Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion-based model MOSAIC

This paper deals with the simulation of microbial degradation of organic matter in soil within the pore space at a microscopic scale. Pore space was analysed with micro-computed tomography and described using a sphere network coming from a geometrical modelling algorithm. The biological model was improved regarding previous work in order to include the transformation of dissolved organic compounds and diffusion processes. We tested our model using experimental results of a simple substrate decomposition experiment (fructose) within a simple medium (sand) in the presence of different bacterial strains. Separate incubations were carried out in microcosms using five different bacterial communities at two different water potentials of −10 and −100 cm of water. We calibrated the biological parameters by means of experimental data obtained at high water content, and we tested the model without changing any parameters at low water content. Same as for the experimental data, our simulation results showed that the decrease in water content caused a decrease of mineralization rate. The model was able to simulate the decrease of connectivity between substrate and microorganism due the decrease of water content

Intertidal finger bars at El Puntal, Bay of Santander, Spain: observation and forcing analysis

A system of 15 small-scale finger bars has been observed, by using video imagery, between 23 June 2008 and 2 June 2010. The bar system is located in the intertidal zone of the swell-protected beaches of El Puntal Spit, in the Bay of Santander (northern coast of Spain). The bars appear on a planar beach (slope = 0.015) with fine, uniform sand (<i>D</i>₅₀ = 0.27 mm) and extend 600 m alongshore. The cross-shore span of the bars is determined by the tidal horizontal excursion (between 70 and 130 m). They have an oblique orientation with respect to the low-tide shoreline; specifically, they are down-current-oriented with respect to the dominant sand transport computed (mean angle of 26° from the shore normal). Their mean wavelength is 26 m and their amplitude varies between 10 and 20 cm. The full system slowly migrates to the east (sand transport direction) with a mean speed of 0.06 m day^-1, a maximum speed in winter (up to 0.15 m day^-1) and a minimum speed in summer. An episode of merging has been identified as bars with larger wavelength seem to migrate more slowly than shorter bars. The wind blows predominantly from the west, generating waves that transport sediment across the bars during high-tide periods. This is the main candidate to explain the eastward migration of the system. In particular, the wind can generate waves of up to 20 cm (root-mean-squared wave height) over a fetch that can reach 4.5 km at high tide. The astronomical tide seems to be important in the bar dynamics, as the tidal level changes the fetch and also determines the time of exposure of the bars to the surf-zone waves and currents. Furthermore, the river discharge could act as input of suspended sediment in the bar system and play a role in the bar dynamics

Work fluctuation theorems for harmonic oscillators

The work fluctuations of an oscillator in contact with a thermostat and driven out of equilibrium by an external force are studied experimentally and theoretically within the context of Fluctuation Theorems (FTs). The oscillator dynamics is modeled by a second order Langevin equation. Both the transient and stationary state fluctuation theorems hold and the finite time corrections are very different from those of a first order Langevin equation. The periodic forcing of the oscillator is also studied; it presents new and unexpected short time convergences. Analytical expressions are given in all cases

Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate

Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion Lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it

Integrating Species Traits into Species Pools

Despite decades of research on the species‐pool concept and the recent explosion of interest in trait‐based frameworks in ecology and biogeography, surprisingly little is known about how spatial and temporal changes in species‐pool functional diversity (SPFD) influence biodiversity and the processes underlying community assembly. Current trait‐based frameworks focus primarily on community assembly from a static regional species pool, without considering how spatial or temporal variation in SPFD alters the relative importance of deterministic and stochastic assembly processes. Likewise, species‐pool concepts primarily focus on how the number of species in the species pool influences local biodiversity. However, species pools with similar richness can vary substantially in functional‐trait diversity, which can strongly influence community assembly and biodiversity responses to environmental change. Here, we integrate recent advances in community ecology, trait‐based ecology, and biogeography to provide a more comprehensive framework that explicitly considers how variation in SPFD, among regions and within regions through time, influences the relative importance of community assembly processes and patterns of biodiversity. First, we provide a brief overview of the primary ecological and evolutionary processes that create differences in SPFD among regions and within regions through time. We then illustrate how SPFD may influence fundamental processes of local community assembly (dispersal, ecological drift, niche selection). Higher SPFD may increase the relative importance of deterministic community assembly when greater functional diversity in the species pool increases niche selection across environmental gradients. In contrast, lower SPFD may increase the relative importance of stochastic community assembly when high functional redundancy in the species pool increases the influence of dispersal history or ecological drift. Next, we outline experimental and observational approaches for testing the influence of SPFD on assembly processes and biodiversity. Finally, we highlight applications of this framework for restoration and conservation. This species‐pool functional diversity framework has the potential to advance our understanding of how local‐ and regional‐scale processes jointly influence patterns of biodiversity across biogeographic regions, changes in biodiversity within regions over time, and restoration outcomes and conservation efforts in ecosystems altered by environmental change

On the Linearization of the Painleve' III-VI Equations and Reductions of the Three-Wave Resonant System

We extend similarity reductions of the coupled (2+1)-dimensional three-wave resonant interaction system to its Lax pair. Thus we obtain new 3x3 matrix Fuchs--Garnier pairs for the third and fifth Painleve' equations, together with the previously known Fuchs--Garnier pair for the fourth and sixth Painleve' equations. These Fuchs--Garnier pairs have an important feature: they are linear with respect to the spectral parameter. Therefore we can apply the Laplace transform to study these pairs. In this way we found reductions of all pairs to the standard 2x2 matrix Fuchs--Garnier pairs obtained by M. Jimbo and T. Miwa. As an application of the 3x3 matrix pairs, we found an integral auto-transformation for the standard Fuchs--Garnier pair for the fifth Painleve' equation. It generates an Okamoto-like B\"acklund transformation for the fifth Painleve' equation. Another application is an integral transformation relating two different 2x2 matrix Fuchs--Garnier pairs for the third Painleve' equation.Comment: Typos are corrected, journal and DOI references are adde

An optimal IV technique for identifying continuous-time transfer function model of multiple input systems

An instrumental variable method for continuous-time model identification is proposed for multiple input single output systems where the characteristic polynomials of the transfer functions associated with each input are not constrained to be identical. An associated model order determination procedure is shown to be reasonably successful. Monte Carlo simulation analyses are used to demonstrate the properties and general robustness of the model order selection and parameter estimation schemes. The results obtained to model a winding process and an industrial binary distillation column illustrate the practical applicability of the proposed identification scheme

Pressure profiles of plasmas confined in the field of a magnetic dipole

Equilibrium pressure profiles of plasmas confined in the field of a dipole magnet are reconstructed using magnetic and x-ray measurements on the levitated dipole experiment (LDX). LDX operates in two distinct modes: with the dipole mechanically supported and with the dipole magnetically levitated. When the dipole is mechanically supported, thermal particles are lost along the field to the supports, and the plasma pressure is highly peaked and consists of energetic, mirror-trapped electrons that are created by electron cyclotron resonance heating. By contrast, when the dipole is magnetically levitated losses to the supports are eliminated and particles are lost via slower cross-field transport that results in broader, but still peaked, plasma pressure profiles.United States. Dept. of Energy (National Science Foundation (U.S.). Partnership in Plasma Science. Grant DE-FG02-00ER54585)United States. Dept. of Energy (National Science Foundation (U.S.). Partnership in Plasma Science. Award PHY-1201896