Lanying Zeng

Wall-induced forces on a rigid sphere at finite Reynolds number

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

Forces on a finite-sized particle located close to a wall in a linear shear flow

Re\,{ , 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

Interactions of a stationary finite-sized particle with wall turbulence

Re

Single-virus tracking reveals a spatial receptor-dependent search mechanism

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.

Cell fate decisions emerge as phages cooperate or compete inside their host

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 wit...

Lysis-lysogeny coexistence: prophage integration during lytic development

Reliable information on forces on a finite-sized particle in a turbulent boundary layer is lacking, so workers continue to use standard drag and lift correlations developed for a laminar flow to predict drag and lift forces. Here we consider direct numerical simulations of a turbulent channel flow over an isolated particle of finite size. The size of the particle and its location within the turbulent channel are systematically varied. All relevant length and time scales of turbulence, attached boundary layers on the particle, and particle wake are faithfully resolved, and thus we consider fully resolved direct numerical simulations. The results from the direct numerical simulation are compared with corresponding predictions based on the standard drag relation with and without the inclusion of added-mass and shear-induced lift forces. The influence of turbulent structures, such as streaks, quasi-streamwise vortices and hairpin packets, on particle force is explored. The effect of vortex shedding is also observed to be important for larger particles, whose Re exceeds a threshold.

Genomic and proteomic features of mycobacteriophage SWU1 isolated from China soil

Viral infection begins with the binding of a virus to a specific target on the surface of the host cell, followed by viral genome delivery into the host and a continuation of the infection process. Before binding occurs, the virus must first find its receptor by a process whose details are largely unknown. We applied high-resolution fluorescence microscopy and single-particle tracking to elucidate the target-finding process in bacteriophage λ as it infects an Escherichia coli cell. By monitoring the motion of individual viruses through the early stages of infection, we identified a unique spatial focusing process that allows a virus to arrive from its initial random landing site to its destination at the cell pole. The search process is governed by the interaction between the virus and the LamB receptors, and by the spatial organization of the receptor network on the cell surface. Our findings allowed us to develop a theoretical model for the target-finding process that reproduces the key features observed in experiment. We discuss the possible implications of our findings for the process of viral receptor-finding in higher systems.

Fluorescent nanodiamond‐bacteriophage conjugates maintain host specificity

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.

The Global Reciprocal Reprogramming between Mycobacteriophage SWU1 and Mycobacterium Reveals the Molecular Strategy of Subversion and Promotion of Phage Infection

The infection of Escherichia coli cells by bacteriophage lambda results in bifurcated means of propagation, where the phage decides between the lytic and lysogenic pathways. Although traditionally thought to be mutually exclusive, increasing evidence suggests that this lysis‐lysogeny decision is more complex than once believed, but exploring its intricacies requires an improved resolution of study. Here, with a newly developed fluorescent reporter system labeling single phage and E. coli DNAs, these two distinct pathways can be visualized by following the DNA movements in vivo. Surprisingly, we frequently observed an interesting “lyso‐lysis” phenomenon in lytic cells, where phage integrates its DNA into the host, a characteristic event of the lysogenic pathway, followed by cell lysis. Furthermore, the frequency of lyso‐lysis increases with the number of infecting phages, and specifically, with CII activity. Moreover, in lytic cells, the integration site attB on the E. coli genome migrates toward the polar region over time, leading to more spatial overlap with the phage DNA and frequent colocalization/collision of attB and phage DNA, possibly contributing to a higher chance for DNA integration.

Coupling of DNA Replication and Negative Feedback Controls Gene Expression for Cell-Fate Decisions

Mycobacteriophage SWU1 is a newly isolated phage from soil sample collected in Sichuan province, China using Mycobacterium smegmatis mc(2)155 as host. Plaque, phage morphology and one-step growth curve were characterized. The complete genomic sequence of phage SWU1 was determined by shotgun sequencing. The ends of SWU1 were determined. Structural proteins of SWU1 were analyzed by NanoLC-ESI-MS/MS. Seven ORFs were identified as structural protein encoded by SWU1 genome. The genetic basis underlying the SWU1 plaque was explored using comparative genomics. Prophages homologous to SWU1 were identified in two pathogens, Segniliparus rugosus ATCC BAA-974 and Mycobacterium rhodesiae JS60. Genus Segniliparus is a member of the order Corynebacteriales. To our knowledge, this is the first report of Mycobacterium prophages in different genera.