Cluster formation and anomalous fundamental diagram in an ant trail model

A recently proposed stochastic cellular automaton model ({\it J. Phys. A 35, L573 (2002)}), motivated by the motions of ants in a trail, is investigated in detail in this paper. The flux of ants in this model is sensitive to the probability of evaporation of pheromone, and the average speed of the ants varies non-monotonically with their density. This remarkable property is analyzed here using phenomenological and microscopic approximations thereby elucidating the nature of the spatio-temporal organization of the ants. We find that the observations can be understood by the formation of loose clusters, i.e. space regions of enhanced, but not maximal, density.Comment: 11 pages, REVTEX, with 11 embedded EPS file

Optimizing Traffic Lights in a Cellular Automaton Model for City Traffic

We study the impact of global traffic light control strategies in a recently proposed cellular automaton model for vehicular traffic in city networks. The model combines basic ideas of the Biham-Middleton-Levine model for city traffic and the Nagel-Schreckenberg model for highway traffic. The city network has a simple square lattice geometry. All streets and intersections are treated equally, i.e., there are no dominant streets. Starting from a simple synchronized strategy we show that the capacity of the network strongly depends on the cycle times of the traffic lights. Moreover we point out that the optimal time periods are determined by the geometric characteristics of the network, i.e., the distance between the intersections. In the case of synchronized traffic lights the derivation of the optimal cycle times in the network can be reduced to a simpler problem, the flow optimization of a single street with one traffic light operating as a bottleneck. In order to obtain an enhanced throughput in the model improved global strategies are tested, e.g., green wave and random switching strategies, which lead to surprising results.Comment: 13 pages, 10 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

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

Counter Chemotactic Flow in Quasi-One-Dimensional Path

Quasi-one-dimensional bidirectional particle flow including the effect of chemotaxis is investigated through a modification of the John-Schadschneider-Chowdhury-Nishinari model. Specifically, we permit multiple lanes to be shared by both directionally traveling particles. The relation between particle density and flux is studied for several evaporation rates of pheromone, and the following results are obtained: i) in the low-particle-density range, the flux is enlarged by pheromone if the pheromone evaporation rate is sufficiently low, ii) in the high particle-density range, the flux is largest at a reasonably high evaporation rate and, iii) if the evaporation rate is at the level intermediate between the above two cases, the flux is kept small in the entire range of particle densities. The mechanism of these behaviors is investigated by observing the spatial-temporal evolution of particles and the average cluster size in the system.Comment: 4 pages, 9 figure

Low-Background In-Trap Decay Spectroscopy with TITAN at TRIUMF

An in-trap decay spectroscopy setup has been developed and constructed for use with the TITAN facility at TRIUMF. The goal of this device is to observe weak electron-capture (EC) branching ratios for the odd-odd intermediate nuclei in the $\beta\beta$ decay process. This apparatus consists of an up-to 6 Tesla, open-access spectroscopy ion-trap, surrounded radially by up to 7 planar Si(Li) detectors which are separated from the trap by thin Be windows. This configuration provides a significant increase in sensitivity for the detection of low-energy photons by providing backing-free ion storage and eliminating charged-particle-induced backgrounds. An intense electron beam is also employed to increase the charge-states of the trapped ions, thus providing storage times on the order of minutes, allowing for decay-spectroscopy measurements. The technique of multiple ion-bunch stacking was also recently demonstrated, which further extends the measurement possibilities of this apparatus. The current status of the facility and initial results from a $^{116}$In measurement are presented.Comment: Proceedings for the 2nd International Conference on Advances in Radioactive Isotope Science (ARIS2014

Instability of dilute granular flow on rough slope

We study numerically the stability of granular flow on a rough slope in collisional flow regime in the two-dimension. We examine the density dependence of the flowing behavior in low density region, and demonstrate that the particle collisions stabilize the flow above a certain density in the parameter region where a single particle shows an accelerated behavior. Within this parameter regime, however, the uniform flow is only metastable and is shown to be unstable against clustering when the particle density is not high enough.Comment: 4 pages, 6 figures, submitted to J. Phys. Soc. Jpn.; Fig. 2 replaced; references added; comments added; misprints correcte