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Flows in confined micro-structures: coupling physical heterogeneity and bio-chemical processes

English title Flows in confined micro-structures: coupling physical heterogeneity and bio-chemical processes
Applicant de Anna Pietro
Number 172587
Funding scheme Project funding (Div. I-III)
Research institution Institut de géographie et de durabilité Faculté des géosciences et environnement Université de Lausanne
Institution of higher education University of Lausanne - LA
Main discipline Hydrology, Limnology, Glaciology
Start/End 01.10.2017 - 30.09.2021
Approved amount 500'000.00
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All Disciplines (2)

Discipline
Hydrology, Limnology, Glaciology
Fluid Dynamics

Keywords (6)

filtration; horizontal gene transfer; modeling and upscaling; flow in porous media; reactive transport; microfluidics

Lay Summary (Italian)

Lead
La maggior parte della biomassa sulla Terra è composta da batteri e una gran parte di essi e' localizzata in condizioni confinate (come nel sottosuolo), dove si trovano a essere agenti viventi di una complessa rete di processi: contribuiscono a catalizzare reazioni chimiche, aumentano la loro cinetica o degradano / producono inquinanti. Da una parte la mancanza di studi sulla dinamica e l'accoppiamento tra questi processi biochimici e il moto dei fluidi, e dall'altra la necessità di robusti modelli predittivi suggeriscono che un quadro meccanicistico a piccola scala costituisca un passo indispensabile per fare previsioni significative di sistemi biologici in ambiente naturale.
Lay summary
L'eterogeneità della velocità dei fluidi si riferisce alla sua variabilità spaziale: un concetto intuitivo per sistemi "aperti", come i flussi di superficie o atmosferici. In ambienti confinati (come il sotto-suolo o i sistemi di filtrazione industriale) il movimento dei fluidi è limitato a spazi molto piccoli e di dimensioni molto diverse: è stato dimostrato che ciò porta ad una ricca struttura del flusso di liquidi e all'eterogeneità di tali flussi, anche se confinati a scale molto piccole (cosa che non avviene in un ambiente aperto con flussi turbolenti).

Ho intenzione di studiare come il movimento di fluidi in strutture piccole e confinate (come il sottosuolo o sistemi di filtrazione industriale) influenzeranno processi reattivi che dipendono dal mescolamento tra diverse sostanze. In particolare, studierò come l'eterogeneità di questi flussi confinati abbia un impatto su: i) la miscelazione di soluti trasportati (come i contaminanti); ii) la cinetica delle reazioni chimiche che hanno luogo al fronte dove si mescolano diverse sostanze; iii) il trasporto e la filtrazione di colloidi e microrganismi (che determina il modo con cui un tale mezzo viene da essi colonizzato) e iv) il tasso di trasferimento di elementi genetici mobili nei batteri (recentemente riconosciuto come una delle cause della persistente resistenza di alcuni batteri agli antibiotici).

Questo studio si basa sull'utilizzo di microscopia, "microfluidics" (piccoli dispositivi trasparenti la cui struttura interna puo essere lavorata con alta precisione), fotografia scientifica e analisi di immagini. Se da una parte l'intento e' quello di scoprire fenomeni nuovi, dall'altra si vuole capire il funzionamento di tali fenomeni per proporre modelli fisici per descriverne e predirne il comportamento.
Direct link to Lay Summary Last update: 20.09.2017

Responsible applicant and co-applicants

Employees

Project partner

Publications

Publication
Trait-specific dispersal of bacteria in heterogeneous porous environments: from pore to porous medium scale
Scheidweiler David, Miele Filippo, Peter Hannes, Battin Tom J., de Anna Pietro (2020), Trait-specific dispersal of bacteria in heterogeneous porous environments: from pore to porous medium scale, in Journal of The Royal Society Interface, 17(164), 20200046-20200046.
Stochastic model for filtration by porous materials
Miele Filippo, de Anna Pietro, Dentz Marco (2019), Stochastic model for filtration by porous materials, in Physical Review Fluids, 4(9), 094101-094101.

Datasets

Scheidweiler_JRSI_2020_dataset

Author Scheidweiler, David; Miele, Filippo; Peter, Hannes; Battin, Tom; de Anna, Pietro
Publication date 04.03.2020
Persistent Identifier (PID) 10.5281/zenodo.3696539
Repository Zeondo
Abstract
The data set contains four folders with all the data published in Scheidweiler et. al, JRSI 2020, about BreakThrough Curves, Deposition Profiles, Particle Tracking and CTRW simulation of motile and non-motile bacteria suspended in porous media flow.A text file named Scheidweiler_JRSI2020_DATA_read_me.txt, decsribes the folder content and how to read it.

Collaboration

Group / person Country
Types of collaboration
Stream Biofilm and Ecosystem Research Laboratory SBER Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Mixing in Porous Media Talk given at a conference Mixing and filtration by heterogeneous and confined porous media 03.02.2020 Lorentz Center, Netherlands Miele Filippo; Hamada Mayumi; de Anna Pietro; Dentz Marco;
Interpore conference Talk given at a conference A stochastic model for filtration by porous media 06.05.2019 Valencia, Spain Miele Filippo; de Anna Pietro; Dentz Marco;
Interpore conference Talk given at a conference Diffusion limited mixing in confined media 06.05.2019 Valencia, Spain de Anna Pietro; Hamada Mayumi;
Interpore conference Talk given at a conference Biophysical controls on the trait-specific dispersal of bacteria in heterogeneous porous environments across spatial scales 06.05.2019 Valencia, Spain Miele Filippo; de Anna Pietro;
EGU meeting Talk given at a conference Diffusion limited mixing in confined media 07.04.2019 Vienna, Austria de Anna Pietro; Hamada Mayumi;
EGU meeting Talk given at a conference A stochastic model for filtration by porous media 07.04.2019 Vienna, Austria Miele Filippo; Dentz Marco; de Anna Pietro;


Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
Gordon Research Seminar Talk 07.07.2018 Jordan Hotel at Sunday River, United States of America Dentz Marco; de Anna Pietro; Miele Filippo;


Abstract

Within the shallow subsurface, soil, rock, fluids, gases and living organisms are in close interactions as a result of the coupling between fluid flows, mixing, solutes availability and microorganisms displacement and adaptation. The common challenge in all these processes is their spatial variability (heterogeneity). The consequent complexity that rises from the coupling of these processes, makes predictions based on rates measured under homogenized, well-mixed, conditions different by orders of magnitudes from observations in the field.In this context, the proposed project aims to investigate the impact of heterogeneous flows in subsurface environments on i) mixing of solutes, ii) the kinetics of moving reactive fronts, iii) transport and filtration of microorganisms and iv) the rate of mobile genetic elements uptake by bacteria (horizontal gene transfer by natural transformation). These four processes are intimately related by heterogeneity which characterizes, at multiple scales, many confined systems, like the shallow sub-surface.The two main expected outcomes of this research project can be summarized as follows. First, microfluidics experimental techniques will be used and developed to produce new knowledge on fundamental biochemical processes coupled to physical heterogeneity, by directly observing relevant quantities such as displacing chemical fronts, microorganisms attachment/detachment processes and chemical reactions. Second, upscaled theoretical models will be derived, based on the micro-scale picture obtained with microfluidics experiments, in order to predict the overall behavior of the considered systems. The upscaling issue is a central scientific question guiding this research project that I will address with two main approaches: i) integrating the statistics of individual processes considered as stochastic (like Random Walk models) and ii) relating the overall evolution of some topological properties (like the length of an invading front or the interface between different phases) to basic mechanical (like fluid stretching and shear) or biological (swimming strategy, biofilm growth) processes.The proposed research will provide a theoretical framework for the fundamental processes mixing, transport, chemical reactions and microbial activities that are key for the spread of pathogens, chemical contamination and remediation in soils and aquifers, geothermal energy exploration, the assessment of geological storage of CO2 and radioactive waste repositories. Optimal mixing strategies represents a central concern in mining for the extraction of minerals or other geological materials from the underground. These are applications that require a solid quantitative approach to predict the large scale consequences of these processes under flow heterogeneity. Moreover, transport processes in confined media of different nature are very similar, thus, the expected impact of the proposed research is not limited to applications in geological environments.
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