Publications

2025

• 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.

• 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

• Wei, W. , Palalay J., Sanfilippo J., and Yang, J. Q. (2025) Flagellar-Driven Motility Enhances Pseudomonas aeruginosa Biofilm Formation by Altering Cell Orientation, Applied and Environmental Microbiology, 0:e00821-25. 

In Review

• 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. (under review).

• Li, Y, Hondzo, M., & Yang, J.Q. (2025), Clay-Based HAB Control: The Role of Turbulence in Aggregate Formation and Settling. (under review)

• 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 2 from Rheometry and Flume Experiments. (under review).

2024

• 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. 

• 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. 

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

• S. Benaich, and 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)

• 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. 

• 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.

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

2023

• 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.

• 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.

• Huang, S., & Yang, J. Q. (2023). Impacts of channel-spanning log jams on hyporheic flow. Water Resources Research, 59, e2023WR035217.

2022

• Huang, S., & Yang, J. Q. (2022). Impacts of emergent vegetation on hyporheic exchange. Geophysical Research Letters, 49, e2022GL099095.

• 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.

2021

• Yang, J. Q., J. Sanfilippo, N. Abbasi, Z. Gitai, B. Bassler, and 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.

• Yang, J. Q., X. Zhang, I. C. Bourg, and H. A. Stone (2021), 4D imaging reveals mechanisms of clay carbon protection and release. Nature Communications, 12, 622.

2016-2020

• Yang, J. Q., and H. M. Nepf (2019), Impacts of vegetation on bed load transport rate and bedform characteristics. Water Resources Research, 55.

• Yang, J.Q., and H.M Nepf (2018), A turbulence-based bed-load transport model for bare and vegetated channels. Geophysical Research Letters, 45.

• Yang, J. Q., C. Hayoon, and 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.

• Yang, J.Q., F. Kerger, and H.M. Nepf (2015), Estimation of the bed shear stress in vegetated and bare channels. Water Resources Research, 51, 3647-3663.

• Kinsey, J.C., Q. Yang, and 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.