Cover page of Stochastic transition in synchronized spiking nanooscillators.

Stochastic transition in synchronized spiking nanooscillators.


This work reports that synchronization of Mott material-based nanoscale coupled spiking oscillators can be drastically different from that in conventional harmonic oscillators. We investigated the synchronization of spiking nanooscillators mediated by thermal interactions due to the close physical proximity of the devices. Controlling the driving voltage enables in-phase 1:1 and 2:1 integer synchronization modes between neighboring oscillators. Transition between these two integer modes occurs through an unusual stochastic synchronization regime instead of the loss of spiking coherence. In the stochastic synchronization regime, random length spiking sequences belonging to the 1:1 and 2:1 integer modes are intermixed. The occurrence of this stochasticity is an important factor that must be taken into account in the design of large-scale spiking networks for hardware-level implementation of novel computational paradigms such as neuromorphic and stochastic computing.

How turbulent transport broadens the heat flux width: local SOL production or edge turbulence spreading?


Abstract: This paper uses data from limited HL-2A Ohmic-plasma to answer the question of how turbulent transport broadens the heat flux width. A key issue in this study is the determination of the origin of SOL turbulence. We develop the concept of the energy production ratio R_a, which compares the flux of turbulence energy across the LCFS to the net, integrated energy production in the SOL. The flux of turbulence energy (i.e., spreading) is measured directly, using Langmuir probes. Experimental data is used to evaluate R_a. Results show that usually R_a>1, indicating that SOL turbulence is energized primarily by edge turbulence spreading. The exceptions – cases where R_a<1 – are those with relatively stronger E×B shear near the LCFS. The latter inhibits both turbulence spreading and local SOL production, but has greater effects on spreading. High blob fraction in the turbulence correlates with large values of R_a. The implications for heat flux width physics are discussed.

Cover page of Surfactant-Mediated Structural Modulations to Planar, Amphiphilic Multilamellar Stacks.

Surfactant-Mediated Structural Modulations to Planar, Amphiphilic Multilamellar Stacks.


The hydrophobic effect, a ubiquitous process in biology, is a primary thermodynamic driver of amphiphilic self-assembly. It leads to the formation of unique morphologies including two highly important classes of lamellar and micellar mesophases. The interactions between these two types of structures and their involved components have garnered significant interest because of their importance in key biochemical technologies related to the isolation, purification, and reconstitution of membrane proteins. This work investigates the structural organization of mixtures of the lamellar-forming phospholipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and two zwitterionic micelle-forming surfactants, being n-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (Zwittergent 3-12 or DDAPS) and 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (O-Lyso-PC), when assembled by water vapor hydration with X-ray diffraction measurements, brightfield optical microscopy, wide-field fluorescence microscopy, and atomic force microscopy. The results reveal that multilamellar mesophases of these mixtures can be assembled across a wide range of POPC to surfactant (POPC:surfactant) concentration ratios, including ratios far surpassing the classical detergent-saturation limit of POPC bilayers without significant morphological disruptions to the lamellar motif. The mixed mesophases generally decreased in lamellar spacing (D) and headgroup-to-headgroup distance (Dhh) with a higher concentration of the doped surfactant, but trends in water layer thickness (Dw) between each bilayer in the stack are highly variable. Further structural characteristics including mesophase topography, bilayer thickness, and lamellar rupture force were revealed by atomic force microscopy (AFM), exhibiting homogeneous multilamellar stacks with no significant physical differences with changes in the surfactant concentration within the mesophases. Taken together, the outcomes present the assembly of unanticipated and highly unique mixed mesophases with varied structural trends from the involved surfactant and lipidic components. Modulations in their structural properties can be attributed to the surfactants chemical specificity in relation to POPC, such as the headgroup hydration and the hydrophobic chain tail mismatch. Taken together, our results illustrate how specific chemical complexities of surfactant-lipid interactions can alter the morphologies of mixed mesophases and thereby alter the kinetic pathways by which surfactants dissolve lipid mesophases in bulk aqueous solutions.

Observation of long-radial-range-correlation in turbulence in high-collisionality high-confinement on DIII-D


Abstract: We report on the observation of spatially asymmetric turbulent structures with a long radial correlation length in the core of high-collisionality \emph{H}-mode plasmas on DIII-D tokamak. These turbulent structures develop from shorter wavelength turbulence and have a radially elongated structure. The envelope of turbulence spans a broad radial range in the mid-radius region, leading to streamer-like transport events. The underlying turbulence is featured by intermittency, long-term memory effect, and the characteristic spectrum of self-organized criticality. The amplitude and the radial scale increase substantially when the shearing rate of the mean flow is reduced below the turbulent scattering rate. The enhanced LRRC transport events are accompanied by apparent normalized energy confinement time degradation. The emergence of such LRRC transport events may serve as a candidate explanation for the degrading nature of H-mode core plasma confinement at high-collisionality on DIII-D tokamak.

Cover page of Endoplasmic reticulum network heterogeneity guides diffusive transport and kinetics

Endoplasmic reticulum network heterogeneity guides diffusive transport and kinetics


The endoplasmic reticulum (ER) is a dynamic network of interconnected sheets and tubules that orchestrates the distribution of lipids, ions, and proteins throughout the cell. The impact of its complex, dynamic morphology on its function as an intracellular transport hub remains poorly understood. To elucidate the functional consequences of ER network structure and dynamics, we quantify how the heterogeneity of the peripheral ER in COS7 cells affects diffusive protein transport. In vivo imaging of photoactivated ER membrane proteins demonstrates their nonuniform spreading to adjacent regions, in a manner consistent with simulations of diffusing particles on extracted network structures. Using a minimal network model to represent tubule rearrangements, we demonstrate that ER network dynamics are sufficiently slow to have little effect on diffusive protein transport. Furthermore, stochastic simulations reveal a novel consequence of ER network heterogeneity: the existence of "hot spots" where sparse diffusive reactants are more likely to find one another. ER exit sites, specialized domains regulating cargo export from the ER, are shown to be disproportionately located in highly accessible regions, further from the outer boundary of the cell. Combining in vivo experiments with analytic calculations, quantitative image analysis, and computational modeling, we demonstrate how structure guides diffusive protein transport and reactions in the ER.

Cover page of FAIR for AI: An interdisciplinary and international community building perspective.

FAIR for AI: An interdisciplinary and international community building perspective.


A foundational set of findable, accessible, interoperable, and reusable (FAIR) principles were proposed in 2016 as prerequisites for proper data management and stewardship, with the goal of enabling the reusability of scholarly data. The principles were also meant to apply to other digital assets, at a high level, and over time, the FAIR guiding principles have been re-interpreted or extended to include the software, tools, algorithms, and workflows that produce data. FAIR principles are now being adapted in the context of AI models and datasets. Here, we present the perspectives, vision, and experiences of researchers from different countries, disciplines, and backgrounds who are leading the definition and adoption of FAIR principles in their communities of practice, and discuss outcomes that may result from pursuing and incentivizing FAIR AI research. The material for this report builds on the FAIR for AI Workshop held at Argonne National Laboratory on June 7, 2022.

Cover page of An Updated Dust-to-Star Geometry: Dust Attenuation Does Not Depend on Inclination in 1.3 ≤z ≤2.6 Star-forming Galaxies from MOSDEF

An Updated Dust-to-Star Geometry: Dust Attenuation Does Not Depend on Inclination in 1.3 ≤z ≤2.6 Star-forming Galaxies from MOSDEF


Abstract: We investigate dust attenuation and its dependence on viewing angle for 308 star-forming galaxies at 1.3 ≤ z ≤ 2.6 from the MOSFIRE Deep Evolution Field survey. We divide galaxies with a detected Hα emission line and coverage of Hβ into eight groups by stellar mass, star formation rate (SFR), and inclination (i.e., axis ratio), and we then stack their spectra. From each stack, we measure the Balmer decrement and gas-phase metallicity, and then we compute the median A V and UV continuum spectral slope (β). First, we find that none of the dust properties (Balmer decrement, A V, or β) varies with the axis ratio. Second, both stellar and nebular attenuation increase with increasing galaxy mass, showing little residual dependence on SFR or metallicity. Third, nebular emission is more attenuated than stellar emission, and this difference grows even larger at higher galaxy masses and SFRs. Based on these results, we propose a three-component dust model in which attenuation predominantly occurs in star-forming regions and large, dusty star-forming clumps, with minimal attenuation in the diffuse ISM. In this model, nebular attenuation primarily originates in clumps, while stellar attenuation is dominated by star-forming regions. Clumps become larger and more common with increasing galaxy mass, creating the above mass trends. Finally, we argue that a fixed metal yield naturally leads to mass regulating dust attenuation. Infall of low-metallicity gas increases the SFR and lowers the metallicity, but leaves the dust column density mostly unchanged. We quantify this idea using the Kennicutt–Schmidt and fundamental metallicity relations, showing that galaxy mass is indeed the primary driver of dust attenuation.