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

Robust seismic velocity change estimation using ambient noise recordings

We consider the problem of seismic velocity change estimation using ambient noise recordings. Motivated by [23] we study how the velocity change estimation is affected by seasonal fluctuations in the noise sources. More precisely, we consider a numerical model and introduce spatio-temporal seasonal fluctuations in the noise sources. We show that indeed, as pointed out in [23], the stretching method is affected by these fluctuations and produces misleading apparent velocity variations which reduce dramatically the signal to noise ratio of the method. We also show that these apparent velocity variations can be eliminated by an adequate normalization of the cross-correlation functions. Theoretically we expect our approach to work as long as the seasonal fluctuations in the noise sources are uniform, an assumption which holds for closely located seismic stations. We illustrate with numerical simulations and real measurements that the proposed normalization significantly improves the accuracy of the velocity change estimation

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

On the physics behind coastal morphodynamic patterns

Peer ReviewedPostprint (published version

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

Western Mediterranean precipitation over the last 300 years from instrumental observations

The paper reports the results of the analysis of the 14 longest precipitation instrumental series, covering the last 300 years, that have been recovered in six subareas of the Western Mediterranean basin, i.e., Portugal, Northern and Southern Spain, Southern France, Northern and Southern Italy. This study extends back by one century our knowledge about the instrumental precipitation over theWestern Mediterranean, and by two centuries in some specific subareas. All the time series show repeated swings. No specific trends have been found over the whole period, except in a few cases, but with modest time changes and sometimes having opposite tendency. The same can be said for the most recent decades although with some more marked departures from the average. The correlation between the various Mediterranean subareas is generally not significant, or almost uncorrelated. The Wavelet Spectral Analysis applied to the precipitation identifies only a minor 56-year cycle in autumn, i.e., the same return period that has been found in literature for the Sea Surface Temperature over North Atlantic. A comparison with a gridded dataset reconstruction based on mixed multiproxy and instrumental observations, shows that the grid reconstruction is in good agreement with the observed data for the period after 1900, less for the previous period

Elementary structural building blocks encountered in silicon surface reconstructions

Driven by the reduction of dangling bonds and the minimization of surface stress, reconstruction of silicon surfaces leads to a striking diversity of outcomes. Despite this variety even very elaborate structures are generally comprised of a small number of structural building blocks. We here identify important elementary building blocks and discuss their integration into the structural models as well as their impact on the electronic structure of the surface