A linear lower bound for incrementing a space-optimal integer representation in the bit-probe model

We present the first linear lower bound for the number of bits required to be accessed in the worst case to increment an integer in an arbitrary space- optimal binary representation. The best previously known lower bound was logarithmic. It is known that a logarithmic number of read bits in the worst case is enough to increment some of the integer representations that use one bit of redundancy, therefore we show an exponential gap between space-optimal and redundant counters. Our proof is based on considering the increment procedure for a space optimal counter as a permutation and calculating its parity. For every space optimal counter, the permutation must be odd, and implementing an odd permutation requires reading at least half the bits in the worst case. The combination of these two observations explains why the worst-case space-optimal problem is substantially different from both average-case approach with constant expected number of reads and almost space optimal representations with logarithmic number of reads in the worst case.Comment: 12 pages, 4 figure

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

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

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

The role of dredge-up in double white dwarf mergers

We present the results of an investigation of the dredge-up and mixing during the merger of two white dwarfs with different chemical compositions by conducting hydrodynamic simulations of binary mergers for three representative mass ratios. In all the simulations, the total mass of the two white dwarfs is $\lesssim1.0~{\rm M_\odot}$. Mergers involving a CO and a He white dwarf have been suggested as a possible formation channel for R Coronae Borealis type stars, and we are interested in testing if such mergers lead to conditions and outcomes in agreement with observations. Even if the conditions during the merger and subsequent nucleosynthesis favor the production of $^{18}{\mathrm O}$, the merger must avoid dredging up large amounts of $^{16}{\mathrm O}$, or else it will be difficult to produce sufficient $^{18}{\mathrm O}$ to explain the oxygen ratio observed to be of order unity. We performed a total of 9 simulations using two different grid-based hydrodynamics codes using fixed and adaptive meshes, and one smooth particle hydrodynamics (SPH) code. We find that in most of the simulations, $>10^{-2}~{\rm M_\odot}$ of $^{16}{\mathrm O}$ is indeed dredged up during the merger. However, in SPH simulations where the accretor is a hybrid He/CO white dwarf with a $\sim 0.1~{\rm M_\odot}$ layer of helium on top, we find that no $^{16}{\mathrm O}$ is being dredged up, while in the $q=0.8$ simulation $<10^{-4}~{\rm M_\odot}$ of $^{16}{\mathrm O}$ has been brought up, making a WD binary consisting of a hybrid CO/He WD and a companion He WD an excellent candidate for the progenitor of RCB stars.Comment: Accepted for publication in Ap

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

Low temperature tunneling current enhancement in silicide/Si Schottky contacts with nanoscale barrier width

The low temperature electrical behavior of adjacent silicide/Si Schottky contacts with or without dopant segregation is investigated. The electrical characteristics are very well modeled by thermionic-field emission for non-segregated contacts separated by micrometer-sized gaps. Still, an excess of current occurs at low temperature for short contact separations or dopant-segregated contacts when the voltage applied to the device is sufficiently high. From two-dimensional self-consistent non-equilibrium Green's function simulations, the dependence of the Schottky barrier profile on the applied voltage, unaccounted for in usual thermionic-field emission models, is found to be the source of this deviation