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

Min-oscillations in Escherichia coli induced by interactions of membrane-bound proteins

During division it is of primary importance for a cell to correctly determine the site of cleavage. The bacterium Escherichia coli divides in the center, producing two daughter cells of equal size. Selection of the center as the correct division site is in part achieved by the Min-proteins. They oscillate between the two cell poles and thereby prevent division at these locations. Here, a phenomenological description for these oscillations is presented, where lateral interactions between proteins on the cell membrane play a key role. Solutions to the dynamic equations are compared to experimental findings. In particular, the temporal period of the oscillations is measured as a function of the cell length and found to be compatible with the theoretical prediction.Comment: 17 pages, 5 figures. Submitted to Physical Biolog

High-frequency performance of Schottky source/drain silicon pMOS devices

A radio-frequency performance of 85-nm gate-length p-type Schottky barrier (SB) with PtSi source/drain materials is investigated. The impact of silicidation annealing temperature on the high-frequency behavior of SB MOSFETs is analyzed using an extrinsic small-signal equivalent circuit. It is demonstrated that the current drive and the gate transconductance strongly depend on the silicidation anneal temperature, whereas the unity-gain cutoff frequency of the measured devices remains nearly unchanged

Predictions from a stochastic polymer model for the MinDE dynamics in E.coli

The spatiotemporal oscillations of the Min proteins in the bacterium Escherichia coli play an important role in cell division. A number of different models have been proposed to explain the dynamics from the underlying biochemistry. Here, we extend a previously described discrete polymer model from a deterministic to a stochastic formulation. We express the stochastic evolution of the oscillatory system as a map from the probability distribution of maximum polymer length in one period of the oscillation to the probability distribution of maximum polymer length half a period later and solve for the fixed point of the map with a combined analytical and numerical technique. This solution gives a theoretical prediction of the distributions of both lengths of the polar MinD zones and periods of oscillations -- both of which are experimentally measurable. The model provides an interesting example of a stochastic hybrid system that is, in some limits, analytically tractable.Comment: 16 page

Dynamic compartmentalization of bacteria: accurate division in E. coli

Positioning of the midcell division plane within the bacterium E. coli is controlled by the min system of proteins: MinC, MinD and MinE. These proteins coherently oscillate from end to end of the bacterium. We present a reaction--diffusion model describing the diffusion of min proteins along the bacterium and their transfer between the cytoplasmic membrane and cytoplasm. Our model spontaneously generates protein oscillations in good agreement with experiments. We explore the oscillation stability, frequency and wavelength as a function of protein concentration and bacterial length.Comment: 4 pages, 4 figures, Latex2e, Revtex

A stochastic model of Min oscillations in Escherichia coli and Min protein segregation during cell division

The Min system in Escherichia coli directs division to the centre of the cell through pole-to-pole oscillations of the MinCDE proteins. We present a one dimensional stochastic model of these oscillations which incorporates membrane polymerisation of MinD into linear chains. This model reproduces much of the observed phenomenology of the Min system, including pole-to-pole oscillations of the Min proteins. We then apply this model to investigate the Min system during cell division. Oscillations continue initially unaffected by the closing septum, before cutting off rapidly. The fractions of Min proteins in the daughter cells vary widely, from 50%-50% up to 85%-15% of the total from the parent cell, suggesting that there may be another mechanism for regulating these levels in vivo.Comment: 19 pages, 12 figures (25 figure files); published at http://www.iop.org/EJ/journal/physbi

Inclusive versus Exclusive EM Processes in Relativistic Nuclear Systems

Connections are explored between exclusive and inclusive electron scattering within the framework of the relativistic plane-wave impulse approximation, beginning with an analysis of the model-independent kinematical constraints to be found in the missing energy--missing momentum plane. From the interplay between these constraints and the spectral function basic features of the exclusive and inclusive nuclear responses are seen to arise. In particular, the responses of the relativistic Fermi gas and of a specific hybrid model with confined nucleons in the initial state are compared in this work. As expected, the exclusive responses are significantly different in the two models, whereas the inclusive ones are rather similar. By extending previous work on the relativistic Fermi gas, a reduced response is introduced for the hybrid model such that it fulfills the Coulomb and the higher-power energy-weighted sum rules. While incorporating specific classes of off-shellness for the struck nucleons, it is found that the reducing factor required is largely model-independent and, as such, yields a reduced response that is useful for extracting the Coulomb sum rule from experimental data. Finally, guided by the difference between the energy-weighted sum rules of the two models, a version of the relativistic Fermi gas is devised which has the 0$^{\rm th}$, 1$^{\rm st}$ and 2$^{\rm nd}$ moments of the charge response which agree rather well with those of the hybrid model: this version thus incorporates {\em a priori} the binding and confinement effects of the stuck nucleons while retaining the simplicity of the original Fermi gas.Comment: LaTex file with 15 .ps figure

An Inner Gaseous Disk around the Herbig Be Star MWC 147

We present high-spectral-resolution, optical spectra of the Herbig Be star MWC 147, in which we spectrally resolve several emission lines, including the [O I] lines at 6300 and 6363\deg. Their highly symmetric, double-peaked line profiles indicate that the emission originates in a rotating circumstellar disk. We deconvolve the Doppler-broadened [O I] emission lines to obtain a measure of emission as a function of distance from the central star. The resulting radial surface brightness profiles are in agreement with a disk structure consisting of a flat, inner, gaseous disk and a flared, outer, dust disk. The transition between these components at 2 to 3 AU corresponds to the estimated dust sublimation radius. The width of the double-peaked Mg II line at 4481\deg suggests that the inner disk extends to at least 0.10 AU, close to the corotation radius.Comment: accepted for ApJ Letters (Oct. 2010

Nitrogen and Sulfur Concentrations and Flow Rates of Corn Wet‐Milling Streams

Nitrogen (N) and sulfur (S) concentrations can affect the market value of coproducts from corn wet‐milling. The composition of parent streams would be expected to affect composition of the resulting coproducts but there are few published data available to examine this relationship. Concentration and flow data are needed to determine which streams are important in modifying N and S coproduct concentrations. The objective was to measure concentrations and flows of N and S in corn wet‐milling streams. Samples were taken from 21 process streams from 3 wet‐milling plants during two periods of three weeks each; N and S concentrations of each sample were determined. There were large differences in N and S concentrations among processing streams; within most streams, N and S concentrations were similar among plants. Concentrations of N and S were related inversely to flow rates. Steepwater and gluten streams contained most of the N and S flow and provide an opportunity for modification. The process water stream carried large quantities of N and S and represents another opportunity for improving process efficiency and coproduct value.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141537/1/cche0260.pd

Timed Parity Games: Complexity and Robustness

We consider two-player games played in real time on game structures with clocks where the objectives of players are described using parity conditions. The games are \emph{concurrent} in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to play strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to \emph{turn-based} (i.e., not concurrent) \emph{finite-state} (i.e., untimed) parity games. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. The states of the resulting game are based on clock regions of the original game, and the state space of the finite game is linear in the size of the region graph. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, \emph{limit-robust} and \emph{bounded-robust} winning strategies. Using a limit-robust winning strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust winning. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust winning strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers