DataVXACS Biomaterials Science & EngineeringPaper
journal article·2023-07-10

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

Eesha Khare, Xiangjun Peng, Zaira Martín-Moldes, Guy M. Genin, David L. Kaplan, Markus J. Buehler

ACS Biomaterials Science & Engineering· Volume 9· Issue 7
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Source abstract

Abstract

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.
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Research context

OpenAlex topics: Diatoms and Algae Research · Physiological and biochemical adaptations · Genomics and Phylogenetic Studies

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States

Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States

NSF Science and Technology Center for Engineering Mechanobiology, Washington University, St. Louis, Missouri 63130, United States

Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States

Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts 02139, United States

Center for Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts 02139, United States

Funding

National Science Foundation · U.S. Department of Health and Human Services

References (37)

Show source-provided references
1. 10.1038/525025a10.1038/525025a ↗
2. 10.1038/533452a10.1038/533452a ↗
3. 10.1038/533437a10.1038/533437a ↗
4. 10.1038/531011f10.1038/531011f ↗
5. 10.1073/pnas.170827211410.1073/pnas.1708272114 ↗
6. 10.1145/299403110.1145/2994031 ↗
7. 10.5840/jphil2018115123910.5840/jphil20181151239 ↗
8. National Aeronautics and Space Administration Standard for Models and Simulations. NASA-STD-7009. 2016. https://standards.nasa.gov/standard/NASA/NASA-STD-7009
9. 10.48550/arXiv.2107.0538610.48550/arXiv.2107.05386 ↗
10. 10.1016/j.coisb.2021.06.00110.1016/j.coisb.2021.06.001 ↗
11. 10.17226/1339510.17226/13395 ↗
12. 10.1109/JBHI.2019.294988810.1109/JBHI.2019.2949888 ↗
13. 10.1097/MAT.000000000000099610.1097/MAT.0000000000000996 ↗
14. 10.3389/fninf.2018.0001810.3389/fninf.2018.00018 ↗
15. 10.1186/s12967-020-02540-410.1186/s12967-020-02540-4 ↗
16. 10.1016/j.clinbiomech.2005.01.01010.1016/j.clinbiomech.2005.01.010 ↗
17. 10.1016/j.ymeth.2020.01.01110.1016/j.ymeth.2020.01.011 ↗
18. 10.1016/j.pbiomolbio.2016.08.00710.1016/j.pbiomolbio.2016.08.007 ↗
19. 10.1146/annurev-bioeng-082219-05174010.1146/annurev-bioeng-082219-051740 ↗
20. 10.1002/jor.2455110.1002/jor.24551 ↗
21. 10.1002/adfm.20170257010.1002/adfm.201702570 ↗
22. 10.1371/journal.pone.001574610.1371/journal.pone.0015746 ↗
23. 10.1002/jcc.2029110.1002/jcc.20291 ↗
24. 10.1007/s00894010004510.1007/s008940100045 ↗
25. 10.1016/0010-4655(95)00042-E10.1016/0010-4655(95)00042-E ↗
26. 10.1007/978-94-007-1611-7_410.1007/978-94-007-1611-7_4 ↗
27. 10.1021/cm500365c10.1021/cm500365c ↗
28. 10.1021/ct900549r10.1021/ct900549r ↗
29. 10.1145/3341525.339399710.1145/3341525.3393997 ↗
30. 10.1109/ACCESS.2018.287476710.1109/ACCESS.2018.2874767 ↗
31. 10.1007/978-1-4842-6649-6_210.1007/978-1-4842-6649-6_2 ↗
32. 10.1109/CLOUD53861.2021.0010110.1109/CLOUD53861.2021.00101 ↗
33. 10.1021/acs.jcim.1c0099810.1021/acs.jcim.1c00998 ↗
34. 10 Simple Rules with Conformance Rubric. Interagency Modeling and Analysis Group. https://www.imagwiki.nibib.nih.gov/content/10-simple-rules-conformance-rubric (accessed Oct 22, 2021).
35. Buehler, M. J.; Kaplan, D. L. [RCA] Integrated multiscale biomaterials experiment and modeling group. Interagency Modeling and Analysis Group. https://www.imagwiki.nibib.nih.gov/resource_credibility_assessment/rca-integrated-multiscale-biomaterials-experiment-and-modeling (accessed Oct 22, 2021).
36. 10.1021/acs.jctc.1c0052610.1021/acs.jctc.1c00526 ↗
37. 10.1371/journal.pone.021596210.1371/journal.pone.0215962 ↗