skip to main content

Search for: All records

Creators/Authors contains: "Thomas, G."

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. In this paper, we discuss some of the key challenges in the study of time-dependent processes and non-equilibrium behaviour in warm dense matter. We outline some of the basic physics concepts that have underpinned the definition of warm dense matter as a subject area in its own right and then cover, in a selective, non-comprehensive manner, some of the current challenges, pointing along the way to topics covered by the papers presented in this volume. This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.
    Free, publicly-accessible full text available August 21, 2024
  2. Warm dense matter is a material state in the region of parameter space connecting condensed matter to classical plasma physics. In this intermediate regime, we investigate the significance of non-adiabatic electron-ion interactions upon ion dynamics. To disentangle non-adiabatic from adiabatic electron-ion interactions, we compare the ion self-diffusion coefficient from the non-adiabatic electron force field computational model with an adiabatic, classical molecular dynamics simulation. A classical pair potential developed through a force-matching algorithm ensures the only difference between the models is due to the electronic inertia. We implement this new method to characterize non-adiabatic effects on the self-diffusion of warm dense hydrogen over a wide range of temperatures and densities. Ultimately we show that the impact of non-adiabatic effects is negligible for equilibrium ion dynamics in warm dense hydrogen. This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.
    Free, publicly-accessible full text available August 21, 2024
  3. Beard, Daniel A (Ed.)
    The geometry of the blood vessel wall plays a regulatory role on the motion of red blood cells (RBCs). The overall topography of the vessel wall depends on many features, among which the endothelial lining of the endothelial surface layer (ESL) is an important one. The endothelial lining of vessel walls presents a large surface area for exchanging materials between blood and tissues. The ESL plays a critical role in regulating vascular permeability, hindering leukocyte adhesion as well as inhibiting coagulation during inflammation. Changes in the ESL structure are believed to cause vascular hyperpermeability and entrap immune cells during sepsis, which could significantly alter the vessel wall geometry and disturb interactions between RBCs and the vessel wall, including the wall-induced migration of RBCs and the thickening of a cell-free layer. To investigate the influence of the vessel wall geometry particularly changed by the ESL under various pathological conditions, such as sepsis, on the motion of RBCs, we developed two models to represent the ESL using the immersed boundary method in two dimensions. In particular, we used simulations to study how the lift force and drag force on a RBC near the vessel wall vary with different wall thickness, spatial variation,more »and permeability associated with changes in the vessel wall geometry. We find that the spatial variation of the wall has a significant effect on the wall-induced migration of the RBC for a high permeability, and that the wall-induced migration is significantly inhibited as the vessel diameter is increased.« less
    Free, publicly-accessible full text available July 17, 2024
  4. Abstract

    We review recent developments in Jackiw–Teitelboim gravity. This is a simple solvable model of quantum gravity in two dimensions (that arises e.g. from the s-wave sector of higher dimensional gravity systems with spherical symmetry). Due to its solvability, it has proven to be a fruitful toy model to analyze important questions such as the relation between black holes and chaos, the role of wormholes in black hole physics and holography, and the way in which information that falls into a black hole can be recovered.

  5. Ahmed, Ferdous (Ed.)
    We addressed the hypothesis that intraspecific genetic variation in plant traits from different sites along a distance/elevation gradient would influence the communities they support when grown at a new site. Answers to this hypothesis are important when considering the community consequences of assisted migration under climate change; i.e., if you build it will they come?. We surveyed arthropod communities occurring on the foundation riparian tree species Populus angustifolia along a distance/elevation gradient and in a common garden where trees from along the gradient were planted 20–22 years earlier. Three major patterns were found: 1) In the wild, arthropod community composition changed significantly. Trees at the lower elevation site supported up to 58% greater arthropod abundance and 26% greater species richness than more distant, high elevation trees. 2) Trees grown in a common garden sourced from the same locations along the gradient, supported arthropod communities more similar to their corresponding wild trees, but the similarity declined with transfer distance and elevation. 3) Of five functional traits examined, leaf area, a trait under genetic control that decreases at higher elevations, is correlated with differences in arthropod species richness and abundance. Our results suggest that genetic differences in functional traits are stronger driversmore »of arthropod community composition than phenotypic plasticity of plant traits due to environmental factors. We also show that variation in leaf area is maintained and has similar effects at the community level while controlling for environment. These results demonstrate how genetically based traits vary across natural gradients and have community-level effects that are maintained, in part, when they are used in assisted migration. Furthermore, optimal transfer distances for plants suffering from climate change may not be the same as optimal transfer distances for their dependent communities.« less
    Free, publicly-accessible full text available May 8, 2024
  6. Semipermeable membranes are a key feature of all living organisms. While specialized membrane transporters in cells can import otherwise impermeable nutrients, the earliest cells would have lacked a mechanism to import nutrients rapidly under nutrient-rich circumstances. Using both experiments and simulations, we find that a process akin to passive endocytosis can be recreated in model primitive cells. Molecules that are too impermeable to be absorbed can be taken up in a matter of seconds in an endocytic vesicle. The internalized cargo can then be slowly released over hours, into the main lumen or putative cytoplasm. This work demonstrates a way by which primitive life could have broken the symmetry of passive permeation prior to the evolution of protein transporters.
    Free, publicly-accessible full text available June 13, 2024
  7. Gupton, Stephanie (Ed.)
    Following exocytosis at active zones, synaptic vesicle membranes and membrane-bound proteins must be recycled. The endocytic machinery that drives this recycling accumulates in the periactive zone (PAZ), a region of the synapse adjacent to active zones, but the organization of this machinery within the PAZ, and how PAZ composition relates to active zone release properties, remains unknown. The PAZ is also enriched for cell adhesion proteins, but their function at these sites is poorly understood. Here, using Airyscan and stimulated emission depletion imaging of Drosophila synapses, we develop a quantitative framework describing the organization and ultrastructure of the PAZ. Different endocytic proteins localize to distinct regions of the PAZ, suggesting that subdomains are specialized for distinct biochemical activities, stages of membrane remodeling, or synaptic functions. We find that the accumulation and distribution of endocytic but not adhesion PAZ proteins correlate with the abundance of the scaffolding protein Bruchpilot at active zones—a structural correlate of release probability. These data suggest that endocytic and exocytic activities are spatially correlated. Taken together, our results identify novel relationships between the exocytic and endocytic apparatus at the synapse and provide a new conceptual framework to quantify synaptic architecture.
    Free, publicly-accessible full text available May 15, 2024

    We present a study of the molecular gas of seven early-type galaxies with high angular resolution data obtained as part of the mm-Wave Interferometric Survey of Dark Object Masses (WISDOM) project with the Atacama Large Millimeter/submillimeter Array. Using a fixed spatial-scale approach, we study the mass surface density (Σ) and velocity dispersion (σ) of the molecular gas on spatial scales ranging from 60 to 120 pc. Given the spatial resolution of our data (20–70 pc), we characterize these properties across many thousands of individual sightlines (≈50 000 at our highest physical resolution). The molecular gas along these sightlines has a large range (≈2 dex) of mass surface densities and velocity dispersions $\approx 40~{{\ \rm per\ cent}}$ higher than those of star-forming spiral galaxies. It has virial parameters αvir that depend weakly on the physical scale observed, likely due to beam smearing of the bulk galactic rotation, and is generally supervirial. Comparing the internal turbulent pressure (Pturb) to the pressure required for dynamic equilibrium (PDE), the ratio Pturb/PDE is significantly less than unity in all galaxies, indicating that the gas is not in dynamic equilibrium and is strongly compressed, in apparent contradiction to the virial parameters. This may be due to ourmore »neglect of shear and tidal forces, and/or the combination of three-dimensional and vertical diagnostics. Both αvir and Pturb anticorrelate with the global star-formation rate of our galaxies. We therefore conclude that the molecular gas in early-type galaxies is likely unbound, and that large-scale dynamics likely plays a critical role in its regulation. This contrasts to the giant molecular clouds in the discs of late-type galaxies, that are much closer to dynamical equilibrium.

    « less
  9. Plant growth-promoting bacteria (PGPB) are valuable for supporting sustainable food production and may alleviate the negative impacts of chemical fertilizers on human health and the environment. While single-strain inoculations have proven unreliable due to poor survival and colonization in the rhizosphere, application of PGPB in multispecies consortia has the potential to improve these outcomes. Here, we describe a new approach for screening and identifying bacterial consortia that improve the growth of corn relative to plants inoculated with a single strain. The method uses the microwell recovery array (MRA), a microfabricated high-throughput screening device, to rapidly explore the maize ( Zea mays L .) rhizobiome for higher-order combinations of bacteria that promote the growth and colonization of the nitrogen-fixing PGPB, Azospirillum brasilense . The device simultaneously generates thousands of random, unique combinations of bacteria that include A. brasilense and members of the maize rhizobiome, then tracks A. brasilense growth in each combination during co-culture. Bacteria that show the highest levels of A. brasilense growth promotion are then recovered from the device using a patterned light extraction technique and are identified. With this approach, the screen uncovered growth-promoting consortia consisting primarily of bacteria from the Acinetobacter - Enterobacter - Serratia genera, whichmore »were then co-inoculated with A. brasilense on axenic maize seedlings that were monitored inside a plant growth chamber. Compared to maize plants inoculated with A. brasilense alone, plants that were co-inoculated with these consortia showed accelerated growth after 15 days. Follow-up root colonization assays revealed that A. brasilense colonized at higher levels on roots from the co-inoculated seedlings. These findings demonstrate a new method for rapid bioprospecting of root and soil communities for complementary PGPB and for developing multispecies consortia with potential use as next-generation biofertilizers.« less
    Free, publicly-accessible full text available April 18, 2024
  10. Free, publicly-accessible full text available March 23, 2024