Publications

2026

1. Assis, W. R. , Naeem, I., Shen, L., & Yang, J. Q. (2026). Influence of biofilms and extracellular polymeric substances on high-frequency acoustic backscatter. Journal of Geophysical Research: Biogeosciences, 131, e2025JG009446. https://doi.org/10.1029/2025JG009446 

2. Wei, G. & Yang, J. Q. (2026), Biofilm-Induced Microplastic Transport under Subcritical Shear Stress, Water Research, 125818. https://doi.org/10.1016/j.watres.2026.125818 

3. Agles, A. A., Albrecht, J. J., & Yang, J. Q. (2026), Efficient Removal of Cyanobacterial Harmful Algal Blooms through Chitosan-Clay Flocculation: Effects of Dosage and Application Procedure, Harmful Algae.103124. https://doi.org/10.1016/j.hal.2026.103124 

In Review

4. Yoon, S., Liu, Y., Shen, L., Yang, J.Q, & Kang, P.K. (2026), Adhesive Particle Transport in Vegetated Hyporheic Zones: Pore-scale Simulation and Stochastic Upscaling. (major revision)

5. Y. Li, M.Hondzo, & Yang, J.Q (2026), Adsorption of Microcystins onto Synthetic and Natural Clay Minerals (in review).

6. Cúñez, E. A., & Yang, J. Q. (2026), Evidence for Biofilm-induced Self-sustaining Meandering Channels (in review).

7. Jing, S. & Yang, J. Q. (2026), Effects of Microplastic Particles on Sandy Bedform Migration. (in review)

8. Assis, W. R. , Shen, L., and Yang, J. Q. (2026), Finite Biofilm Patch Drives Transitions from Current Ripples to Discrete Bedforms and Alters Sediment Transport and Topography (in review).

2025

1. Pirdavari, P., Zadehali, E., Wei, G., & Yang, J. Q. (2025). Evaporation-induced clay bridge formation in porous microchannels. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 139216. https://doi.org/10.1016/j.colsurfa.2025.139216 

2. Wei, W. , Palalay J., Sanfilippo J., & Yang, J. Q. (2025) Flagellar-Driven Motility Enhances Pseudomonas aeruginosa Biofilm Formation by Altering Cell Orientation, Applied and Environmental Microbiology, 0:e00821-25. https://doi.org/10.1128/aem.00821-25 

3. Zadehali, E., Benaich, S., Huang, S.H., Bourg, I., & Yang, J. Q. (2025).  Salinity Reduces Yield Stress and Erosion Threshold in Sand-Clay Mixtures: Evidence from Rheometry and Flume Experiments,Water Resources Research, 61,e2024WR039529. https://doi.org/10.1029/2024WR039529 

4. Assis, W. R., Shen, L., & Yang, J. Q. (2025). Role of Synthetic Biofilms in Bed Evolution and the Formation of Sedimentary Structures. Geophysical Research Letters, 52, e2024GL113826. https://doi.org/10.1029/2024GL113826 

5. Huang, S. H., Nuli, R., Kang, P. K., Shen, L., & Yang, J. Q. (2025). Experimental and Numerical Investigation on the Impact of Emergent Vegetation on the Hyporheic Exchange, Water Resources Research, 61: e2025WR040217. https://doi.org/10.1029/2025WR040217 

6. Li, Y, Hondzo, M., & Yang, J.Q. (2025), Clay-Based HAB Control: The Role of Turbulence in Aggregate Formation and Settling,  Environmental Fluid Mechanics, 10.1007/s10652-025-10057-x. https://doi.org/10.1007/s10652-025-10057-x  

7. Huang, S., Sawyer, A., Wohl, E., & Yang, J. Q. (2025). Flume experiments with refractive‐index matched sediment revealing the impact of two in‐line channel‐spanning logs on hyporheic exchange. Water Resources Research, 61, e2024WR038355. https://doi.org/10.1029/2024WR038355 

2024

1. San Juan, J. E., Wei, W. G., & Yang, J. Q. (2024). Impact of salinity on the erosion threshold, yield stress, and gelatinous state of a cohesive clay. Journal of Geophysical Research: Earth Surface, 129, e2023JF007485. https://doi.org/10.1029/2023JF007485 

2. Yang, J. Q. (2024). “Solute flow and particle transport in aquatic ecosystems: A review on the effect of emergent and rigid vegetation,” Environmental Science & Ecotechnology, 2666-4984, 2024. https://doi.org/10.1016/j.ese.2024.100429 

3. Y. Li, M.Hondzo, & J. Yang, "A synthetic clay removes Microcystis aeruginosa efficiently," Harmful Algae, 2024. https://doi.org/10.1016/j.hal.2024.102667

4. S. Benaich, & J. Yang, “Impact of Salt on Cohesive Sediment Transport,” In Sediment Transport Research - Further Recent Advances, edited by Prof. Andrew J. Manning, IntechOpen, 2024. http://dx.doi.org/10.5772/intechopen.1005893

5. Voigtländer, A., Houssais, M., Bacik, K. A., Bourg, I. C., Burton, J. C., Daniels, K. E., ... , and J.~Yang, ``Soft matter physics of the ground beneath our feet,'' Soft Matter, 2024. https://doi.org/10.1039/D4SM00391H  

6. Brittany; Lima, Bruno; Chen, Ruoqiong; Yang, Judy Q.; Wei, Guanju; Chumber, Ashwani K.; Herzberg, M; "Effects of fluid shear stress on oral biofilm formation and composition and the transcriptional response of Streptococcus gordonii," Molecular Oral Microbiology, 1–14. 2024. https://doi.org/10.1111/omi.12481 

7. Huang, S.H. & Yang, J.Q., 2024. Direct visualization of hyporheic exchange in an emergent vegetation canopy. In River Flow 2022 (pp. 716-723). CRC Press. (link)

2023

1. Wei, G., & Yang, J. Q. (2023). Microfluidic investigation of the impacts of flow fluctuations on the development of Pseudomonas putida biofilms. npj Biofilms and Microbiomes,  9 , 73. https://doi.org/10.1038/s41522-023-00442-z 

2. Wei, G., & Yang, J. Q. (2023). Impacts of hydrodynamic conditions and microscale surface roughness on the critical shear stress to develop and thickness of early-stage Pseudomonas putida biofilms. Biotechnology and Bioengineering, 1– 12. https://doi.org/10.1002/bit.28409 

3. Huang, S., & Yang, J. Q. (2023). Impacts of channel-spanning log jams on hyporheic flow. Water Resources Research, 59, e2023WR035217. https://doi.org/10.1029/2023WR035217 

2022

1. Huang, S., & Yang, J. Q. (2022). Impacts of emergent vegetation on hyporheic exchange. Geophysical Research Letters, 49, e2022GL099095. https://doi.org/10.1029/2022GL099095 

2. Li, Y., Sanfilippo, J. E., Kearns, D., & Yang, J. Q. (2022). Corner flows induced by surfactant-producing bacteria Bacillus subtilis and Pseudomonas fluorescens. Microbiology Spectrum, 10(5), e03233-22. https://doi.org/10.1128/spectrum.03233-22 

2021

1. Yang, J. Q., J. Sanfilippo, N. Abbasi, Z. Gitai, B. Bassler, & H. Stone (2021), Evidence for biosurfactant induced flow in corners and bacterial spreading in unsaturated porous media. Proceedings of the National Academy of Sciences, 118, e2111060118. https://doi.org/10.1073/pnas.2111060118 

2. Yang, J. Q., X. Zhang, I. C. Bourg, & H. A. Stone (2021), 4D imaging reveals mechanisms of clay carbon protection and release. Nature Communications, 12, 622. https://doi.org/10.1038/s41467-020-20798-6 

Before 2020

1. Yang, J. Q., & H. M. Nepf (2019), Impacts of vegetation on bed load transport rate and bedform characteristics. Water Resources Research, 55. https://doi.org/10.1029/2018WR024404 

2. Yang, J.Q., & H.M Nepf (2018), A turbulence-based bed-load transport model for bare and vegetated channels. Geophysical Research Letters, 45. https://doi.org/10.1029/2018GL079319 

3. Yang, J. Q., C. Hayoon, & H. M. Nepf (2016), The onset of sediment transport in vegetated channels predicted by turbulent kinetic energy. Geophysical Research Letters , 43 , 11,261–11,268. https://doi.org/10.1002/2016GL071092 

4. Yang, J.Q., F. Kerger, & H.M. Nepf (2015), Estimation of the bed shear stress in vegetated and bare channels. Water Resources Research, 51, 3647-3663. https://doi.org/10.1002/2014WR016042 

5. Kinsey, J.C., Q. Yang, & J.C. Howland (2014). Nonlinear Dynamic Model-Based State Estimators for Underwater Navigation of Remotely Operated Vehicles. IEEE Transactions on Control Systems Technology, 22(5), 1845-1854. https://doi.org/10.1109/TCST.2013.2293958