Application of the Interagency and Modeling Analysis Group Model Verification Approach for Scientific Reproducibility in a Study of Biomineralization.
Application of the Interagency and Modeling Analysis Group Model Verification Approach for Scientific Reproducibility in a Study of Biomineralization.
复制标题
科学再现性的机构间和建模分析组模型验证方法在生物矿化研究中的应用。
DOI：
10.1021/acsbiomaterials.3c00147
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发表时间：
2023
影响因子：
5.8
通讯作者：
Buehler,MarkusJ
中科院分区：
文献类型：
--
作者：
Khare,Eesha;Peng,Xiangjun;Martín-Moldes,Zaira;Genin,GuyM;Kaplan,DavidL;Buehler,MarkusJ
模型验证是科学问责制、透明度和学习的一个重要方面。在这里，我们展示了一个应用程序的模型验证方法的分子动力学（MD）模拟，二氧化硅和丝蛋白之间的相互作用进行了实验研究，了解生物矿化。遵循Erdemir等人提出的生物科学可信建模和模拟的十条规则，原始论文的作者与外部建模小组合作，以验证其原始模拟模型的关键发现，并记录这种验证方法。这一过程成功地复制了原始模型的主要结论。除了验证，从一个新的角度研究模型产生了新的见解的基本假设。我们讨论了如何更普遍地改进模型验证过程的关键知识，特别是通过改进的文档方法。我们预计，我们的模型验证协议的这种应用程序可以进一步复制和改进，以验证和验证其他模拟。
Model verification is a critical aspect of scientific accountability, transparency, and learning. Here, we demonstrate an application of a model verification approach for a molecular dynamics (MD) simulation, where the interactions between silica and silk protein were studied experimentally toward understanding biomineralization. Following the ten rules for credible modeling and simulation of biosciences as developed in Erdemir et al., the authors of the original paper collaborated with an external modeling group to verify the key findings of their original simulation model and to document this verification approach. The process resulted in successful replication of the key findings of the original model. Beyond verification, study of the model from a new perspective generated new insight into the basic assumptions. We discuss key learnings for how model validation processes can be improved more generally, specifically through improved documentation methods. We anticipate that this application of our protocol for model verification can be further replicated and improved to verify and validate other simulations.