Possible Origin of Stagnation and Variability of Earth's Biodiversity

The magnitude and variability of Earth's biodiversity have puzzled scientists ever since paleontologic fossil databases became available. We identify and study a model of interdependent species where both endogenous and exogenous impacts determine the nonstationary extinction dynamics. The framework provides an explanation for the qualitative difference of marine and continental biodiversity growth. In particular, the stagnation of marine biodiversity may result from a global transition from an imbalanced to a balanced state of the species dependency network. The predictions of our framework are in agreement with paleontologic databases.Comment: 5 pages, 6 pages supplemen

Unfair and Anomalous Evolutionary Dynamics from Fluctuating Payoffs

Evolution occurs in populations of reproducing individuals. Reproduction depends on the payoff a strategy receives. The payoff depends on the environment that may change over time, on intrinsic uncertainties, and on other sources of randomness. These temporal variations in the payoffs can affect which traits evolve. Understanding evolutionary game dynamics that are affected by varying payoffs remains difficult. Here we study the impact of arbitrary amplitudes and covariances of temporally varying payoffs on the dynamics. The evolutionary dynamics may be "unfair", meaning that, on average, two coexisting strategies may persistently receive different payoffs. This mechanism can induce an anomalous coexistence of cooperators and defectors in the Prisoner's Dilemma, and an unexpected selection reversal in the Hawk-Dove game.Comment: 6 pages, 8 pages supplemen

Sustainable computational science: the ReScience initiative

Computer science o ers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel con dent their research is reproducible. But this is not exactly true. Jonathan Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. e actual scholarship is the full so ware environment, code, and data that produced the result. is implies new work ows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically di erent from other traditional scienti c journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and so ware tests

A Voronoi Grid and a Particle Tracking Algorithm for DSMC

The DSMC method simulates a gas by three uncoupled steps: moving representative particles through a physical domain, performing probabilistic collisions and estimating the macroscopic state by ensemble averaging. In order to ease computational treatment of these three steps it is convenient to discretize the space with a grid that fits into the boundaries of the physical domain. For efficient particle tracking it is useful that the cells of this grid are convex polyhedra which preferably have no indirect neighbors. To reduce discretization errors in the collision step and to take reasonable averages the cells should be nearly isotropic, whereas their volume is primarily determined by the local flow gradients. Especially the latter condition requires the density of the grid to be continuously adaptable in space and time. We show that grids derived from Voronoi diagrams fulfill these requirements very well

[Re] A simple rule for the evolution of cooperation on graphs and social networks

A simple rule for the evolution of cooperation on graphs and social networks, ReScience 3(5), 201

A Voronoi Grid and a Particle Tracking Algorithm for DSMC

Abstract. The DSMC method simulates a gas by three uncoupled steps: moving representative particles through a physical domain, performing probabilistic collisions and estimating the macroscopic state by ensemble averaging. In order to ease computational treatment of these three steps it is convenient to discretize the space with a grid that fits into the boundaries of the physical domain. For efficient particle tracking it is useful that the cells of this grid are convex polyhedra which preferably have no indirect neighbors. To reduce discretization errors in the collision step and to take reasonable averages the cells should be nearly isotropic, whereas their volume is primarily determined by the local flow gradients. Especially the latter condition requires the density of the grid to be continuously adaptable in space and time. We show that grids derived from Voronoi diagrams fulfill these requirements very well