The HPx software for multicomponent reactive transport during variably-saturated flow: Recent developments and applications

Abstract HPx is a multicomponent reactive transport model which uses HYDRUS as the flow and transport solver and PHREEQC-3 as the biogeochemical solver. Some recent adaptations have significantly increased the flexibility of the software for different environmental and engineering applications. This paper gives an overview of the most significant changes of HPx, such as coupling transport properties to geochemical state variables, gas diffusion, and transport in two and three dimensions. OpenMP allows for parallel computing using shared memory. Enhancements for scripting may eventually simplify input definitions and create possibilities for defining templates for generic (sub)problems. We included a discussion of root solute uptake and colloid-affected solute transport to show that most or all of the comprehensive features of HYDRUS can be extended with geochemical information. Finally, an example is used to demonstrate how HPx, and similar reactive transport models, can be helpful in implementing different factors relevant for soil organic matter dynamics in soils. HPx offers a unique framework to couple spatial-temporal variations in water contents, temperatures, and water fluxes, with dissolved organic matter and CO2 transport, as well as bioturbation processes

Coupled heat-mass transport modelling of radionuclide migration from a nuclear waste disposal borehole

Disposal of radioactive waste originating from reprocessing of spent research reactor fuel typically includes stainless steel canisters with waste immobilised in a glass matrix. In a deep borehole disposal concept, waste packages could be stacked in a disposal zone at a depth of one to potentially several kilometres. This waste will generate heat for several hundreds of years. The influence of combining a natural geothermal gradient with heat from decaying nuclear waste on radionuclide transport from deep disposal boreholes is studied by implementing a coupled heat-solute mass transport modelling framework, subjected to depth-dependent temperature, pressure, and viscosity profiles. Several scenarios of waste-driven heat loads were investigated to test to what degree, if any, the additional heat affects radionuclide migration by generating convection-driven transport. Results show that the heat output and the calculated radioactivity at a hypothetical near-surface observation point are directly correlated; however, the overall impact of convection-driven transport is small due to the short duration (a few hundred years) of the heat load. Results further showed that the calculated radiation dose at the observation point was very sensitive to the magnitude of the effective diffusion parameter of the host rock. Coupled heat-solute mass transport models are necessary tools to identify influential processes regarding deep borehole disposal of heat-generating long-lived radioactive waste

Sensitivity of groundwater recharge using climatic analogues and HYDRUS-1D

The sensitivity of groundwater recharge to different climate conditions was simulated using the approach of climatic analogue stations, i.e. stations presently experiencing climatic conditions corresponding to a possible future climate state. The study was conducted in the context of a safety assessment of a future near-surface disposal facility for low and intermediate level short-lived radioactive waste in Belgium; this includes estimation of groundwater recharge for the next millennia. Groundwater recharge was simulated using the Richards based soil water balance model HYDRUS-1D and meteorological time series from analogue stations. This study used four analogue stations for a warmer subtropical climate with changes of average annual precipitation and potential evapotranspiration from −42% to +5% and from +8% to +82%, respectively, compared to the present-day climate. Resulting water balance calculations yielded a change in groundwater recharge ranging from a decrease of 72% to an increase of 3% for the four different analogue stations. The Gijon analogue station (Northern Spain), considered as the most representative for the near future climate state in the study area, shows an increase of 3% of groundwater recharge for a 5% increase of annual precipitation. Calculations for a colder (tundra) climate showed a change in groundwater recharge ranging from a decrease of 97% to an increase of 32% for four different analogue stations, with an annual precipitation change from −69% to −14% compared to the present-day climate

Utilisation de l'expérience de drainage à pas de pression multiples pour la détermination des fonctions hydrauliques du sol par la méthode inverse : résultats expérimentaux

La méthode de drainage à pas de pression multiples, combinée avec la méthode inverse, permet la détermination des fonctions hydrauliques du sol (têta(h) et K(h)) simultanément. Cependant, le choix des fonctions décrivant têta(h) et K(h) du sol est d'une importance capitale dans cette méthode. Les résultats expérimentaux montrent que le modèle de CAMPBELL (1974) dans sa version améliorée par HUTSON et CASS (1987) permet une description raisonnable du processus du drainage en fonction du temps et correspondant à des pas de pression croissants. Les courbes de rétention d'eau déduites des paramètres optimisés par la méthode inverse ont les mêmes allures que celles déterminées par la méthode standard (bac de sable et cellules à basses et hautes pressions). Ces résultats sont plus représentatifs de la réalité lorsque les paramètres têta(s) et K(s) sont fixes et égaux aux valeurs expérimentales, avec une précision sensiblement la même dans les cas d'optimisation, où têta(s) est fixe et têta(s) et K(s) fixes et égaux aux valeurs expérimentales; le premier cas où seulement le paramètre têta(s) est fixe est suggéré (il y a moins de paramètres à mesurer). (Résumé d'auteur

Utilisation de l'expérience de drainage à pas de pression multiples pour la détermination des fonctions hydrauliques du sol par la méthode inverse : présentation et évaluation de la méthode

L'optimisation des paramètres des fonctions décrivant les propriétés hydrauliques du sol têta(h) et K(h), basée sur les résultats de l'expérience de drainage interne à pas de pression multiples est une méthode prometteuse. En effet, cette dernière fournit suffisamment d'informations sur les propriétés hydrauliques essentielles d'un sol. Le modèle utilisé pour décrire les relations entre la teneur en eau volumique têta et la pression de l'eau h, d'une part, et entre la conductivité hydraulique K et h, d'autre part, est celui de CAMPBELL (1974) dans sa version améliorée par HUTSON et CASS (1987). Les résultats montrent que ce modèle décrit raisonnablement le processus du drainage en fonction du temps correspondant à des pas de pressions croissantes. La solution de la méthode d'identification des paramètres est unique tant que les valeurs assignées aux paramètres au départ sont proches (plus ou moins 20 %) de celles du sol étudié. L'effet d'une erreur expérimentale allant jusqu'à 10 % n'est pas significatif pour les résultats des paramètres optimisés. (Résumé d'auteur

Centimeter-scale secondary information on hydraulic conductivity using a hand-held air permeameter on borehole cores

Saturated hydraulic conductivity (Ks) is one of the most important parameters determining groundwater flow and contaminant transport in both unsaturated and saturated porous media. Determining the small-scale variability of this parameter is key to evaluate implications on effective parameters at the larger scale. Moreover, for stochastic simulations of groundwater flow and contaminant transport, accurate models on the spatial variability of Ks are very much needed. While several well-established laboratory methods exist for determining Ks, investigating the small-scale variability remains a challenge. If several tens to hundreds of metres of borehole core has to be hydraulically characterised at the centimetre to decimetre scale, several hundreds to thousands of Ks measurements are required, which makes it very costly and time-consuming should traditional methods be used. With reliable air permeameters becoming increasingly available from the late 80’s, a fast and effective indirect method exists to determine Ks. Therefore, the use of hand-held air permeameter measurements for determining very accurate small-scale heterogeneity about Ks is very appealing. Very little is known, however, on its applicability for borehole cores that typically carry a small sediment volume. Therefore, the method was tested on several borehole cores of different size, originating from the Campine basin, Northern Belgium. The studied sediments are of Miocene to Pleistocene age, with a marine to continental origin, and consist of sand to clayey sand with distinct clay lenses, resulting in a Ks range of 7 orders of magnitude. During previous studies, two samples were taken from borehole cores each two meters for performing constant head lab permeameter tests. This data is now used as a reference for the air permeameter measurements that are performed with a resolution of 5 centimetres. Preliminary results indicate a very good correlation between the previously gathered constant head Ks data and the air permeability measurements, but a systematic bias seems to exist. A geostatistical analysis with cross-validation is performed to assess the predictive uncertainty on Ks, using both types of data. We conclude that performing hand-held air permeameter measurements on undisturbed borehole cores provides a very cost-effective way to obtain very detailed information in the framework of stochastic simulation and conditioning of heterogeneous hydraulic conductivity fields

Hydrogeological conceptual model building and testing: A review

© 2018 Elsevier BV. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 24 month embargo from date of publication (December 2018) in accordance with the publisher’s archiving policyHydrogeological conceptual models are collections of hypotheses describing the understanding of groundwater systems and they are considered one of the major sources of uncertainty in groundwater flow and transport modelling. A common method for characterizing the conceptual uncertainty is the multi-model approach, where alternative plausible conceptual models are developed and evaluated. This review aims to give an overview of how multiple alternative models have been developed, tested and used for predictions in the multi-model approach in international literature and to identify the remaining challenges. The review shows that only a few guidelines for developing the multiple conceptual models exist, and these are rarely followed. The challenge of generating a mutually exclusive and collectively exhaustive range of plausible models is yet to be solved. Regarding conceptual model testing, the reviewed studies show that a challenge remains in finding data that is both suitable to discriminate between conceptual models and relevant to the model objective. We argue that there is a need for a systematic approach to conceptual model building where all aspects of conceptualization relevant to the study objective are covered. For each conceptual issue identified, alternative models representing hypotheses that are mutually exclusive should be defined. Using a systematic, hypothesis based approach increases the transparency in the modelling workflow and therefore the confidence in the final model predictions, while also anticipating conceptual surprises. While the focus of this review is on hydrogeological applications, the concepts and challenges concerning model building and testing are applicable to spatio-temporal dynamical environmental systems models in general

A robust pipeline with high replication rate for detection of somatic variants in the adaptive immune system as a source of common genetic variation in autoimmune disease

The role of somatic variants in diseases beyond cancer is increasingly being recognized, with potential roles in autoinflammatory and autoimmune diseases. However, as mutation rates and allele fractions are lower, studies in these diseases are substantially less tolerant of false positives, and bio-informatics algorithms require high replication rates. We developed a pipeline combining two variant callers, MuTect2 and VarScan2, with technical filtering and prioritization. Our pipeline detects somatic variants with allele fractions as low as 0.5% and achieves a replication rate of > 55%. Validation in an independent data set demonstrates excellent performance (sensitivity > 57%, specificity > 98%, replication rate > 80%). We applied this pipeline to the autoimmune disease multiple sclerosis (MS) as a proof-of-principle. We demonstrate that 60% of MS patients carry 2-10 exonic somatic variants in their peripheral blood T and B cells, with the vast majority (80%) occurring in T cells and variants persisting over time. Synonymous variants significantly co-occur with non-synonymous variants. Systematic characterization indicates somatic variants are enriched for being novel or very rare in public databases of germline variants and trend towards being more damaging and conserved, as reflected by higher phred-scaled combined annotation-dependent depletion (CADD) and genomic evolutionary rate profiling (GERP) scores. Our pipeline and proof-of-principle now warrant further investigation of common somatic genetic variation on top of inherited genetic variation in the context of autoimmune disease, where it may offer subtle survival advantages to immune cells and contribute to the capacity of these cells to participate in the autoimmune reaction.Peer reviewe

Comparison of three stream tube models predicting field-scale solute transport

International audienceIn this paper the relation between local- and field-scale solute transport parameters in an unsaturated soil profile is investigated. At two experimental sites, local-scale steady-state solute transport was measured in-situ using 120 horizontally installed TDR probes at 5 depths. Local-scale solute transport parameters determined from BTCs were used to predict field-scale solute transport using stochastic stream tube models (STM). Local-scale solute transport was described by two transport models: (1) the convection-dispersion transport model (CDE), and (2) the stochastic convective lognormat transfer model (CLT). The parameters of the CDE-model were found to be lognormally distributed, whereas the parameters of the CLT model were normally distributed. Local-scale solute transport heterogeneity within the measurement volume of a TDR-probe was an important factor causing field-scale solute dispersion. The study of the horizontal scale-dependency revealed that the variability in the solute transport parameters contributes more to the field-scale dispersion at deeper depths than at depths near the surface. Three STMs were used to upscale the local transport parameters: (i) the stochastic piston flow STM-I assuming local piston flow transport, (ii) the convective-dispersive STM-II assuming local CDE transport, and (iii) the stochastic convective lognormal STM-III assuming local CLT. The STM-I considerably underpredicted the field-scale solute dispersion indicating that local-scale dispersion processes, which are captured within the measurement volume of the TDR-probe, are important to predict field-scale solute transport. STM-II and STM-III both described the field-scale breakthrough curves (BTC) accurately if depth dependent parameters were used. In addition, a reasonable description of the horizontal variance of the local BTCs was found. STM-III was (more) superior to STM-II if only one set of parameters from one depth is used to predict the field-scale solute BTCs at several depths. This indicates that the local-scale solute transport process, as measured with TDR in this study, is in agreement with the CLT-hypothesis

Multiple sclerosis risk variants alter expression of co-stimulatory genes in B cells.

The increasing evidence supporting a role for B cells in the pathogenesis of multiple sclerosis prompted us to investigate the influence of known susceptibility variants on the surface expression of co-stimulatory molecules in these cells. Using flow cytometry we measured surface expression of CD40 and CD86 in B cells from 68 patients and 162 healthy controls that were genotyped for the multiple sclerosis associated single nucleotide polymorphisms (SNPs) rs4810485, which maps within the CD40 gene, and rs9282641, which maps within the CD86 gene. We found that carrying the risk allele rs4810485*T lowered the cell-surface expression of CD40 in all tested B cell subtypes (in total B cells P ≤ 5.10 × 10-5 in patients and ≤4.09 × 10-6 in controls), while carrying the risk allele rs9282641*G increased the expression of CD86, with this effect primarily seen in the naïve B cell subset (P = 0.048 in patients and 5.38 × 10-5 in controls). In concordance with these results, analysis of RNA expression demonstrated that the risk allele rs4810485*T resulted in lower total CD40 expression (P = 0.057) but with an increased proportion of alternative splice-forms leading to decoy receptors (P = 4.00 × 10-7). Finally, we also observed that the risk allele rs4810485*T was associated with decreased levels of interleukin-10 (P = 0.020), which is considered to have an immunoregulatory function downstream of CD40. Given the importance of these co-stimulatory molecules in determining the immune reaction that appears in response to antigen our data suggest that B cells might have an important antigen presentation and immunoregulatory role in the pathogenesis of multiple sclerosis