Abstract:We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid.
“…In the video, the upstream displacements are clearly identifiable as well as the motion towards the rear of the grains and the displacements on the surfaces and the final release. This succession of steps was also recently identified by computer simulations using molecular dynamics coupled with lattice Boltzmann (Lee et al 2021) as the scenario characterizing the entrapment and release of motile bacteria moving near an obstacle. The critical shear rate is reached when θ = arcsin( γc 0 /4U).…”
Section: Appendix D Asymptotic Dispersion and Retardation Coefficient...supporting
confidence: 53%
“…This succession of steps was also recently identified by computer simulations using molecular dynamics coupled with lattice Boltzmann (Lee et al. 2021) as the scenario characterizing the entrapment and release of motile bacteria moving near an obstacle. Figure 11.Illustration of the model.…”
Section: Figurementioning
confidence: 53%
“…When flow was increased and concomitantly the shear rate, they observed a depletion of the central part of the profile that they attributed to a transverse flux of bacteria from low shear to high shear regions located near the surfaces (Rusconi et al 2014). Motility was also observed to lead to bacteria accumulation at the rear of a constriction (Altshuler et al 2013) or downstream of circular obstacles (Miño et al 2018;Secchi et al 2020;Lee et al 2021). Addition of pillars to microfluidic rectangular channels offers the possibility to design a bi-dimensional heterogeneous porous system suited to exploring the influence of flow heterogeneities and pore structures on the transport and retention of bacteria (Creppy et al 2019;Dehkharghani et al 2019;Scheidweiler et al 2020;Secchi et al 2020;de Anna et al 2020).…”
Section: Introductionmentioning
confidence: 98%
“…2020; Lee et al. 2021). Addition of pillars to microfluidic rectangular channels offers the possibility to design a bi-dimensional heterogeneous porous system suited to exploring the influence of flow heterogeneities and pore structures on the transport and retention of bacteria (Creppy et al.…”
Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization and enhanced oil recovery. While physicochemical bacteria filtration is well documented, recent studies showed that bacterial motility plays a key role in the transport process. Flow and transport experiments performed in microfluidic chips containing randomly placed obstacles confirmed that the distributions of non-motile bacteria stays compact, whereas for the motile strains, the distributions are characterized by both significant retention as well as fast downstream motion. For motile bacteria, the detailed microscopic study of individual bacteria trajectories reveals two salient features: (i) the emergence of an active retention process triggered by motility, (ii) enhancement of dispersion due to the exchange between fast flow channels and low flow regions in the vicinity of the solid grains. We propose a physical model based on a continuous time random walk approach. This approach accounts for bacteria dispersion via variable pore-scale flow velocities through a Markov model for equidistant particle speeds. Motility of bacteria is modelled by a two-rate trapping process that accounts for the motion towards and active trapping at the obstacles. This approach captures the forward tails observed for the distribution of bacteria displacements, and quantifies an enhanced hydrodynamic dispersion effect that originates in the combined effect of pore-scale flow variability and bacterial motility. The model reproduces the experimental observations, and predicts bacteria dispersion and transport at the macroscale.
“…In the video, the upstream displacements are clearly identifiable as well as the motion towards the rear of the grains and the displacements on the surfaces and the final release. This succession of steps was also recently identified by computer simulations using molecular dynamics coupled with lattice Boltzmann (Lee et al 2021) as the scenario characterizing the entrapment and release of motile bacteria moving near an obstacle. The critical shear rate is reached when θ = arcsin( γc 0 /4U).…”
Section: Appendix D Asymptotic Dispersion and Retardation Coefficient...supporting
confidence: 53%
“…This succession of steps was also recently identified by computer simulations using molecular dynamics coupled with lattice Boltzmann (Lee et al. 2021) as the scenario characterizing the entrapment and release of motile bacteria moving near an obstacle. Figure 11.Illustration of the model.…”
Section: Figurementioning
confidence: 53%
“…When flow was increased and concomitantly the shear rate, they observed a depletion of the central part of the profile that they attributed to a transverse flux of bacteria from low shear to high shear regions located near the surfaces (Rusconi et al 2014). Motility was also observed to lead to bacteria accumulation at the rear of a constriction (Altshuler et al 2013) or downstream of circular obstacles (Miño et al 2018;Secchi et al 2020;Lee et al 2021). Addition of pillars to microfluidic rectangular channels offers the possibility to design a bi-dimensional heterogeneous porous system suited to exploring the influence of flow heterogeneities and pore structures on the transport and retention of bacteria (Creppy et al 2019;Dehkharghani et al 2019;Scheidweiler et al 2020;Secchi et al 2020;de Anna et al 2020).…”
Section: Introductionmentioning
confidence: 98%
“…2020; Lee et al. 2021). Addition of pillars to microfluidic rectangular channels offers the possibility to design a bi-dimensional heterogeneous porous system suited to exploring the influence of flow heterogeneities and pore structures on the transport and retention of bacteria (Creppy et al.…”
Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization and enhanced oil recovery. While physicochemical bacteria filtration is well documented, recent studies showed that bacterial motility plays a key role in the transport process. Flow and transport experiments performed in microfluidic chips containing randomly placed obstacles confirmed that the distributions of non-motile bacteria stays compact, whereas for the motile strains, the distributions are characterized by both significant retention as well as fast downstream motion. For motile bacteria, the detailed microscopic study of individual bacteria trajectories reveals two salient features: (i) the emergence of an active retention process triggered by motility, (ii) enhancement of dispersion due to the exchange between fast flow channels and low flow regions in the vicinity of the solid grains. We propose a physical model based on a continuous time random walk approach. This approach accounts for bacteria dispersion via variable pore-scale flow velocities through a Markov model for equidistant particle speeds. Motility of bacteria is modelled by a two-rate trapping process that accounts for the motion towards and active trapping at the obstacles. This approach captures the forward tails observed for the distribution of bacteria displacements, and quantifies an enhanced hydrodynamic dispersion effect that originates in the combined effect of pore-scale flow variability and bacterial motility. The model reproduces the experimental observations, and predicts bacteria dispersion and transport at the macroscale.
“…Many bacterial habitats also have fluid flow 278 , which can further alter oxygen, nutrient, and cellular profiles in interesting ways. Near surfaces, the torque from fluid shear causes the cells to rotate and swim along periodic helical-like trajectories near the surface [279][280][281][282] or even swim upstream near the surface [283][284][285][286][287][288] , possibly promoting 271,289 or alternatively suppressing 290 attachment at specific locations. In 2D porous media, these effects can lead to retention of cells at the solid surfaces 291 , but enhanced spreading of cells through the spaces between 291,292 (Fig.…”
The ability of many living systems to actively self-propel underlies critical biomedical, environmental, and industrial processes. While such active transport is well-studied in uniform settings, environmental complexities such as geometric constraints, mechanical cues, and external stimuli such as chemical gradients and fluid flow can strongly influence transport. In this chapter, we describe recent progress in the study of active transport in such complex environments, focusing on two prominent biological systems-bacteria and eukaryotic cells-as archetypes of active matter. We review research findings highlighting how environmental factors can fundamentally alter cellular motility, hindering or promoting active transport in unexpected ways, and giving rise to fascinating behaviors such as directed migration and large-scale clustering. In parallel, we describe specific open questions and promising avenues for future research. Furthermore, given the diverse forms of active matterranging from enzymes and driven biopolymer assemblies, to microorganisms and synthetic microswimmers, to larger animals and even robots-we also describe connections to other active systems as well as more general theoretical/computational models of transport processes in complex environments. * Preprint of a chapter in the book Out-of-Equilibrium Soft Matter: Active Fluids, to be published by the Royal Society of Chemistry.
Microbes thrive in diverse porous environments—from soil and riverbeds to human lungs and cancer tissues—spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decades. With a focus on bacteria, here we review recent advances in self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback that mediates microbial survival and fitness. We discuss open questions and opportunities for using integrative approaches to advance our understanding of the biophysical strategies which microbes employ at various scales to make porous settings habitable.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
