I'm currently trying to simulate the calcium carbonate mineralization process on the surface of nanoparticles. In here, I've already borrowed the classical force-field parameters on here(https://pubs.acs.org/doi/10.1021/ja108508k), in which the interactions for calcium/carbonate ions and water are described as the mixing of Electrostatic/Lennard Jones/Buckingham potential.

The very obstacle for classical MD simulation is that when I'm trying to observe the calcium carbonate mineralization (or nucleation) process by setting the initial structure of nanoparticles and calcium/carbonate ions in a separate way, both ions try to adsorb to the surface of nanoparticles but with a highly disordered manner. Even without the nanoparticles, the aggregation of calcium/carbonate ions in solution phase is quite favorable, but again, it's very hard to observe that such aggregated clusters exist with any crystalline order. Referring to the previous literature (https://www.nature.com/articles/ncomms1604), the authors only analyzed the very early stages of calcium carbonate formation as stable prenucleation clusters, without extending the scope to observe the full mineralization process. Although the purpose of my research is aimed to address why certain type of crystal structure (among the three polymorphs of calcium carbonate) is favorably mineralized on nanoparticles surface, it seems that just implementing the usual classical force-field is quite unfeasible to observe the transition from solvated calcium/carbonate ions into the crystalline structure.

My question here is that is there any way to simulate/analyze the mineralization process on here. I expect that such incapability of simulating the mineralization process in classical MD simulation would be originated from the poor transferability of force field parameters between solvated/mineral phase of calcium carbonate ions. It'd be really appreciated if one could recommend any reference for simulating mineralization process using classical MD simulation. Sharing any experience for the one who've already done the similar work would be highly informative for me!

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1 Answer 1


Fair Note: I have experience with only studying aggregation of small molecules at the solid - liquid interface.

If you are trying to study the formation of an ordered structure from a solution phase using classical MD simulations, you would need to run the simulations for a very long time, atleast to hope that you get close to an ordered structure. For example, in this paper we had to perform a 750 ns simulation to get an ordered structure. But even if you perform such long simulations, there is no guarantee that you will converge to the state that you are hoping to achieve, because classical FF parameters are empirically tuned to reproduce certain properties only. Then your best bet becomes to repeat the simulations multiple times, and look at the statistics to form a general idea.

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    $\begingroup$ Thanks for sharing your experience. I've already ran the MD simulation for such system with more than >1 microsec trajectory length and also come to the conclusion that the spatiotemporal scale which is required to observe the mineralization process is very challenging. $\endgroup$
    – Arete
    May 31, 2023 at 17:02
  • $\begingroup$ I agree that it is challenging. You can refer to papers by Prof. Aurora Clark, where they study the the interfacial dynamics of aluminate minerals. $\endgroup$ May 31, 2023 at 17:29

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