Three‐Dimensional Tracking of Colloids at the Pore Scale Using Epifluorescence Microscopy

Abstract

The transport of micrometer-and submicrometer-sized par cles of bio c and abio c origin through both natural and engineered porous media is relevant to a wide variety of disciplines. While the infl uence on colloid transport of chemical factors such as colloid and media surface chemistry and the ionic strength of the carrying fl uid are fairly well understood, the role of physical factors s ll needs clarifi ca on from a mechanis c standpoint. Along with recent recogni on that pore-scale processes may depend on the coupling of chemistry and local hydrodynamics, which in turn depends on pore topography, there is a growing need for experimental systems that enable visualiza on of individual colloids in pores and pore networks that contain relevant three-dimensional features. We introduce a single camera-epifl uorescence microscope system to track fl uorescent colloids in three dimensions using the apparent diameter of out-of-focus colloids to es mate their z-axis loca on. The current system, using a Plan Achromat 5× objec ve, enables z es ma on of 4.7-μm-diameter fl uorescent microspheres across a range of 1200 μm with accuracy of approximately 34 μm. In addi on to discussion of system limita ons and poten al improvements, we present results from two mini-studies illustra ng the use of three-dimensional par cle tracking to inves gate (i) the behavior of colloids approaching orthogonally oriented grain-to-grain contacts, and (ii) the potenal reten on mechanisms in porous media under chemical condi ons unfavorable to deposi on. The ability to track individual colloids in three dimensions brings experimental capabili es closer in line with computer-modeling capabili es, se ng the stage for synergis c pairing of experimental and theore cal inves ga ons.

Micro-scale determinants of bacterial diversity in soil

“…An exciting development in this respect is the use of porous media consisting of transparent particles that allow for nondestructive, three-dimensional microscopic observation and tracking of the spatial dynamics of biofilms and potentially even individual bacterial cells in real time (Leis et al, 2005;Ochiai et al, 2010). An exciting development in this respect is the use of porous media consisting of transparent particles that allow for nondestructive, three-dimensional microscopic observation and tracking of the spatial dynamics of biofilms and potentially even individual bacterial cells in real time (Leis et al, 2005;Ochiai et al, 2010).…”

“…As mentioned above, the opaque nature of soil (real or artificial) limits microscopic in situ observation to surfaces or requires the use of laborious methods to preserve soil structure. An exciting development in this respect is the use of porous media consisting of transparent particles that allow for nondestructive, three-dimensional microscopic observation and tracking of the spatial dynamics of biofilms and potentially even individual bacterial cells in real time (Leis et al, 2005;Ochiai et al, 2010). To allow optical transmission, it is necessary that the refractive index value of the solid particles is close to the value of the surrounding liquid.…”

“…To allow optical transmission, it is necessary that the refractive index value of the solid particles is close to the value of the surrounding liquid. One material fulfilling this criterion is the hydrophilic, amorphous fluoropolymer Nafion (Leis et al, 2005;Ochiai et al, 2010). Using confocal microscopy, biofilms growing in flow cells packed with granules could be observed even throughout multiple layers of the material (Fig.…”

On bias of kinetic temperature measurements in complex plasmas

“…The results demonstrated in this paper are applicable not only to complex plasmas but also to colloids [26][27][28][29] and granular materials. [30][31][32][33][34] In Sec.…”

Quantitative Pore‐Scale Investigations of Multiphase Bio/Geo/Chemical Processes

“…This special section of Vadose Zone Journal contains five articles covering pore‐scale research relevant for flow and transport in the vadose zone. The experimental study by Ochiai et al (2010) deals with the tracking of individual fluorescent micrometer‐sized colloids around glass beads using epifluorescence microscopy. This method allows the tracking of colloid trajectories in three dimensions and in time.…”