Tag Archives: Markus J. Buehler

Sonifying proteins to make music and brand new proteins

Markus Buehler at the Massachusetts Institute of Technology (MIT) has been working with music and science for a number of years. My December 9, 2011 posting, Music, math, and spiderwebs, was the first one here featuring his work. My November 28, 2012 posting, Producing stronger silk musically, was a followup to Buehler’s previous work.

A June 28, 2019 news item on Azonano provides a recent update,

Composers string notes of different pitch and duration together to create music. Similarly, cells join amino acids with different characteristics together to make proteins.

Now, researchers have bridged these two seemingly disparate processes by translating protein sequences into musical compositions and then using artificial intelligence to convert the sounds into brand-new proteins. …

Caption: Researchers at MIT have developed a system for converting the molecular structures of proteins, the basic building blocks of all living beings, into audible sound that resembles musical passages. Then, reversing the process, they can introduce some variations into the music and convert it back into new proteins never before seen in nature. Credit: Zhao Qin and Francisco Martin-Martinez

A June 26, 2019 American Chemical Society (ACS) news release, which originated the news item, provides more detail and a video,

To make proteins, cellular structures called ribosomes add one of 20 different amino acids to a growing chain in combinations specified by the genetic blueprint. The properties of the amino acids and the complex shapes into which the resulting proteins fold determine how the molecule will work in the body. To better understand a protein’s architecture, and possibly design new ones with desired features, Markus Buehler and colleagues wanted to find a way to translate a protein’s amino acid sequence into music.

The researchers transposed the unique natural vibrational frequencies of each amino acid into sound frequencies that humans can hear. In this way, they generated a scale consisting of 20 unique tones. Unlike musical notes, however, each amino acid tone consisted of the overlay of many different frequencies –– similar to a chord. Buehler and colleagues then translated several proteins into audio compositions, with the duration of each tone specified by the different 3D structures that make up the molecule. Finally, the researchers used artificial intelligence to recognize specific musical patterns that corresponded to certain protein architectures. The computer then generated scores and translated them into new-to-nature proteins. In addition to being a tool for protein design and for investigating disease mutations, the method could be helpful for explaining protein structure to broad audiences, the researchers say. They even developed an Android app [Amino Acid Synthesizer] to allow people to create their own bio-based musical compositions.

Here’s the ACS video,

A June 26, 2019 MIT news release (also on EurekAlert) provides some specifics and the MIT news release includes two embedded audio files,

Want to create a brand new type of protein that might have useful properties? No problem. Just hum a few bars.

In a surprising marriage of science and art, researchers at MIT have developed a system for converting the molecular structures of proteins, the basic building blocks of all living beings, into audible sound that resembles musical passages. Then, reversing the process, they can introduce some variations into the music and convert it back into new proteins never before seen in nature.

Although it’s not quite as simple as humming a new protein into existence, the new system comes close. It provides a systematic way of translating a protein’s sequence of amino acids into a musical sequence, using the physical properties of the molecules to determine the sounds. Although the sounds are transposed in order to bring them within the audible range for humans, the tones and their relationships are based on the actual vibrational frequencies of each amino acid molecule itself, computed using theories from quantum chemistry.

The system was developed by Markus Buehler, the McAfee Professor of Engineering and head of the Department of Civil and Environmental Engineering at MIT, along with postdoc Chi Hua Yu and two others. As described in the journal ACS Nano, the system translates the 20 types of amino acids, the building blocks that join together in chains to form all proteins, into a 20-tone scale. Any protein’s long sequence of amino acids then becomes a sequence of notes.

While such a scale sounds unfamiliar to people accustomed to Western musical traditions, listeners can readily recognize the relationships and differences after familiarizing themselves with the sounds. Buehler says that after listening to the resulting melodies, he is now able to distinguish certain amino acid sequences that correspond to proteins with specific structural functions. “That’s a beta sheet,” he might say, or “that’s an alpha helix.”

Learning the language of proteins

The whole concept, Buehler explains, is to get a better handle on understanding proteins and their vast array of variations. Proteins make up the structural material of skin, bone, and muscle, but are also enzymes, signaling chemicals, molecular switches, and a host of other functional materials that make up the machinery of all living things. But their structures, including the way they fold themselves into the shapes that often determine their functions, are exceedingly complicated. “They have their own language, and we don’t know how it works,” he says. “We don’t know what makes a silk protein a silk protein or what patterns reflect the functions found in an enzyme. We don’t know the code.”

By translating that language into a different form that humans are particularly well-attuned to, and that allows different aspects of the information to be encoded in different dimensions — pitch, volume, and duration — Buehler and his team hope to glean new insights into the relationships and differences between different families of proteins and their variations, and use this as a way of exploring the many possible tweaks and modifications of their structure and function. As with music, the structure of proteins is hierarchical, with different levels of structure at different scales of length or time.

The team then used an artificial intelligence system to study the catalog of melodies produced by a wide variety of different proteins. They had the AI system introduce slight changes in the musical sequence or create completely new sequences, and then translated the sounds back into proteins that correspond to the modified or newly designed versions. With this process they were able to create variations of existing proteins — for example of one found in spider silk, one of nature’s strongest materials — thus making new proteins unlike any produced by evolution.

Although the researchers themselves may not know the underlying rules, “the AI has learned the language of how proteins are designed,” and it can encode it to create variations of existing versions, or completely new protein designs, Buehler says. Given that there are “trillions and trillions” of potential combinations, he says, when it comes to creating new proteins “you wouldn’t be able to do it from scratch, but that’s what the AI can do.”

“Composing” new proteins

By using such a system, he says training the AI system with a set of data for a particular class of proteins might take a few days, but it can then produce a design for a new variant within microseconds. “No other method comes close,” he says. “The shortcoming is the model doesn’t tell us what’s really going on inside. We just know it works.

This way of encoding structure into music does reflect a deeper reality. “When you look at a molecule in a textbook, it’s static,” Buehler says. “But it’s not static at all. It’s moving and vibrating. Every bit of matter is a set of vibrations. And we can use this concept as a way of describing matter.”

The method does not yet allow for any kind of directed modifications — any changes in properties such as mechanical strength, elasticity, or chemical reactivity will be essentially random. “You still need to do the experiment,” he says. When a new protein variant is produced, “there’s no way to predict what it will do.”

The team also created musical compositions developed from the sounds of amino acids, which define this new 20-tone musical scale. The art pieces they constructed consist entirely of the sounds generated from amino acids. “There are no synthetic or natural instruments used, showing how this new source of sounds can be utilized as a creative platform,” Buehler says. Musical motifs derived from both naturally existing proteins and AI-generated proteins are used throughout the examples, and all the sounds, including some that resemble bass or snare drums, are also generated from the sounds of amino acids.

The researchers have created a free Android smartphone app, called Amino Acid Synthesizer, to play the sounds of amino acids and record protein sequences as musical compositions.

Here’s a link to and a citation for the paper,

A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence by Chi-Hua Yu, Zhao Qin, Francisco J. Martin-Martinez, Markus J. Buehler. ACS Nano 2019 XXXXXXXXXX-XXX DOI: https://doi.org/10.1021/acsnano.9b02180 Publication Date:June 26, 2019 Copyright © 2019 American Chemical Society

This paper is behind a paywall.

ETA October 23, 2019 1000 hours: Ooops! I almost forgot the link to the Aminot Acid Synthesizer.

Worm-inspired gel material and soft robots

The Nereis virens worm inspired new research out of the MIT Laboratory for Atomistic and Molecular Mechanics. Its jaw is made of soft organic material, but is as strong as harder materials such as human dentin. Photo: Alexander Semenov/Wikimedia Commons

What an amazing worm! Here’s more about robots inspired by the Nereis virens worm in a March 20, 2017 news item on Nanowerk,

A new material that naturally adapts to changing environments was inspired by the strength, stability, and mechanical performance of the jaw of a marine worm. The protein material, which was designed and modeled by researchers from the Laboratory for Atomistic and Molecular Mechanics (LAMM) in the Department of Civil and Environmental Engineering (CEE) [at the Massachusetts Institute of Technology {MIT}], and synthesized in collaboration with the Air Force Research Lab (AFRL) at Wright-Patterson Air Force Base, Ohio, expands and contracts based on changing pH levels and ion concentrations. It was developed by studying how the jaw of Nereis virens, a sand worm, forms and adapts in different environments.

The resulting pH- and ion-sensitive material is able to respond and react to its environment. Understanding this naturally-occurring process can be particularly helpful for active control of the motion or deformation of actuators for soft robotics and sensors without using external power supply or complex electronic controlling devices. It could also be used to build autonomous structures.

A March 20, 2017 MIT news release, which originated the news item, provides more detail,

“The ability of dramatically altering the material properties, by changing its hierarchical structure starting at the chemical level, offers exciting new opportunities to tune the material, and to build upon the natural material design towards new engineering applications,” wrote Markus J. Buehler, the McAfee Professor of Engineering, head of CEE, and senior author of the paper.

The research, recently published in ACS Nano, shows that depending on the ions and pH levels in the environment, the protein material expands and contracts into different geometric patterns. When the conditions change again, the material reverts back to its original shape. This makes it particularly useful for smart composite materials with tunable mechanics and self-powered roboticists that use pH value and ion condition to change the material stiffness or generate functional deformations.

Finding inspiration in the strong, stable jaw of a marine worm

In order to create bio-inspired materials that can be used for soft robotics, sensors, and other uses — such as that inspired by the Nereis — engineers and scientists at LAMM and AFRL needed to first understand how these materials form in the Nereis worm, and how they ultimately behave in various environments. This understanding involved the development of a model that encompasses all different length scales from the atomic level, and is able to predict the material behavior. This model helps to fully understand the Nereis worm and its exceptional strength.

“Working with AFRL gave us the opportunity to pair our atomistic simulations with experiments,” said CEE research scientist Francisco Martin-Martinez. AFRL experimentally synthesized a hydrogel, a gel-like material made mostly of water, which is composed of recombinant Nvjp-1 protein responsible for the structural stability and impressive mechanical performance of the Nereis jaw. The hydrogel was used to test how the protein shrinks and changes behavior based on pH and ions in the environment.

The Nereis jaw is mostly made of organic matter, meaning it is a soft protein material with a consistency similar to gelatin. In spite of this, its strength, which has been reported to have a hardness ranging between 0.4 and 0.8 gigapascals (GPa), is similar to that of harder materials like human dentin. “It’s quite remarkable that this soft protein material, with a consistency akin to Jell-O, can be as strong as calcified minerals that are found in human dentin and harder materials such as bones,” Buehler said.

At MIT, the researchers looked at the makeup of the Nereis jaw on a molecular scale to see what makes the jaw so strong and adaptive. At this scale, the metal-coordinated crosslinks, the presence of metal in its molecular structure, provide a molecular network that makes the material stronger and at the same time make the molecular bond more dynamic, and ultimately able to respond to changing conditions. At the macroscopic scale, these dynamic metal-protein bonds result in an expansion/contraction behavior.

Combining the protein structural studies from AFRL with the molecular understanding from LAMM, Buehler, Martin-Martinez, CEE Research Scientist Zhao Qin, and former PhD student Chia-Ching Chou ’15, created a multiscale model that is able to predict the mechanical behavior of materials that contain this protein in various environments. “These atomistic simulations help us to visualize the atomic arrangements and molecular conformations that underlay the mechanical performance of these materials,” Martin-Martinez said.

Specifically, using this model the research team was able to design, test, and visualize how different molecular networks change and adapt to various pH levels, taking into account the biological and mechanical properties.

By looking at the molecular and biological makeup of a the Nereis virens and using the predictive model of the mechanical behavior of the resulting protein material, the LAMM researchers were able to more fully understand the protein material at different scales and provide a comprehensive understanding of how such protein materials form and behave in differing pH settings. This understanding guides new material designs for soft robots and sensors.

Identifying the link between environmental properties and movement in the material

The predictive model explained how the pH sensitive materials change shape and behavior, which the researchers used for designing new PH-changing geometric structures. Depending on the original geometric shape tested in the protein material and the properties surrounding it, the LAMM researchers found that the material either spirals or takes a Cypraea shell-like shape when the pH levels are changed. These are only some examples of the potential that this new material could have for developing soft robots, sensors, and autonomous structures.

Using the predictive model, the research team found that the material not only changes form, but it also reverts back to its original shape when the pH levels change. At the molecular level, histidine amino acids present in the protein bind strongly to the ions in the environment. This very local chemical reaction between amino acids and metal ions has an effect in the overall conformation of the protein at a larger scale. When environmental conditions change, the histidine-metal interactions change accordingly, which affect the protein conformation and in turn the material response.

“Changing the pH or changing the ions is like flipping a switch. You switch it on or off, depending on what environment you select, and the hydrogel expands or contracts” said Martin-Martinez.

LAMM found that at the molecular level, the structure of the protein material is strengthened when the environment contains zinc ions and certain pH levels. This creates more stable metal-coordinated crosslinks in the material’s molecular structure, which makes the molecules more dynamic and flexible.

This insight into the material’s design and its flexibility is extremely useful for environments with changing pH levels. Its response of changing its figure to changing acidity levels could be used for soft robotics. “Most soft robotics require power supply to drive the motion and to be controlled by complex electronic devices. Our work toward designing of multifunctional material may provide another pathway to directly control the material property and deformation without electronic devices,” said Qin.

By studying and modeling the molecular makeup and the behavior of the primary protein responsible for the mechanical properties ideal for Nereis jaw performance, the LAMM researchers are able to link environmental properties to movement in the material and have a more comprehensive understanding of the strength of the Nereis jaw.

Here’s link to and a citation for the paper,

Ion Effect and Metal-Coordinated Cross-Linking for Multiscale Design of Nereis Jaw Inspired Mechanomutable Materials by Chia-Ching Chou, Francisco J. Martin-Martinez, Zhao Qin, Patrick B. Dennis, Maneesh K. Gupta, Rajesh R. Naik, and Markus J. Buehler. ACS Nano, 2017, 11 (2), pp 1858–1868 DOI: 10.1021/acsnano.6b07878 Publication Date (Web): February 6, 2017

Copyright © 2017 American Chemical Society

This paper is behind a paywall.

Fusing graphene flakes for 3D graphene structures that are 10x as strong as steel

A Jan. 6, 2017 news item on Nanowerk describes how geometry may have as much or more to do with the strength of 3D graphene structures than the graphene used to create them,

A team of researchers at MIT [Massachusetts Institute of Technology] has designed one of the strongest lightweight materials known, by compressing and fusing flakes of graphene, a two-dimensional form of carbon. The new material, a sponge-like configuration with a density of just 5 percent, can have a strength 10 times that of steel.

In its two-dimensional form, graphene is thought to be the strongest of all known materials. But researchers until now have had a hard time translating that two-dimensional strength into useful three-dimensional materials.

The new findings show that the crucial aspect of the new 3-D forms has more to do with their unusual geometrical configuration than with the material itself, which suggests that similar strong, lightweight materials could be made from a variety of materials by creating similar geometric features.

The findings are being reported today [Jan. 6, 2017\ in the journal Science Advances, in a paper by Markus Buehler, the head of MIT’s Department of Civil and Environmental Engineering (CEE) and the McAfee Professor of Engineering; Zhao Qin, a CEE research scientist; Gang Seob Jung, a graduate student; and Min Jeong Kang MEng ’16, a recent graduate.

A Jan. 6, 2017 MIT news release (also on EurekAlert), which originated the news item, describes the research in more detail,

Other groups had suggested the possibility of such lightweight structures, but lab experiments so far had failed to match predictions, with some results exhibiting several orders of magnitude less strength than expected. The MIT team decided to solve the mystery by analyzing the material’s behavior down to the level of individual atoms within the structure. They were able to produce a mathematical framework that very closely matches experimental observations.

Two-dimensional materials — basically flat sheets that are just one atom in thickness but can be indefinitely large in the other dimensions — have exceptional strength as well as unique electrical properties. But because of their extraordinary thinness, “they are not very useful for making 3-D materials that could be used in vehicles, buildings, or devices,” Buehler says. “What we’ve done is to realize the wish of translating these 2-D materials into three-dimensional structures.”

The team was able to compress small flakes of graphene using a combination of heat and pressure. This process produced a strong, stable structure whose form resembles that of some corals and microscopic creatures called diatoms. These shapes, which have an enormous surface area in proportion to their volume, proved to be remarkably strong. “Once we created these 3-D structures, we wanted to see what’s the limit — what’s the strongest possible material we can produce,” says Qin. To do that, they created a variety of 3-D models and then subjected them to various tests. In computational simulations, which mimic the loading conditions in the tensile and compression tests performed in a tensile loading machine, “one of our samples has 5 percent the density of steel, but 10 times the strength,” Qin says.

Buehler says that what happens to their 3-D graphene material, which is composed of curved surfaces under deformation, resembles what would happen with sheets of paper. Paper has little strength along its length and width, and can be easily crumpled up. But when made into certain shapes, for example rolled into a tube, suddenly the strength along the length of the tube is much greater and can support substantial weight. Similarly, the geometric arrangement of the graphene flakes after treatment naturally forms a very strong configuration.

The new configurations have been made in the lab using a high-resolution, multimaterial 3-D printer. They were mechanically tested for their tensile and compressive properties, and their mechanical response under loading was simulated using the team’s theoretical models. The results from the experiments and simulations matched accurately.

The new, more accurate results, based on atomistic computational modeling by the MIT team, ruled out a possibility proposed previously by other teams: that it might be possible to make 3-D graphene structures so lightweight that they would actually be lighter than air, and could be used as a durable replacement for helium in balloons. The current work shows, however, that at such low densities, the material would not have sufficient strength and would collapse from the surrounding air pressure.

But many other possible applications of the material could eventually be feasible, the researchers say, for uses that require a combination of extreme strength and light weight. “You could either use the real graphene material or use the geometry we discovered with other materials, like polymers or metals,” Buehler says, to gain similar advantages of strength combined with advantages in cost, processing methods, or other material properties (such as transparency or electrical conductivity).

“You can replace the material itself with anything,” Buehler says. “The geometry is the dominant factor. It’s something that has the potential to transfer to many things.”

The unusual geometric shapes that graphene naturally forms under heat and pressure look something like a Nerf ball — round, but full of holes. These shapes, known as gyroids, are so complex that “actually making them using conventional manufacturing methods is probably impossible,” Buehler says. The team used 3-D-printed models of the structure, enlarged to thousands of times their natural size, for testing purposes.

For actual synthesis, the researchers say, one possibility is to use the polymer or metal particles as templates, coat them with graphene by chemical vapor deposit before heat and pressure treatments, and then chemically or physically remove the polymer or metal phases to leave 3-D graphene in the gyroid form. For this, the computational model given in the current study provides a guideline to evaluate the mechanical quality of the synthesis output.

The same geometry could even be applied to large-scale structural materials, they suggest. For example, concrete for a structure such a bridge might be made with this porous geometry, providing comparable strength with a fraction of the weight. This approach would have the additional benefit of providing good insulation because of the large amount of enclosed airspace within it.

Because the shape is riddled with very tiny pore spaces, the material might also find application in some filtration systems, for either water or chemical processing. The mathematical descriptions derived by this group could facilitate the development of a variety of applications, the researchers say.

“This is an inspiring study on the mechanics of 3-D graphene assembly,” says Huajian Gao, a professor of engineering at Brown University, who was not involved in this work. “The combination of computational modeling with 3-D-printing-based experiments used in this paper is a powerful new approach in engineering research. It is impressive to see the scaling laws initially derived from nanoscale simulations resurface in macroscale experiments under the help of 3-D printing,” he says.

This work, Gao says, “shows a promising direction of bringing the strength of 2-D materials and the power of material architecture design together.”

There’s a video describing the work,

Here’s a link to and a citation for the paper,

The mechanics and design of a lightweight three-dimensional graphene assembly by Zhao Qin, Gang Seob Jung, Min Jeong Kang, and Markus J. Buehler. Science Advances  06 Jan 2017: Vol. 3, no. 1, e1601536 DOI: 10.1126/sciadv.1601536  04 January 2017

This paper appears to be open access.

Making better concrete by looking to nature for inspiration

Researchers from the Masssachusetts Institute of Technology (MIT) are working on a new formula for concrete based on bones, shells, and other such natural materials. From a May 25, 2016 news item on Nanowerk (Note: A link has been removed),

Researchers at MIT are seeking to redesign concrete — the most widely used human-made material in the world — by following nature’s blueprints.

In a paper published online in the journal Construction and Building Materials (“Roadmap across the mesoscale for durable and sustainable cement paste – A bioinspired approach”), the team contrasts cement paste — concrete’s binding ingredient — with the structure and properties of natural materials such as bones, shells, and deep-sea sponges. As the researchers observed, these biological materials are exceptionally strong and durable, thanks in part to their precise assembly of structures at multiple length scales, from the molecular to the macro, or visible, level.

A May 26, 2016 MIT news release (also on EurekAlert), which originated the news item, provides more detail,

From their observations, the team, led by Oral Buyukozturk, a professor in MIT’s Department of Civil and Environmental Engineering (CEE), proposed a new bioinspired, “bottom-up” approach for designing cement paste.

“These materials are assembled in a fascinating fashion, with simple constituents arranging in complex geometric configurations that are beautiful to observe,” Buyukozturk says. “We want to see what kinds of micromechanisms exist within them that provide such superior properties, and how we can adopt a similar building-block-based approach for concrete.”

Ultimately, the team hopes to identify materials in nature that may be used as sustainable and longer-lasting alternatives to Portland cement, which requires a huge amount of energy to manufacture.

“If we can replace cement, partially or totally, with some other materials that may be readily and amply available in nature, we can meet our objectives for sustainability,” Buyukozturk says.

“The merger of theory, computation, new synthesis, and characterization methods have enabled a paradigm shift that will likely change the way we produce this ubiquitous material, forever,” Buehler says. “It could lead to more durable roads, bridges, structures, reduce the carbon and energy footprint, and even enable us to sequester carbon dioxide as the material is made. Implementing nanotechnology in concrete is one powerful example [of how] to scale up the power of nanoscience to solve grand engineering challenges.”

From molecules to bridges

Today’s concrete is a random assemblage of crushed rocks and stones, bound together by a cement paste. Concrete’s strength and durability depends partly on its internal structure and configuration of pores. For example, the more porous the material, the more vulnerable it is to cracking. However, there are no techniques available to precisely control concrete’s internal structure and overall properties.

“It’s mostly guesswork,” Buyukozturk says. “We want to change the culture and start controlling the material at the mesoscale.”

As Buyukozturk describes it, the “mesoscale” represents the connection between microscale structures and macroscale properties. For instance, how does cement’s microscopic arrangement affect the overall strength and durability of a tall building or a long bridge? Understanding this connection would help engineers identify features at various length scales that would improve concrete’s overall performance.

“We’re dealing with molecules on the one hand, and building a structure that’s on the order of kilometers in length on the other,” Buyukozturk says. “How do we connect the information we develop at the very small scale, to the information at the large scale? This is the riddle.”

Building from the bottom, up

To start to understand this connection, he and his colleagues looked to biological materials such as bone, deep sea sponges, and nacre (an inner shell layer of mollusks), which have all been studied extensively for their mechanical and microscopic properties. They looked through the scientific literature for information on each biomaterial, and compared their structures and behavior, at the nano-, micro-, and macroscales, with that of cement paste.

They looked for connections between a material’s structure and its mechanical properties. For instance, the researchers found that a deep sea sponge’s onion-like structure of silica layers provides a mechanism for preventing cracks. Nacre has a “brick-and-mortar” arrangement of minerals that generates a strong bond between the mineral layers, making the material extremely tough.

“In this context, there is a wide range of multiscale characterization and computational modeling techniques that are well established for studying the complexities of biological and biomimetic materials, which can be easily translated into the cement community,” says Masic.

Applying the information they learned from investigating biological materials, as well as knowledge they gathered on existing cement paste design tools, the team developed a general, bioinspired framework, or methodology, for engineers to design cement, “from the bottom up.”

The framework is essentially a set of guidelines that engineers can follow, in order to determine how certain additives or ingredients of interest will impact cement’s overall strength and durability. For instance, in a related line of research, Buyukozturk is looking into volcanic ash [emphasis mine] as a cement additive or substitute. To see whether volcanic ash would improve cement paste’s properties, engineers, following the group’s framework, would first use existing experimental techniques, such as nuclear magnetic resonance, scanning electron microscopy, and X-ray diffraction to characterize volcanic ash’s solid and pore configurations over time.

Researchers could then plug these measurements into models that simulate concrete’s long-term evolution, to identify mesoscale relationships between, say, the properties of volcanic ash and the material’s contribution to the strength and durability of an ash-containing concrete bridge. These simulations can then be validated with conventional compression and nanoindentation experiments, to test actual samples of volcanic ash-based concrete.

Ultimately, the researchers hope the framework will help engineers identify ingredients that are structured and evolve in a way, similar to biomaterials, that may improve concrete’s performance and longevity.

“Hopefully this will lead us to some sort of recipe for more sustainable concrete,” Buyukozturk says. “Typically, buildings and bridges are given a certain design life. Can we extend that design life maybe twice or three times? That’s what we aim for. Our framework puts it all on paper, in a very concrete way, for engineers to use.”

This is not the only team looking at new methods for producing the material, my Dec. 24, 2012 posting features a number of ‘concrete’ research projects.

Also, I highlighted the reference to ‘volcanic ash’ as it reminded me of Roman concrete which has lasted for over 2000 years and includes volcanic sand and volcanic rock.  You can read more about it in a Dec. 18, 2014 article by Mark Miller for Ancient Origins where he describes the wonders of the material and what was then a recent discovery of the Romans’ recipe.

I have two links and citations, first, the MIT paper, then the paper on Roman concrete.

Roadmap across the mesoscale for durable and sustainable cement paste – A bioinspired approach by Steven D. Palkovic, Dieter B. Brommer, Kunal Kupwade-Patil, Admir Masic, Markus J. Buehler, Oral Büyüköztürk.Construction and Building Materials Volume 115, 15 July 2016, Pages 13–31.  doi:10.1016/j.conbuildmat.2016.04.020

Mechanical resilience and cementitious processes in Imperial Roman architectural mortar by Marie D. Jackson, Eric N. Landis, Philip F. Brune, Massimo Vitti, Heng Chen, Qinfei Li, Martin Kunz, Hans-Rudolf Wenk, Paulo J. M. Monteiro, and Anthony R. Ingraffea. Proceedings of the National Academy of Sciences  vol. 111 no. 52 18484–18489, doi: 10.1073/pnas.1417456111

The first paper is behind a paywall but the second one appears to be open access.

Congratulations to Markus Buehler on his Foresight Institute Feynman Prize for advances in nanotechnology

A May 24, 2016 Massachusetts Institute of Technology (MIT) news release celebrates Markus Buehler’s latest award,

On May 21 [2016], Department of Civil and Environmental Engineering head and McAfee Professor of Engineering Markus J. Buehler received the 2015 Foresight Institute Feynman Prize in Theoretical Molecular Nanotechnology. Buehler’s award was one of three prizes presented by the Foresight Institute, a leading think tank and public interest organization, at its annual conference in Palo Alto, California. …

The Foresight Institute recognized Buehler for his important contributions to making nanotechnology scalable for large-scale materials applications, enabled by bottom-up multiscale computational methods, and linking new manufacturing and characterization methods.

Focusing on mechanical properties — especially deformation and failure — and translation from biological materials and structures to bio-inspired synthetic materials, his work has led to the development and application of new modeling, design, and manufacturing approaches for advanced materials that offer greater resilience and a wide range of controllable properties from the nano- to the macroscale.

Buehler’s signature achievement, according to the Institute, is the application of molecular and chemical principles in the analysis of mechanical systems, with the aim to design devices and materials that provide a defined set of functions.

“It’s an incredible honor to receive such an esteemed award. I owe this to the outstanding students and postdocs whom I had a pleasure to work with over the years, my colleagues, as well my own mentors,” Buehler said. “Richard Feynman was a revolutionary scientist of his generation. It’s a privilege to share his goals of researching molecular technology at very small scale to create new, more efficient, and better lasting materials at much larger scale that will help transform lives and industries.”

The two other award winners are Professor Michelle Y. Simmons of the University of New South Wales [Australia], who won the Feynman Prize for Experimental Molecular Nanotechnology, and Northwestern University graduate student Chuyang Cheng, who won the Distinguished Student Award.

I have featured Buehler’s work here a number of times. The most recent appearance was in  a May 29, 2015 posting about synthesizing spider’s silk.

Synthesizing spider silk

Most of the research on spider silk and spider webs that’s featured here is usually from the Massachusetts Institute of Technology (MIT) and, more specifically, from professor Markus J. Buehler. This May 28, 2015 news item on ScienceDaily, which heralds the development of synthetic spider silk, is no exception,

After years of research decoding the complex structure and production of spider silk, researchers have now succeeded in producing samples of this exceptionally strong and resilient material in the laboratory. The new development could lead to a variety of biomedical materials — from sutures to scaffolding for organ replacements — made from synthesized silk with properties specifically tuned for their intended uses.

The findings are published this week in the journal Nature Communications by MIT professor of civil and environmental engineering (CEE) Markus Buehler, postdocs Shangchao Lin and Seunghwa Ryu, and others at MIT, Tufts University, Boston University, and in Germany, Italy, and the U.K.

The research, which involved a combination of simulations and experiments, paves the way for “creating new fibers with improved characteristics” beyond those of natural silk, says Buehler, who is also the department head in CEE. The work, he says, should make it possible to design fibers with specific characteristics of strength, elasticity, and toughness.

The new synthetic fibers’ proteins — the basic building blocks of the material — were created by genetically modifying bacteria to make the proteins normally produced by spiders. These proteins were then extruded through microfluidic channels designed to mimic the effect of an organ, called a spinneret, that spiders use to produce natural silk fibers.

A May 28, 2015 MIT news release (also on EurekAlert), which originated the news item, describes the work in more detail,

While spider silk has long been recognized as among the strongest known materials, spiders cannot practically be bred to produce harvestable fibers — so this new approach to producing a synthetic, yet spider-like, silk could make such strong and flexible fibers available for biomedical applications. By their nature, spider silks are fully biocompatible and can be used in the body without risk of adverse reactions; they are ultimately simply absorbed by the body.

The researchers’ “spinning” process, in which the constituent proteins dissolved in water are extruded through a tiny opening at a controlled rate, causes the molecules to line up in a way that produces strong fibers. The molecules themselves are a mixture of hydrophobic and hydrophilic compounds, blended so as to naturally align to form fibers much stronger than their constituent parts. “When you spin it, you create very strong bonds in one direction,” Buehler says.

The team found that getting the blend of proteins right was crucial. “We found out that when there was a high proportion of hydrophobic proteins, it would not spin any fibers, it would just make an ugly mass,” says Ryu, who worked on the project as a postdoc at MIT and is now an assistant professor at the Korea Advanced Institute of Science and Technology. “We had to find the right mix” in order to produce strong fibers, he says.

The researchers made use of computational modelling to speed up the process of synthesizing proteins for synthetic spider silk, from the news release,

This project represents the first use of simulations to understand silk production at the molecular level. “Simulation is critical,” Buehler explains: Actually synthesizing a protein can take several months; if that protein doesn’t turn out to have exactly the right properties, the process would have to start all over.

Using simulations makes it possible to “scan through a large range of proteins until we see changes in the fiber stiffness,” and then home in on those compounds, says Lin, who worked on the project as a postdoc at MIT and is now an assistant professor at Florida State University.

Controlling the properties directly could ultimately make it possible to create fibers that are even stronger than natural ones, because engineers can choose characteristics for a particular use. For example, while spiders may need elasticity so their webs can capture insects without breaking, those designing fibers for use as surgical sutures would need more strength and less stretchiness. “Silk doesn’t give us that choice,” Buehler says.

The processing of the material can be done at room temperature using water-based solutions, so scaling up manufacturing should be relatively easy, team members say. So far, the fibers they have made in the lab are not as strong as natural spider silk, but now that the basic process has been established, it should be possible to fine-tune the materials and improve its strength, they say.

“Our goal is to improve the strength, elasticity, and toughness of artificially spun fibers by borrowing bright ideas from nature,” Lin says. This study could inspire the development of new synthetic fibers — or any materials requiring enhanced properties, such as in electrical and thermal transport, in a certain direction.

Here’s a link to and a citation for the paper,

Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres by Shangchao Lin, Seunghwa Ryu, Olena Tokareva, Greta Gronau, Matthew M. Jacobsen, Wenwen Huang, Daniel J. Rizzo, David Li, Cristian Staii, Nicola M. Pugno, Joyce Y. Wong, David L. Kaplan, & Markus J. Buehler. Nature Communications 6, Article number: 6892 doi:10.1038/ncomms7892 Published 28 May 2015

This paper is behind a paywall.

My two most recent (before this one) postings about Buehler’s work are an August 5, 2014 piece about structural failures and a June 4, 2014 piece about spiderwebs and music.

Finally, I recognized one of the authors, Nicola Pugno from Italy. He’s been mentioned here more than once in regard to his biomimicry work which has often been focused on geckos and their adhesive qualities as per this April 3, 2014 post announcing his book ‘An Experimental Study on Adhesive or Anti-Adhesive, Bio-Inspired Experimental Nanomaterials‘ (co-authored with Emiliano Lepore).

Things falling apart: both a Nigerian novel and research at the Massachusetts Intitute of Technology

First the Nigerian novel ‘Things Fall Apart‘ (from its Wikipedia entry; Note: Links have been removed),

Things Fall Apart is an English-language novel by Nigerian author Chinua Achebe published in 1958 by William Heinemann Ltd in the UK; in 1962, it was also the first work published in Heinemann’s African Writers Series. Things Fall Apart is seen as the archetypal modern African novel in English, one of the first to receive global critical acclaim. It is a staple book in schools throughout Africa and is widely read and studied in English-speaking countries around the world. The title of the novel comes from William Butler Yeats’ poem “The Second Coming”.[1]

For those unfamiliar with the Yeats poem, this is the relevant passage (from Wikipedia entry for The Second Coming),

Turning and turning in the widening gyre
The falcon cannot hear the falconer;
Things fall apart; the centre cannot hold;
Mere anarchy is loosed upon the world,
The blood-dimmed tide is loosed, and everywhere
The ceremony of innocence is drowned;
The best lack all conviction, while the worst
Are full of passionate intensity.

The other ‘Things fall apart’ item, although it’s an investigation into ‘how things fall apart’, is mentioned in an Aug. 4, 2014 news item on Nanowerk,

Materials that are firmly bonded together with epoxy and other tough adhesives are ubiquitous in modern life — from crowns on teeth to modern composites used in construction. Yet it has proved remarkably difficult to study how these bonds fracture and fail, and how to make them more resistant to such failures.

Now researchers at MIT [Massachusetts Institute of Technology] have found a way to study these bonding failures directly, revealing the crucial role of moisture in setting the stage for failure. Their findings are published in the journal Proceedings of the National Academy of Science in a paper by MIT professors of civil and environmental engineering Oral Buyukozturk and Markus Buehler; research associate Kurt Broderick of MIT’s Microsystems Technology Laboratories; and doctoral student Denvid Lau, who has since joined the faculty at the City University of Hong Kong.

An Aug. 4, 2014 MIT news release written by David Chandler (also on EurekAlert), which originated the news item, provides an unexpectedly fascinating discussion of bonding, interfaces, and infrastructure,

“The bonding problem is a general problem that is encountered in many disciplines, especially in medicine and dentistry,” says Buyukozturk, whose research has focused on infrastructure, where such problems are also of great importance. “The interface between a base material and epoxy, for example, really controls the properties. If the interface is weak, you lose the entire system.”

“The composite may be made of a strong and durable material bonded to another strong and durable material,” Buyukozturk adds, “but where you bond them doesn’t necessarily have to be strong and durable.”

Besides dental implants and joint replacements, such bonding is also critical in construction materials such as fiber-reinforced polymers and reinforced concrete. But while such materials are widespread, understanding how they fail is not simple.

There are standard methods for testing the strength of materials and how they may fail structurally, but bonded surfaces are more difficult to model. “When we are concerned with deterioration of this interface when it is degraded by moisture, classical methods can’t handle that,” Buyukozturk says. “The way to approach it is to look at the molecular level.”

When such systems are exposed to moisture, “it initiates new molecules at the interface,” Buyukozturk says, “and that interferes with the bonding mechanism. How do you assess how weak the interface becomes when it is affected? We came up with an innovative method to assess the interface weakening as a result of exposure to environmental effects.”

The team used a combination of molecular simulations and laboratory tests in its assessment. The modeling was based on fundamental principles of molecular interactions, not on empirical data, Buyukozturk says.

In the laboratory tests, Buyukozturk and his colleagues controlled the residual stresses in a metal layer that was bonded and then forcibly removed. “We validated the method, and showed that moisture has a degrading effect,” he says.

The findings could lead to exploration of new ways to prevent moisture from reaching into the bonded layer, perhaps using better sealants. “Moisture is the No. 1 enemy,” Buyukozturk says.

“I think this is going to be an important step toward assessment of the bonding, and enable us to design more durable composites,” he adds. “It gives a quantitative knowledge of the interface” — for example, predicting that under specific conditions, a given bonded material will lose 30 percent of its strength.

Interface problems are universal, Buyukozturk says, occurring in many areas besides biomedicine and construction. “They occur in mechanical devices, in aircraft, electrical equipment, in the packaging of electronic components,” he says. “We feel this will have very broad applications.”

Bonded composite materials are beginning to be widely used in airplane manufacturing; often these composites are then bonded to traditional materials, like aluminum. “We have not had enough experience to prove the durability of these composite systems is going to be there after 20 years,” Buyukozturk says.

Here’s a link to and a citation for the research paper,

A robust nanoscale experimental quantification of fracture energy in a bilayer material system by Denvid Lau, Kurt Broderick, Markus J. Buehler, and Oral Büyüköztürk. PNAS, doi: 10.1073/pnas.1402893111 published August 5, 2014

This paper is behind a paywall.

Gossamer silk that withstands hurricane force winds

I’ve written about spiderwebs before (mostly recently in my Dec. 9, 2011 posting titled, Music, math, and spiderwebs. Researcher, Markus J. Buehler, was featured in the Dec. 2011 posting and he is featured in this one too. I imagine he’s the ‘go to’ spiderweb researcher at MIT (Massachusetts Institute of Technology).

The most discussed characteristic of spiderwebs is their strength, a topic of endless fascination. The Feb. 1, 2012 news item on physorg.com offers a new take on this phenomenon,

While researchers have long known of the incredible strength of spider silk, the robust nature of the tiny filaments cannot alone explain how webs survive multiple tears and winds that exceed hurricane strength.

Now, a study that combines experimental observations of spider webs with complex computer simulations has shown that web durability depends not only on silk strength, but on how the overall web design compensates for damage and the response of individual strands to continuously varying stresses.

Reporting in the cover story of the Feb. 2, 2012, issue of Nature, researchers from the Massachusetts Institute of Technology (MIT) [team leader Markus Buehler, associate professor of civil and environmental engineering at MIT] and the Politecnico di Torino [team leader Nicola Pugno, Professor of Solid and Structural Mechanics at the Politecnico di Torino] in Italy show how spider web-design localizes strain and damage, preserving the web as a whole.

Very simply, two of the types of spider silk that give the webs their strength were examined separately and together. From the news item,

Viscid silk is stretchy, wet and sticky, and it is the silk that winds out in increasing spirals from the web center. Its primary function is to capture prey. Dragline silk is stiff and dry, and it serves as the threads that radiate out from a web’s center, providing structural support. Dragline silk is crucial to the mechanical behavior of the web.

If you’re a weaver, that description will like remind you of warp and weft. The warp threads provide the strength and remain immobile while the the weft threads are the ones you weave in and out and use to create patterns, etc. if you are so inclined.

These observations about viscid and dragline silk have practical applications (from the news item),

The concept of selective, localized failure for spider webs is interesting since it is a distinct departure from the structural principles that seem to be in play for many biological materials and components,” adds Dennis Carter, the NSF program director for biomechanics and mechanobiology who helped support the study. [emphasis mine]

“For example, the distributed material components in bone spread stress broadly, adding strength. There is no ‘wasted’ material, minimizing the weight of the structure. While all of the bone is being used to resist force, bone everywhere along the structure tends to be damaged prior to failure.”

In contrast, a spider’s web is organized to sacrifice local areas so that failure will not prevent the remaining web from functioning, even if in a diminished capacity, says Carter. “This is a clever strategy when the alternative is having to make an entire, new web!,” he adds. “As Buehler suggests, engineers can learn from nature and adapt the design strategies that are most appropriate for specific applications.”

According to David Kaplan’s Feb. 2, 2012 article for MIT News, the spiderweb’s localized failure was a considered a sign of weakness,

It turns out that a key property of spider silk that helps make webs robust is something previously considered a weakness: the way it can stretch and soften at first when pulled, and then stiffen again as the force of the pulling increases.

This stiffening response is crucial to the way spider silk resists damage. Buehler and his team analyzed how materials with different properties, arranged in the same web pattern, respond to localized stresses. They found that materials with other responses — those that either behave as a simple linear spring as they’re pulled, or start out stretchy and then become more “plastic” — perform much less effectively.

Spider webs, it turns out, can take quite a beating without failing. Damage tends to be localized, affecting just a few threads — the place where a bug got caught in the web and flailed around, for example. This localized damage can simply be repaired, rather than replaced, or even left alone if the web continues to function as before. “Even if it has a lot of defects, the web actually still functions mechanically virtually the same way,” Buehler says. “It’s a very flaw-tolerant system.”

Here’s an image that illustrates how spiderwebs react to stress,

Images show the successive deformation states as loading is increased on a spider web, with red marking high stresses. Simulation picture by S. Cranford & M.J. Buehler/MIT, photographic image by Francesco Tomasinelli & Emanuele Biggi.

The researchers’ article in Nature, Nonlinear material behaviour of spider silk yields robust webs by Steven W. Cranford, Anna Tarakanova, Nicola M. Pugno & Markus J. Buehler is available behind a paywall.

Note: I’m pretty sure I searched to find out if it should be spiderwebs or spider webs. I will investigate further but do not have time now. Meanwhile, I committed to spiderwebs in Dec. 2011.

Canada Foundation for Innovation “World’s Best”?; Ping hoodie, clothing that networks socially; life protection clothing; getting spiders to weave building materials?; open access archive for nano papers

The headline for the news release on Marketwire (via the Canadian Science Policy site) is: Canada Foundation for Innovation(CFI) Practices is Called ‘World’s Best’. As it’s been a bit slow for news here I began wondering ‘which practices in which countries are being compared’? After reviewing the reports quickly, I can’t answer the question. There are no bibliographies in any of the three reports related to this KPMG study while the footnotes make reference only to other KPMG and Canadian studies. It was a bit of surprise, I was expecting to see reports from other countries and/or from international organizations and some insight into their analysis as comparing agencies in different countries can be complicated.

I’m not sure how they arrived at their conclusion although they provide some interesting data. From the Overall Evaluation report (p. 28 PDF, p. 24 print),

Exhibit [Table] 4.16 shows that, on average, there have been about 6.4 collaborations with end-users per PL/PU in the past year, three-quarters of which used the CFI projects as key resources, and about 10.2 collaborations per Department Head, about 70% of which using CFI projects in a significant way. For PLs/PUs, there are only small differences in use of CFI projects as a key resource by type of end-user, but Department Heads show more variation in the use of CFI project by type of user; it is unknown if this is significant.

Note that 64% of PL/PUs’ and 80% of Department Heads’ end-user collaborations, respectively, are with Canadian organizations; there is a significant international component (with OMS data suggesting that the CFI projects are a significant attractor for international organizations to collaborate [emphasis mine]).

It certainly seems laudable although I question whether you can conclude that the CFI is a significant international organization attractor by inference alone. Shouldn’t this be backed up with another instrument, such as a questionnaire for a survey/poll of the international organizations, asking why they are collaborating with Canadian scientists? I was not able to find any mention of such a survey or poll taking place.

From everything I hear, Canadians are excellent at academic science research and attracting researchers from around the world and because of our penchant for collaboration we (as they say) “punch above our weight.” I just wish this report did a better job of providing evidence for its assertions about the CFI’s ‘best practices’.

Ping hoodie

Thanks to Adrian Covert’s article on Fast Company, I found information about a prototype for a piece of wearable computing, the Ping hoodie. From Covert’s article,

The Ping clothing concept makes use of embedded electronics and haptics controlled by the Arduino Lilypad system, which transmits to your device (most likely a smartphone) using the Lylipad Xbee. This tech serves as the core interface between you and the information you need. If someone special is sending you a call or text, you can set the hoodie to vibrate in a specific manner, letting you know it’s them. Actions as simple as lifting or dropping the hood can be used to send status updates and messages on Facebook, with the potential to target certain groups of friends.

There’s more at Fast Company or you can check out electricfoxy where the designer, Jennifer Darmour has her site which is where I found this image,

Ping hoodie (wearable computing) designed by Jennifer Darmour at electricfoxy

Do go to Darmour’s site (although Fast Company offers a pretty good selection) if you want to see all the images including close ups of the fabric (don’t forget to scroll horizontally as well as vertically).

Clothing that protects your life

P2i, a company I’ve mentioned here before, has announced a ‘new’ revolutionary form of protective clothing. Actually, it sounds like an improvement rather than a revolutionary concept but maybe I’m getting jaded. From the news item on Nanowerk,

A revolutionary new generation of high-performance body armour, launched today, is lighter, more comfortable and more protective than any previous design, thanks to P2i’s liquid-repellent nano-coating technology.

The new G Tech Vest is a joint development between two world-class UK companies with very strong credentials for the life protection market: P2i, whose technology was originally developed to make soldiers’ protective clothing more effective against chemical attack; and Global Armour, which has been at the leading edge of product innovation in the armour industry for over 30 years.

The G Tech Vest employs brand-new lightweight materials, both in the physical armour itself (a closely-guarded trade secret) and the fabric that forms the armour into a garment. P2i’s technology reduces weight by avoiding the need for bulky durable water repellents and increases comfort by preserving the natural airflow and drape of the garment material.

I recently (April 15, 2010) made a comment about how modern soldiers are beginning to resemble medieval knights and this talk of armour certainly reinforces the impression.

Spiders weaving building materials?

Michael Berger at Nanowerk has written an in-depth article about spider silk and its possible application, amongst others, as a building material. He’s interviewed one of the authors (Markus J. Buehler) of a recent paper that lays out “… a framework for predicting the nanostructure of spider silk using atomistic principles.” More from the Spotlight article on Nanowerk,

In a paper published as the cover article in Applied Physics Letters on April 12, 2010 (“Atomistic model of the spider silk nanostructure”), [Sinan] Keten and Buehler demonstrate an innovative application of replica exchange molecular dynamics simulations on a key spider silk repeating sequence, resulting in the first atomistic level structure of spider silk.

More specifically, the MIT researchers found the formation of beta-sheet structures in poly-Ala rich parts of the structure, the presence of semi-extended GGX domains that form H-bonded 31 helix type structures and a complete lack of alpha-helical conformations in the molecular structures formed by the self-assembly of MaSp1 proteins. These results resolve controversies around the structure of the amorphous domains in silk, by illustrating for the first time that these semi-extended, well-oriented and more sparsely H-bonded structures that resemble 31 helices could be the molecular source of the large semi-crystalline fraction of silks and the so-called ‘pre-stretched’ configuration proposed for these domains.

Shy of reading the original research, which I likely wouldn’t understand easily, Berger’s article provides an excellent entry into the subject.

Open access archive for nano papers

My final item for today is about a project to give free access to papers on nanotechnology that they host and/or publish.  Hooray! It’s very frustrating to get stuck behind paywalls so I’m thrilled that there’s an agency offering free access. From the news item on Nanowerk,

The Nano Archive, the online open-access repository for nanoscience and nanotechnology, invites you to submit research papers to be published free online for users across the globe.

Submitted papers can include peer-reviewed articles, journal articles, review articles, conference and workshop papers, theses and dissertations, book chapters and sections, as well as multimedia and audio-visual materials. The Nano Archive also welcomes new, unpublished research results to be shared with the wider community.

The Nano Archive is part of the ICPC NanoNet project, funded by the EU under FP7. It brings together partners from the EU, Russia, India, China and Africa, and provides wider access to published nanoscience research and opportunities for collaboration between scientists in the EU and International Cooperation Partner Countries.

The Nano Archive currently hosts over 6000 papers. You can read more about the sponsoring agency, the ICPC (International Cooperation Partner Countries) NanoNet here. It has funding for four years and was started in 2008.