Chemosensing in microorganisms to practical biosensors

Microorganisms like bacteria can sense concentration of chemo-attractants in its medium very accurately. They achieve this through interaction between the receptors on their cell surface and the chemo-attractant molecules (like sugar). But the physical processes like diffusion set some limits on the accuracy of detection which was discussed by Berg and Purcell in the late seventies. We have a re-look at their work in order to assess what insight it may offer towards making efficient, practical biosensors. We model the functioning of a typical biosensor as a reaction-diffusion process in a confined geometry. Using available data first we characterize the system by estimating the kinetic constants for the binding/unbinding reactions between the chemo-attractants and the receptors. Then we compute the binding flux for this system which Berg and Purcell had discussed. But unlike in microorganisms where the interval between successive measurements determines the efficiency of the nutrient searching process, it turns out that biosensors depend on long time properties like signal saturation time which we study in detail. We also develop a mean field description of the kinetics of the system.Comment: 6 pages, 7 figure

Multiscaling in Models of Magnetohydrodynamic Turbulence

From a direct numerical simulation of the MHD equations we show, for the first time, that velocity and magnetic-field structure functions exhibit multiscaling, extended self similarity (ESS), and generalized extended self similarity (GESS). We also propose a new shell model for homogeneous and isotropic MHD turbulence, which preserves all the invariants of ideal MHD, reduces to a well-known shell model for fluid turbulence for zero magnetic field, has no adjustable parameters apart from Reynolds numbers, and exhibits the same multiscaling, ESS, and GESS as the MHD equations. We also study dissipation-range asymptotics and the inertial- to dissipation-range crossover.Comment: 5 pages, REVTEX, 4 figures (eps

Predicting the coherence resonance curve using a semi-analytical treatment

Emergence of noise induced regularity or Coherence Resonance in nonlinear excitable systems is well known. We explain theoretically why the normalized variance ($V_{N}$) of inter spike time intervals, which is a measure of regularity in such systems, has a unimodal profile. Our semi-analytic treatment of the associated spiking process produces a general yet simple formula for $V_{N}$, which we show is in very good agreement with numerics in two test cases, namely the FitzHugh-Nagumo model and the Chemical Oscillator model.Comment: 5 pages, 5 figure

Stuttering Min oscillations within E. coli bacteria: A stochastic polymerization model

We have developed a 3D off-lattice stochastic polymerization model to study subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding, and fragmentation of MinD filaments due to MinE. Each of processivity, protection, and fragmentation reduces stuttering, speeds oscillations, and reduces MinD filament lengths. Neither processivity or tip-protection were, on their own, sufficient to produce fast stutter-free oscillations. While filament fragmentation could, on its own, lead to fast oscillations with infrequent stuttering; high levels of fragmentation degraded oscillations. The infrequent stuttering observed in standard Min oscillations are consistent with short filaments of MinD, while we expect that mutants that exhibit higher stuttering frequencies will exhibit longer MinD filaments. Increased stuttering rate may be a useful diagnostic to find observable MinD polymerization in experimental conditions.Comment: 21 pages, 7 figures, missing unit for k_f inserte

Inertial- and Dissipation-Range Asymptotics in Fluid Turbulence

We propose and verify a wave-vector-space version of generalized extended self similarity and broaden its applicability to uncover intriguing, universal scaling in the far dissipation range by computing high-order (\leq 20\/) structure functions numerically for: (1) the three-dimensional, incompressible Navier Stokes equation (with and without hyperviscosity); and (2) the GOY shell model for turbulence. Also, in case (2), with Taylor-microscale Reynolds numbers 4 \times 10^{4} \leq Re_{\lambda} \leq 3 \times 10^{6}\/, we find that the inertial-range exponents (\zeta_{p}\/) of the order - p\/ structure functions do not approach their Kolmogorov value p/3\/ as Re_{\lambda}\/ increases.Comment: RevTeX file, with six postscript figures. epsf.tex macro is used for figure insertion. Packaged using the 'uufiles' utilit