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