Kinetic models of ion transport through a nanopore

Kinetic equations for the stationary state distribution function of ions moving through narrow pores are solved for a number of one-dimensional models of single ion transport. Ions move through pores of length $L$, under the action of a constant external field and of a concentration gradient. The interaction of single ions with the confining pore surface and with water molecules inside the pore are modelled by a Fokker-Planck term in the kinetic equation, or by uncorrelated collisions with thermalizing centres distributed along the pore. The temporary binding of ions to polar residues lining the pore is modelled by stopping traps or energy barriers. Analytic expressions for the stationary ion current through the pore are derived for several versions of the model, as functions of key physical parameters. In all cases, saturation of the current at high fields is predicted. Such simple models, for which results are analytic, may prove useful in the study of the current/voltage relations of ion channels through membranes

Oral medicine case book 68: Oral ulceration caused by rifampicin-resistant tuberculosis

A 53-year old female was referred by her local general medical practitioner to an oral medicine specialist for the management of a persistent ulcer on the left side of her tongue. The lesion had been present for at least three months and was not responding to treatment by topical antiseptic agents. The earlier removal of a molar in close proximity to the lesion, in an attempt to exclude the possibility of traumatic ulceration, had also yielded no beneficial effects. Upon examination, the patient appeared clinically healthy but presented with a history of emphysema due to chronic cigarette smoking. The emphysema was currently being managed by oral inhalation steroids. Even though smoking cessation had previously been advised, she failed to comply and was currently still smoking more than 10 cigarettes per day.DHE

Absence of bound states for waveguides in 2D periodic structures

We study a Helmholtz-type spectral problem in a two-dimensional medium consisting of a fully periodic background structure and a perturbation in form of a line defect. The defect is aligned along one of the coordinate axes, periodic in that direction (with the same periodicity as the background), and bounded in the other direction. This setting models a so-called "soft-wall" waveguide problem. We show that there are no bound states, i.e., the spectrum of the operator under study contains no point spectrum.Comment: This is an updated version of our paper (in slightly different form in Journal of Mathematical Physics). An anonymous reviewer kindly made us aware that ref. 10 is not applicable in our situation. An application of the theorem in ref. 10 would have proved the absence of singular continuous spectrum also. Our result on the absence of point spectrum is not affected by thi

Fluctuations of a driven membrane in an electrolyte

We develop a model for a driven cell- or artificial membrane in an electrolyte. The system is kept far from equilibrium by the application of a DC electric field or by concentration gradients, which causes ions to flow through specific ion-conducting units (representing pumps, channels or natural pores). We consider the case of planar geometry and Debye-H\"{u}ckel regime, and obtain the membrane equation of motion within Stokes hydrodynamics. At steady state, the applied field causes an accumulation of charges close to the membrane, which, similarly to the equilibrium case, can be described with renormalized membrane tension and bending modulus. However, as opposed to the equilibrium situation, we find new terms in the membrane equation of motion, which arise specifically in the out-of-equilibrium case. We show that these terms lead in certain conditions to instabilities.Comment: 7 pages, 2 figures. submitted to Europhys. Let

Anaerobic digestion of Spirulina sp. and Scenedesmus sp.: a comparison and investigation of the impact of mechanical pre-treatment

AAnaerobic digestion (AD) is a unit process that integrates beneficially and sustainably into many bioprocesses. This study assesses and compares the production of methane from the biomass of the microalga Scenedesmus sp. and the cyanobacterium Spirulina sp. in batch anaerobic digesters. Anaerobic digestion of whole cell Spirulina resulted in a substantially higher methane productivity (0.18 L CH4 Lreactor −1 day−1) and methane yield (0.113 L CH4 g−1 volatile solids (VS)) compared to the digestion of whole cell Scenedesmus (0.12 L CH4 Lreactor −1 day−1 and 0.054 L CH4 g VS−1). Spirulina, possibly due to a combination of osmotic shock, the filamentous nature of the cells and lower mechanical strength of the non-cellulosic cell wall, was more readily degraded by hydrolytic and acidogenic microorganisms, resulting in the generation of a greater amount of acetic acid. This in turn provided greater substrate for methanogens and hence higher methane yields. In addition, Spirulina cells could be disrupted mechanically more quickly (1 h) than Scenedesmus cells (4 h) in a bead mill. Mechanical pre-treatment improved the final methane yields (L CH4 g VS−1) obtained from digestion of both substrates; however, the improvement was greater for Scenedesmus. Mechanical pre-treatment resulted in a 47 % increase in methane production for Spirulina compared to 76 % increase for Scenedesmus fed digesters. The more substantial increase observed for Scenedesmus was due to the relatively inefficient digestion of the whole, unruptured cells

First Order Relativistic Three-Body Scattering

Relativistic Faddeev equations for three-body scattering at arbitrary energies are formulated in momentum space and in first order in the two-body transition-operator directly solved in terms of momentum vectors without employing a partial wave decomposition. Relativistic invariance is incorporated within the framework of Poincare invariant quantum mechanics, and presented in some detail. Based on a Malfliet-Tjon type interaction, observables for elastic and break-up scattering are calculated up to projectile energies of 1 GeV. The influence of kinematic and dynamic relativistic effects on those observables is systematically studied. Approximations to the two-body interaction embedded in the three-particle space are compared to the exact treatment.Comment: 26 pages, 13 figure

Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair

CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA repair pathways, either by regulating their expression or via direct protein-protein contact and enzymatic activity. The integrase Cas1 is usually involved in the adaptation phase of CRISPR-Cas immunity but an additional role in cellular DNA repair pathways has been proposed previously. Here, we analysed the capacity of an archaeal Cas1 from Haloferax volcanii to act upon DNA damage induced by oxidative stress and found that a deletion of the cas1 gene led to reduced survival rates following stress induction. In addition, our results indicate that Cas1 is directly involved in DNA repair as the enzymatically active site of the protein is crucial for growth under oxidative conditions. Based on biochemical assays, we propose a mechanism by which Cas1 plays a similar function to DNA repair protein Fen1 by cleaving branched intermediate structures. The present study broadens our understanding of the functional link between CRISPR-Cas immunity and DNA repair by demonstrating that Cas1 and Fen1 display equivalent roles during archaeal DNA damage repair

Linear superposition in nonlinear wave dynamics

We study nonlinear dispersive wave systems described by hyperbolic PDE's in R^{d} and difference equations on the lattice Z^{d}. The systems involve two small parameters: one is the ratio of the slow and the fast time scales, and another one is the ratio of the small and the large space scales. We show that a wide class of such systems, including nonlinear Schrodinger and Maxwell equations, Fermi-Pasta-Ulam model and many other not completely integrable systems, satisfy a superposition principle. The principle essentially states that if a nonlinear evolution of a wave starts initially as a sum of generic wavepackets (defined as almost monochromatic waves), then this wave with a high accuracy remains a sum of separate wavepacket waves undergoing independent nonlinear evolution. The time intervals for which the evolution is considered are long enough to observe fully developed nonlinear phenomena for involved wavepackets. In particular, our approach provides a simple justification for numerically observed effect of almost non-interaction of solitons passing through each other without any recourse to the complete integrability. Our analysis does not rely on any ansatz or common asymptotic expansions with respect to the two small parameters but it uses rather explicit and constructive representation for solutions as functions of the initial data in the form of functional analytic series.Comment: New introduction written, style changed, references added and typos correcte

Analysis of the microbial community associated with a bioprocess system for bioremediation of thiocyanate- and cyanide-laden mine water effluents

Gold extraction by cyanidation from refractory gold ores results in the formation of thiocyanate- and cyanide-contaminated wastewater effluents that must be treated before recycle or discard. Activated sludge processes, such as ASTER™, can be used for biodegradation of these effluent streams. The destruction of these compounds is catalyzed by a mixed microbial culture, however, very little is known about the community composition and metabolic potential of the thiocyanate- and cyanide-degrading microorganisms within the community. Here we describe our on-going attempts to better understand the key microorganisms, within the ASTER™ bioprocess, that contribute to the destruction of thiocyanate and cyanide, and how this knowledge relates to further process optimisation

Research of factors affecting the development of municipalities in Russia: creating a database for econometric modeling

This paper describes the preparatory stage of forming a database for the study of factors affecting the development of municipalities in Russia. The sources of information were identified and the combination of information from various databases was used in order to significantly expand the system of indicators for subsequent research. The created system of indicators is comparable with the systems of indicators used in foreign studies and will allow to identify similarities and differences in the behavior of municipalities of Russia and foreign countries. The generated database is panel data, which is enough for applying modern econometric methods for analyzing panel data, in particular, using regression models with fixed or random effects