Yang Research Group

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Data supporting Biofilm Formation Promotes Microplastic Mobility via Hydrodynamic Forces
(2025-10-27) Wei, Guanju; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; Yang Research Group
This dataset supports the manuscript “Biofilm Formation Promotes Microplastic Mobility via Hydrodynamic Forces.” It includes measurements of biofilm area and the percentage of transported beads under five different flow rates, as well as an example set of microscopy images and a MATLAB dataset used for image processing. In the manuscript, we demonstrate that the presence of biofilms alters the hydrodynamic forces acting on microplastic particles. Specifically, biofilms modify the local pressure field and generate lift forces strong enough to mobilize particles even under weak shear conditions.
Data supporting the paper Influence of Biofilms and Extracellular Polymeric Substances on High-Frequency Acoustic Backscatter
(2025-09-25) Assis, Willian; Yang, Judy Q; wassis@umn.edu; Assis, Willian; University of Minnesota, Saint Anthony Falls Laboratory; Yang Research Lab
This dataset contains the data collected and presented in the manuscript "Influence of Biofilms and Extracellular Polymeric Substances on High-Frequency Acoustic Backscatter". It includes acoustic signals (voltage and time) for each tested case (and replicates), hydrophone tests, and acoustic calibration using two transducers. Additionally, it contains the MATLAB codes used to process the data.
High Salinity Increases the Fluidity and Decreases the Yield Stress and Erosion Threshold of Sand-Clay Mixtures – New Data in 2025
(2025-06-30) Zadehali, Ehsan; Yang, Judy Q; zadeh006@umn.edu; Zadehali, Ehsan; University of Minnesota - SAFL - Yang Research Group
This dataset presents raw videos and frames captured from flume erosion test and rheological measurements on bentonite clay - silica sand mixture at seven different salinity concentrations (0ppt, 3ppt, 5ppt, 10ppt, 15ppt, 20ppt, 35ppt). There are three replicates per each experiment that make it: - 21 flume tests (about 30 minutes after sample preparation) (3 rep for each salinity concentration) - 21 flow sweep tests (6hrs after preparation) (3 rep for each salinity concentration) - 21 amplitude oscillation tests (6hrs after preparation) (3 rep for each salinity concentration) - 21 flow sweep tests (30hrs after preparation) (3 rep for each salinity concentration) - 21 amplitude oscillation tests (30hrs after preparation) (3 rep for each salinity concentration) Video data for each flume experiment include side-view and top-view for all runs and there is angled-view for some tests. Cameras were synchronized by briefly turning the flume room lights off and on at the start of each test. Erosion observed from top and angled views, while simultaneously, the water depth is measured using the corresponding frames from the side camera. Having water depth in erosion time, critical shear stress calculated by slope method. Rheological data consist of flow sweep tests and oscillatory amplitude tests at 6hrs post-preparation, give us insights about viscosity, shear thinning behavior of the mixture, yield stress and flow-point stress and effect of ageing. Together, these data quantify how increasing salt concentration collapses the electrostatic double layer, lowers yield and flow-point stresses, and reduces—but does not eliminate—the shear stress required to erode sand-clay beds.
Data for the flume experiments and numerical simulations of the surface and subsurface flows in an emergent vegetation canopy at St. Anthony Falls Laboratory in 2024.
(2025-01-21) Huang, Shih-Hsun; Nuli, Rohit; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; University of Minnesota Environmental Transport Lab
We combined laboratory experiments and coupled numerical simulations to study the hyporheic exchange process within an emergent vegetation canopy in a channel with a permeable bed.
Data supporting the manuscript Role of microbial mats in bed evolution and the formation of sedimentary structures
(2024-12-05) Assis, Willian; Yang, Judy Q; wassis@umn.edu; Assis, Willian; University of Minnesota, Saint Anthony Falls Laboratory
This dataset contains the data collected and presented in the manuscript "Role of microbial mats in bed evolution and the formation of sedimentary structures". It includes the bed topographies along the centerline of the channel for each tested case. Additionally, it contains the matlab codes used to process the data.
High Salinity Increases the Fluidity and Erodibility of Sand-Clay Mixtures
(2024-09-12) Benaich, Soukaina; Huang, Shih-Hsun; Bourg, Ian; Yang, Judy Q; benai015@umn.edu; Soukaina , Benaich; St.Anthony Falls Laboratory, University of Minnesota Twin Cities
Mud, consisting of clay and sand, is commonly found in freshwater and saltwater ecosystems including wetlands, coastal regions, and estuaries. However, our understanding of how mud behaves under various salinity levels is still limited. In this research, we investigated the impact of salinity on the rheological properties and erosion resistance of sand-clay mixtures through flume experiments. To simulate natural mud under various salinity conditions, we mixed sand and clay in ratios representative of natural mud and added pore water with salinities ranging from 0 to 35 ppt. We used a rheometer to measure the viscosity and yield stress of the mixtures and determined the critical bed shear stress needed to erode them in a water-recirculating flume. Our results indicate that as salinity increases, the critical bed shear stress and yield stress decrease by one order magnitude and two order magnitude, respectively. This dependency on salinity reflects a transition of the sand-clay mixture from a cohesive gel-like state at lower salinity levels (<10 ppt) to a liquid state as salinity increases to a higher level (≥ 10 ppt). Our research underscores the important role of salt in controlling the erosion threshold of mud. The results will help design erosion prevention structures and forecast sediment movement in coastal areas.
Data supporting Motility directs Pseudomonas aeruginosa towards surfaces and enhances biofilm formation
(2024-08-08) Wei, Guanju; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; University of Minnesota, Saint Anthony Falls Laboratory
This dataset contains all the angles and trajectories for both motile and non-motile Pseudomonas aeruginosa cells. In the manuscript, we demonstrated that the cell motility can enhance biofilm formation and utilized the orientation angle and trajectory data to support this conclusion.
Experimental data of the log-induced hyporheic flow experiment in the 6-inch flume of St. Anthony Falls Laboratory in 2023
(2024-06-17) Huang, Shih-Hsun; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; University of Minnesota Environmental Transport Lab
We conducted flume experiments to study how two in-line channel-spanning logs affect surface flow and hyporheic flow in a channel. The dataset comprises data and results obtained from measurements of water surface elevation profiles, particle image velocimetry (PIV) measurements, and visualizations of fluorescent dye transport in the sediment bed around the channel-spanning log. The Matlab scripts used to process the data are also included.
Experimental data of biofilm development experiments under fluctuating flow conditions taken and processed at SAFL in 2022
(2023-05-04) Wei, Guanju; Yang, Judy Q; judyyang@umn.edu; Yang, Judy; University of Minnesota, Saint Anthony Falls Laboratory, Environmental Transport Lab
This dataset consists of the Matlab codes, experimental data, and raw images of the biofilm development experiments under fluctuating flow conditions. They are all collected in the Saint Anthony Falls Laboratory at the University of Minnesota. The codes are used for processing the raw images to calculate the biofilm thickness and biofilm area coverage. The experimental data file contains the data after processing. The image file contains the raw images collected during the experiments using the Nikon confocal microscope.
Experimental data of log jam-induced hyporheic flow experiment in Ecoflume of St. Anthony Falls Laboratory in 2022
(2023-04-26) Huang, Shih-Hsun; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; University of Minnesota Environmental Transport Lab
We conducted flume experiments to study how a channel-spanning log jam affects hyporheic flow. The dataset comprises data and results obtained from measurements of water surface elevation profiles, particle image velocimetry (PIV) measurements, and visualizations of fluorescent dye transport in the sediment bed beneath the log jam.
Flow and clay erosion data taken and processed at SAFL in a grid-turbulence tank Summer 2022
(2022-10-03) San Juan, Jorge E; Wei, William G; Yang, Judy Q; jsanjuan@umn.edu; San Juan, Jorge E; Environmental Transport Laboratory at St Anthony Falls Lab
Here we present a dataset containing raw imaging and processed data on clay erosion. This new dataset expands and complements the information located at https://doi.org/10.13020/vxrv-7e20. This dataset supports our study of the impact of salinity and consolidation on the microstructure and erosion threshold of cohesive sediments. The erosion measurements were taken inside a grid-turbulence tank at the St. Anthony Falls Laboratory at the University of Minnesota Twin Cities. We set the water salinity at a prescribed concentration in part-per-thousands and two clay consolidation conditions (unconsolidated and consolidated after 17 hours) for each experimental case. Here we incorporate laponite (smectite clay)'s surface erosion from laser-induced fluorescence and image processing.
Flow and clay erosion data taken and processed at SAFL in a grid-turbulence tank Fall 2021-Spring 2022
(2022-05-23) San Juan, Jorge E; Wei, William G; Yang, Judy Q; jsanjuan@umn.edu; San Juan, Jorge E; Environmental Transport Laboratory at St Anthony Falls Lab
Here we present a data set containing raw imaging and processed data of clay erosion and near-bed turbulence. This data set supports our study of the impact of salinity and consolidation on the microstructure and erosion threshold of cohesive sediments. The flow and erosion measurements were taken inside a grid-turbulence tank at the St. Anthony Falls Laboratory at the University of Minnesota Twin Cities. We set up the water salinity at a prescribed concentration in part-per-thousands and two clay consolidation conditions (unconsolidated and consolidated after 17 hours) for each experimental case. Here we incorporate detailed near-bed turbulence measurements to quantify the erosive effect of the turbulent water flow. We also include laponite (smectite clay)'s surface erosion from laser-induced fluorescence and image processing.
Experimental data of Pseudomonas putida biofilm development experiments in flat and rough microfluidic channels
(2022-05-09) Wei, Guanju; Yang, Judy Q; judyyang@umn.edu; Yang, Judy; University of Minnesota, Saint Anthony Falls Laboratory, Environmental Transport Lab
This dataset consists of the codes, experimental data, and raw images of the Pseudomonas putida biofilm development experiments. They are all collected in the Saint Anthony Falls Laboratory at the University of Minnesota. The codes are used for processing the raw images to calculate the biofilm thickness. The experimental data file contains the experiment parameters and the data after processing. The image file contains the raw images collected using the Nikon confocal microscope.
Data supporting Inhibition of the Growth of Harmful Algal Bloom-forming Freshwater Cyanobacteria by Clay
(2022-03-14) Yang, Judy Q; Tomaska, Katherine R; Wei, Guanju; tomas098@umn.edu; Tomaska, Katherine R; Yang Research Group
This dataset contains cell density measurements and confocal images of Microcystis Aeruginosa. The raw data from hand counting cells under a microscope with a hemocytometer is included, as well as the calculated cell density based on the hemocytometer measurements. The bacteria cells were grown in one of three growth conditions. Each growth condition was simulated in three different flasks. For each date, the cell densities of identical growth conditions were averaged. Cell densities for each date and growth condition were subsequently plotted with error bars to determine any trends. Additionally, data on the environmental conditions of cell growth are included on dates when the measurements were taken. The physical interactions between cyanobacteria and clay particles were visualized using a confocal laser scanning microscope (Nikon C2 plus). Each image is around 2048 by 2048 pixels at a resolution of 0.08 um/pixel. We used a 20X objective magnification. A sequence of images was taken at 10-second intervals for 5 minutes. The laser used for excitation has a wavelength of 488 nm (FITC) and the emission wavelength is 525 nm.
Experimental data of vegetation-induced hyporheic exchange experiment in Ecoflume of St. Anthony Falls Laboratory on 2021 (29GB)
(2021-11-19) Huang, Shih-Hsun; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; University of Minnesota Environmental Transport Lab
The dye injection experiments were conducted to investigate the impacts of the vegetation-generated turbulence on hyporheic exchange. The data set includes the results and raw data of solute washout experiments and the flow measurements.

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