16,506 research outputs found
Length control of microtubules by depolymerizing motor proteins
In many intracellular processes, the length distribution of microtubules is
controlled by depolymerizing motor proteins. Experiments have shown that,
following non-specific binding to the surface of a microtubule, depolymerizers
are transported to the microtubule tip(s) by diffusion or directed walk and,
then, depolymerize the microtubule from the tip(s) after accumulating there. We
develop a quantitative model to study the depolymerizing action of such a
generic motor protein, and its possible effects on the length distribution of
microtubules. We show that, when the motor protein concentration in solution
exceeds a critical value, a steady state is reached where the length
distribution is, in general, non-monotonic with a single peak. However, for
highly processive motors and large motor densities, this distribution
effectively becomes an exponential decay. Our findings suggest that such motor
proteins may be selectively used by the cell to ensure precise control of MT
lengths. The model is also used to analyze experimental observations of
motor-induced depolymerization.Comment: Added section with figures and significantly expanded text, current
version to appear in Europhys. Let
Comment on "Four-body charge transfer processes in proton--helium collisions"
We found, within the plane-wave first Born approximation (PWFBA), that the
proton-helium fully differential cross section (FDCS) for transfer excitation
agrees well with the experimental one at the proton energy Ep = 300 keV and
small scattering angles both in shape and in magnitude. This result is in a
contradiction with that obtained in [1].Comment: 4 pages, 2 figure
Collective traffic-like movement of ants on a trail: dynamical phases and phase transitions
The traffic-like collective movement of ants on a trail can be described by a
stochastic cellular automaton model. We have earlier investigated its unusual
flow-density relation by using various mean field approximations and computer
simulations. In this paper, we study the model following an alternative
approach based on the analogy with the zero range process, which is one of the
few known exactly solvable stochastic dynamical models. We show that our theory
can quantitatively account for the unusual non-monotonic dependence of the
average speed of the ants on their density for finite lattices with periodic
boundary conditions. Moreover, we argue that the model exhibits a continuous
phase transition at the critial density only in a limiting case. Furthermore,
we investigate the phase diagram of the model by replacing the periodic
boundary conditions by open boundary conditions.Comment: 8 pages, 6 figure
Doping Dependence of Thermal Oxidation on n-type 4H-SiC
The doping dependence of dry thermal oxidation rates in n-type 4H-SiC was
investigated. The oxidation was performed in the temperature range 1000C to
1200C for samples with nitrogen doping in the range of 6.5e15/cm3 to
9.3e18/cm3, showing a clear doping dependence. Samples with higher doping
concentrations displayed higher oxidation rates. The results were interpreted
using a modified Deal-Grove model. Linear and parabolic rate constants and
activation energies were extracted. Increasing nitrogen led to an increase in
linear rate constant pre-exponential factor from 10-6m/s to 10-2m/s and the
parabolic rate constant pre-exponential factor from 10e9m2/s to 10e6m2/s. The
increase in linear rate constant was attributed to defects from doping-induced
lattice mismatch, which tend to be more reactive than bulk crystal regions. The
increase in the diffusion-limited parabolic rate constant was attributed to
degradation in oxide quality originating from the doping-induced lattice
mismatch. This degradation was confirmed by the observation of a decrease in
optical density of the grown oxide films from 1.4 to 1.24. The linear
activation energy varied from 1.6eV to 2.8eV, while the parabolic activation
energy varied from 2.7eV to 3.3eV, increasing with doping concentration. These
increased activation energies were attributed to higher nitrogen content,
leading to an increase in effective bond energy stemming from the difference in
C-Si (2.82eV) and Si-N (4.26eV) binding energies. This work provides crucial
information in the engineering of SiO2 dielectrics for SiC MOS structures,
which typically involve regions of very different doping concentrations, and
suggests that thermal oxidation at high doping concentrations in SiC may be
defect mediated.Comment: 13 pages. 9 figures, accepted as a transiction in IEEE electron
device. TED MS#8035
Stochastic kinetics of ribosomes: single motor properties and collective behavior
Synthesis of protein molecules in a cell are carried out by ribosomes. A
ribosome can be regarded as a molecular motor which utilizes the input chemical
energy to move on a messenger RNA (mRNA) track that also serves as a template
for the polymerization of the corresponding protein. The forward movement,
however, is characterized by an alternating sequence of translocation and
pause. Using a quantitative model, which captures the mechanochemical cycle of
an individual ribosome, we derive an {\it exact} analytical expression for the
distribution of its dwell times at the successive positions on the mRNA track.
Inverse of the average dwell time satisfies a ``Michaelis-Menten-like''
equation and is consistent with the general formula for the average velocity of
a molecular motor with an unbranched mechano-chemical cycle. Extending this
formula appropriately, we also derive the exact force-velocity relation for a
ribosome. Often many ribosomes simultaneously move on the same mRNA track,
while each synthesizes a copy of the same protein. We extend the model of a
single ribosome by incorporating steric exclusion of different individuals on
the same track. We draw the phase diagram of this model of ribosome traffic in
3-dimensional spaces spanned by experimentally controllable parameters. We
suggest new experimental tests of our theoretical predictions.Comment: Final published versio
Disaster-Resilient Control Plane Design and Mapping in Software-Defined Networks
Communication networks, such as core optical networks, heavily depend on
their physical infrastructure, and hence they are vulnerable to man-made
disasters, such as Electromagnetic Pulse (EMP) or Weapons of Mass Destruction
(WMD) attacks, as well as to natural disasters. Large-scale disasters may cause
huge data loss and connectivity disruption in these networks. As our dependence
on network services increases, the need for novel survivability methods to
mitigate the effects of disasters on communication networks becomes a major
concern. Software-Defined Networking (SDN), by centralizing control logic and
separating it from physical equipment, facilitates network programmability and
opens up new ways to design disaster-resilient networks. On the other hand, to
fully exploit the potential of SDN, along with data-plane survivability, we
also need to design the control plane to be resilient enough to survive network
failures caused by disasters. Several distributed SDN controller architectures
have been proposed to mitigate the risks of overload and failure, but they are
optimized for limited faults without addressing the extent of large-scale
disaster failures. For disaster resiliency of the control plane, we propose to
design it as a virtual network, which can be solved using Virtual Network
Mapping techniques. We select appropriate mapping of the controllers over the
physical network such that the connectivity among the controllers
(controller-to-controller) and between the switches to the controllers
(switch-to-controllers) is not compromised by physical infrastructure failures
caused by disasters. We formally model this disaster-aware control-plane design
and mapping problem, and demonstrate a significant reduction in the disruption
of controller-to-controller and switch-to-controller communication channels
using our approach.Comment: 6 page
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