A hybrid discrete bubble-lattice Boltzmann–discrete element model for gas-charged sediments

This paper presents a hybrid discrete bubble-lattice Boltzmann–discrete element modelling framework for simulating gas-charged sediments, especially in the seabed. A discrete bubble model proposed in chemical engineering is adapted in the coupled discrete element/lattice Boltzmann method to model the migration of gas bubbles in saturated sediments involving interactions between gas bubbles and fluid/solid phases. Surface tension is introduced into the discrete bubble model in this work, so that it can handle the complex gas–fluid–solid interface. The lattice Boltzmann and discrete element methods are, respectively, employed to simulate fluid flows and mechanical behaviours of sediments. A velocity interpolation-based immerse boundary method is utilised to resolve the coupling between the fluid flow and the solid/gas phase. The proposed technique is preliminarily validated using simulations of bubble migration in fluids, which is followed by high-resolution investigations of the transport of a gas bubble in seabed sediments. It is demonstrated that this hybrid method can reproduce, to a certain degree, the characters of bubbles moving in seabed sediment tests

Subdiffraction-limit study of Kaede diffusion and spatial distribution in live Escherichia coli.

Photoactivation localization microscopy (PALM) is used to study the spatial distribution and diffusion of single copies of the protein Kaede in the cytoplasm of live Escherichia coli under moderate growth conditions (67 min doubling time). The spatial distribution of Kaede is uniform within the cytoplasm. The cytoplasmic radius of 380 ± 30 nm varies little from cell to cell. Single-particle tracking using 4 ms exposure times reveals negatively curved plots of mean-square displacement versus time. A detailed comparison with Monte Carlo simulations in a spherocylindrical volume shows that the curvature can be quantitatively understood in terms of free diffusion within a confining volume. The mean diffusion coefficient across cells is = 7.3 ± 1.1 μm(2)·s(-1), consistent with a homotetrameric form of Kaede. The distribution of squared displacements along the long axis for individual Kaede molecules is consistent with homogeneous diffusion. However, for longer cells, a spatial map of one-step estimates of the diffusion coefficient along x suggests that diffusion is ∼20-40% faster within nucleoids than in the ribosome-rich region lying between nucleoid lobes at the cell mid-plane. Fluorescence recovery after photobleaching yielded = 8.3 ± 1.6 μm(2)·s(-1), in agreement with the single-particle tracking results

Nonperturbative imaging of nucleoid morphology in live bacterial cells during an antimicrobial peptide attack.

Studies of time-dependent drug and environmental effects on single, live bacterial cells would benefit significantly from a permeable, nonperturbative, long-lived fluorescent stain specific to the nucleoids (chromosomal DNA). The ideal stain would not affect cell growth rate or nucleoid morphology and dynamics, even during laser illumination for hundreds of camera frames. In this study, time-dependent, single-cell fluorescence imaging with laser excitation and a sensitive electron-multiplying charge-coupled-device (EMCCD) camera critically tested the utility of "dead-cell stains" (SYTOX orange and SYTOX green) and "live-cell stains" (DRAQ5 and SYTO 61) and also 4',6-diamidino-2-phenylindole (DAPI). Surprisingly, the dead-cell stains were nearly ideal for imaging live Escherichia coli, while the live-cell stains and DAPI caused nucleoid expansion and, in some cases, cell permeabilization and the halting of growth. SYTOX orange performed well for both the Gram-negative E. coli and the Gram-positive Bacillus subtilis. In an initial application, we used two-color fluorescence imaging to show that the antimicrobial peptide cecropin A destroyed nucleoid-ribosome segregation over 20 min after permeabilization of the E. coli cytoplasmic membrane, reminiscent of the long-term effects of the drug rifampin. In contrast, the human cathelicidin LL-37, while similar to cecropin A in structure, length, charge, and the ability to permeabilize bacterial membranes, had no observable effect on nucleoid-ribosome segregation. Possible underlying causes are suggested

The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane

Accumulating evidence suggests that molecular motors contribute to the apparent diffusion of molecules in cells. However, current literature lacks evidence for an active process that drives diffusive-like motion in the bacterial membrane. One possible mechanism is cell wall synthesis, which involves the movement of protein complexes in the cell membrane circumferentially around the cell envelope and may generate currents in the lipid bilayer that advectively transport other transmembrane proteins. We test this hypothesis in Escherichia coli using drug treatments that slow cell wall synthesis and measure their effect on the diffusion of the transmembrane protein mannitol permease using fluorescence recovery after photobleaching. We found no clear decrease in diffusion in response to vancomycin and no decrease in response to mecillinam treatment. These results suggest that cell wall synthesis is not an active contributor to mobility in the cytoplasmic membrane