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# Conda environment in Jupyter

## Customize Ipython Kernel on NERSC

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This post is about customizing your kernel on Jupyterhub. Here I will use my_env as my new environment name. Also see the documentation here Read more

## Portfolio item number 1

Short description of portfolio item number 1

## Portfolio item number 2

Short description of portfolio item number 2

## Groundwater flow, nutrient, and stable isotope dynamics in the parafluvial-hyporheic zone of the regulated Lower Colorado River (Texas, USA) over the course of a small flood

Published in Hydrogeology Journal, 2016

Abstract: Periodic releases from an upstream dam cause rapid stage fluctuations in the Lower Colorado River near Austin, Texas, USA. These daily pulses modulate fluid exchange and residence times in the hyporheic zone where biogeochemical reactions are typically pronounced. The effects of a small flood pulse under low-flow conditions on surface-water/groundwater exchange and biogeochemical processes were studied by monitoring and sampling from two dense transects of wells perpendicular to the river. The first transect recorded water levels and the second transect was used for water sample collection at three depths. Samples were collected from 12 wells every 2 h over a 24-h period which had a 16-cm flood pulse. Analyses included nutrients, carbon, major ions, and stable isotopes of water. The relatively small flood pulse did not cause significant mixing in the parafluvial zone. Under these conditions, the river and groundwater were decoupled, showed potentially minimal mixing at the interface, and did not exhibit any discernible denitrification of river-borne nitrate. The chemical patterns observed in the parafluvial zone can be explained by evaporation of groundwater with little mixing with river water. Thus, large pulses may be necessary in order for substantial hyporheic mixing and exchange to occur. The large regulated river under a low-flow and small flood pulse regime functioned mainly as a gaining river with little hydrologic connectivity beyond a narrow hyporheic zone. Read more

Recommended citation: ﻿Briody, A. C., Cardenas, M. B., Shuai, P., Knappett, P. S. K., & Bennett, P. C. (2016). Groundwater flow, nutrient, and stable isotope dynamics in the parafluvial-hyporheic zone of the regulated Lower Colorado River (Texas, USA) over the course of a small flood. Hydrogeology Journal, 24(4), 923–935. https://doi.org/10.1007/s10040-016-1365-3 ﻿http://link.springer.com/10.1007/s10040-016-1365-3

## Vulnerability of low-arsenic aquifers to municipal pumping in Bangladesh

Published in Journal of Hydrology, 2016

Abstract: Sandy aquifers deposited > 12,000 years ago, some as shallow as 30 m, have provided a reliable supply of low-arsenic (As) drinking water in rural Bangladesh. This study concerns the potential risk of contaminating these aquifers in areas surrounding the city of Dhaka where hydraulic heads in aquifers > 150 m deep have dropped by 70 m in a few decades due to municipal pumping. Water levels measured continuously from 2012 to 2014 in 12 deep ( > 150 m), 3 intermediate (90-150 m) and 6 shallow ( < 90 m) community wells, 1 shallow private well, and 1 river piezometer show that the resulting drawdown cone extends 15-35 km east of Dhaka. Water levels in 4 low-As community wells within the 62-147 m depth range closest to Dhaka were inaccessible by suction for up to a third of the year. Lateral hydraulic gradients in the deep aquifer system ranged from 1.7 × 10 -4 to 3.7 × 10 -4 indicating flow towards Dhaka throughout 2012-2014. Vertical recharge on the edge of the drawdown cone was estimated at 0.21 ± 0.06 m/yr. The data suggest that continued municipal pumping in Dhaka could eventually contaminate some relatively shallow community wells. Read more

Recommended citation: ﻿Knappett, P. S. K., Mailloux, B. J., Choudhury, I., Khan, M. R., Michael, H. A., Barua, S., et al. (2016). Vulnerability of low-arsenic aquifers to municipal pumping in Bangladesh. Journal of Hydrology, 539, 674–686. https://doi.org/10.1016/j.jhydrol.2016.05.035 ﻿https://linkinghub.elsevier.com/retrieve/pii/S002216941630302X

## ﻿Tracking the fate of arsenic in groundwater discharged to the Meghna River

Published in Arsenic Research and Global Sustainability - Proceedings of the 6th International Congress on Arsenic in the Environment, AS 2016, 2016

Abstract: ﻿The fate of arsenic fluxes to rivers from shallow aquifers is influenced by hydraulic head differences, and the geochemistry and geometry of aquifers and aquitards adjacent to the river. In our study area the eastern side of the Meghna River is generally strongly gaining year-round with some exceptions. The distribution of solid-phase Fe, Mn and As in riverbank sediments was correlated to variations in hydraulic gradients and hydraulic conductivity. The 30 m deep shallow aquifer was mapped 500 m parallel and orthogonal to the river bank at 3 locations, on both sides of the river, using Electrical Resistivity Tomography (ERT). The aquifer dimensions and properties are remarkably consistent between sites. The continuity of the 3–4 m capping clay layer will prevent shallow groundwater from discharging along the shallow river banks. Substantial seasonal fluctuations in dissolved As and Fe concentrations within the aquifer are related to irrigation pumping and natural river level fluctuations. Read more

Recommended citation: ﻿Knappett, P. S. K., Myers, K., Shuai, P., Rhodes, K., Jewell, K., Peterson, J., et al. (2016). Tracking the fate of arsenic in groundwater discharged to the Meghna River. In Arsenic Research and Global Sustainability - Proceedings of the 6th International Congress on Arsenic in the Environment, AS 2016. https://doi.org/10.1071/EN17104 https://www.crcpress.com/Arsenic-Research-and-Global-Sustainability-Proceedings-of-the-Sixth-International/Bhattacharya-Vahter-Jarsjo-Kumpiene-Ahmad-Sparrenbom-Jacks-Donselaar-Bundschuh-Naidu/p/book/9781138029415

## The Impact of the Degree of Aquifer Confinement and Anisotropy on Tidal Pulse Propagation

Published in ﻿Groundwater, 2017

Abstract: Oceanic tidal fluctuations which propagate long distances up coastal rivers can be exploited to constrain hydraulic properties of riverbank aquifers. These estimates, however, may be sensitive to degree of aquifer confinement and aquifer anisotropy. We analyzed the hydraulic properties of a tidally influenced aquifer along the Meghna River in Bangladesh using: (1) slug tests combined with drilling logs and surface resistivity to estimate Transmissivity (T); (2) a pumping test to estimate T and Storativity (S) and thus Aquifer Diffusivity (DPT); and (3) the observed reduction in the amplitude and velocity of a tidal pulse to calculate D using the Jacob‐Ferris analytical solution. Average Hydraulic Conductivity (K) and T estimated with slug tests and borehole lithology were 27.3 m/d and 564 m2/d, respectively. Values of T and S determined from the pumping test ranged from 400 to 500 m2/d and 1 to 5 × 10−4, respectively with DPT ranging from 9 to 40 × 105 m2/d. In contrast, D estimated from the Jacob‐Ferris model ranged from 0.5 to 9 × 104 m2/d. We hypothesized this error resulted from deviations of the real aquifer conditions from those assumed by the Jacob‐Ferris model. Using a 2D numerical model tidal pulses were simulated across a range of conditions and D was calculated with the Jacob‐Ferris model. Moderately confined (Ktop/Kaquifer < 0.01) or anisotropic aquifers (Kx/Kz > 10) yield D within a factor of 2 of the actual value. The order of magnitude difference in D between pumping test and Jacob‐Ferris model at our site argues for little confinement or anisotropy. Read more

Recommended citation: ﻿Shuai, P., Knappett, P. S. K., Hossain, S., Hosain, A., Rhodes, K., Ahmed, K. M., & Cardenas, M. B. (2017). The Impact of the Degree of Aquifer Confinement and Anisotropy on Tidal Pulse Propagation. Groundwater, 55(4), 519–531. https://doi.org/10.1111/gwat.12509 ﻿http://doi.wiley.com/10.1111/gwat.12509

## Denitrification in the banks of fluctuating rivers: The effects of river stage amplitude, sediment hydraulic conductivity and dispersivity, and ambient groundwater flow

Published in ﻿Water Resources Research, 2017

Abstract: Hyporheic exchange induced by periodic river fluctuations leads to important biogeochemical processes, particularly nitrogen cycling, in riparian zones (RZs) where chemically distinct surface water and groundwater mix. We developed a two‐dimensional coupled flow, reactive transport model to study the role of bank storage induced by river fluctuations on removing river‐borne nitrate. Sensitivity analyses were conducted to quantify the effects of river amplitude, sediment hydraulic conductivity and dispersivity, and ambient groundwater flow on nitrate removal rate. The simulations showed that nitrification occurred in the shallower zone adjacent to the bank where oxic river water and groundwater interacted while denitrification occurred deeper into the aquifer and in the riverbed sediments where oxygen was depleted. River fluctuations greatly increased the amount of nitrate being removed; the nitrate removal rate increased as river amplitude increased. Similarly, increasing hydraulic conductivity increased overall nitrate removal since it expanded the denitrifying zone but decreased efficiency. In contrast, increasing sediment dispersivity increased the removal efficiency of nitrate because it promoted mixing between electron acceptors and donors. The presence and direction of ambient groundwater flow had a significant impact on nitrate removal rate when compared to neutral conditions. A losing river showed a larger nitrate removal rate, whereas a gaining river showed a smaller nitrate removal rate. Our results demonstrated that daily river fluctuations created denitrification hot spots within the RZ that would not otherwise exist under naturally neutral or gaining conditions. Read more

Recommended citation: ﻿Shuai, P., Cardenas, M. B., Knappett, P. S. K., Bennett, P. C., & Neilson, B. T. (2017). Denitrification in the banks of fluctuating rivers: The effects of river stage amplitude, sediment hydraulic conductivity and dispersivity, and ambient groundwater flow. Water Resources Research, 53(9), 7951–7967. https://doi.org/10.1002/2017WR020610 https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2017WR020610

## The fate of arsenic in groundwater discharged to the Meghna River, Bangladesh

Published in Environmental Chemistry, 2018

Abstract: ﻿Environmental context Arsenic contamination of groundwater is a major environmental problem in many areas of the world. In south-east Asia, iron-rich reducing groundwater mixes with oxidising river water in hyporheic zones, precipitating iron oxides. These oxides can act as a natural reactive barrier capable of accumulating elevated solid-phase concentrations of arsenic. Abstract Shallow, anoxic aquifers within the Ganges-Brahmaputra-Meghna Delta (GBMD) commonly contain elevated concentrations of arsenic (As), iron (Fe) and manganese (Mn). Highly enriched solid-phase concentrations of these elements have been observed within sediments lining the banks of the Meghna River. This zone has been described as a Natural Reactive Barrier (NRB). The impact of hydrological processes on NRB formation, such as transient river levels, which drive mixing between rivers and aquifers, is poorly understood. We evaluated the impact of groundwater flow dynamics on hydrobiogeochemical processes that led to the formation of an Fe- and Mn-rich NRB containing enriched As, within a riverbank aquifer along the Meghna River. The NRB dimensions were mapped using four complementary elemental analysis methods on sediment cores: X-ray fluorescence (XRF), aqua regia bulk extraction, and HCl and sodium phosphate leaching. It extended from 1.2 to 2.4 m in depth up to 15 m from the river's edge. The accumulated As was advected to the NRB from offsite and released locally in response to mixing with aged river water. Nearly all of the As was subsequently deposited within the NRB before discharging to the Meghna. Significant Fe II release to the aqueous phase was observed within the NRB. This indicates the NRB is a dynamic zone defined by the interplay between oxidative and reductive processes, causing the NRB to grow and recede in response to rapid and seasonal hydrologic processes. This implies that natural and artificially induced changes in river stages and groundwater-tables will impact where As accumulates and is released to aquifers. Read more

Recommended citation: ﻿Berube, M., Jewell, K., Myers, K. D., Knappett, P. S. K., Shuai, P., Hossain, A., et al. (2018). The fate of arsenic in groundwater discharged to the Meghna River, Bangladesh. Environmental Chemistry, 15(2), 29. https://doi.org/10.1071/EN17104 http://www.publish.csiro.au/en/EN17104

## Dam Operations and Subsurface Hydrogeology Control Dynamics of Hydrologic Exchange Flows in a Regulated River Reach

Published in ﻿Water Resources Research, 2019

Abstract: Hydrologic exchange flows (HEFs) across the river‐aquifer interface have important implications for biogeochemical processes and contaminant plume migration in the river corridor, yet little is known about the hydrogeomorphic factors that control HEFs dynamics under dynamic flow conditions. Here, we developed a 3‐D numerical model for a large regulated river corridor along the Columbia River to study how HEFs are controlled by the interplays between dam‐regulated flow conditions and hydrogeomorphic features of such river corridor system. Our results revealed highly variable intra‐annual spatiotemporal patterns in HEFs along the 75‐km river reach, as well as strong interannual variability with larger exchange volumes in wet years than dry years. In general, the river was losing during late spring to early summer when the river stage was high, and river was gaining in fall and winter when river stage was low. The magnitude and timing of river stage fluctuations controlled the timing of high exchange rates. Both river channel geomorphology and the thickness of a highly permeable river bank geologic layer controlled the locations of exchange hot spots, while the latter played a dominant role. Dam‐induced, subdaily to daily river stage fluctuations drove high‐frequency variations in HEFs across the river‐aquifer interfaces, resulting in greater overall exchange volumes as compared to the case without high‐frequency flows. Our results demonstrated that upstream dam operations enhanced the exchange between river water and groundwater with strong potential influence on the associated biogeochemical processes and on the fate and transport of groundwater contaminant plumes in such river corridors. Read more

Recommended citation: ﻿Shuai, P., Chen, X., Song, X., Hammond, G. E., Zachara, J., Royer, P., et al. (2019). Dam operations and subsurface hydrogeology control dynamics of hydrologic exchange flows in a Regulated River reach. Water Resources Research, 55. https://doi.org/ 10.1029/2018WR024193 https://doi.org/10.1029/2018WR024193

## Kilometer‐Scale Hydrologic Exchange Flows in a Gravel Bed River Corridor and Their Implications to Solute Migration

Published in ﻿Water Resources Research, 2020

Abstract: A well‐characterized field site along a major, gravel bed river corridor was used to investigate the dynamic pathways and impacts of subsurface hydrogeologic structure on kilometer‐scale hydrologic exchange flows between river water and groundwater. An aqueous uranium (Uaq) plume exists within a hyporheic alluvial aquifer at the site that discharges to the Columbia River. We performed temporally intensive monitoring of specific conductance (SpC) and Uaq concentrations within the plume for a 2‐year period at varying distances from the river shoreline, both within and outside a presumed subsurface pathway of lateral hydrologic exchange. SpC and Uaq were utilized as in situ tracers of hydrologic exchange and associated groundwater‐surface water mixing. Seasonal river stage variations by more than 2 m caused distinct events of river water intrusion and retreat from the nearshore, hyporheic alluvial aquifer, resulting in highly dynamic SpC and Uaq patterns in monitoring wells. Simulations of hydrologic exchange and mixing were performed with PFLOTRAN to understand the observed SpC and Uaq behaviors linked to predominant flow directions and velocities in the river corridor as influenced by river stage dynamics and variable aquitard topography. By coupling robust monitoring with numerical flow and transport modeling, we demonstrate complicated multidirectional flow behaviors at the kilometer scale that strongly influenced plume dynamics. Therefore, hyporheic aquifer must be frequently monitored under different flow conditions if water quality is of concern. The resulting hydrologic understanding enables improved interpretation of hydrogeochemical data from this site and other large gravel bed river corridors in the United States and elsewhere. Read more

Recommended citation: Zachara J., X. Chen, X. Song, P. Shuai, C. Murray, C. Resch. (2020). Kilometer-scale hydrologic exchange flows in a river corridor and their implications to solute migration. Water Resources Research. https://doi.org/10.1029/2019WR025258 https://doi.org/10.1029/2019WR025258

## Talk 1 on Relevant Topic in Your Field

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This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown! Read more

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## Conference Proceeding talk 3 on Relevant Topic in Your Field

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This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field. Read more

## Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post. Read more

## Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post. Read more