2,123 research outputs found
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, 1 and 2 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
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