Miloš Šormaz

Near surface swimming of Salmonella Typhimurium explains target-site selection and cooperative invasion.

Targeting of permissive entry sites is crucial for bacterial infection. The targeting mechanisms are incompletely understood. We have analyzed target-site selection by S. Typhimurium. This enteropathogenic bacterium employs adhesins (e.g. fim) and the type III secretion system 1 (TTSS-1) for host cell binding, the triggering of ruffles and invasion. Typically, S. Typhimurium invasion is focused on a subset of cells and multiple bacteria invade via the same ruffle. It has remained unclear how this is achieved. We have studied target-site selection in tissue culture by time lapse microscopy, movement pattern analysis and modeling. Flagellar motility (but not chemotaxis) was required for reaching the host cell surface in vitro. Subsequently, physical forces trapped the pathogen for ∼1.5–3 s in “near surface swimming”. This increased the local pathogen density and facilitated “scanning” of the host surface topology. We observed transient TTSS-1 and fim-independent “stopping” and irreversible TTSS-1-mediated docking, in particular at sites of prominent topology, i.e. the base of rounded-up cells and membrane ruffles. Our data indicate that target site selection and the cooperative infection of membrane ruffles are attributable to near surface swimming. This mechanism might be of general importance for understanding infection by flagellated bacteria.

Stochastic modeling of light scattering with fluorescence using a Monte Carlo-based multiscale approach

This work deals with the efficient and accurate modeling of fluorescence in the context of stochastic Monte Carlo methods for which we propose a novel multiscale method. As in other approaches of this category, the transport theory is employed to describe the physics. The new framework was successfully applied for a quantitative assessment of halftone reflectance measurements with three different devices. It could be demonstrated that the described method is faster than classical Monte Carlo by multiple orders of magnitude, and that it is capable of correctly handling the geometrical device differences. It is also shown that optical dot gain is accurately predicted for the whole ink coverage range.

Contrast improvement by selecting ballistic-photons using polarization gating

In this paper a new approach to improve contrast in optical subsurface imaging is presented. The method is based on time-resolved reflectance and selection of ballistic photons using polarization gating. Numerical studies with a statistical Monte Carlo method also reveal that weakly scattered diffuse photons can be eliminated by employing a small aperture and that the contrast improvement strongly depends on the single-scattering phase function. A possible experimental setup is discussed in the conclusions.

Stochastic modeling of polarized light scattering using a Monte Carlo based stencil method.

This paper deals with an efficient and accurate simulation algorithm to solve the vector Boltzmann equation for polarized light transport in scattering media. The approach is based on a stencil method, which was previously developed for unpolarized light scattering and proved to be much more efficient (speedup factors of up to 10 were reported) than the classical Monte Carlo while being equally accurate. To validate what we believe to be the new stencil method, a substrate composed of spherical non-absorbing particles embedded in a non-absorbing medium was considered. The corresponding single scattering Mueller matrix, which is required to model scattering of polarized light, was determined based on the Lorenz-Mie theory. From simulations of a reflected polarized laser beam, the Mueller matrix of the substrate was computed and compared with an established reference. The agreement is excellent, and it could be demonstrated that a significant speedup of the simulations is achieved due to the stencil approach compared with the classical Monte Carlo.

Influence of linear birefringence in the computation of scattering phase functions

Birefringent media, like biological tissues, are usually assumed to be uniaxial. For biological tissues, the influence of linear birefringence on the scattering phase function is assumed to be neglectable. In order to examine this, a numerical study of the influence of linear birefringence on the scattering phase function and the resulting backscattering Mueller matrices was performed. It is assumed that the media consist of spherical scattering particles embedded in a nonabsorbing medium, which allows us to employ the Lorenz-Mie theory. In the Monte Carlo framework, the influence of linear birefringence on the components of the electric field vector is captured through the Jones N-matrix formalism. The Lorenz-Mie theory indicates that a given linear birefringence value Δn has a bigger impact on the scattering phase function for large particles. This conclusion is further supported by Monte Carlo simulations, where the phase function was calculated based on the refractive index once in the ordinary direction and once in the extraordinary one. For large particles, comparisons of the resulting backscattering Mueller matrices show significant differences even for small Δn values.

Empirical model for target depth estimation used in the time-domain subsurface imaging

Monte Carlo simulations were performed in order to obtain reflectance measurements from phantoms typically used in biomedical optics when either unpolarized or circularly polarized incident light is used. Phantoms contain spherical targets of different diameters, placed at different depths, with higher absorption than the surrounding medium, which are detected using a coaxial setup of laser and detector. The considered turbid media have highly anisotropic scattering phase functions, so detected light for the considered times of flight is not diffuse, but rather in the multiple-scattering regime. Therefore, the target reconstruction methods typically used in diffuse optical imaging cannot be employed. However, spatially resolved reflectance measurements in the time domain allow use of a novel reconstruction method based on the approximation of average photon trajectories, which are functions of the separation distance from the point of incidence and of the time of flight. With the approximated average photon trajectories, one can estimate the depth of the target.