Tag Archives: David Spivak

Producing stronger silk musically

Markus Buehler and his interdisciplinary team (my previous posts on their work includes Gossamer silk that withstands hurricane force winds and Music, math, and spiderwebs) have synthesized a new material based on spider silk. From the Nov. 28, 2012 news item on ScienceDaily,

Pound for pound, spider silk is one of the strongest materials known: Research by MIT’s [Massachusetts Institute of Technology] Markus Buehler has helped explain that this strength arises from silk’s unusual hierarchical arrangement of protein building blocks.

Now Buehler — together with David Kaplan of Tufts University and Joyce Wong of Boston University — has synthesized new variants on silk’s natural structure, and found a method for making further improvements in the synthetic material.

And an ear for music, it turns out, might be a key to making those structural improvements.

Here’s Buehler describing the work in an MIT video clip,

The Nov. 28, 2012 MIT news release by David Chandler provides more details,

Buehler’s previous research has determined that fibers with a particular structure — highly ordered, layered protein structures alternating with densely packed, tangled clumps of proteins (ABABAB) — help to give silk its exceptional properties. For this initial attempt at synthesizing a new material, the team chose to look instead at patterns in which one of the structures occurred in triplets (AAAB and BBBA).

Making such structures is no simple task. Kaplan, a chemical and biomedical engineer, modified silk-producing genes to produce these new sequences of proteins. Then Wong, a bioengineer and materials scientist, created a microfluidic device that mimicked the spider’s silk-spinning organ, which is called a spinneret.

Even after the detailed computer modeling that went into it, the outcome came as a bit of a surprise, Buehler says. One of the new materials produced very strong protein molecules — but these did not stick together as a thread. The other produced weaker protein molecules that adhered well and formed a good thread. “This taught us that it’s not sufficient to consider the properties of the protein molecules alone,” he says. “Rather, [one must] think about how they can combine to form a well-connected network at a larger scale.”

The different levels of silk’s structure, Buehler says, are analogous to the hierarchical elements that make up a musical composition — including pitch, range, dynamics and tempo. The team enlisted the help of composer John McDonald, a professor of music at Tufts, and MIT postdoc David Spivak, a mathematician who specializes in a field called category theory. Together, using analytical tools derived from category theory to describe the protein structures, the team figured out how to translate the details of the artificial silk’s structure into musical compositions.

The differences were quite distinct: The strong but useless protein molecules translated into music that was aggressive and harsh, Buehler says, while the ones that formed usable fibers sound much softer and more fluid.

Combining materials modeling with mathematical and musical tools, Buehler says, could provide a much faster way of designing new biosynthesized materials, replacing the trial-and-error approach that prevails today. Genetically engineering organisms to produce materials is a long, painstaking process, he says, but this work “has taught us a new approach, a fundamental lesson” in combining experiment, theory and simulation to speed up the discovery process.

Materials produced this way — which can be done under environmentally benign, room-temperature conditions — could lead to new building blocks for tissue engineering or other uses, Buehler says: scaffolds for replacement organs, skin, blood vessels, or even new materials for use in civil engineering.

It may be that the complex structures of music can reveal the underlying complex structures of biomaterials found in nature, Buehler says. “There might be an underlying structural expression in music that tells us more about the proteins that make up our bodies. After all, our organs — including the brain — are made from these building blocks, and humans’ expression of music may inadvertently include more information that we are aware of.”

“Nobody has tapped into this,” he says, adding that with the breadth of his multidisciplinary team, “We could do this — making better bio-inspired materials by using music, and using music to better understand biology.”

At the end of Chandler’s news release there’s a notice about a summer course with Markus Buehler,

For those interested in the work Professor Buehler is doing, you may also be interested to know that he is offering a short course on campus this summer called Materials By Design.

Materials By Design
June 17-20, 2013

Through lectures and hands-on labs, participants will learn how materials failure, studied from a first principles perspective, can be applied in an effective “learning-from-failure approach” to design and make novel materials. Participants will also learn how superior material properties in nature and biology can be mimicked in bioinspired materials for applications in new technology. This course will be of interest to scientists, engineers, managers, and policy makers working in the area of materials design, development, manufacturing, and testing. [emphasis mine]

I wasn’t expecting to see managers and policy makers as possible students for this course.

By the way, Buehler is not the only scientist to make a connection between music and biology (although he seems to be the only person using the concept for applications), there’s also geneticist and biophysicist, Mae Wan Ho and her notion of quantum jazz. From the Quantum Jazz Biology* article by David Reilly in the June 23, 2010 Isis Report,

I use the analogy of ‘quantum jazz’ to express the quantum coherence of the organism. It goes through a fantastic range of space and time scales, from the tiniest atom or subatomic particle to the whole organism and beyond. Organisms communicate with other organisms, and are attuned to natural rhythms, so they have circadian rhythms, annual rhythms, and so on. At the other extreme, you have very fast reactions that take place in femtoseconds. And all these rhythms are coordinated, there is evidence for that.

Music, math, and spiderwebs

I pricked up my ears when I saw the word ‘analogy’. As a writer, I tend to be quite interested in analogies and metaphors, especially as they relate to science. I certainly never expected to find an analogy established by mathematical rigour—it never occurred to the poet in my soul. Thankfully, mathematicians at MIT (Massachusetts Institute of Technology) were not constrained by my lack of imagination. From the Dec. 8, 2011 news item written by Denise Brehm on Nanowerk,

Using a new mathematical methodology, researchers at MIT have created a scientifically rigorous analogy that shows the similarities between the physical structure of spider silk and the sonic structure of a melody, proving that the structure of each relates to its function in an equivalent way.

The step-by-step comparison begins with the primary building blocks of each item — an amino acid and a sound wave — and moves up to the level of a beta sheet nanocomposite (the secondary structure of a protein consisting of repeated hierarchical patterns) and a musical riff (a repeated pattern of notes or chords). The study explains that structural patterns are directly related to the functional properties of lightweight strength in the spider silk and, in the riff, sonic tension that creates an emotional response in the listener.

The Dec. 8, 2011 news release at MIT goes on to explain,

While likening spider silk to musical composition may appear to be more novelty than breakthrough, the methodology behind it represents a new approach to comparing research findings from disparate scientific fields. Such analogies could help engineers develop materials that make use of the repeating patterns of simple building blocks found in many biological materials that, like spider silk, are lightweight yet extremely failure-resistant. The work also suggests that engineers may be able to gain new insights into biological systems through the study of the structure-function relationships found in music and other art forms.

The MIT researchers — David Spivak, a postdoc in the Department of Mathematics, Associate Professor Markus Buehler of the Department of Civil and Environmental Engineering (CEE) and CEE graduate student Tristan Giesa — published their findings in the December issue of BioNanoScience.

Here’s part of how they developed the analogy between spider silk and music using mathematics (from the MIT news release),

They created the analogy using ontology logs, or “ologs,” a concept introduced about a year ago by Spivak, who specializes in a branch of mathematics called category theory. Ologs provide an abstract means for categorizing the general properties of a system — be it a material, mathematical concept or phenomenon — and showing inherent relationships between function and structure.

To build the ologs, the researchers used information from Buehler’s previous studies of the nanostructure of spider silk and other biological materials.

“There is mounting evidence that similar patterns of material features at the nanoscale, such as clusters of hydrogen bonds or hierarchical structures, govern the behavior of materials in the natural environment, yet we couldn’t mathematically show the analogy between different materials,” Buehler says. “The olog lets us compile information about how materials function in a mathematically rigorous way and identify those patterns that are universal to a very broad class of materials. Its potential for engineering the built environment — in the design of new materials, structures or infrastructure — is immense.”

“This work is very exciting because it brings forth an approach founded on category theory to bridge music (and potentially other aspects of the fine arts) to a new field of materiomics,” says Associate Professor of Biomedical Engineering Joyce Wong of Boston University, a biomaterials scientist and engineer, as well as a musician. “This approach is particularly appropriate for the hierarchical design of proteins, as they show in the silk example. What is particularly exciting is the opportunity to reveal new relationships between seemingly disparate fields with the aim of improving materials engineering and design.”

I always like to have a visual,

Graphic: Christine Daniloff

You can get more details from either the Nanowerk website or the MIT website.

Since it’s a Friday I thought I’d include a video of a song about spiderwebs and found this on YouTube,

Happy Friday!