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Abstract. We introduce a time-dependent, one-dimensional model ofearly diagenesis that we term RADI, an acronym accounting for the mainprocesses included in the model: chemical reactions, advection, molecularand bio-diffusion, and bio-irrigation. RADI is targeted for study ofdeep-sea sediments, in particular those containing calcium carbonates(CaCO3). RADI combines CaCO3 dissolution driven by organic matterdegradation with a diffusive boundary layer and integrates state-of-the-artparameterizations of CaCO3 dissolution kinetics in seawater, thusserving as a link between mechanistic surface reaction modeling andglobal-scale biogeochemical models. RADI also includes CaCO3precipitation, providing a continuum between CaCO3 dissolution andprecipitation. RADI integrates components rather than individual chemicalspecies for accessibility and is straightforward to compare againstmeasurements. RADI is the first diagenetic model implemented in Julia, ahigh-performance programming language that is free and open source, and itis also available in MATLAB/GNU Octave. Here, we first describe thescientific background behind RADI and its implementations. Following this, we evaluateits performance in three selected locations and explore other potentialapplications, such as the influence of tides and seasonality on earlydiagenesis in the deep ocean. RADI is a powerful tool to study thetime-transient and steady-state response of the sedimentary system toenvironmental perturbation, such as deep-sea mining, deoxygenation, oracidification events. 

The dissolution of CaCO 3 minerals in the ocean is a fundamental part of the marine alkalinity and carbon cycles. While there have been decades of work aimed at deriving the relationship between dissolution rate and mineral saturation state (a so-called rate law), no real consensus has been reached. There are disagreements between laboratory- and field-based studies and differences in rates for inorganic and biogenic materials. Rates based on measurements on suspended particles do not always agree with rates inferred from measurements made near the sediment–water interface of the actual ocean. By contrast, the freshwater dissolution rate of calcite has been well described by bulk rate measurements from a number of different laboratories, fit by basic kinetic theory, and well studied by atomic force microscopy and vertical scanning interferometry to document the processes at the atomic scale. In this review, we try to better unify our understanding of carbonate dissolution in the ocean via a relatively new, highly sensitive method we have developed combined with a theoretical framework guided by the success of the freshwater studies. We show that empirical curve fits of seawater data as a function of saturation state do not agree, largely because the curvature is itself a function of the thermodynamics. Instead, we show that models that consider both surface energetic theory and the complicated speciation of seawater and calcite surfaces in seawater are able to explain most of the most recent data.This new framework can also explain features of the historical data that have not been previously explained. The existence of a kink in the relationship between rate and saturation state, reflecting a change in dissolution mechanism, may be playing an important role in accelerating CaCO 3 dissolution in key sedimentary environments.