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

Continuum Modeling and Simulation in Bone Tissue Engineering

Bone tissue engineering is currently a mature methodology from a research perspective. Moreover, modeling and simulation of involved processes and phenomena in BTE have been proved in a number of papers to be an excellent assessment tool in the stages of design and proof of concept through in-vivo or in-vitro experimentation. In this paper, a review of the most relevant contributions in modeling and simulation, in silico, in BTE applications is conducted. The most popular in silico simulations in BTE are classified into: (i) Mechanics modeling and sca old design, (ii) transport and flow modeling, and (iii) modeling of physical phenomena. The paper is restricted to the review of the numerical implementation and simulation of continuum theories applied to di erent processes in BTE, such that molecular dynamics or discrete approaches are out of the scope of the paper. Two main conclusions are drawn at the end of the paper: First, the great potential and advantages that in silico simulation o ers in BTE, and second, the need for interdisciplinary collaboration to further validate numerical models developed in BTE.Ministerio de Economía y Competitividad del Gobierno España DPI2017-82501-

Mass Exchange Dynamics of Surface and Subsurface Oil in Shallow-Water Transport

We formulate a model for the mass exchange between oil at and below the sea surface. This is a particularly important aspect of modeling oil spills. Surface and subsurface oil have different chemical and transport characteristics and lumping them together would compromise the accuracy of the resulting model. Without observational or computational constraints, it is thus not possible to quantitatively predict oil spills based upon partial field observations of surface and/or sub-surface oil. The primary challenge in capturing the mass exchange is that the principal mechanisms are on the microscale. This is a serious barrier to developing practical models for oil spills that are capable of addressing questions regarding the fate of oil at the large spatio-temporal scales, as demanded by environmental questions. We use upscaling to propose an environmental-scale model which incorporates the mass exchange between surface and subsurface oil due to oil droplet dynamics, buoyancy effects, and sea surface and subsurface mechanics. While the mass exchange mechanism detailed here is generally applicable to oil transport models, it addresses the modeling needs of a particular to an oil spill model [1]. This transport model is designed to capture oil spills at very large spatio-temporal scales. It accomplishes this goal by specializing to shallow-water environments, in which depth averaging is a perfectly good approximation for the flow, while at the same time retaining mass conservation of oil over the whole oceanic domain.Comment: 18 pages, 6 figure

Eliciting a predatory response in the eastern corn snake (Pantherophis guttatus) using live and inanimate sensory stimuli: implications for managing invasive populations

North America's Eastern corn snake (Pantherophis guttatus) has been introduced to several islands throughout the Caribbean and Australasia where it poses a significant threat to native wildlife. Invasive snake control programs often involve trapping with live bait, a practice that, as well as being costly and labour intensive, raises welfare and ethical concerns. This study assessed corn snake response to live and inanimate sensory stimuli in an attempt to inform possible future trapping of the species and the development of alternative trap lures. We exposed nine individuals to sensory cues in the form of odour, visual, vibration and combined stimuli and measured the response (rate of tongue-flick [RTF]). RTF was significantly higher in odour and combined cues treatments, and there was no significant difference in RTF between live and inanimate cues during odour treatments. Our findings suggest chemical cues are of primary importance in initiating predation and that an inanimate odour stimulus, absent of simultaneous visual and vibratory cues, is a potential low-cost alternative trap lure for the control of invasive corn snake populations

Cellulose Biodegradation Models; An Example of Cooperative Interactions in Structured Populations

We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the population of micro-organisms. We then use the corresponding models in the context of multiple-trait populations. This leads to classical, logistic type, reproduction rates limiting the growth of large populations but also, and more surprisingly, limiting the growth of populations which are too small in a manner similar to the effects seen in populations requiring cooperative interactions (or sexual reproduction). This study hence offers a striking example of how some mechanisms resembling cooperation can occur in structured biological populations, even in the absence of any actual cooperation.Comment: 37 pages, accepted to ESAIM: Mathematical Modelling and Numerical Analysis (2017

A method for the reconstruction of unknown non-monotonic growth functions in the chemostat

We propose an adaptive control law that allows one to identify unstable steady states of the open-loop system in the single-species chemostat model without the knowledge of the growth function. We then show how one can use this control law to trace out (reconstruct) the whole graph of the growth function. The process of tracing out the graph can be performed either continuously or step-wise. We present and compare both approaches. Even in the case of two species in competition, which is not directly accessible with our approach due to lack of controllability, feedback control improves identifiability of the non-dominant growth rate.Comment: expansion of ideas from proceedings paper (17 pages, 8 figures), proceedings paper is version v