Review of saturated groundwater model codes for Hydro-JULES

This report reviews saturated groundwater model codes, one to be implemented into the Hydro-JULES modelling framework. First, the criteria for the code evaluation is described, and then commercial groundwater modelling codes, codes for thermo-hydro-chemical modelling and finally open source groundwater modelling codes are evaluated using the aforementioned criteria. Considering a groundwater code for the simulation of groundwater flooding or drought, we recommend either MODFLOW-2005, or the newly developed MODFLOW 6, the latter will need to be tested. Alternatively, BGS could develop a custom code that can solve the groundwater flow equation using moving grids, allowing a dynamic representation of the model grid for a moving water table. If also thermo and chemical processes are of interest, then codes such as OpenGeoSys, Dumux, and PFLOTRAN could be good choices, however they will need benchmarking to evaluate their ease of use

On modelling of consolidation processes in geological materials

Low-permeablity materials may be seen as natural geological barriers for radioactive waste repositories. However, to ensure their safe performance, a good understanding of their mechanical properties is required. Although the standard Biot's poroelastic model is widely used to estimate the key properties of these materials, experimental observations differ from this mathematical formulation and suggest that a more complex rock deformation behaviour to include a creep effect is needed. In this study, the Biot's differential equations are modified to include a rheological skeleton. In comparison with other existing models, here we propose a formulation with a minimal parametric uncertainty: we show that with just one additional physically-based parameter, the experimental creep behaviour is properly described. This enhanced model is implemented within a finite element framework and employed in a fitting algorithm to extract the hydro-mechanical properties from experimental data. To illustrate its generality, we analyse laboratory tests performed on three different types of materials: (a) an unlithified lower Oligocene clay from Belgium (Boom Clay), (b) an indurated Jurassic mudrock (Callovo-Oxfordian mudstone) and (c) a Triassic siltstone (Mercia Mudstone Formation). Numerical fits to the data support the validity of this approach and demonstrate its applicability to a range of low-permeability materials regardless of mineralogy or burial history

Stress controls on transport properties of the Mercia Mudstone Group: importance for hydrocarbon depletion and CO 2 injection

The physical properties of the Mercia Mudstone Group (MMG) are of interest to Carbon Capture and Storage (CCS) in the UK, both in terms of the sealing capacity of certain horizons and in order to assess scenarios involving CO2 migration in the overburden above potential CCS sites. In this study, the hydromechanical properties of MMG samples from the Larne Basin, Northern Ireland, were directly measured under steady-state conditions. Test samples were found to be good seals, with hydraulic permeabilities ranging from ≈2.1 x 10−18 to 8.4 x 10−21 m2 (2.1 x 10−3 to 8.5 x 10−6 mD). A detailed examination of the consolidation behaviour of the material yielded values for compressibility, hydraulic permeability and specific storage, as a function of effective pressure. Consolidation testing also provided preconsolidation pressure values of between 30 and 37 MPa. Test data were fitted to a linear elastic model using a two-dimension finite element approach, yielding hydraulic permeability and Young's Modulus, as a function of effective pressure. Findings suggest localisation of flow, due to small-scale heterogeneity, may play a role even in relatively large test samples. Results also highlight the impact of methodology on resulting permeabilities and the importance of using values measured at boundary conditions appropriate for the specific application. Critical state envelopes were derived from test data and used to conduct a scenario analysis, considering a range of stress paths, to examine the impacts of depletion and reinflation during CO2 injection. Initial stress conditions, stress path gradient and caprock heterogeneity were all found to be influencing factors on the potential for yield during depletion and the resulting deformation mode. The response to CO2 injection is less clear, but will be impacted by the initial caprock permeability and resulting drainage response. An awareness of these controls on caprock performance during stress path changes may aid in the selection of depleted CCS sites with geomechanically favourable characteristics for reinjection

Scoping study examining the behaviour of Boom Clay at disposal depths investigated in OPERA

The Onderzoeks Programma Eindberging Radioactief Afval (OPERA) is the third national research programme for the geological disposal of radioactive waste in the Netherlands, operating during the period 2011 to 2017. The rock types to host a geological disposal facility that are currently being considered in the Netherlands are salt and clay. Earlier Dutch work focussed mostly on salt, but the present programme OPERA is focused on a specific clay formation the Boom Clay. Previous studies have primarily focused on examining behaviour at the Belgium reference depth (~220m). The work presented in this study extends this knowledge-base to repository depths of potential interest in the Netherlands (~500m). In this report, results from a scoping study examining the hydromechanical properties of Boom Clay are presented, including investigations on consolidation, swelling, hydraulic, gas and deformation behaviour. These were performed on preserved core material retrieved from the HADES underground research laboratory, Belgium. Sections of core were then consolidated to a depth representative of the Netherlands. Permeability was sensitive to stress state and thermal load, though incremental changes in NaCl concentration had minimal impact. Hysteresis was observed in thermally induced changes in permeability. Gas entry was closely linked to the minimum principal stress component, with mass and volume changes of samples observed as a result of gas migration. Stress, porewater pressure and gas flow were integrally linked with pathways evolving temporally and spatially. A transition from brittle to ductile deformation was noted with increasing stress in both compression and shear. Boom Clay is both complex and anisotropic in its behaviour

Advective gas flow in bentonite: development and comparison of enhanced multi-phase numerical approaches

Understanding the impact of repository gas, generated from degradation of waste and its interaction with the host rock, is essential when assessing the performance and safety function of long-term disposal systems for radioactive waste. Numerical models based on conventional multi-phase flow theory have historically been applied to predict the outcome and impact of gas flow on different repository components. However, they remain unable to describe the full complexity of the physical processes observed in water-saturated experiments (e.g., creation of dilatant pathways) and thus, the development of novel representations for their description is required when assessing fully saturated clay-based systems. This was the primary focus of Task A within the international cooperative project DECOVALEX-2019 (D-2019) and refinement of these approaches is the primary focus of this study (Task B in the current phase of DECOVALEX-2023). This paper summarises development of enhanced numerical representations of key processes and compares the performance of each model against high-quality laboratory test data. Experimental data reveals that gas percolation in water-saturated compacted bentonite is characterised by four key features: (i) a quiescence phase, followed by (ii) the gas breakthrough, which leads to a (iii) peak value, which is then followed by (iv) a negative decay. Three models based on the multiphase flow theory have been developed. These models can provide good initial values and reasonable responses for gas breakthrough (although some of them still predict a too-smooth response). Peak gas pressure values are in general reasonably well captured, although maximum radial stress differences are observed at 48 mm from the base of the sample. Here, numerical peak values of 12.8 MPa are predicted, whereas experimental values are about 11 MPa. These models are also capable of providing a reasonable representation of the negative pressure decay following peak pressure. However, other key specific features (such as the timing of gas breakthrough) still require a better representation. The model simulations and their comparison with experimental data show that these models need to be further improved with respect to model parameter calibration, the numerical representation of spatial heterogeneities in material properties and flow localisation, and the upscaling of the related physical processes and parameters. To further understand gas flow localisation, a new conceptual model has been developed, which shows that discrete channels can possibly be induced through the instability of gas-bentonite interface during gas injection, thus providing a new perspective for modeling gas percolation in low-permeability deformable media

Numerical modelling of gas flow in a compact clay barrier for DECOVALEX-2019

The mechanisms controlling the movement of gases through geological disposal facilities can be described by models accounting for (i) diffusion, (ii) two-phase flow, (iii) localised flow pathways and (iv) gas fracturing of the rock. It is therefore necessary to consider all these phenomena for a better understanding of the processes governing the movement of gases in low permeability materials. The purpose of Task A in the current phase of the DEvelopment of COupled models and their VALidation against Experiments (DECOVALEX) project is to better understand the processes governing the advective movement of gas. In this paper, a synthesis of the ongoing work of eight participating modelling teams is presented. A wide range of 2D and 3D approaches including (i) continuous strategies assuming different mechanical deformation behaviors, (ii) continuous models with distinct phases or embedded fractures and (iii) discrete models with different formulations are validated against a gas flow test on pre-compacted bentonite undertaken by the British Geological Survey. The results of the ongoing work show that after a calibration process, plausible descriptions of the laboratory experiment can be achieved

DECOVALEX-2019 project: Task A - modElliNg Gas INjection ExpERiments (ENGINEER)

In a repository for radioactive waste hosted in a clay formation, hydrogen and other gases may be generated due to the corrosion of metallic materials under anoxic conditions, the radioactive decay of waste and the radiolysis of water. If the gas production rate exceeds the gas diffusion rate within the pores of the clay, a discrete gas phase will form and accumulate until its pressure becomes large enough to exceed the entry pressure of the surrounding material. The purpose of Task A under DECOVALEX-2019 is to better understand the processes governing the advective movement of gas in both low-permeability argillaceous repository host rocks and clay-based engineered barriers. Special attention is given to the mechanisms controlling gas entry, flow and pathway sealing and their impact on the performance of the engineered clay barrier. Previous work suggests gas flow may be accompanied by the creation of dilatant pathways whose properties change temporally and spatially within the medium. Thus, new numerical representations for the quantitative prediction of gas migration fluxes through argillaceous rock formations have been developed. These provide an invaluable tool with which to assess the impact of gas flow on repository layout and therefore design of any future facility. In addition, experience gained through this task is of direct relevance to other clay-based engineering issues where immiscible gas flow is a consideration including shale gas, hydrocarbon migration, carbon capture and storage and landfill design. Task A is organised into four steps, starting with the code development (stage 0) and followed by the modelling of a 1D gas flow test (stage 1) and a spherical gas flow test (stage 2). Then, the previous models are applied to a natural argillaceous material (stage 3). This report summarises the outcomes of work in Task A (stages 0 and 1) with work conducted from May 2016 to March 2018 and provides a brief overview of the experimental data, the current task structure and a synthesis of the ongoing work of the participating modelling teams as of March 2018

A new view of electrochemistry at highly oriented pyrolytic graphite

Major new insights on electrochemical processes at graphite electrodes are reported, following extensive investigations of two of the most studied redox couples, Fe(CN)64–/3– and Ru(NH3)63+/2+. Experiments have been carried out on five different grades of highly oriented pyrolytic graphite (HOPG) that vary in step-edge height and surface coverage. Significantly, the same electrochemical characteristic is observed on all surfaces, independent of surface quality: initial cyclic voltammetry (CV) is close to reversible on freshly cleaved surfaces (>400 measurements for Fe(CN)64–/3– and >100 for Ru(NH3)63+/2+), in marked contrast to previous studies that have found very slow electron transfer (ET) kinetics, with an interpretation that ET only occurs at step edges. Significantly, high spatial resolution electrochemical imaging with scanning electrochemical cell microscopy, on the highest quality mechanically cleaved HOPG, demonstrates definitively that the pristine basal surface supports fast ET, and that ET is not confined to step edges. However, the history of the HOPG surface strongly influences the electrochemical behavior. Thus, Fe(CN)64–/3– shows markedly diminished ET kinetics with either extended exposure of the HOPG surface to the ambient environment or repeated CV measurements. In situ atomic force microscopy (AFM) reveals that the deterioration in apparent ET kinetics is coupled with the deposition of material on the HOPG electrode, while conducting-AFM highlights that, after cleaving, the local surface conductivity of HOPG deteriorates significantly with time. These observations and new insights are not only important for graphite, but have significant implications for electrochemistry at related carbon materials such as graphene and carbon nanotubes

X chromosome inactivation does not necessarily determine the severity of the phenotype in Rett syndrome patients

Rett syndrome (RTT) is a severe neurological disorder usually caused by mutations in the MECP2 gene. Since the MECP2 gene is located on the X chromosome, X chromosome inactivation (XCI) could play a role in the wide range of phenotypic variation of RTT patients; however, classical methylation-based protocols to evaluate XCI could not determine whether the preferentially inactivated X chromosome carried the mutant or the wild-type allele. Therefore, we developed an allele-specific methylation-based assay to evaluate methylation at the loci of several recurrent MECP2 mutations. We analyzed the XCI patterns in the blood of 174 RTT patients, but we did not find a clear correlation between XCI and the clinical presentation. We also compared XCI in blood and brain cortex samples of two patients and found differences between XCI patterns in these tissues. However, RTT mainly being a neurological disease complicates the establishment of a correlation between the XCI in blood and the clinical presentation of the patients. Furthermore, we analyzed MECP2 transcript levels and found differences from the expected levels according to XCI. Many factors other than XCI could affect the RTT phenotype, which in combination could influence the clinical presentation of RTT patients to a greater extent than slight variations in the XCI pattern

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis