Methodological Considerations for Comparison of Cross-species Use of Tactile Contact

Cross-species comparisons are benefited by compatible datasets; conclusions related to phylogenetic comparisons, questions on convergent and divergent evolution, or homologs versus analogs can only be made when the behaviors being measured are comparable. A direct comparison of the social function of physical contact across two disparate taxa is possible only if data collection and analyses methodologies are analogous. We identify and discuss the parameters, assumptions and measurement schemes applicable to multiple taxa and species that facilitate cross-species comparisons. To illustrate our proposed guidelines for evaluating the role played by tactile contact in social behavior across disparate taxa, this paper presents data on mother-offspring relationships in the two species studied by the authors: chimpanzees (Pan troglodytes schweinfurthii) and dolphins (bottlenose and spotted, Tursiops truncatus and Stenella frontalis, respectively). Cross-species comparative studies allow for a more comprehensive assessment of the similarities and differences with respect to how animals traverse the relationships that form their social groups and societies

Competition for finite resources

The resources in a cell are finite, which implies that the various components of the cell must compete for resources. One such resource is the ribosomes used during translation to create proteins. Motivated by this example, we explore this competition by connecting two totally asymmetric simple exclusion processes (TASEPs) to a finite pool of particles. Expanding on our previous work, we focus on the effects on the density and current of having different entry and exit rates.Comment: 15 pages, 9 figures, v2: minor revisions, v3: additional reference & minor correction

Feedback and Fluctuations in a Totally Asymmetric Simple Exclusion Process with Finite Resources

We revisit a totally asymmetric simple exclusion process (TASEP) with open boundaries and a global constraint on the total number of particles [Adams, et. al. 2008 J. Stat. Mech. P06009]. In this model, the entry rate of particles into the lattice depends on the number available in the reservoir. Thus, the total occupation on the lattice feeds back into its filling process. Although a simple domain wall theory provided reasonably good predictions for Monte Carlo simulation results for certain quantities, it did not account for the fluctuations of this feedback. We generalize the previous study and find dramatically improved predictions for, e.g., the density profile on the lattice and provide a better understanding of the phenomenon of "shock localization."Comment: 11 pages, 3 figures, v2: Minor change

Power Spectra of a Constrained Totally Asymmetric Simple Exclusion Process

To synthesize proteins in a cell, an mRNA has to work with a finite pool of ribosomes. When this constraint is included in the modeling by a totally asymmetric simple exclusion process (TASEP), non-trivial consequences emerge. Here, we consider its effects on the power spectrum of the total occupancy, through Monte Carlo simulations and analytical methods. New features, such as dramatic suppressions at low frequencies, are discovered. We formulate a theory based on a linearized Langevin equation with discrete space and time. The good agreement between its predictions and simulation results provides some insight into the effects of finite resoures on a TASEP.Comment: 4 pages, 2 figures v2: formatting change

A beamforming video recorder for integrated observations of dolphin behavior and vocalizations

Author Posting. © Acoustical Society of America, 2005. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 117 (2005): 1005-1008, doi:10.1121/1.1831284.In this Letter we describe a beamforming video recorder consisting of a video camera at the center of a 16 hydrophone array. A broadband frequency-domain beamforming algorithm is used to estimate the azimuth and elevation of each detected sound. These estimates are used to generate a visual cue indicating the location of the sound source within the video recording, which is synchronized to the acoustic data. The system provided accurate results in both lab calibrations and a field test. The system allows researchers to correlate the acoustic and physical behaviors of marine mammals during studies of social interactions.This research was funded by NSF Ocean Sciences CAREER award 9733391

Dynamical Transition in the Open-boundary Totally Asymmetric Exclusion Process

We revisit the totally asymmetric simple exclusion process with open boundaries (TASEP), focussing on the recent discovery by de Gier and Essler that the model has a dynamical transition along a nontrivial line in the phase diagram. This line coincides neither with any change in the steady-state properties of the TASEP, nor the corresponding line predicted by domain wall theory. We provide numerical evidence that the TASEP indeed has a dynamical transition along the de Gier-Essler line, finding that the most convincing evidence was obtained from Density Matrix Renormalisation Group (DMRG) calculations. By contrast, we find that the dynamical transition is rather hard to see in direct Monte Carlo simulations of the TASEP. We furthermore discuss in general terms scenarios that admit a distinction between static and dynamic phase behaviour.Comment: 27 pages, 18 figures. v2 to appear in J Phys A features minor corrections and better-quality figure

Slowest relaxation mode of the partially asymmetric exclusion process with open boundaries

We analyze the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process on a finite lattice and with the most general open boundary conditions. We extend results obtained recently for totally asymmetric diffusion [J. de Gier and F.H.L. Essler, J. Stat. Mech. P12011 (2006)] to the case of partial symmetry. We determine the finite-size scaling of the spectral gap, which characterizes the approach to stationarity at large times, in the low and high density regimes and on the coexistence line. We observe boundary induced crossovers and discuss possible interpretations of our results in terms of effective domain wall theories.Comment: 30 pages, 9 figures, typeset for pdflatex; revised versio

Implementation of Code Properties via Transducers

The FAdo system is a symbolic manipulator of formal language objects, implemented in Python. In this work, we extend its capabilities by implementing methods to manipulate transducers and we go one level higher than existing formal language systems and implement methods to manipulate objects representing classes of independent languages (widely known as code properties). Our methods allow users to define their own code properties and combine them between themselves or with fixed properties such as prefix codes, suffix codes, error detecting codes, etc. The satisfaction and maximality decision questions are solvable for any of the definable properties. The new online system LaSer allows one to query about a code property and obtain the answer in a batch mode. Our work is founded on independence theory as well as the theory of rational relations and transducers, and contributes with improved algorithms on these objects

Exact Spectral Gaps of the Asymmetric Exclusion Process with Open Boundaries

We derive the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process with the most general open boundary conditions. By analysing these equations in detail for the cases of totally asymmetric and symmetric diffusion, we calculate the finite-size scaling of the spectral gap, which characterizes the approach to stationarity at large times. In the totally asymmetric case we observe boundary induced crossovers between massive, diffusive and KPZ scaling regimes. We further study higher excitations, and demonstrate the absence of oscillatory behaviour at large times on the ``coexistence line'', which separates the massive low and high density phases. In the maximum current phase, oscillations are present on the KPZ scale $t\propto L^{-3/2}$. While independent of the boundary parameters, the spectral gap as well as the oscillation frequency in the maximum current phase have different values compared to the totally asymmetric exclusion process with periodic boundary conditions. We discuss a possible interpretation of our results in terms of an effective domain wall theory.Comment: 42 pages, 25 figures; added appendix and minor correction