Heidelberg Institute for Theoretical Studies (Germany)
Local Project ID:
HPC Platform used:
Hornet of HLRS
Composite materials made up of inorganic and biological matter present remarkable properties including fracture resistance, toughness and strength. A team of scientists of the Heidelberg Institute for Theoretical Studies has been investigating the mechanical properties of nacre, a material that possesses great stability due to its elaborate hierarchical nanostructures.
The iridescent shimmer found on the inside of seashells and the outside of pearls is caused by a substance called nacre. It is one of the strongest and most resilient materials found in nature due to its composite structure, pairing stiff but brittle calcium carbonate crystals with soft layers of protein that impart it an elevated resistance against fracture. Biomaterials such as nacre are highly organised at the nanoscale, so by studying this organisation it may be possible to elucidate the source of their remarkable mechanical performance, which often outstrips synthetic analogues.
Structurally, the majority of nacre is made up of calcium carbonate crystals that are several tens of nanometres thick. These are stacked in a very organised manner similar to a traditional ‘bricks and mortar’ arrangement. Intersecting these crystals in parallel stripes are layers of protein and chitin, only a few nanometres thick, which provide extra mechanical stability.
Professor Frauke Gräter of the Heidelberg Institute for Theoretical Studies has been leading a project investigating the separate components of nacre under physical loads. “The calcium carbonate found in nacre comes in the form of aragonite, a crystalline structure commonly found in nature,” she says. “A wider debate in materials science at present is the role that flaws — tiny errors in the molecular structure — have on mechanical performance of crystals. Experimental data shows us that these flaws exist in aragonite, so we want to determine whether or not these nanometer-sized gaps in structure cause the material to fail earlier under stress.”
Behaviour at the nanoscale is notoriously hard to predict, and as such it does not necessarily follow that flaws in a structure at this level will confer the same type of structural weakness that flaws of a similar proportion do at the macroscale. However, Gräter and her team have found that these flaws do indeed impact on the structural mechanics of aragonite. “Using 11.5 million core hours on the Hornet supercomputer, we have extensively simulated crystals of different sizes, with different sized flaws and at differing loading conditions,” she says. “We found that even the smallest flaw of a few atoms causes the crystals to fail earlier.”
As part of their work, the group developed a method called force distribution analysis. When engineers want to test the stability of a structure, they use crash test simulators. Force distribution analysis does the same thing but at a molecular scale. It exists as a patch for GROMACS, a widely used molecular dynamics code, and has been integral to understanding the role of flaws in the crystals. “Our programme highlighted the areas at which stress concentrates when placed under load, and it was clear to see that even tiny flaws cause stress to concentrate at that point,” Gräter states.
This discovery has forced the team to look for alternative sources for nacre’s strength. They now believe that the protein component may compensate for flaws in the crystalline structure of aragonite. “If the protein is able to fill in the gaps of the crystals, it may be acting as a shock absorber, dissipating the forces and stress concentrations and thus allowing the crystal to behave as if it is flawless,” explains Gräter.
The team have already carried out some preliminary studies on the peptides present in the protein layer of nacre and their interaction with the aragonite crystals. Some aminoacids in the peptide, glutamate and aspartate, have negatively charged side chains that bind to the positively charged calcium ions present in the crystal. The study involved binding these peptides to the crystal surface and then pulling them off, and it was shown that the bond is very strong.
The next step for the researchers will be to simulate the two components in action together. “The idea that the protein layer acts as a sort of shock absorber in nacre has been around for a while, but what that idea is really missing is actual data about how the forces are propagated from one layer to the other at the molecular scale,” Gräter states. “We’re aiming to provide a solid basis for what has already been speculated.”
Biocomposite materials such as nacre are found everywhere in nature, including in the human body in the case of teeth and bones. Similar arrangements of stiff crystalline blocks and thin soft organic layers confer them similar structural integrity. At present, materials used to replace bone and teeth such as ceramics are fully inorganic, but Gräter’s work may provide a push towards creating similarly structured synthetic materials that closely mimic the mechanical stability of the original skeletal tissue.
This project was made possible through PRACE (Partnership for Advanced Computing in Europe) with HPC system Hornet of the High Performance Computing Center Stuttgart (HLRS) serving as computing platform.
This is a reprint of the article published in the PRACE Women in HPC Magazine 2015
Dr. Frauke Gräter
Professor for Molecular Biomechanics
Interdisciplinary Center for Scientific Computing (IWR)
Heidelberg University, Mathematikon, INF 205
D69120 Heidelberg (Germany)
Heidelberg Institute for Theoretical Studies
69118 Heidelberg, Germany