SBI Research Feature: A 3D visualization tool for particle transport

Posted: November, 2010

Article Links

Ochiai, N, Dragila, M.I., Parke, J.L. (2010) 3D tracking of colloids at the pore-scale using epifluorescence microscopy.Vadose Zone Journal 9:3, p.576-587. August 2010.

Naoyuki's dissertation is also available online through OSU's online library, Scholar's Archive.

In the August 2010 issue of the Vadose Zone Journal, Naoyuki Ochiai, a recent Ph.D. graduate in Crop and Soil Science, reported on a method to visualize the movement of contaminants or plant pathogens through soils and other porous media.  The method uses micromodels and epi-fluorescence microscopy to trace the three-dimensional pathway of individual particles as they travel through the pore space between two 1 mm-sized grains. Naoyuki’s coauthors were his PhD advisors, professors Maria Dragila (Crop and Soil Science) and Jennifer Parke (Plant Pathology).  In this short Web interview Naoyuki gives an overview of the paper.

What questions and applications drive your work?

Our focus is on understanding how particles move through soil and other porous media.  That’s important for understanding things like how soil contaminants or some plant pathogens spread.  For example, Phytophthora is a genus of plant pathogens that spread as motile zoospores.  The spores are small infectious particles that can reach new plants by traveling with water as they move through soil.

In order to understand how the particles move, it’s important to understand the physics involved.  This paper describes micromodels where we use glass beads to mimic soil grains and then study the physics of how particles move between those grains.  We use a pair of beads that are embedded in glass plates so we are isolating and focusing on the physics of what happens near the contact between two grains. Also, instead of using live zoospores, we use latex microspheres as proxies -- they are approximately the same size as the zoospores. This is to be able to focus on the hydrodynamics without the added complication of zoospore swimming, which we introduce later.   It is a highly simplified model, but it’s a necessary step to understand first principles.

Photo of Naoyuki Ochiai working on experiments.
Naoyuki Ochiai, recent graduate student in the OSU Department of Crop and Soil Science

Your paper describes a way to visualize and map the three dimensional flow paths of individual particles – how does the technique work?

We use an epifluorescence microscope system.  It has a high intensity UV light source that is set to a wavelength that makes our study particles fluoresce.  They emit back light at a particular wavelength that we isolate with a filter.  The result is an image of the particles moving through the model as we circulate water through it.  When we first did experiments we were annoyed to find that many of the particles were out of focus, but then we realized that the focus gave us a way to measure the particle’s position in the third dimension.  As the particle goes out of focus its image gets larger and the size of it correlates with the particle location on the z-axis of the model.  So we can track the position of the particles in three dimensions as they move around and between the glass beads.

Diagram of experimental setup.
Diagram showing the epifluorescence microscope setup.

Your journal article also includes some examples of how the model can be used to study specific physical questions, what are these examples about?

One example focuses on understanding the low flow zone between two particles.  At a solid boundary, like against the side of the glass bead, there is a no-slip boundary where the fluid is not moving.  If there are two surfaces coming together, for example, where the two beads meet, there are two no-slip boundaries and creates a zone with lower velocity flows.  Researchers have theorized that particles can get trapped in this low flow zone.  That’s important when thinking about things like contaminants – if they are stuck in this low flow zone they could be hard to remove.  Our model lets us visualize what is actually happening in that low flow zone – do particles really get trapped there?  What we found is that in our experiments the particles didn’t enter this zone – instead most followed the streamlines of flow and there was a low probability of them entering these zones and getting trapped.

The second example from the paper focuses on particle attachment theory and whether particles can become “stuck” to the grain or glass bead itself. This is related to contaminant and pathogen retention within a porous medium.

Image of particle tracking.
Image showing particle paths as they move between two glass beads. The colors correspond to particle velocities.


Some spores and microbes are able to move themselves and could potentially move against the flow current.  Are you also studying the added complexity that this mobility introduces?

Yes. Because the zoospores we are using aren’t fluorescent, we’re not able to use the out-of-focus method to track them in 3 dimensions. However, we are able to track them in 2d micromodels. Our interest is in understanding how the zoospores ‘swim’ in the presence of moving water. Do they swim with the current? Across the current? Upstream? If so, how does that affect the speed at which they’re transported. In relation to the work I talked about earlier, the zoospores’ swimming ability becomes increasingly relevant in low-flow zones, and, importantly, allows them to explore those slow zones which would be avoided by non-motile particles or organisms.