A general description of the mathematical and numerical formulations used in modern numerical reactive transport codes relevant for subsurface environmental simulations is presented. The formulations are followed by short descriptions of commonly used and available subsurface simulators that consider continuum representations of flow, transport, and reactions in porous media. These formulations are applicable to most of the subsurface environmental benchmark problems included in this special issue. The list of codes described briefly here includes PHREEQC, HPx, PHT3D, OpenGeoSys (OGS), HYTEC, ORCHESTRA, TOUGHREACT, eSTOMP, HYDROGEOCHEM, CrunchFlow, MIN3P, and PFLOTRAN. The descriptions include a high-level list of capabilities for each of the codes, along with a selective list of applications that highlight their capabilities and historical development.

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Reactive transport codes for subsurface environmental simulation

Geomicrobially induced deterioration of stone monuments and buildings contributes to a considerable loss of world cultural heritage, especially when exposed to a changing climate or environment. The active biodeterioration processes typically involve biochemical activities and cooperation among functional microorganisms in epilithic biofilms, which assimilate mineral nutrients and metabolize anthropogenic pollutants through biogeochemical cycles. Development of any effective mitigation strategies requires the comprehensive understanding of such processes. We focus on how microbes contribute to the biodeterioration processes through their activities and biogeochemical cycles of elements, discuss biochemical mechanisms involved and provide innovative strategies for sustainable conservation of stone monuments and buildings. Biodeterioration of stone monuments and buildings can lead to a loss of world cultural heritage. This Review discusses the role of microbes in the deterioration processes, the biochemical mechanisms involved and possible strategies for sustainable conservation of stone monuments and buildings.

Microbial deterioration and sustainable conservation of stone monuments and buildings

Degradation modelling of concrete submitted to sulfuric acid attack

Building materials can be exposed to microorganisms (mainly bacteria, fungi and algae) in almost every aqueous medium or damp environment, water being the indispensable condition for life development. The activity of microorganisms can be responsible for mineralogical, chemical and microstructural damage to the material (biodeterioration). Deleterious effects can also concern the aesthetics of a building (proliferation of colored biological stains on facades and roofs) or the quality of indoor air (presence of microorganisms in damp buildings). However, microorganisms can also have positive effects (healing of materials) and their action is explored through the development of bio-based protective systems intended for building materials. In all cases, understanding interactions between building materials and microorganisms is an indispensable step toward the development of more sustainable, better quality, safer structures in many environments. This paper presents two examples where the action of microorganisms has—or is likely to have—strong impact on the durability and safety of concrete structures. The first example concerns the biodeterioration of concrete in agricultural and agro-food environments. The second example is that of the abiotic and biotic reactivity of nitrates in repository of intermediate-level long-lived nuclear wastes. The paper presents the approaches used to explore and understand the phenomenology of bio-geo-chemical interactions in these complex environments. These studies notably comprise the development of test methods and experimental pilots to enable these explorations to be carried out. Current shortcomings in the scientific literature and in the standardization environment are also highlighted.

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Phillippe Devillers

Papers

Modeling the degradation of Portland cement pastes by biogenic organic acids