Member Login Menu

Laboratory for Atomistic and Molecular Mechanics (LAMM)

MIT Logo General

Multi-scale modeling and simulation of biological and bioinspired materials
Zhao Qin

December 2015


 Multi-scale modeling and simulation of
biological and bioinspired materials and
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
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 mutifunctionalities 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
 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


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.

Selected Publications

[1] L. Dimas, G. Bratzel, I. Eylon, M.J. Buehler, Advanced Functional Materials, 2013
[2] A. Nair, A. Gautieri, S.W. Chang, M.J. Buehler, Nature Communications, 2013
[3] Z. Qin, M.J. Buehler, Nature Communications, 2013
[4] S.W. Cranford, A. Tarakanova, N. Pugno, M.J. Buehler, Nature, 2012
[5] T. Giesa, D. Spivak, M.J. Buehler, Advanced Engineering Materials, 2012
[6] S. Keten, Z. Xu, B. Ihle, M.J. Buehler, Nature Materials, 2010
[7] M.J. Buehler, Nano Today, 2010
[8] Z. Qin, L. Kreplak, M.J. Buehler, PLoS ONE, 2009
[9] M.J. Buehler, Y. Yung, Nature Materials, 2009

Core Competencies

Figure 1. Bottom-up description of the mechanical properties of biological materials by combining simulations and experiments and explicitly considering hierarchical structure from chemical level upwards.

Lead Researchers:
Dr. Zhao Qin (Research 
 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