Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters.

Bacteriophages (phages) defend mucosal surfaces against bacterial infections. However, their complex interactions with their bacterial hosts and with the mucus-covered epithelium remain mostly unexplored. Our previous work demonstrated that T4 phage with Hoc proteins exposed on their capsid adhered to mucin glycoproteins and protected mucus-producing tissue culture cells in vitro. On this basis, we proposed our bacteriophage adherence to mucus (BAM) model of immunity. Here, to test this model, we developed a microfluidic device (chip) that emulates a mucosal surface experiencing constant fluid flow and mucin secretion dynamics. Using mucus-producing human cells and Escherichia coli in the chip, we observed similar accumulation and persistence of mucus-adherent T4 phage and nonadherent T4∆hoc phage in the mucus. Nevertheless, T4 phage reduced bacterial colonization of the epithelium >4,000-fold compared with T4∆hoc phage. This suggests that phage adherence to mucus increases encounters with bacterial hosts by some other mechanism. Phages are traditionally thought to be completely dependent on normal diffusion, driven by random Brownian motion, for host contact. We demonstrated that T4 phage particles displayed subdiffusive motion in mucus, whereas T4∆hoc particles displayed normal diffusion. Experiments and modeling indicate that subdiffusive motion increases phage-host encounters when bacterial concentration is low. By concentrating phages in an optimal mucus zone, subdiffusion increases their host encounters and antimicrobial action. Our revised BAM model proposes that the fundamental mechanism of mucosal immunity is subdiffusion resulting from adherence to mucus. These findings suggest intriguing possibilities for engineering phages to manipulate and personalize the mucosal microbiome.

Interfacial and topological effects on the glass transition in free-standing polystyrene films.

United-atom molecular-dynamics computer simulations of atactic polystyrene (PS) were performed for the bulk and free-standing films of 2 nm-20 nm thickness, for both linear and cyclic polymers comprised of 80 monomers. Simulated volumetric glass-transition temperatures (Tg) show a strong dependence on the film thickness below 10 nm. The glass-transition temperature of linear PS is 13% lower than that of the bulk for 2.5 nm-thick films, as compared to less than 1% lower for 20 nm films. Our studies reveal that the fraction of the chain-end groups is larger in the interfacial layer with its outermost region approximately 1 nm below the surface than it is in the bulk. The enhanced population of the end groups is expected to result in a more mobile interfacial layer and the consequent dependence of Tg on the film thickness. In addition, the simulations show an enrichment of backbone aliphatic carbons and concomitant deficit of phenyl aromatic carbons in the interfacial film layer. This deficit would weaken the strong phenyl-phenyl aromatic (π-π) interactions and, hence, lead to a lower film-averaged Tg in thin films, as compared to the bulk sample. To investigate the relative importance of the two possible mechanisms (increased chain ends at the surface or weakened π-π interactions in the interfacial region), the data for linear PS are compared with those for cyclic PS. For the cyclic PS, the reduction of the glass-transition temperature is also significant in thin films, albeit not as much as for linear PS. Moreover, the deficit of phenyl carbons in the film interface is comparable to that observed for linear PS. Therefore, chain-end effects alone cannot explain the observed pronounced Tg dependence on the thickness of thin PS films; the weakened phenyl-phenyl interactions in the interfacial region seems to be an important cause as well.

Impact of bacteria motility in the encounter rates with bacteriophage in mucus.

Bacteriophages-or phages-are viruses that infect bacteria and are present in large concentrations in the mucosa that cover the internal organs of animals. Immunoglobulin (Ig) domains on the phage surface interact with mucin molecules, and this has been attributed to an increase in the encounter rates of phage with bacteria in mucus. However, the physical mechanism behind this phenomenon remains unclear. A continuous time random walk (CTRW) model simulating the diffusion due to mucin-T4 phage interactions was developed and calibrated to empirical data. A Langevin stochastic method for Escherichia coli (E. coli) run-and-tumble motility was combined with the phage CTRW model to describe phage-bacteria encounter rates in mucus for different mucus concentrations. Contrary to previous theoretical analyses, the emergent subdiffusion of T4 in mucus did not enhance the encounter rate of T4 against bacteria. Instead, for static E. coli, the diffusive T4 mutant lacking Ig domains outperformed the subdiffusive T4 wild type. E. coli's motility dominated the encounter rates with both phage types in mucus. It is proposed, that the local fluid-flow generated by E. coli's motility combined with T4 interacting with mucins may be the mechanism for increasing the encounter rates between the T4 phage and E. coli bacteria.

Microstructural Origins of Nonlinear Response in Associating Polymers under Oscillatory Shear.

The response of associating polymers with oscillatory shear is studied through large-scale simulations. A hybrid molecular dynamics (MD), Monte Carlo (MC) algorithm is employed. Polymer chains are modeled as a coarse-grained bead-spring system. Functionalized end groups, at both ends of the polymer chains, can form reversible bonds according to MC rules. Stress-strain curves show nonlinearities indicated by a non-ellipsoidal shape. We consider two types of nonlinearities. Type I occurs at a strain amplitude much larger than one, type II at a frequency at which the elastic storage modulus dominates the viscous loss modulus. In this last case, the network topology resembles that of the system at rest. The reversible bonds are broken and chains stretch when the system moves away from the zero-strain position. For type I, the chains relax and the number of reversible bonds peaks when the system is near an extreme of the motion. During the movement to the other extreme of the cycle, first a stress overshoot occurs, then a yield accompanied by shear-banding. Finally, the network restructures. Interestingly, the system periodically restores bonds between the same associating groups. Even though major restructuring occurs, the system remembers previous network topologies.

Aggregation kinetics of a simulated telechelic polymer.

We investigate the aggregation kinetics of a simulated telechelic polymer gel. In the hybrid molecular dynamics (MD)/Monte Carlo (MC) algorithm, aggregates of associating end groups form and break according to MC rules, while the position of the polymers in space is dictated by MD. As a result, the aggregate sizes change over time. In order to describe this aggregation process, we employ master equations. They define changes in the number of aggregates of a certain size in terms of reaction rates. These reaction rates indicate the likelihood that two aggregates combine to form a large one, or that a large aggregate splits into two smaller parts. The reaction rates are obtained from the simulations for a range of temperatures. Our results indicate that the rates are not only temperature dependent, but also a function of the sizes of the aggregates involved in the reaction. Using the measured rates, solutions to the master equations are shown to be stable and in agreement with the aggregate size distribution, as obtained directly from simulation data. Furthermore, we show how temperature-induced variations in these rates give rise to the observed changes in the aggregate distribution that characterizes the sol-gel transition.

Eigenvalue spectra of spatial-dependent networks.

Many real-life networks exhibit a spatial dependence; i.e., the probability to form an edge between two nodes in the network depends on the distance between them. We investigate the influence of spatial dependence on the spectral density of the network. When increasing spatial dependence in Erdös-Rényi, scale-free, and small-world networks, it is found that the spectrum changes. Due to the spatial dependence the degree of clustering and the number of triangles increase. This results in a higher asymmetry (skewness). Our results show that the spectrum can be used to detect and quantify clustering and spatial dependence in a network.

Numerical study of the gel transition in reversible associating polymers.

Four temperatures to characterize the gel transition in reversible associating polymers have been calculated in a novel mixed molecular dynamics/Monte Carlo model. (1) The temperature below which relaxation times no longer show Arrhenius dependence on temperature; (2) the Vogel-Fulcher temperature at which the structural relaxation time extrapolates to infinity; (3) the micelle formation temperature at which the number of reversible bonds sharply increases; and (4) a crossover temperature at which the viscosity exhibits a power law divergence as predicted by mode coupling theory. These specific temperatures are obtained from measurements of diffusivity, specific heat, and network topology.

Transitory response of confined polymer films subjected to oscillatory shear.

Molecular-dynamics simulations were used to study the response of a nanometer thin polymer film to oscillatory shear. Several types of response occur, depending on the amplitude of the shear. At low amplitude, the film deforms elastically. At intermediate ones it deforms plastically. Short-range stress-induced structured crystalline domains occur. This flexible elastic state is very dynamic. The crystalline domains oscillate with the applied stress. In the course of repeated cycling, they slowly increase in size. These mesoscopic domains may account for experimentally observed memory behavior. Ultra-thin polymer films typically possess relaxation times that are orders of magnitudes larger than those of the individual polymers. When oscillated at even higher amplitude, stick-slip is observed. In our constant pressure simulations, the film yields when wall spacing is increased to a value at which the polymer segments can smoothly rearrange and hence relax the internal stress.

Percolation of immobile domains in supercooled thin polymeric films.

We present an analysis of heterogeneous dynamics in molecular dynamics simulations of a polymeric film supported by an absorbing surface. Using a bead-spring model for polymers, we show that slow, immobile beads occur throughout the film, with the probability of their occurrence decreasing with distance from the substrate. Still, enough immobile beads are located near the free surface to cause them to percolate in the direction perpendicular to the substrate, at a temperature near the glass transition one. This result is consistent with a recent theoretical model of glass transition.