Stochastic self-assembly of incommensurate clusters

We examine the classic problem of homogeneous nucleation and growth by deriving and analyzing a fully discrete stochastic master equation. Upon comparison with results obtained from the corresponding mean-field Becker-D\"{o}ring equations we find striking differences between the two corresponding equilibrium mean cluster concentrations. These discrepancies depend primarily on the divisibility of the total available mass by the maximum allowed cluster size, and the remainder. When such mass incommensurability arises, a single remainder particle can "emulsify" or "disperse" the system by significantly broadening the mean cluster size distribution. This finite-sized broadening effect is periodic in the total mass of the system and can arise even when the system size is asymptotically large, provided the ratio of the total mass to the maximum cluster size is finite. For such finite ratios we show that homogeneous nucleation in the limit of large, closed systems is not accurately described by classical mean-field mass-action approaches.Comment: 5 pages, 4 figures, 1 tabl

Time-Dependent Density Functional Theory for Driven Lattice Gas Systems with Interactions

We present a new method to describe the kinetics of driven lattice gases with particle-particle interactions beyond hard-core exclusions. The method is based on the time-dependent density functional theory for lattice systems and allows one to set up closed evolution equations for mean site occupation numbers in a systematic manner. Application of the method to a totally asymmetric site exclusion process with nearest-neighbor interactions yields predictions for the current-density relation in the bulk, the phase diagram of non-equilibrium steady states and the time evolution of density profiles that are in good agreement with results from kinetic Monte Carlo simulations.Comment: 11 pages, 3 figure

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

The triple-mode pulsating variable V823 Cas

Based on extended multicolour CCD photometry of the triple-mode radial pulsator V823 Cas we studied the properties of the coupling frequencies invoked by nonlinear processes. Our results support that a resonance connection as suggested by Antonello & Aikawa (1998) affects the mode coupling behaviour. The P1/P0 period ratio of V823 Cas has an "out of range" value if compared with the period ratios of the known double mode pulsators, while the P2/P1 period ratio is normal. The periods and period ratios cannot be consistently interpret without conflict with pulsation and/or evolution models. We attempt to interpret this failure by the suggestion that at present, the periods of V823 Cas are in a transient, resonance affected state, thus do not reflect the true parameters of the object. The anomalous period change behaviour of the fundamental and second overtone modes supports this idea. We have also raised the possibility that a f0 + f2 = 2f1 resonance may act in triple mode pulsators.Comment: 10 pages, 7 figures, 5 tables. Accepted for publication in Astronomy and Astrophysic

Two-Channel Totally Asymmetric Simple Exclusion Processes

Totally asymmetric simple exclusion processes, consisting of two coupled parallel lattice chains with particles interacting with hard-core exclusion and moving along the channels and between them, are considered. In the limit of strong coupling between the channels, the particle currents, density profiles and a phase diagram are calculated exactly by mapping the system into an effective one-channel totally asymmetric exclusion model. For intermediate couplings, a simple approximate theory, that describes the particle dynamics in vertical clusters of two corresponding parallel sites exactly and neglects the correlations between different vertical clusters, is developed. It is found that, similarly to the case of one-channel totally asymmetric simple exclusion processes, there are three stationary state phases, although the phase boundaries and stationary properties strongly depend on inter-channel coupling. An extensive computer Monte Carlo simulations fully support the theoretical predictions.Comment: 13 pages, 10 figure

Power spectra of TASEPs with a localized slow site

The totally asymmetric simple exclusion process (TASEP) with a localized defect is revisited in this article with attention paid to the power spectra of the particle occupancy N(t). Intrigued by the oscillatory behaviors in the power spectra of an ordinary TASEP in high/low density phase(HD/LD) observed by Adams et al. (2007 Phys. Rev. Lett. 99 020601), we introduce a single slow site with hopping rate q<1 to the system. As the power spectrum contains time-correlation information of the particle occupancy of the system, we are particularly interested in how the defect affects fluctuation in particle number of the left and right subsystems as well as that of the entire system. Exploiting Monte Carlo simulations, we observe the disappearance of oscillations when the defect is located at the center of the system. When the defect is off center, oscillations are restored. To explore the origin of such phenomenon, we use a linearized Langevin equation to calculate the power spectrum for the sublattices and the whole lattice. We provide insights into the interactions between the sublattices coupled through the defect site for both simulation and analytical results.Comment: 16 pages, 6 figures; v2: Minor revision

An International Ultraviolet Explorer Archival Study of Dwarf Novae in Outburst

We present a synthetic spectral analysis of nearly the entire far ultraviolet International Ultraviolet Explorer (IUE) archive of spectra of dwarf novae in or near outburst. The study includes 46 systems of all dwarf nova subtypes both above and below the period gap. The spectra were uniformly analyzed using synthetic spectral codes for optically thick accretion disks and stellar photospheres along with the best-available distance measurements or estimates. We present newly estimated accretion rates and discuss the implications of our study for disk accretion physics and CV evolution.Comment: Accepted for publication in the ApJ, Part

Escape of a Uniform Random Walk from an Interval

We study the first-passage properties of a random walk in the unit interval in which the length of a single step is uniformly distributed over the finite range [-a,a]. For a of the order of one, the exit probabilities to each edge of the interval and the exit time from the interval exhibit anomalous properties stemming from the change in the minimum number of steps to escape the interval as a function of the starting point. As a decreases, first-passage properties approach those of continuum diffusion, but non-diffusive effects remain because of residual discreteness effectsComment: 8 pages, 8 figures, 2 column revtex4 forma