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 

4. Yoon, S., Liu, Y., Shen, L., Yang, J.Q, & Kang, P.K. (2026), Adhesive Particle Transport in Idealized Vegetated Hyporheic Zones: Pore-scale Simulation and Stochastic Upscaling, Advances in Water Resources, 105338. https://doi.org/10.1016/j.advwatres.2026.105338

In Review

5. Cúñez, E. A., & Yang, J. Q. (2026), Evidence for Biofilm-induced Self-sustaining Meandering Channels (major revision).

6. 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 (major revision).

7. Jans, M. D., Soulaine, C., & Yang, J. Q., and Bourg, I. C. (2026), A Micro-Continuum Physics-Based Model for Cohesive Sediment Gravity Flows Across Mudslide, Mudflow, and Turbidity Current Regimes (major revision).

8. Zadehali, E., Bourg, I. C., & Yang, J. Q. (2026), Extracellular Polymeric Substances Increase the Erosion Threshold and Yield Stress of Bentonite Clay at Seawater Salinity (major revision).

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

10. Huang, S. H., Zadehali, E., & Yang, J. Q. (2026), Impact of Channel-Spanning Log on the Transport of Microplastics in the Hyporheic Zone (in review).

11. Pirdavari, P., & Yang, J. Q. (2026), Kaolinite Addition Significantly Increases E. coli Retention in Sand Filters (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. B.L. Nairn, B.P. Lima, R. Chen, J.Q. Yang, G. Wei, A.K. Chumber, & M.C. Herzberg "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