Application of the Interagency and Modeling Analysis Group Model Verification Approach for Scientific Reproducibility in a Study of Biomineralization

Model verification is a critical aspect of scientificaccountability,transparency, and learning. Here, we demonstrate an application ofa model verification approach for a molecular dynamics (MD) simulation,where the interactions between silica and silk protein were studiedexperimentally toward understanding biomineralization. Following theten rules for credible modeling and simulation of biosciences as developedin Erdemir et al., the authors of the original paper collaboratedwith an external modeling group to verify the key findings of theiroriginal simulation model and to document this verification approach.The process resulted in successful replication of the key findingsof the original model. Beyond verification, study of the model froma new perspective generated new insight into the basic assumptions.We discuss key learnings for how model validation processes can beimproved more generally, specifically through improved documentationmethods. We anticipate that this application of our protocol for modelverification can be further replicated and improved to verify andvalidate other simulations.

Automated summary

Model verification is critical for scientific accountability, transparency, and learning. In this study, a model verification approach was applied to a molecular dynamics simulation, successfully replicating the key findings of the original model and gaining new insights. Improvements in model validation processes, particularly through enhanced documentation methods, were discussed. This protocol for model verification can be further applied to validate other simulations.