Pattern formation in self-propelled particles with density-dependent motility

We study the behaviour of interacting self-propelled particles, whose self-propulsion speed decreases with their local density. By combining direct simulations of the microscopic model with an analysis of the hydrodynamic equations obtained by explicitly coarse graining the model, we show that interactions lead generically to the formation of a host of patterns, including moving clumps, active lanes and asters. This general mechanism could explain many of the patterns seen in recent experiments and simulations

A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation

Thigmomorphogenesis is viewed as being a response process of acclimation to short repetitive bursts of mechanical stimulation or touch. The underlying molecular mechanisms that coordinate changes in how touch signals lead to long-term morphological changes are enigmatic. Touch responsive gene expression is rapid and transient, and no transcription factor or DNA regulatory motif has been reported that could confer a genome wide mechanical stimulus. We report here on a chromatin modifying enzyme, SDG8/ASHH2, which can regulate the expression of many touch responsive genes identified in Arabidopsis. SDG8 is required for the permissive expression of touch induced genes; and the loss of function of sdg8 perturbs the maximum levels of induction on selected touch gene targets. SDG8 is required to maintain permissive H3K4 trimethylation marks surrounding the Arabidopsis touch-inducible gene TOUCH 3 (TCH3), which encodes a calmodulin-like protein (CML12). The gene neighboring was also slightly down regulated, revealing a new target for SDG8 mediated chromatin modification. Finally, sdg8 mutants show perturbed morphological response to wind-agitated mechanical stimuli, implicating an epigenetic memory-forming process in the acclimation response of thigmomorphogenesis

Field Theory of Propagating Reaction-Diffusion Fronts

The problem of velocity selection of reaction-diffusion fronts has been widely investigated. While the mean field limit results are well known theoretically, there is a lack of analytic progress in those cases in which fluctuations are to be taken into account. Here, we construct an analytic theory connecting the first principles of the reaction-diffusion process to an effective equation of motion via field-theoretic arguments, and we arrive at the results already confirmed by numerical simulations

Objectively measuring subjectively described traits: Geographic variation in body shape and caudal coloration pattern within vieja melanura (Teleostei: Cichlidae)

© 2017, Universidad de Costa Rica. All rights reserved. Vieja melanura is a Neotropical cichlid occurring in the Petén-lake district systems of Guatemala, as well as the Río Grijalva-Usumacinta basin, and other systems in Southern México, Belize, and Guatemala. A caudal stripe, extending forward from the caudal peduncle, is characteristic of this species. This stripe is sloped downward in nearly all individuals of V. melanura, but the degree of the slope is highly variable throughout its range. The slope and shape of the stripe has previously been used in diagnosing and differentiating between species of Vieja. The purpose of this study was to use objective methods to investigate morphological variation in the caudal stripe and body shape throughout the range of V. melanura. We studied geometric morphometric analyses of body shape and empirical measurements of the slope of the caudal stripe in 215 specimens of V. melanura. We also used the mitochondrial cytochrome b marker to study population level patterns within V. melanura. Results from our analyses showed significant geographic variation in body shape and patterns of coloration with little mitochondrial phylogeographic structure. These patterns likely correspond to differences in riverine habitats throughout the species’ distribution. In conclusion, these results can be used to inform other studies of color and shape variation as it applies to taxonomy and systematics

State-dependent diffusion: thermodynamic consistency and its path integral formulation

The friction coefficient of a particle can depend on its position as it does when the particle is near a wall. We formulate the dynamics of particles with such state-dependent friction coefficients in terms of a general Langevin equation with multiplicative noise, whose evaluation requires the introduction of specific rules. Two common conventions, the Ito and the Stratonovich, provide alternative rules for evaluation of the noise, but other conventions are possible. We show the requirement that a particle's distribution function approach the Boltzmann distribution at long times dictates that a drift term must be added to the Langevin equation. This drift term is proportional to the derivative of the diffusion coefficient times a factor that depends on the convention used to define the multiplicative noise. We explore the consequences of this result in a number examples with spatially varying diffusion coefficients. We also derive path integral representations for arbitrary interpretation of the noise, and use it in a perturbative study of correlations in a simple system.Comment: 18 pages, 8 figures, Accepted to PR

Rare Events Statistics in Reaction--Diffusion Systems

We develop an efficient method to calculate probabilities of large deviations from the typical behavior (rare events) in reaction--diffusion systems. The method is based on a semiclassical treatment of underlying "quantum" Hamiltonian, encoding the system's evolution. To this end we formulate corresponding canonical dynamical system and investigate its phase portrait. The method is presented for a number of pedagogical examples.Comment: 12 pages, 6 figure

Screening for developmental disabilities in HIV positive and HIV negative children in South Africa: Results from the Asenze Study

Background While neurodevelopmental abnormalities are common in children with HIV infection, their detection can be challenging in settings with limited availability of health professionals. The aim of this study was to assess the ability to identify developmental disability among HIV positive and HIV negative children living in South Africa with an internationally used screen. Methods and findings This analysis uses a sample of 1,330 4–6 year old children and 1,231 of their caregivers in KwaZulu-Natal, South Africa, including administration of the Ten Questions (TQ) screen, a standardized medical history and physical examination conducted by a medical doctor, with hearing and vision screening, psychological assessment for cognition and language delay, and voluntary HIV testing. There was a high prevalence of disability among the sample. Compared to HIV negative children, HIV positive children were more likely to screen positive on at least one TQ item (59.3 vs 42.8%, p = 0.01), be delayed in sitting, standing or walking (OR 3.89, 95% CI = 2.1–7.2) and have difficulty walking or weakness in the arms or legs (OR = 2.7, 95%CI = 0.8–9.37). By medical doctor assessment, HIV positive children were more likely to be diagnosed with gross motor disability (OR = 3.5, 95%CI = 1.3–9.2) and hearing disability (OR = 2.5, 95%CI = 1.2–5.3). By independent psychological assessment, HIV positive children were more likely to have cognitive delay (OR = 2.2, 95%CI = 1.2–3.9) and language delay (OR = 4.3, 95%CI = 2.2–8.4). Among HIV positive children, the sensitivity and specificity of the TQ for serious disability (vs. no disability) was 100% and 51.2%, respectively. Among HIV-negative children, the sensitivity and specificity of the TQ for serious disability (vs. no disability) was 90.2% and 63.9%, respectively. Conclusions In this first report of the use of the TQ screen in the isiZulu language, it was found to have high sensitivity for detecting serious developmental disabilities in children, especially HIV positive children. The performance of the TQ in this sample indicates utility for making best use of limited neurodevelopmental resources by screening HIV positive children

A Generalized Epidemic Process and Tricritical Dynamic Percolation

The renowned general epidemic process describes the stochastic evolution of a population of individuals which are either susceptible, infected or dead. A second order phase transition belonging to the universality class of dynamic isotropic percolation lies between endemic or pandemic behavior of the process. We generalize the general epidemic process by introducing a fourth kind of individuals, viz. individuals which are weakened by the process but not yet infected. This sensibilization gives rise to a mechanism that introduces a global instability in the spreading of the process and therefore opens the possibility of a discontinuous transition in addition to the usual continuous percolation transition. The tricritical point separating the lines of first and second order transitions constitutes a new universality class, namely the universality class of tricritical dynamic isotropic percolation. Using renormalized field theory we work out a detailed scaling description of this universality class. We calculate the scaling exponents in an $\epsilon$-expansion below the upper critical dimension $d_{c}=5$ for various observables describing tricritical percolation clusters and their spreading properties. In a remarkable contrast to the usual percolation transition, the exponents $\beta$ and ${\beta}^{\prime}$ governing the two order parameters, viz. the mean density and the percolation probability, turn out to be different at the tricritical point. In addition to the scaling exponents we calculate for all our static and dynamic observables logarithmic corrections to the mean-field scaling behavior at $d_c=5$.Comment: 21 pages, 10 figures, version to appear in Phys. Rev.

Heat kernel regularization of the effective action for stochastic reaction-diffusion equations

The presence of fluctuations and non-linear interactions can lead to scale dependence in the parameters appearing in stochastic differential equations. Stochastic dynamics can be formulated in terms of functional integrals. In this paper we apply the heat kernel method to study the short distance renormalizability of a stochastic (polynomial) reaction-diffusion equation with real additive noise. We calculate the one-loop {\emph{effective action}} and its ultraviolet scale dependent divergences. We show that for white noise a polynomial reaction-diffusion equation is one-loop {\emph{finite}} in $d=0$ and $d=1$, and is one-loop renormalizable in $d=2$ and $d=3$ space dimensions. We obtain the one-loop renormalization group equations and find they run with scale only in $d=2$.Comment: 21 pages, uses ReV-TeX 3.