In-depth analysis of the Naming Game dynamics: the homogeneous mixing case

Language emergence and evolution has recently gained growing attention through multi-agent models and mathematical frameworks to study their behavior. Here we investigate further the Naming Game, a model able to account for the emergence of a shared vocabulary of form-meaning associations through social/cultural learning. Due to the simplicity of both the structure of the agents and their interaction rules, the dynamics of this model can be analyzed in great detail using numerical simulations and analytical arguments. This paper first reviews some existing results and then presents a new overall understanding.Comment: 30 pages, 19 figures (few in reduced definition). In press in IJMP

Hofstadter butterflies of carbon nanotubes: Pseudofractality of the magnetoelectronic spectrum

The electronic spectrum of a two-dimensional square lattice in a perpendicular magnetic field has become known as the Hofstadter butterfly [Hofstadter, Phys. Rev. B 14, 2239 (1976).]. We have calculated quasi-one-dimensional analogs of the Hofstadter butterfly for carbon nanotubes (CNTs). For the case of single-wall CNTs, it is straightforward to implement magnetic fields parallel to the tube axis by means of zone folding in the graphene reciprocal lattice. We have also studied perpendicular magnetic fields which, in contrast to the parallel case, lead to a much richer, pseudofractal spectrum. Moreover, we have investigated magnetic fields piercing double-wall CNTs and found strong signatures of interwall interaction in the resulting Hofstadter butterfly spectrum, which can be understood with the help of a minimal model. Ubiquitous to all perpendicular magnetic field spectra is the presence of cusp catastrophes at specific values of energy and magnetic field. Resolving the density of states along the tube circumference allows recognition of the snake states already predicted for nonuniform magnetic fields in the two-dimensional electron gas. An analytic model of the magnetic spectrum of electrons on a cylindrical surface is used to explain some of the results.Comment: 14 pages, 12 figures update to published versio

Sharp transition towards shared vocabularies in multi-agent systems

What processes can explain how very large populations are able to converge on the use of a particular word or grammatical construction without global coordination? Answering this question helps to understand why new language constructs usually propagate along an S-shaped curve with a rather sudden transition towards global agreement. It also helps to analyze and design new technologies that support or orchestrate self-organizing communication systems, such as recent social tagging systems for the web. The article introduces and studies a microscopic model of communicating autonomous agents performing language games without any central control. We show that the system undergoes a disorder/order transition, going trough a sharp symmetry breaking process to reach a shared set of conventions. Before the transition, the system builds up non-trivial scale-invariant correlations, for instance in the distribution of competing synonyms, which display a Zipf-like law. These correlations make the system ready for the transition towards shared conventions, which, observed on the time-scale of collective behaviors, becomes sharper and sharper with system size. This surprising result not only explains why human language can scale up to very large populations but also suggests ways to optimize artificial semiotic dynamics.Comment: 12 pages, 4 figure

Exploring variation in surgical practice : does the surgeon's personality influence anastomotic decision-making?'

Funding This work was kindly supported by Bowel Research UK and the Ileostomy and Internal Pouch Association. The funders had no influence in the design, delivery, or interpretation of this study. Acknowledgements The study authors are grateful to all participants who took part, as well as those individuals and professional bodies who shared the Plato Project survey, including: the Association of Coloproctology of Great Britain and Ireland, the COVIDSurg Collaborative Group, the Turkish Society of Colon and Rectal Surgery and the Italian Surgical Research Group.Peer reviewedPublisher PD

Full sphere hydrodynamic and dynamo benchmarks

Convection in planetary cores can generate fluid flow and magnetic fields, and a number of sophisticated codes exist to simulate the dynamic behaviour of such systems. We report on the first community activity to compare numerical results of computer codes designed to calculate fluid flow within a whole sphere. The flows are incompressible and rapidly rotating and the forcing of the flow is either due to thermal convection or due to moving boundaries. All problems defined have solutions that allow easy comparison, since they are either steady, slowly drifting or perfectly periodic. The first two benchmarks are defined based on uniform internal heating within the sphere under the Boussinesq approximation with boundary conditions that are uniform in temperature and stress-free for the flow. Benchmark 1 is purely hydrodynamic, and has a drifting solution. Benchmark 2 is a magnetohydrodynamic benchmark that can generate oscillatory, purely periodic, flows and magnetic fields. In contrast, Benchmark 3 is a hydrodynamic rotating bubble benchmark using no slip boundary conditions that has a stationary solution. Results from a variety of types of code are reported, including codes that are fully spectral (based on spherical harmonic expansions in angular coordinates and polynomial expansions in radius), mixed spectral and finite difference, finite volume, finite element and also a mixed Fourier–finite element code. There is good agreement between codes. It is found that in Benchmarks 1 and 2, the approximation of a whole sphere problem by a domain that is a spherical shell (a sphere possessing an inner core) does not represent an adequate approximation to the system, since the results differ from whole sphere results

Experiences of support garments following bowel stoma formation: analysis of free-text responses in a cross-sectional survey

Aim: To explore the experiences of support garments when adjusting to bodily change following bowel stoma formation. Design: Thematic analyses of free-text responses in a cross-sectional survey of the stoma population in 2018. Methods: Free-text responses were invited so that respondents could describe their experiences in more detail. A process of induction was chosen to allow for themes to emerge directly from the data. The concept ‘embodiment’ was used as a theoretical framework during interpretation. Results: 1425 people with a bowel stoma responded to the survey, of whom 598 provided free-text responses. Four themes about experiences of support garments in the context of changed bodily experiences following stoma formation were identified: body complications, which is about experiences of using support garments to prevent or self-manage parastomal hernia; body appearance, which is about hiding the stoma and stoma appliance; body function, which is about managing stoma appliance complications; and body sensation, which is mainly about negative experiences of ill-fitting garments. Conclusion: Support garments can be understood as items that are used by people during an ongoing process of adjusting to bodily changes following stoma formation and as part of an ongoing process of reconstructing new embodied selves. Impact: This is the first study to explore people’s experiences of support garments following bowel stoma formation. Support garments are used in the self-management of body complications, appearance, function and sensations. Stoma nurses may draw on the findings of this study to advise patients about the benefits of garments for adjusting to bodily change, and garment suppliers should address people’s negative experiences by improving garments

Recombination rate and selection strength in HIV intra-patient evolution

The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the parameters governing genetic diversification and the strength of selection need to be known. While mutation rates can be measured in single replication cycles, the relevant effective recombination rate depends on the probability of coinfection of a cell with more than one virus and can only be inferred from population data. However, most population genetic estimators for recombination rates assume absence of selection and are hence of limited applicability to HIV, since positive and purifying selection are important in HIV evolution. Here, we estimate the rate of recombination and the distribution of selection coefficients from time-resolved sequence data tracking the evolution of HIV within single patients. By examining temporal changes in the genetic composition of the population, we estimate the effective recombination to be r=1.4e-5 recombinations per site and generation. Furthermore, we provide evidence that selection coefficients of at least 15% of the observed non-synonymous polymorphisms exceed 0.8% per generation. These results provide a basis for a more detailed understanding of the evolution of HIV. A particularly interesting case is evolution in response to drug treatment, where recombination can facilitate the rapid acquisition of multiple resistance mutations. With the methods developed here, more precise and more detailed studies will be possible, as soon as data with higher time resolution and greater sample sizes is available.Comment: to appear in PLoS Computational Biolog

Bistability in Apoptosis by Receptor Clustering

Apoptosis is a highly regulated cell death mechanism involved in many physiological processes. A key component of extrinsically activated apoptosis is the death receptor Fas, which, on binding to its cognate ligand FasL, oligomerize to form the death-inducing signaling complex. Motivated by recent experimental data, we propose a mathematical model of death ligand-receptor dynamics where FasL acts as a clustering agent for Fas, which form locally stable signaling platforms through proximity-induced receptor interactions. Significantly, the model exhibits hysteresis, providing an upstream mechanism for bistability and robustness. At low receptor concentrations, the bistability is contingent on the trimerism of FasL. Moreover, irreversible bistability, representing a committed cell death decision, emerges at high concentrations, which may be achieved through receptor pre-association or localization onto membrane lipid rafts. Thus, our model provides a novel theory for these observed biological phenomena within the unified context of bistability. Importantly, as Fas interactions initiate the extrinsic apoptotic pathway, our model also suggests a mechanism by which cells may function as bistable life/death switches independently of any such dynamics in their downstream components. Our results highlight the role of death receptors in deciding cell fate and add to the signal processing capabilities attributed to receptor clustering.Comment: Accepted by PLoS Comput Bio

A variational method based on weighted graph states

In a recent article [Phys. Rev. Lett. 97 (2006), 107206], we have presented a class of states which is suitable as a variational set to find ground states in spin systems of arbitrary spatial dimension and with long-range entanglement. Here, we continue the exposition of our technique, extend from spin 1/2 to higher spins and use the boson Hubbard model as a non-trivial example to demonstrate our scheme.Comment: 36 pages, 13 figure

Information transmission in oscillatory neural activity

Periodic neural activity not locked to the stimulus or to motor responses is usually ignored. Here, we present new tools for modeling and quantifying the information transmission based on periodic neural activity that occurs with quasi-random phase relative to the stimulus. We propose a model to reproduce characteristic features of oscillatory spike trains, such as histograms of inter-spike intervals and phase locking of spikes to an oscillatory influence. The proposed model is based on an inhomogeneous Gamma process governed by a density function that is a product of the usual stimulus-dependent rate and a quasi-periodic function. Further, we present an analysis method generalizing the direct method (Rieke et al, 1999; Brenner et al, 2000) to assess the information content in such data. We demonstrate these tools on recordings from relay cells in the lateral geniculate nucleus of the cat.Comment: 18 pages, 8 figures, to appear in Biological Cybernetic