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Matriarch: A Python Library for Materials Architecture.

Tristan Giesa1, Ravi Jagadeesan1,2, David I Spivak3

  • 1Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.

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|August 30, 2016
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Summary
This summary is machine-generated.

A new mathematical language and open-source Python library, Matriarch, enables precise design of complex biological material structures. This tool facilitates the creation of arbitrary protein architectures for advanced materials engineering.

Keywords:
building blockcategory theoryhierarchical protein materialsmolecular designopen-source softwarestructure creation

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Area of Science:

  • Biomaterials Science
  • Computational Biology
  • Materials Engineering

Background:

  • Biological materials exhibit hierarchical structures from nanoscale building blocks to macroscale assemblies.
  • Existing software lacks flexibility in geometrically arranging unequilibrated structures for simulations.
  • Designing complex hierarchical structures is currently difficult and time-consuming.

Purpose of the Study:

  • To develop a flexible mathematical framework for describing hierarchical material architecture.
  • To implement this framework as an open-source Python library (Matriarch) for protein structure generation.
  • To enable the design and modification of biologically inspired materials with desired functionalities.

Main Methods:

  • Utilized category theory to define a mathematical language for material building blocks and assembly instructions.
  • Developed Matriarch, an open-source Python library, to implement the mathematical language.
  • Generated Protein Data Bank (PDB) files from user-defined arbitrary protein structures.
  • Performed a case study altering tropocollagen building blocks and instructions.

Main Results:

  • Matriarch allows the creation of virtually any protein structure with specified amino acid sequences.
  • The software offers greater flexibility and power compared to existing commercial tools.
  • The case study demonstrated the impact of altered building blocks and instructions on tropocollagen structure and mechanics.
  • Matriarch integrates with molecular dynamics simulations for enhanced materials design.

Conclusions:

  • Matriarch provides a powerful, domain-specific language for designing complex hierarchical biological materials.
  • The library facilitates the exploration of structure-property relationships in proteins.
  • This approach advances the engineering of novel biomaterials with tailored functionalities.