Chemical sensing by nonequilibrium cooperative receptors

Cooperativity arising from local interactions in equilibrium receptor systems provides gain, but does not increase sensory performance, as measured by the signal-to-noise ratio (SNR) due to a fundamental tradeoff between gain and intrinsic noise. Here we allow sensing to be a nonequilibrium process and show that energy dissipation cannot circumvent the fundamental tradeoff, so that SNR is still optimal for independent receptors. For systems requiring high gain, nonequilibrium 2D-coupled receptors maximize SNR, revealing a new design principle for biological sensors

Dynamics of cooperativity in chemical sensing among cell-surface receptors

Cooperative interactions among sensory receptors provide a general mechanism to increase the sensitivity of signal transduction. In particular, bacterial chemotaxis receptors interact cooperatively to produce an ultrasensitive response to chemoeffector concentrations. However, cooperativity between receptors in large macromolecular complexes is necessarily based on local interactions and consequently is fundamentally connected to slowing of receptor conformational dynamics, which increases intrinsic noise. Therefore, it is not clear whether or under what conditions cooperativity actually increases the precision of the concentration measurement. We explictly calculate the signal-to-noise ratio (SNR) for sensing a concentration change using a simple, Ising-type model of receptor-receptor interactions, generalized via scaling arguments, and find that the optimal SNR is always achieved by independent receptors.Comment: 5 pages, 2 figure

Receptor-Receptor Coupling in Bacterial Chemotaxis: Evidence for Strongly Coupled Clusters

AbstractReceptor coupling is believed to explain the high sensitivity of the Escherichia coli chemotaxis network to small changes in levels of chemoattractant. We compare in detail the activity response of coupled two-state receptors for different models of receptor coupling: weakly-coupled extended one-dimensional and two-dimensional lattice models and the Monod-Wyman-Changeux model of isolated strongly-coupled clusters. We identify features in recent data that distinguish between the models. Specifically, researchers have measured the receptor activity response to steps of chemoattractant for a variety of engineered E. coli strains using in vivo fluorescence resonance energy transfer. We find that the fluorescence resonance energy transfer results for wild-type and for a low-activity mutant are inconsistent with the lattice models of receptor coupling, but consistent with the Monod-Wyman-Changeux model of receptor coupling, suggesting that receptors form isolated strongly-coupled clusters

Black Hole-Neutron Star Binaries in General Relativity: Quasiequilibrium Formulation

We present a new numerical method for the construction of quasiequilibrium models of black hole-neutron star binaries. We solve the constraint equations of general relativity, decomposed in the conformal thin-sandwich formalism, together with the Euler equation for the neutron star matter. We take the system to be stationary in a corotating frame and thereby assume the presence of a helical Killing vector. We solve these coupled equations in the background metric of a Kerr-Schild black hole, which accounts for the neutron star's black hole companion. In this paper we adopt a polytropic equation of state for the neutron star matter and assume large black hole--to--neutron star mass ratios. These simplifications allow us to focus on the construction of quasiequilibrium neutron star models in the presence of strong-field, black hole companions. We summarize the results of several code tests, compare with Newtonian models, and locate the onset of tidal disruption in a fully relativistic framework.Comment: 17 pages, 7 figures; added discussion, tables; PRD in pres

Comparing Criteria for Circular Orbits in General Relativity

We study a simple analytic solution to Einstein's field equations describing a thin spherical shell consisting of collisionless particles in circular orbit. We then apply two independent criteria for the identification of circular orbits, which have recently been used in the numerical construction of binary black hole solutions, and find that both yield equivalent results. Our calculation illustrates these two criteria in a particularly transparent framework and provides further evidence that the deviations found in those numerical binary black hole solutions are not caused by the different criteria for circular orbits.Comment: 4 pages; to appear in PRD as a Brief Report; added and corrected reference

Comparison of public key cryptography algorithms

In the present work we study comparison of basic public key encryption algorithms - RSA, Rabin and ElGamel method. We derive theoretic complexity of encrypting / decrypting of one block and we derive an expected model of its behavior with the key of double size. We also take practical measurements of speed of each algorithm using keys sized 64 - 4096 bits and we statistically analyze the results. We also mention special cases of some algorithms and discuss the advantages and disadvantages of their practical usage. At the end of this thesis we make a comparison of the speed of algorithms and we also compare the measured data with theoretical hypothesis

Dicty World Race _ team 11 tracks

<p>Skoge M, Wong E, Hamza B, Bae A, Martel J, Kataria, R, Keizer-Gunnink, I, Kortholt A, van Haastert, P J M, Charras G, Janetopoulos C, Irimia D.  A Worldwide Competition to Compare the Speed and Chemotactic Accuracy of Neutrophil-like Cells. PLOS One 2016</p

Dicty World Race _ team 12 tracks

<p>Skoge M, Wong E, Hamza B, Bae A, Martel J, Kataria, R, Keizer-Gunnink, I, Kortholt A, van Haastert, P J M, Charras G, Janetopoulos C, Irimia D.  A Worldwide Competition to Compare the Speed and Chemotactic Accuracy of Neutrophil-like Cells. PLOS One 2016</p

Dicty World Race _ team 04 tracks

<p>Skoge M, Wong E, Hamza B, Bae A, Martel J, Kataria, R, Keizer-Gunnink, I, Kortholt A, van Haastert, P J M, Charras G, Janetopoulos C, Irimia D.  A Worldwide Competition to Compare the Speed and Chemotactic Accuracy of Neutrophil-like Cells. PLOS One 2016</p