Competition and cooperation in one-dimensional stepping stone models

Cooperative mutualism is a major force driving evolution and sustaining ecosystems. Although the importance of spatial degrees of freedom and number fluctuations is well-known, their effects on mutualism are not fully understood. With range expansions of microbes in mind, we show that, even when mutualism confers a distinct selective advantage, it persists only in populations with high density and frequent migrations. When these parameters are reduced, mutualism is generically lost via a directed percolation process, with a phase diagram strongly influenced by an exceptional DP2 transition.Comment: 8 pages, 4 figure

Opening of DNA double strands by helicases. Active versus passive opening

Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA). We describe helicase opening of dsNA, based on helicases which bind single NA strands and move towards the double-stranded region, using a discrete ``hopping'' model. The interaction between the helicase and the junction where the double strand opens is characterized by an interaction potential. The form of the potential determines whether the opening is active or passive. We calculate the rate of passive opening for the helicase PcrA, and show that the rate increases when the opening is active. Finally, we examine how to choose the interaction potential to optimize the rate of strand separation. One important result is our finding that active opening can increase the unwinding rate by 7 fold compared to passive opening.Comment: 13 pages, 3 figure

On the kinetic equation approach to pair production by time-dependent electric field

We investigate the quantum kinetic approach to pair production from vacuum by time-dependent electric field. Equivalence between this approach and the more familiar S-matrix approach is explicitly established for both scalar and fermion cases. For the particular case of a constant electric field exact solution for kinetic equations is provided and the accuracy of low-density approximation is estimated.Comment: 8 pages, 4 figure

Fisher waves in the strong noise limit

We investigate the effects of strong number fluctuations on traveling waves in the Fisher-Kolmogorov reaction-diffusion system. Our findings are in stark contrast to the commonly used deterministic and weak-noise approximations. We compute the wave velocity in one and two spatial dimensions, for which we find a linear and a square-root dependence of the speed on the particle density. Instead of smooth sigmoidal wave profiles, we observe fronts composed of a few rugged kinks that diffuse, annihilate, and rarely branch; this dynamics leads to power-law tails in the distribution of the front sizes.Comment: 4 pages, 2 figures, updat

A multi-dimensional numerical scheme for two-fluid Relativistic MHD

The paper describes an explicit multi-dimensional numerical scheme for Special Relativistic Two-Fluid Magnetohydrodynamics of electron-positron plasma and a suit of test problems. The scheme utilizes Cartesian grid and the third order WENO interpolation. The time integration is carried out using the third order TVD method of Runge-Kutta type, thus ensuring overall third order accuracy on smooth solutions. The magnetic field is kept near divergence-free by means of the method of generalized Lagrange multiplier. The test simulations, which include linear and non-linear continuous plasma waves, shock waves, strong explosions and the tearing instability, show that the scheme is sufficiently robust and confirm its accuracy

Velocity and processivity of helicase unwinding of double-stranded nucleic acids

Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase unwinding velocity and processivity vary if the base-pair binding free energy is changed.Comment: To appear in special issue on molecular motors, Journal of Physics - Condensed Matte

Determination of Ethanol Content in Fuels with Phononic Crystal Sensor

Introduction. In-line analysis of ethanol content in gasoline blends is currently one of the urgent needs of fuel industry. Developing safe and secure approaches is critical for real applications. A phononic crystal sensor have been introduced as an innovative approach to high performance gasoline sensing. Distinguishing feature of proposed sensor is the absence of any electrical contact with analysed gasoline blend, which allows the use of sensors directly in pipelines without the risk of explosion in an emergency.Aim. Investigation of the possibilities of using phononic sensor structures to determine the ethanol content in liquid hydrocarbons.Materials and methods. A theoretical analysis of sensor structure was carried out on the basis of numerical simulation using COMSOL Multiphysics software. For measurement, substances of ordinary gasoline and gasoline 63–80 with ethanol concentrations in the range of 1–10 % by volume in increments of 2 % were prepared. The phononic crystal sensor was designed as a stainless steel plate with cylindrical holes and a resonant cavity, formed as a running across the wave propagation path slit between two lattices.Results. In-line analysis of measuring the concentration of ethanol in alcohol-containing fuels on a phononic crystal structure with a resonant cavity was carried out. Using the Agilent4395A admittance meter, the transmission spectra of longitudinal acoustic waves through the gasoline-filled sensor structure with were obtained. The non-linear correlation between the composition and the speed of sound of the blend is presented in the article is due to the ability to reduce the speed of sound of the mixture with an increase in ethanol concentration in the range of 0–10 % by volume.Conclusion. A measurement structure on the basis of phononic crystal was created. The measurements of various gasoline-ethanol mixtures show that the sensor has significant sensitivity (0.91 kHz/ms−1 ) with quality factor of 200) to distinguish between regular fuels, gasoline based blends and the presence of additives in standard fuels. The sensor has prospects for in-line analyzes the composition of liquid hydrocarbons.Introduction. In-line analysis of ethanol content in gasoline blends is currently one of the urgent needs of fuel industry. Developing safe and secure approaches is critical for real applications. A phononic crystal sensor have been introduced as an innovative approach to high performance gasoline sensing. Distinguishing feature of proposed sensor is the absence of any electrical contact with analysed gasoline blend, which allows the use of sensors directly in pipelines without the risk of explosion in an emergency.Aim. Investigation of the possibilities of using phononic sensor structures to determine the ethanol content in liquid hydrocarbons.Materials and methods. A theoretical analysis of sensor structure was carried out on the basis of numerical simulation using COMSOL Multiphysics software. For measurement, substances of ordinary gasoline and gasoline 63–80 with ethanol concentrations in the range of 1–10 % by volume in increments of 2 % were prepared. The phononic crystal sensor was designed as a stainless steel plate with cylindrical holes and a resonant cavity, formed as a running across the wave propagation path slit between two lattices.Results. In-line analysis of measuring the concentration of ethanol in alcohol-containing fuels on a phononic crystal structure with a resonant cavity was carried out. Using the Agilent4395A admittance meter, the transmission spectra of longitudinal acoustic waves through the gasoline-filled sensor structure with were obtained. The non-linear correlation between the composition and the speed of sound of the blend is presented in the article is due to the ability to reduce the speed of sound of the mixture with an increase in ethanol concentration in the range of 0–10 % by volume.Conclusion. A measurement structure on the basis of phononic crystal was created. The measurements of various gasoline-ethanol mixtures show that the sensor has significant sensitivity (0.91 kHz/ms−1 ) with quality factor of 200) to distinguish between regular fuels, gasoline based blends and the presence of additives in standard fuels. The sensor has prospects for in-line analyzes the composition of liquid hydrocarbons

Guided random walk calculation of energies and <\sq {r^2} > values of the 1Σg^1\Sigma_g state of H_2 in a magnetic field

Energies and spatial observables for the $^1\Sigma_g$ state of the hydrogen molecule in magnetic fields parallel to the proton-proton axis are calculated with a guided random walk Feynman-Kac algorithm. We demonstrate that the accuracy of the results and the simplicity of the method may prove it a viable alternative to large basis set expansions for small molecules in applied fields.Comment: 10 pages, no figure