Mark R. Paul

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In order for the cell's genome to be passed intact from one generation to the next, the events of the cell cycle (DNA replication, mitosis, cell division) must be executed in the correct order, despite the considerable molecular noise inherent in any protein-based regulatory system residing in the small confines of a eukaryotic cell. To assess the effects(More)
The stochastic response of nanoscale oscillators of arbitrary geometry immersed in a viscous fluid is studied. Using the fluctuation-dissipation theorem, it is shown that deterministic calculations of the governing fluid and solid equations can be used in a straightforward manner to directly calculate the stochastic response that would be measured in(More)
The origin of the power-law decay measured in the power spectra of low Prandtl number Rayleigh-Bénard convection near the onset of chaos is addressed using long time numerical simulations of the three-dimensional Boussinesq equations in cylindrical domains. The power law is found to arise from quasidiscontinuous changes in the slope of the time series of(More)
We study the nonlinear dynamics of a tapping mode atomic force microscope with tip-surface interactions that include attractive, repulsive, and capillary force contributions using numerical techniques tailored for hybrid or discontinuous dynamical systems that include forward-time simulation with event handling and numerical pseudo-arclength continuation.(More)
We describe a numerical procedure to construct a modified velocity field that does not have any mean flow. Using this procedure, we present two results. First, we show that, in the absence of the mean flow, spiral defect chaos collapses to a stationary pattern comprising textures of stripes with angular bends. The quenched patterns are characterized by mean(More)
Numerical simulations of the Boussinesq equations with rotation for realistic no-slip boundary conditions and a finite annular domain are presented. These simulations reproduce traveling waves observed experimentally. Traveling waves are studied near threshold by using the complex Ginzburg-Landau equation (CGLE): a mode analysis enables the CGLE(More)
The results of an analysis of turbulent pipe flow based on a Karhunen-Lò eve decomposition are presented. The turbulent flow is generated by a direct numerical simulation of the Navier-Stokes equations using a spectral element algorithm at a Reynolds number Reτ = 150. This simulation yields a set of basis functions that captures 90% of the energy after 2,(More)
The free-living aquatic bacterium, Caulobacter crescentus, exhibits two different morphologies during its life cycle. The morphological change from swarmer cell to stalked cell is a result of changes of function of two bi-functional histidine kinases, PleC and CckA. Here, we describe a detailed molecular mechanism by which the function of PleC changes(More)
Using large-scale parallel numerical simulations we explore spatiotemporal chaos in Rayleigh-Bénard convection in a cylindrical domain with experimentally relevant boundary conditions. We use the variation of the spectrum of Lyapunov exponents and the leading-order Lyapunov vector with system parameters to quantify states of high-dimensional chaos in fluid(More)
  • Nicholas L O 'connor, Mark R Paul, Danesh K Tafti, Traian Iliescu
  • 2008
The nonlinear and chaotic dynamics of a shallow fluid layer are investigated numerically using large-scale parallel numerical simulations. Two particular situations are studied in detail. First, a fluid layer is placed between rigid boundaries and heated from below to yield the chaotic dynamics of thermal convection rolls (Rayleigh-Bénard convection).(More)