Statistical Analysis of Genealogical Trees for Polygamic Species

Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point transformations. In particular we show that the tree features strongly depend on the fractions of males and females in the population, and also on the offspring probability distribution. We check different possibilities, some of them relevant to human groups, and compare them with simulations.Comment: 2 eps figs, Fig.2 changed to meet cond-mat size criteri

Self-organization of hierarchical structures in nonlocally coupled replicator models

We study a simple replicator model with non-symmetric and nonlocal interactions. Hierarchical structures with prey-predator relations are self-organized from a homogeneous state, induced by the dynamical instability of nonlinear interactions.Comment: 7 pages, 2 figure

Author-Based Analysis of Conference versus Journal Publication in Computer Science

Conference publications in computer science (CS) have attracted scholarly attention due to their unique status as a main research outlet unlike other science fields where journals are dominantly used for communicating research findings. One frequent research question has been how different conference and journal publications are, considering a paper as a unit of analysis. This study takes an author-based approach to analyze publishing patterns of 517,763 scholars who have ever published both in CS conferences and journals for the last 57 years, as recorded in DBLP. The analysis shows that the majority of CS scholars tend to make their scholarly debut, publish more papers, and collaborate with more coauthors in conferences than in journals. Importantly, conference papers seem to serve as a distinct channel of scholarly communication, not a mere preceding step to journal publications: coauthors and title words of authors across conferences and journals tend not to overlap much. This study corroborates findings of previous studies on this topic from a distinctive perspective and suggests that conference authorship in CS calls for more special attention from scholars and administrators outside CS who have focused on journal publications to mine authorship data and evaluate scholarly performance

Comprehending environmental and economic sustainability: Comparative analysis of stability principles in the biosphere and free market economy

Using the formalism of Lyapunov potential function it is shown that the stability principles for biomass in the ecosystem and for employment in economics are mathematically similar. The ecosystem is found to have a stable and an unstable stationary state with high (forest) and low (grasslands) biomass, respectively. In economics, there is a stable stationary state with high employment, which corresponds to mass production of conventional goods sold at low cost price, and an unstable stationary state with lower employment, which corresponds to production of novel goods appearing in the course of technological progress. An additional stable stationary state is described for economics, the one corresponding to very low employment in production of life essentials such as energy and raw materials. In this state the civilization currently pays 10% of global GDP for energy produced by a negligible minority of the working population (currently ~0.2%) and sold at prices greatly exceeding the cost price by 40 times. It is shown that economic ownership over energy sources is equivalent to equating measurable variables of different dimensions (stores and fluxes), which leads to effective violation of the laws of energy and matter conservation.Comment: 51 pages, 6 figure

Power laws, Pareto distributions and Zipf's law

When the probability of measuring a particular value of some quantity varies inversely as a power of that value, the quantity is said to follow a power law, also known variously as Zipf's law or the Pareto distribution. Power laws appear widely in physics, biology, earth and planetary sciences, economics and finance, computer science, demography and the social sciences. For instance, the distributions of the sizes of cities, earthquakes, solar flares, moon craters, wars and people's personal fortunes all appear to follow power laws. The origin of power-law behaviour has been a topic of debate in the scientific community for more than a century. Here we review some of the empirical evidence for the existence of power-law forms and the theories proposed to explain them.Comment: 28 pages, 16 figures, minor corrections and additions in this versio

"Quantum phase transitions" in classical nonequilibrium processes

Diffusion limited reaction of the Lotka-Volterra type is analyzed taking into account the discrete nature of the reactants. In the continuum approximation, the dynamics is dominated by an elliptic fixed-point. This fixed-point becomes unstable due to discretization effects, a scenario similar to quantum phase transitions. As a result, the long-time asymptotic behavior of the system changes and the dynamics flows into a limit cycle. The results are verified by numerical simulations.Comment: 9 pages, 3 figures include

Four-state rock-paper-scissors games on constrained Newman-Watts networks

We study the cyclic dominance of three species in two-dimensional constrained Newman-Watts networks with a four-state variant of the rock-paper-scissors game. By limiting the maximal connection distance $R_{max}$ in Newman-Watts networks with the long-rang connection probability $p$, we depict more realistically the stochastic interactions among species within ecosystems. When we fix mobility and vary the value of $p$ or $R_{max}$, the Monte Carlo simulations show that the spiral waves grow in size, and the system becomes unstable and biodiversity is lost with increasing $p$ or $R_{max}$. These results are similar to recent results of Reichenbach \textit{et al.} [Nature (London) \textbf{448}, 1046 (2007)], in which they increase the mobility only without including long-range interactions. We compared extinctions with or without long-range connections and computed spatial correlation functions and correlation length. We conclude that long-range connections could improve the mobility of species, drastically changing their crossover to extinction and making the system more unstable.Comment: 6 pages, 7 figure

Computational inference in systems biology

Parameter inference in mathematical models of biological pathways, expressed as coupled ordinary differential equations (ODEs), is a challenging problem. The computational costs associated with repeatedly solving the ODEs are often high. Aimed at reducing this cost, new concepts using gradient matching have been proposed. This paper combines current adaptive gradient matching approaches, using Gaussian processes, with a parallel tempering scheme, and conducts a comparative evaluation with current methods used for parameter inference in ODEs

The literature of chemoinformatics : 1978–2018

This article presents a study of the literature of chemoinformatics, updating and building upon an analogous bibliometric investigation that was published in 2008. Data on outputs in the field, and citations to those outputs, were obtained by means of topic searches of the Web of Science Core Collection. The searches demonstrate that chemoinformatics is by now a well-defined sub-discipline of chemistry, and one that forms an essential part of the chemical educational curriculum. There are three core journals for the subject: The Journal of Chemical Information and Modeling, the Journal of Cheminformatics, and Molecular Informatics, and, having established itself, chemoinformatics is now starting to export knowledge to disciplines outside of chemistry

Spontaneous emergence of spatial patterns ina a predator-prey model

We present studies for an individual based model of three interacting populations whose individuals are mobile in a 2D-lattice. We focus on the pattern formation in the spatial distributions of the populations. Also relevant is the relationship between pattern formation and features of the populations' time series. Our model displays travelling waves solutions, clustering and uniform distributions, all related to the parameters values. We also observed that the regeneration rate, the parameter associated to the primary level of trophic chain, the plants, regulated the presence of predators, as well as the type of spatial configuration.Comment: 17 pages and 15 figure