Rutenberg, Andrew
Permanent URI for this collectionhttps://hdl.handle.net/10222/22132
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Item Open Access Classical Antiferromagnets on the Kagome Lattice(1992-04) HUSE, DA; RUTENBERG, ADNo abstract available.Item Open Access Clocking out: modeling phage-induced lysis of Escherichia coli(2007-07) Ryan, G. L.; Rutenberg, A. D.Phage lambda lyses the host Escherichia coli at a precisely scheduled time after induction. Lysis timing is determined by the action of phage holins, which are small proteins that induce hole formation in the bacterium's cytoplasmic membrane. We present a two-stage nucleation model of lysis timing, with the nucleation of condensed holin rafts on the inner membrane followed by the nucleation of a hole within those rafts. The nucleation of holin rafts accounts for most of the delay of lysis after induction. Our simulations of this model recover the accurate lysis timing seen experimentally and show that the timing accuracy is optimal. An enhanced holin-holin interaction is needed in our model to recover experimental lysis delays after the application of membrane poison, and such early triggering of lysis is possible only after the inner membrane is supersaturated with holin. Antiholin reduces the delay between membrane depolarization and lysis and leads to an earlier time after which triggered lysis is possible.Item Open Access Diffusion of Asymmetric Swimmers(American Physical Society, 2003) Rutenberg, Andrew D.; Richardson, Andrew J.; Montgomery, Claire J.Asymmetric swimmers that would move at a constant speed in perfect circles in the absence of fluctuations were studied. Particles moving at a constant speed with either a fixed or a Gaussian distributed magnitude of curvature were considered. It was found that at small speeds the diffusivity was independent of the speed and at large particle speeds, the diffusivity depended on the speed through a novel exponent.Item Open Access Temperature dependence of MinD oscillation in Escherichia coli: Running hot and fast(2006-11) Touhami, Ahmed; Jericho, Manfred; Rutenberg, Andrew D.No abstract available.Item Open Access Item Open Access Unwinding scaling violations in phase ordering(1995-05) Rutenberg, A. D.; Bray, A. J.No abstract available.Item Open Access Anisotropic coarsening: Grain shapes and nonuniversal persistence(1999-11) Rutenberg, AD; Vollmayr-Lee, BPNo abstract available.Item Open Access Persistence, poisoning, and autocorrelations in dilute coarsening(1997) Lee, Benjamin P.; Rutenberg, Andrew D.No abstract available.Item Open Access Pattern formation inside bacteria: Fluctuations due to the low copy number of proteins(2003-03) Howard, M.; Rutenberg, ADNo abstract available.Item Open Access Dynamic compartmentalization of bacteria: Accurate division in E-coli(2001-12) Howard, M.; Rutenberg, AD; de Vet, S.No abstract available.Item Open Access Dynamics of dislocations and surface instabilities in misfitting heteroepitaxial films(2002-01) Haataja, M.; Muller, J.; Rutenberg, AD; Grant, M.No abstract available.Item Open Access Steady-state helices of the actin homolog MreB inside bacteria: dynamics without motors(2007-09) Allard, J. F.; Rutenberg, A. D.Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasistatic evolution of the helical pitch with cell growth, as well as time scales of helix turnover and de novo establishment. We find that while the body of a polarized MreB helix treadmills toward its slow-growing end, the fast-growing tips of laterally associated protofilaments move toward the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.Item Open Access Self-organization of the MinE protein ring in subcellular Min oscillations(2009-07) Derr, J.; Hopper, J. T.; Sain, A.; Rutenberg, A. D.We model the self-organization of the MinE ring that is observed during subcellular oscillations of the proteins MinD and MinE within the rod-shaped bacterium Escherichia coli. With a steady-state approximation, we can study the MinE ring generically--apart from the other details of the Min oscillation. Rebinding of MinE to depolymerizing MinD-filament tips controls MinE-ring formation through a scaled cell shape parameter r. We find two types of E-ring profiles near the filament tip: either a strong plateaulike E ring controlled by one-dimensional diffusion of MinE along the bacterial length or a weak cusplike E ring controlled by three-dimensional diffusion near the filament tip. While the width of a strong E ring depends on r, the occupation fraction of MinE at the MinD-filament tip is saturated and hence the depolymerization speed does not depend strongly on r. Conversely, for weak E rings both r and the MinE to MinD stoichiometry strongly control the tip occupation and hence the depolymerization speed. MinE rings in vivo are close to the threshold between weak and strong, and so MinD-filament depolymerization speed should be sensitive to cell shape, stoichiometry, and MinE-rebinding rate. We also find that the transient to MinE-ring formation is quite long in the appropriate open geometry for assays of ATPase activity in vitro, explaining the long delays of ATPase activity observed for smaller MinE concentrations in those assays without the need to invoke cooperative MinE activity.Item Open Access Subcellular Min Oscillations as a Single-Cell Reporter of the Action of Polycations, Protamine, and Gentamicin on Escherichia coli(2009-09) Downing, Benjamin P. B.; Rutenberg, Andrew D.; Touhami, Ahmed; Jericho, ManfredNo abstract available.Item Open Access Monodisperse domains by proteolytic control of the coarsening instability(American Physical Society, 2011) Derr, Julien; Rutenberg, Andrew D.The coarsening instability typically disrupts steady-state cluster-size distributions. We show that degradation coupled to the cluster size, such as arising from biological proteolysis, leads to a fixed-point cluster size. Stochastic evaporative and condensative fluxes determine the width of the fixed-point size distribution. At the fixed point, we show how the peak size and width depend on number, interactions, and proteolytic rate. This proteolytic size-control mechanism is consistent with the phenomenology of pseudopilus length control in the general secretion pathway of bacteria. 2011 American Physical Society.Item Open Access Pulling helices inside bacteria: imperfect helices and rings(2009-04) Allard, J. F.; Rutenberg, A. D.We study steady-state configurations of intrinsically-straight elastic filaments constrained within rod-shaped bacteria that have applied forces distributed along their length. Perfect steady-state helices result from axial or azimuthal forces applied at filament ends, however azimuthal forces are required for the small pitches observed for MreB filaments within bacteria. Helix-like configurations can result from distributed forces, including coexistence between rings and imperfect helices. Levels of expression and/or bundling of the polymeric protein could mediate this coexistence.Item Open Access Dislocations and morphological instabilities: Continuum modeling of misfitting heteroepitaxial films(2002-04) Haataja, M.; Muller, J.; Rutenberg, AD; Grant, M.No abstract available.Item Open Access Maximally fast coarsening algorithms(2005-11) Cheng, M.; Rutenberg, A. D.We present maximally fast numerical algorithms for conserved coarsening systems that are stable and accurate with a growing natural time step Deltat=At2/3s. We compare the scaling structure obtained from our maximally fast conserved systems directly against the standard fixed time-step Euler algorithm, and find that the error scales as square root of A--so arbitrary accuracy can be achieved. For nonconserved systems, only effectively finite time steps are accessible for similar unconditionally stable algorithms.