Multi-scale modeling and simulation of biological and bioinspired materials

Massachusetts Institute of Technology

Zhao Qin


  • Multi-scale modeling and simulation of biological and bioinspired materials and structures Biological materials have fascinating mechanical and properties and functions, including their capacity to integrate strength, toughness, mutability, adaptability, self-healing and mutifunctionality, achieved from a basis of simple material building blocks (Fig. 1). We aim to understand the paradigm by which biological materials are constructed, and apply the knowledge to realize new materials designs, from concept to physical realization.
  • Collagenous materials and tissues: Structure, deformation and failure Bone serves a variety of mechanical, synthetic, and metabolic functions in the body. This tough, lightweight, elastic, and highly dissipative material acts as a protective load-bearing framework and shows remarkable mechanical properties. Knowledge of how collagen molecules assemble into fibrils and form higher-level structures is critical for understanding bone mechanics and diseases and can lead to bio-inspired materials (Fig. 2).
  • Beta-sheet rich protein materials: Silks and amyloid proteins Beta-sheets structures, composed of hierarchical assemblies of H-bonds, form the basic building block of many protein materials such as spider silk, muscle tissue or amyloid fibers. These materials feature outstanding mechanical properties that combine exceptional strength, robustness and resilience. Our studies focus on how nano structures are able to tune the mechanics of those materials and enable them to achieve the highest strength (Figs. 2, 3).
  • Alpha-helix rich intermediate filament protein materials Intermediate filaments, largely composed of alpha helix structures, serve as an important component of the cytoskeleton in metazoan cells. These fibrous proteins have also been linked to serious human diseases including muscle dystrophies and rapid aging disease (Progeria). Our study focuses on their biomechanical properties and the mechanism of those diseases, in joint work with experimental collaborators (Fig. 2).
  • Rational material design and manufacturing inspired by biological materials The existence of multiple advantages in biological materials go beyond our current capacity in designing and synthesizing engineered materials. Learning the mechanics and process of those materials will eventually enable us to produce advanced engineering materials with comparable material properties and multifunctionalities as their natural counterparts (Fig. 4).


  • Bottom-up multiscale modeling of hierarchical protein materials Theoretical and experimental studies show that the nanostructure and nanomechanical properties of protein materials are the key to understanding the mechanisms of the diseases related to mutated protein structure and chemistry. Molecular modeling by ab initio methods has shown that a single point mutation can only locally affect the mechanical features of a protein molecule, but its influence on the material and tissue level appears in the hierarchical context. Therefore, any study restricted to a single scale level is far from enough to model and understand the full biomechanics and biomateriomics of a protein material. Thus the multiscale modeling approach that starts from the fundamental level and is up-scaled by a finertrains-coarser computational strategy provides the efficient way to study the hierarchical structures and material functions at multiple scales as summarized in Fig. 1.
  • Comparative study of multiple protein materials We have used computational modeling tools to systematically investigate several key biological materials including bone, nacre, spider silk and intermediate filament network (Fig. 2). We have also applied mathematical tools including category theory to perform comparative studies and find that the synergistic organization of the building blocks is critical for those materials to reach superior properties, including an ability to translate insights from one material domain into another. By utilizing what we learn from nature and computational studies, we can achieve complex and optimized material functions by using limited types of raw materials but tuning their arrangements.
  • Material design aided by computation and advanced manufacturing A recently developed additive manufacturing technique is used in our work by using the information extracted from our computational study to inform 3D printing of functional materials (Fig. 4). Advanced 3D printers can precisely print the designed architecture with a multitude of materials of designed mechanics in one structure where we can achieve microstructural variation at any point in its design. The ability to achieve microstructural variation can make the material have much more possible mechanics than single values of the raw materials. Such a characteristic is similar to many carbon-based materials with different microscopic morphologies (diamond, amorphous carbon, graphene and carbon nanotube) to achieve diverse mechanical features.


Large scale modeling of collagenous tissues and bone We have built a mineralized collagen microfibril model and used it to investigated how mineral density in bone affects its mechanical characteristics under tensile loading. This model enabled fullatomistic calculations of the three-dimensional molecular structure of a mineralized collagen matrix and elucidated its mechanical features at various mineral densities. It was identified based on using the model that the existence of mineral crystals is important for the mechanics of bone, which agrees with earlier studies of the nanoscopic bone structure, indicating that bone' structure is synergistically integrated at different scales. De novo silk and silk-inspired materials Experimental efforts were combined with our modeling work to investigate the sequencestructure-function relationships of recombinant spider silk (Fig. 5). By designing different arrangement of the hydrophobic and hydrophilic domain in the silk sequence, we now have the ability to assess the propensity of the polypeptide to form β-sheets or crystalline structures and these features can also be related to differences in functional outcomes.

Nacre-inspired structural material with defect tolerance A recent study in our group explored a novel design process for nacreinspired materials with maximum defect tolerance. In this process (Fig. 6) computational structure optimization was combined with advanced multi-material 3D printer to create composites with fracture characteristics far superior to their stronger constituents. Printed composites with brick-and-mortar topology exhibited fracture resistances more than 20 times larger than that of their strongest constituents.


The new understanding of bone's molecular structure and function could help in unraveling the mechanisms of certain diseases, including osteoporosis and brittle bone disease. Using the model we can systematically understand how a protein sequence change causes a conformation change in the molecule level and thus alters the modulus of a mineralized fibril.

One important function of spider silk is its ability to be subjected to extreme loading and return its initial conformation after relaxation. Our multiscale models of silk can be used for studying the fabrication and mechanics of silk materials, and will facilitate the optimization of silk material design.

Our model suggests a reliable way to construct superior material with high fracture toughness by using raw materials with inferior mechanics. This combined technique will enable the rational design of materials with advanced mechanical properties.

Lead researchers

  • Dr. Zhao Qin (Research Scientist)
  • Dr. Markus J. Buehler (Professor of Civil and Environmental Engineering)

Current research team members

  • Dr. Shangchao Lin
  • Dr. Baptiste Depalle
  • Dr. Alfonso Gautieri
  • Dr. Reza Mirzaeifar
  • Talal Al-Mulla
  • Dieter Brosnan Brommer
  • Shu-Wei Chang
  • Chun-Teh Chen
  • Chia-Ching Chou
  • Leon Dimas
  • Tristan Giesa
  • Kai Jin
  • Gang Seob Jung
  • Max Solar
  • Anna Tarakanova
    See also:

Recent graduates

  • Prof. Sinan Keten
  • Prof. Steven Cranford
  • Prof. Zhiping Xu