Fractional Chemotaxis Diffusion Equations

We introduce mesoscopic and macroscopic model equations of chemotaxis with anomalous subdiffusion for modelling chemically directed transport of biological organisms in changing chemical environments with diffusion hindered by traps or macro-molecular crowding. The mesoscopic models are formulated using Continuous Time Random Walk master equations and the macroscopic models are formulated with fractional order differential equations. Different models are proposed depending on the timing of the chemotactic forcing. Generalizations of the models to include linear reaction dynamics are also derived. Finally a Monte Carlo method for simulating anomalous subdiffusion with chemotaxis is introduced and simulation results are compared with numerical solutions of the model equations. The model equations developed here could be used to replace Keller-Segel type equations in biological systems with transport hindered by traps, macro-molecular crowding or other obstacles.Comment: 25page

Anomalous thermodynamics at the micro-scale

Particle motion at the micro-scale is an incessant tug-of-war between thermal fluctuations and applied forces on one side, and the strong resistance exerted by fluid viscosity on the other. Friction is so strong that completely neglecting inertia - the overdamped approximation - gives an excellent effective description of the actual particle mechanics. In sharp contrast with this result, here we show that the overdamped approximation dramatically fails when thermodynamic quantities such as the entropy production in the environment is considered, in presence of temperature gradients. In the limit of vanishingly small, yet finite inertia, we find that the entropy production is dominated by a contribution that is anomalous, i.e. has no counterpart in the overdamped approximation. This phenomenon, that we call entropic anomaly, is due to a symmetry-breaking that occurs when moving to the small, finite inertia limit. Strong production of anomalous entropy is traced back to intense sweeps down the temperature gradient.Comment: 4 pages, 1 figure, supplementary information uploaded as a separate pdf file (see other formats link

Hydrodynamic object recognition using pressure sensing

Hydrodynamic sensing is instrumental to fish and some amphibians. It also represents, for underwater vehicles, an alternative way of sensing the fluid environment when visual and acoustic sensing are limited. To assess the effectiveness of hydrodynamic sensing and gain insight into its capabilities and limitations, we investigated the forward and inverse problem of detection and identification, using the hydrodynamic pressure in the neighbourhood, of a stationary obstacle described using a general shape representation. Based on conformal mapping and a general normalization procedure, our obstacle representation accounts for all specific features of progressive perceptual hydrodynamic imaging reported experimentally. Size, location and shape are encoded separately. The shape representation rests upon an asymptotic series which embodies the progressive character of hydrodynamic imaging through pressure sensing. A dynamic filtering method is used to invert noisy nonlinear pressure signals for the shape parameters. The results highlight the dependence of the sensitivity of hydrodynamic sensing not only on the relative distance to the disturbance but also its bearing

Asexual and sexual replication in sporulating organisms

This paper develops models describing asexual and sexual replication in sporulating organisms. Replication via sporulation is the replication strategy for all multicellular life, and may even be observed in unicellular life (such as with budding yeast). We consider diploid populations replicating via one of two possible sporulation mechanisms: (1) Asexual sporulation, whereby adult organisms produce single-celled diploid spores that grow into adults themselves. (2) Sexual sporulation, whereby adult organisms produce single-celled diploid spores that divide into haploid gametes. The haploid gametes enter a haploid "pool", where they may recombine with other haploids to form a diploid spore that then grows into an adult. We consider a haploid fusion rate given by second-order reaction kinetics. We work with a simplified model where the diploid genome consists of only two chromosomes, each of which may be rendered defective with a single point mutation of the wild-type. We find that the asexual strategy is favored when the rate of spore production is high compared to the characteristic growth rate from a spore to a reproducing adult. Conversely, the sexual strategy is favored when the rate of spore production is low compared to the characteristic growth rate from a spore to a reproducing adult. As the characteristic growth time increases, or as the population density increases, the critical ratio of spore production rate to organism growth rate at which the asexual strategy overtakes the sexual one is pushed to higher values. Therefore, the results of this model suggest that, for complex multicellular organisms, sexual replication is favored at high population densities, and low growth and sporulation rates.Comment: 8 pages, 5 figures, to be submitted to Journal of Theoretical Biology, figures not included in this submissio

The Effect of Proton Temperature Anisotropy on the Solar Minimum Corona and Wind

A semi-empirical, axisymmetric model of the solar minimum corona is developed by solving the equations for conservation of mass and momentum with prescribed anisotropic temperature distributions. In the high-latitude regions, the proton temperature anisotropy is strong and the associated mirror force plays an important role in driving the fast solar wind; the critical point where the outflow velocity equals the parallel sound speed is reached already at 1.5 Rsun from Sun center. The slow wind arises from a region with open field lines and weak anisotropy surrounding the equatorial streamer belt. The model parameters were chosen to reproduce the observed latitudinal extent of the equatorial streamer in the corona and at large distance from the Sun. We find that the magnetic cusp of the closed-field streamer core lies at about 1.95 Rsun. The transition from fast to slow wind is due to a decrease in temperature anisotropy combined with the non-monotonic behavior of the non-radial expansion factor in flow tubes that pass near the streamer cusp. In the slow wind, the plasma beta is of order unity and the critical point lies at about 5 Rsun, well beyond the magnetic cusp. The predicted outflow velocities are consistent with OVI Doppler dimming measurements from UVCS/SOHO. We also find good agreement with polarized brightness (pB) measurements from LASCO/SOHO and HI Ly-alpha images from UVCS/SOHO.Comment: 36 pages, 13 figures. AAS LaTeX Macros v5.0. To appear in The Astrophysical Journal, Vol. 598, No. 2, Issue December 1, 200

Low-frequency components in harbor porpoise (Phocoena phocoena) clicks : communication signal, by-products, or artifacts?

Author Posting. © Acoustical Society of America, 2008. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 124 (2008): 4059-4068, doi:10.1121/1.2945154.Underwater sound signals for biosonar and communication normally have different source properties to serve the purposes of generating efficient acoustic backscatter from small objects or conveying information to conspecifics. Harbor porpoises (Phocoena phocoena) are nonwhistling toothed whales that produce directional, narrowband, high-frequency (HF) echolocation clicks. This study tests the hypothesis that their 130 kHz HF clicks also contain a low-frequency (LF) component more suited for communication. Clicks from three captive porpoises were analyzed to quantify the LF and HF source properties. The LF component is 59 (S.E.M=1.45 dB) dB lower than the HF component recorded on axis, and even at extreme off-axis angles of up to 135°, the HF component is 9 dB higher than the LF component. Consequently, the active space of the HF component will always be larger than that of the LF component. It is concluded that the LF component is a by-product of the sound generator rather than a dedicated pulse produced to serve communication purposes. It is demonstrated that distortion and clipping in analog tape recorders can explain some of the prominent LF components reported in earlier studies, emphasizing the risk of erroneous classification of sound types based on recording artifacts.This work was supported by the Carlsberg Foundation and Oticon, and via a Steno Scholarship from the Danish Natural Science Research Council to PTM

Cell morphology governs directional control in swimming bacteria

The ability to rapidly detect and track nutrient gradients is key to the ecological success of motile bacteria in aquatic systems. Consequently, bacteria have evolved a number of chemotactic strategies that consist of sequences of straight runs and reorientations. Theoretically, both phases are affected by fluid drag and Brownian motion, which are themselves governed by cell geometry. Here, we experimentally explore the effect of cell length on control of swimming direction. We subjected Escherichia coli to an antibiotic to obtain motile cells of different lengths, and characterized their swimming patterns in a homogeneous medium. As cells elongated, angles between runs became smaller, forcing a change from a run-and-tumble to a run-and-stop/reverse pattern. Our results show that changes in the motility pattern of microorganisms can be induced by simple morphological variation, and raise the possibility that changes in swimming pattern may be triggered by both morphological plasticity and selection on morphology

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

MicroRNAs in pulmonary arterial remodeling

Pulmonary arterial remodeling is a presently irreversible pathologic hallmark of pulmonary arterial hypertension (PAH). This complex disease involves pathogenic dysregulation of all cell types within the small pulmonary arteries contributing to vascular remodeling leading to intimal lesions, resulting in elevated pulmonary vascular resistance and right heart dysfunction. Mutations within the bone morphogenetic protein receptor 2 gene, leading to dysregulated proliferation of pulmonary artery smooth muscle cells, have been identified as being responsible for heritable PAH. Indeed, the disease is characterized by excessive cellular proliferation and resistance to apoptosis of smooth muscle and endothelial cells. Significant gene dysregulation at the transcriptional and signaling level has been identified. MicroRNAs are small non-coding RNA molecules that negatively regulate gene expression and have the ability to target numerous genes, therefore potentially controlling a host of gene regulatory and signaling pathways. The major role of miRNAs in pulmonary arterial remodeling is still relatively unknown although research data is emerging apace. Modulation of miRNAs represents a possible therapeutic target for altering the remodeling phenotype in the pulmonary vasculature. This review will focus on the role of miRNAs in regulating smooth muscle and endothelial cell phenotypes and their influence on pulmonary remodeling in the setting of PAH

Dissimilar responses of fungal and bacterial communities to soil transplantation simulating abrupt climate changes.

Both fungi and bacteria play essential roles in regulating soil carbon cycling. To predict future carbon stability, it is imperative to understand their responses to environmental changes, which is subject to large uncertainty. As current global warming is causing range shifts toward higher latitudes, we conducted three reciprocal soil transplantation experiments over large transects in 2005 to simulate abrupt climate changes. Six years after soil transplantation, fungal biomass of transplanted soils showed a general pattern of changes from donor sites to destination, which were more obvious in bare fallow soils than in maize cropped soils. Strikingly, fungal community compositions were clustered by sites, demonstrating that fungi of transplanted soils acclimatized to the destination environment. Several fungal taxa displayed sharp changes in relative abundance, including Podospora, Chaetomium, Mortierella and Phialemonium. In contrast, bacterial communities remained largely unchanged. Consistent with the important role of fungi in affecting soil carbon cycling, 8.1%-10.0% of fungal genes encoding carbon-decomposing enzymes were significantly (p < 0.01) increased as compared with those from bacteria (5.7%-8.4%). To explain these observations, we found that fungal occupancy across samples was mainly determined by annual average air temperature and rainfall, whereas bacterial occupancy was more closely related to soil conditions, which remained stable 6 years after soil transplantation. Together, these results demonstrate dissimilar response patterns and resource partitioning between fungi and bacteria, which may have considerable consequences for ecosystem-scale carbon cycling