Persistent random walk on a one-dimensional lattice with random asymmetric transmittances

We study the persistent random walk of photons on a one-dimensional lattice of random asymmetric transmittances. Each site is characterized by its intensity transmittance t (t') for photons moving to the right (left) direction. Transmittances at different sites are assumed independent, distributed according to a given probability density Distribution. We use the effective medium approximation and identify two classes of probability density distribution of transmittances which lead to the normal diffusion of photons. Monte Carlo simulations confirm our predictions.Comment: 7 pages, submitted to Phys. Rev.

Statistical Mechanics of Glass Formation in Molecular Liquids with OTP as an Example

We extend our statistical mechanical theory of the glass transition from examples consisting of point particles to molecular liquids with internal degrees of freedom. As before, the fundamental assertion is that super-cooled liquids are ergodic, although becoming very viscous at lower temperatures, and are therefore describable in principle by statistical mechanics. The theory is based on analyzing the local neighborhoods of each molecule, and a statistical mechanical weight is assigned to every possible local organization. This results in an approximate theory that is in very good agreement with simulations regarding both thermodynamical and dynamical properties

Diffusive transport of light in a two-dimensional disordered packing of disks: Analytical approach to transport-mean-free path

We study photon diffusion in a two-dimensional random packing of monodisperse disks as a simple model of granular media and wet foams. We assume that the intensity reflectance of disks is a constant. We present an analytic expression for the transport-mean-free path in terms of the velocity of light in the disks and host medium, radius and packing fraction of the disks, and the intensity reflectance. For the glass beads immersed in the air or water, we estimate transport-mean-free paths about half the experimental ones. For the air bubbles immersed in the water, transport-mean-free paths is an inverse function of liquid volume fraction of the model wet foam. This throws new light on the empirical law of Vera et. al, and promotes more realistic models.Comment: 9 pages, 6 figure

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

Natural History of Tuberculosis: Duration and Fatality of Untreated Pulmonary Tuberculosis in HIV Negative Patients: A Systematic Review

Background The prognosis, specifically the case fatality and duration, of untreated tuberculosis is important as many patients are not correctly diagnosed and therefore receive inadequate or no treatment. Furthermore, duration and case fatality of tuberculosis are key parameters in interpreting epidemiological data. Methodology and Principal Findings To estimate the duration and case fatality of untreated pulmonary tuberculosis in HIV negative patients we reviewed studies from the pre-chemotherapy era. Untreated smear-positive tuberculosis among HIV negative individuals has a 10-year case fatality variously reported between 53% and 86%, with a weighted mean of 70%. Ten-year case fatality of culture-positive smear-negative tuberculosis was nowhere reported directly but can be indirectly estimated to be approximately 20%. The duration of tuberculosis from onset to cure or death is approximately 3 years and appears to be similar for smear-positive and smear-negative tuberculosis. Conclusions Current models of untreated tuberculosis that assume a total duration of 2 years until self-cure or death underestimate the duration of disease by about one year, but their case fatality estimates of 70% for smear-positive and 20% for culture-positive smear-negative tuberculosis appear to be satisfactory

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.

We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglial cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene-gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research

Space-and time-resolved diffusion-limited binary reaction kinetics in capillaries: experimental observation of segregation, anomalous exponents, and depletion zone

An experimental investigation of one-dimensional, diffusion-limited A+B→C chemical reactions is reported. The persistence of reactant segregation and the formation of a depletion zone is observed and expressed in terms of the universal time exponents: α (motion of the boundary zone), β (width of instantaneous product formation zone), γ (rate of instantaneous local formation of product), δ (rate of instantaneous global formation of product), etc. There is good agreement with the recently predicted and/or simulated values: α =1/2, β =1/6, γ =2/3, δ =1/2, in contrast to classical predictions ( α =0, β =1/2, γ =0, δ =−1/2). Furthermore, classically the segregation would not be preserved and there would be no formation of a depletion zone and no motion (just dissipation) of the reaction zone. We also discuss the relations to electrode oxidation-reduction reactions, i.e., A+C→C where C is a catalyst, electrode, or “trap.”Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45162/1/10955_2005_Article_BF01049588.pd