Biomedical subjects

Andrew D Rutenberg

Publications and source records attributed to Andrew D Rutenberg.

6 recordsLinked to original sources

PubMed2006

Temperature dependence of MinD oscillation in Escherichia coli: running hot and fast.

We observed that the oscillation period of MinD within rod-like and filamentous cells of Escherichia coli varied by a factor of 4 in the temperature range from 20 degrees C to 40 degrees C. The detailed dependence was Arrhenius, with a slope similar to the overall temperature-dependent growth curve of E. coli. The detailed pattern of oscillation, including the characteristic wavelength in filamentous cells, remained independent of temperature. A quantitative model of MinDE oscillation exhibited similar behavior, with an activated temperature dependence of the MinE-stimulated MinD-ATPase rate.

Adenosine Triphosphatases↗

PubMed2006

Scaling state of dry two-dimensional froths: universal angle-deviations and structure.

We characterize the late-time scaling state of dry, coarsening, two-dimensional froths using a detailed force-based dynamical model. We find that the slow evolution of bubbles leads to small and decreasing deviations from 120-degree angles at threefold vertices in the froth, but with a side-number dependence that is independent of time and apparently universal. We also find that a significant number of T1 side-switching processes occur for macroscopic bubbles in the scaling state, though most bubble annihilations involve four-sided bubbles at microscopic scales.

Journal Article↗

PubMed2005

Maximally fast coarsening algorithms.

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.

Journal Article↗

PubMed2003

Fast and accurate coarsening simulation with an unconditionally stable time step.

We present Cahn-Hilliard and Allen-Cahn numerical integration algorithms that are unconditionally stable and so provide significantly faster accuracy-controlled simulation. Our stability analysis is based on Eyre's theorem and unconditional von Neumann stability analysis, both of which we present. Numerical tests confirm the accuracy of the von Neumann approach, which is straightforward and should be widely applicable in phase-field modeling. For the Cahn-Hilliard case, we show that accuracy can be controlled with an unbounded time step Delta t that grows with time t as Delta t approximately t(alpha). We develop a classification scheme for the step exponent alpha and demonstrate that a class of simple linear algorithms gives alpha=1/3. For this class the speedup relative to a fixed time step grows with N, the linear size of the system, as N/ln N. With conservative choices for the parameters controlling accuracy and finite-size effects we find that an 8192(2) lattice can be integrated 300 times faster than with the Euler method.

Journal Article↗

PubMed2003

Diffusion of asymmetric swimmers.

Particles moving along curved trajectories will diffuse if the curvature fluctuates sufficiently in either magnitude or orientation. We consider particles moving at a constant speed with either a fixed or a Gaussian distributed magnitude of curvature. At small speeds the diffusivity is independent of the speed. At larger particle speeds, the diffusivity depends on the speed through a novel exponent. We apply our results to intracellular transport of vesicles. In sharp contrast to thermal diffusion, the effective diffusivity increases with vesicle size and so may provide an effective means of intracellular transport.

Actins↗

PubMed2003

Pattern formation inside bacteria: fluctuations due to the low copy number of proteins.

We examine fluctuation effects due to the low copy number of proteins involved in pattern-forming dynamics within a bacterium. We focus on a stochastic model of the oscillating MinCDE protein system regulating accurate cell division in E. coli. We find that, for some parameter regions, the protein concentrations are low enough that fluctuations are essential for the generation of patterns. We also examine the role of fluctuations in constraining protein concentration levels.

Adenosine Triphosphatases↗