Spatial Scaling in Model Plant Communities

We present an analytically tractable variant of the voter model that provides a quantitatively accurate description of beta-diversity (two-point correlation function) in two tropical forests. The model exhibits novel scaling behavior that leads to links between ecological measures such as relative species abundance and the species area relationship.Comment: 10 pages, 3 figure

Coherent and incoherent atomic scattering: Formalism and application to pionium interacting with matter

The experimental determination of the lifetime of pionium provides a very important test on chiral perturbation theory. This quantity is determined in the DIRAC experiment at CERN. In the analysis of this experiment, the breakup probabilities of of pionium in matter are needed to high accuracy as a theoretical input. We study in detail the influence of the target electrons. They contribute through screening and incoherent effects. We use Dirac-Hartree- Fock-Slater wavefunctions in order to determine the corresponding form factors. We find that the inner-shell electrons contribute less than the weakly bound outer electrons. Furthermore, we establish a more rigorous estimate for the magnitude of the contributions form the transverse current (magnetic terms thus far neglected in the calculations).Comment: Journal of Physics B: Atomic, Molecular and Optical Physics; (accepted; 22 pages, 6 figures, 26 references) Revised version: more detailed description of DIRAC experiment; failure of simplest models for incoherent scattering demonstrated by example

Voter Model with Time dependent Flip-rates

We introduce time variation in the flip-rates of the Voter Model. This type of generalisation is relevant to models of ageing in language change, allowing the representation of changes in speakers' learning rates over their lifetime and may be applied to any other similar model in which interaction rates at the microscopic level change with time. The mean time taken to reach consensus varies in a nontrivial way with the rate of change of the flip-rates, varying between bounds given by the mean consensus times for static homogeneous (the original Voter Model) and static heterogeneous flip-rates. By considering the mean time between interactions for each agent, we derive excellent estimates of the mean consensus times and exit probabilities for any time scale of flip-rate variation. The scaling of consensus times with population size on complex networks is correctly predicted, and is as would be expected for the ordinary voter model. Heterogeneity in the initial distribution of opinions has a strong effect, considerably reducing the mean time to consensus, while increasing the probability of survival of the opinion which initially occupies the most slowly changing agents. The mean times to reach consensus for different states are very different. An opinion originally held by the fastest changing agents has a smaller chance to succeed, and takes much longer to do so than an evenly distributed opinion.Comment: 16 pages, 6 figure

Radiative and Auger decay data for modelling nickel K lines

Radiative and Auger decay data have been calculated for modelling the K lines in ions of the nickel isonuclear sequence, from Ni$^+$ up to Ni$^{27+}$. Level energies, transition wavelengths, radiative transition probabilities, and radiative and Auger widths have been determined using Cowan's Hartree--Fock with Relativistic corrections (HFR) method. Auger widths for the third-row ions (Ni$^+$--Ni$^{10+}$) have been computed using single-configuration average (SCA) compact formulae. Results are compared with data sets computed with the AUTOSTRUCTURE and MCDF atomic structure codes and with available experimental and theoretical values, mainly in highly ionized ions and in the solid state.Comment: submitted to ApJS. 42 pages. 12 figure

Integrating ecology into macroevolutionary research

On 9 March, over 150 biologists gathered in London for the Centre for Ecology and Evolution spring symposium, ‘Integrating Ecology into Macroevolutionary Research’. The event brought together researchers from London-based institutions alongside others from across the UK, Europe and North America for a day of talks. The meeting highlighted methodological advances and recent analyses of exemplar datasets focusing on the exploration of the role of ecological processes in shaping macroevolutionary patterns

Neutral Evolution as Diffusion in phenotype space: reproduction with mutation but without selection

The process of `Evolutionary Diffusion', i.e. reproduction with local mutation but without selection in a biological population, resembles standard Diffusion in many ways. However, Evolutionary Diffusion allows the formation of local peaks with a characteristic width that undergo drift, even in the infinite population limit. We analytically calculate the mean peak width and the effective random walk step size, and obtain the distribution of the peak width which has a power law tail. We find that independent local mutations act as a diffusion of interacting particles with increased stepsize.Comment: 4 pages, 2 figures. Paper now representative of published articl

Universal and non-universal features of the generalized voter class for ordering dynamics

By considering three different spin models belonging to the generalized voter class for ordering dynamics in two dimensions [I. Dornic, \textit{et al.} Phys. Rev. Lett. \textbf{87}, 045701 (2001)], we show that they behave differently from the linear voter model when the initial configuration is an unbalanced mixture up and down spins. In particular we show that for nonlinear voter models the exit probability (probability to end with all spins up when starting with an initial fraction $x$ of them) assumes a nontrivial shape. The change is traced back to the strong nonconservation of the average magnetization during the early stages of dynamics. Also the time needed to reach the final consensus state $T_N(x)$ has an anomalous nonuniversal dependence on $x$.Comment: 7 pages, 7 figure

Comparing process-based and constraint-based approaches for modeling macroecological patterns

Ecological patterns arise from the interplay of many different processes, and yet the emergence of consistent phenomena across a diverse range of ecological systems suggests that many patterns may in part be determined by statistical or numerical constraints. Differentiating the extent to which patterns in a given system are determined statistically, and where it requires explicit ecological processes, has been difficult. We tackled this challenge by directly comparing models from a constraint-based theory, the Maximum Entropy Theory of Ecology (METE) and models from a process-based theory, the size-structured neutral theory (SSNT). Models from both theories were capable of characterizing the distribution of individuals among species and the distribution of body size among individuals across 76 forest communities. However, the SSNT models consistently yielded higher overall likelihood, as well as more realistic characterizations of the relationship between species abundance and average body size of conspecific individuals. This suggests that the details of the biological processes contain additional information for understanding community structure that are not fully captured by the METE constraints in these systems. Our approach provides a first step towards differentiating between process- and constraint-based models of ecological systems and a general methodology for comparing ecological models that make predictions for multiple patterns.Comment: 45 pages, 3 main figures, 3 tables, 2 appendices. arXiv admin note: text overlap with arXiv:1308.073

Lymphatic drainage function and its immunological implications: From dendritic cell homing to vaccine design

The slow interstitial flow that drains fluid from the blood capillaries into the lymphatic capillaries provides transport of macromolecular nutrients to cells in the interstitium. We discuss herein how this flow also provides continuous access to immune cells residing in the lymph nodes of antigens from self or from pathogens residing in the interstitium. We also address mechanisms by which dendritic cells in the periphery sense interstitial flow to home efficiently into the lymphatics after activation, and how lymphatic endothelium can be activated by this flow, including how it can act as a lymphatic morphoregulator. Further, we present concepts on how interstitial flow can be exploited with biomaterial systems to deliver antigen and adjuvant molecules directly into the lymphatics, to target dendritic cells residing in the lymph nodes rather than in the peripheral tissues, using particles that are small enough to be carried along by flow through the network structure of the interstitium. Finally, we present recent work on lymphatic and lymphoid tissue engineering, including how interstitial flow can be used as a design principle. Thus, an understanding of the physiological processes that govern transport in the interstitium guides new understanding of both immune cell interactions with the lymphatics as well as therapeutic interventions exploiting the lymphatics as a target

Careful prior specification avoids incautious inference for log-Gaussian Cox point processes

The BCI forest dynamics research project was founded by S.P. Hubbell and R.B. Foster and is now managed by R. Condit, S. Lao, and R. Perez under the Center for Tropical Forest Science and the Smithsonian Tropical Research in Panama. Numerous organizations have provided funding, principally the U.S. National Science Foundation, and hundreds of field workers have contributed. The data used can be requested and generally granted at http://ctfs.si.edudatarequest. Kriged estimates for concentration of the soil nutrients were downloaded from http://ctfs.si.edu/webatlas/datasets/bci/soilmaps/BCIsoil.html. We acknowledge the principal investigators that were responsible for collecting and analysing the soil maps (Jim Dallin, Robert John, Kyle Harms, Robert Stallard and Joe Yavitt), the funding sources (NSF DEB021104,021115, 0212284,0212818 and OISE 0314581, STRI Soils Initiative and CTFS) and field assistants (Paolo Segre and Juan Di Trani).Peer reviewedPostprin