We perform direct numerical simulations of a rigid sphere translating parallel to a flat wall in an otherwise quiescent ambient fluid. A spectral element method is employed to perform the simulations with high accuracy. For $Re\,{<}\,100$, we observe the lift coefficient to decrease with both Reynolds number and distance from the wall. In this regime the present results are in good agreement with the low-Reynolds-number theory of Vasseur & Cox (1977), with the recent experiments of Takemura & Magnaudet (2003) and with the simulations of Kim et al. (1993). The most surprising result from the present simulations is that the wall-induced lift coefficient increases dramatically with increasing $Re$ above about 100. Detailed analysis of the flow field around the sphere suggests that this increase is due to an imperfect bifurcation resulting in the formation of a double-threaded wake vortical structure. In addition to a non-rotating sphere, we also simulate a freely rotating sphere in order to assess the importance of free rotation on the translational motion of the sphere. We observe the effect of sphere rotation on lift and drag forces to be small. We also explore the effect of the wall on the onset of unsteadiness.

Bacterial type IV secretion systems (T4SSs) are a functionally diverse translocation superfamily. They consist mainly of two large subfamilies: (i) conjugation systems that mediate interbacterial DNA transfer and (ii) effector translocators that deliver effector macromolecules into prokaryotic or eukaryotic cells. A few other T4SSs export DNA or proteins to the milieu, or import exogenous DNA. The T4SSs are defined by 6 or 12 conserved “core” subunits that respectively elaborate “minimized” systems in Gram‐positive or ‐negative bacteria. However, many “expanded” T4SSs are built from “core” subunits plus numerous others that are system‐specific, which presumptively broadens functional capabilities. Recently, there has been exciting progress in defining T4SS assembly pathways and architectures using a combination of fluorescence and cryoelectron microscopy. This review will highlight advances in our knowledge of structure–function relationships for model Gram‐negative bacterial T4SSs, including “minimized” systems resembling the Agrobacterium tumefaciens VirB/VirD4 T4SS and “expanded” systems represented by the Helicobacter pylori Cag, Legionella pneumophila Dot/Icm, and F plasmid‐encoded Tra T4SSs. Detailed studies of these model systems are generating new insights, some at atomic resolution, to long‐standing questions concerning mechanisms of substrate recruitment, T4SS channel architecture, conjugative pilus assembly, and machine adaptations contributing to T4SS functional versatility.

To understand and better model the hydrodynamic force acting on a finite-sized particle moving in a wall-bounded linear shear flow, here we consider the two limiting cases of (a) a rigid stationary spherical particle in a linear wall-bounded shear flow and (b) a rigid spherical particle in rectilinear motion parallel to a wall in a quiescent ambient flow. In the present computations, the particle Reynolds number ranges from 2 to 250 at separation distances to the wall from nearly sitting on the wall to far away from the wall. First we characterize the structure of the wake for a stationary particle in a linear shear flow and compare with those for a particle moving parallel to a wall in a quiescent ambient [see L. Zeng, S. Balachandar, and P. Fischer, J. Fluid Mech. 536, 1 (2005)]. For both these cases we present drag and lift results and obtain composite drag and lift correlations that are valid for a wide range of Re and distance from the wall. These correlations have been developed to be consistent with all available low Reynolds number theories and approach the appropriate uniform flow results at large distance from the wall. Particular attention is paid to the case of particle in contact with the wall and the computational results are compared with those from experiments.

Prokaryotes evolved numerous systems that defend against predation by bacteriophages. In addition to well-known restriction-modification and CRISPR-Cas immunity systems, many poorly characterized systems exist. One class of such systems, named BREX, consists of a putative phosphatase, a methyltransferase and four other proteins. A Bacillus cereus BREX system provides resistance to several unrelated phages and leads to modification of specific motif in host DNA. Here, we study the action of BREX system from a natural Escherichia coli isolate. We show that while it makes cells resistant to phage λ infection, induction of λ prophage from cells carrying BREX leads to production of viruses that overcome the defense. The induced phage DNA contains a methylated adenine residue in a specific motif. The same modification is found in the genome of BREX-carrying cells. The results establish, for the first time, that immunity to BREX system defense is provided by an epigenetic modification.

The system of the bacterium Escherichia coli and its virus, bacteriophage lambda, is paradigmatic for gene regulation in cell-fate development, yet insight about its mechanisms and complexities are limited due to insufficient resolution of study. Here we develop a 4-colour fluorescence reporter system at the single-virus level, combined with computational models to unravel both the interactions between phages and how individual phages determine cellular fates. We find that phages cooperate during lysogenization, compete among each other during lysis, and that confusion between the two pathways occasionally occurs. Additionally, we observe that phage DNAs have fluctuating cellular arrival times and vie for resources to replicate, enabling the interplay during different developmental paths, where each phage genome may make an individual decision. These varied strategies could separate the selection for replication-optimizing beneficial mutations during lysis from sequence diversification during lysogeny, allowing rapid adaptation of phage populations for various environments.