Tag Archives: Nicholas A. Kotov

Nanobiotics and a new machine learning model

A May 16, 2022 news item on phys.org announces work on a new machine learning model that could be useful in the research into engineered nanoparticles for medical purposes (Note: Links have been removed),

With antibiotic-resistant infections on the rise and a continually morphing pandemic virus, it’s easy to see why researchers want to be able to design engineered nanoparticles that can shut down these infections.

A new machine learning model that predicts interactions between nanoparticles and proteins, developed at the University of Michigan, brings us a step closer to that reality.

A May 16, 2022 University of Michigan news release by Kate McAlpine, which originated the news item, delves further into the work (Note: Links have been removed),

“We have reimagined nanoparticles to be more than mere drug delivery vehicles. We consider them to be active drugs in and of themselves,” said J. Scott VanEpps, an assistant professor of emergency medicine and an author of the study in Nature Computational Science.

Discovering drugs is a slow and unpredictable process, which is why so many antibiotics are variations on a previous drug. Drug developers would like to design medicines that can attack bacteria and viruses in ways that they choose, taking advantage of the “lock-and-key” mechanisms that dominate interactions between biological molecules. But it was unclear how to transition from the abstract idea of using nanoparticles to disrupt infections to practical implementation of the concept. 

“By applying mathematical methods to protein-protein interactions, we have streamlined the design of nanoparticles that mimic one of the proteins in these pairs,” said Nicholas Kotov, the Irving Langmuir Distinguished University Professor of Chemical Sciences and Engineering and corresponding author of the study. 

“Nanoparticles are more stable than biomolecules and can lead to entirely new classes of antibacterial and antiviral agents.”

The new machine learning algorithm compares nanoparticles to proteins using three different ways to describe them. While the first was a conventional chemical description, the two that concerned structure turned out to be most important for making predictions about whether a nanoparticle would be a lock-and-key match with a specific protein.

Between them, these two structural descriptions captured the protein’s complex surface and how it might reconfigure itself to enable lock-and-key fits. This includes pockets that a nanoparticle could fit into, along with the size such a nanoparticle would need to be. The descriptions also included chirality, a clockwise or counterclockwise twist that is important for predicting how a protein and nanoparticle will lock in.

“There are many proteins outside and inside bacteria that we can target. We can use this model as a first screening to discover which nanoparticles will bind with which proteins,” said Emine Sumeyra Turali Emre, a postdoctoral researcher in chemical engineering and co-first author of the paper, along with Minjeong Cha, a PhD student in materials science and engineering.

Emre and Cha explained that researchers could follow up on matches identified by their algorithm with more detailed simulations and experiments. One such match could stop the spread of MRSA, a common antibiotic-resistant strain, using zinc oxide nanopyramids that block metabolic enzymes in the bacteria.  

“Machine learning algorithms like ours will provide a design tool for nanoparticles that can be used in many biological processes. Inhibition of the virus that causes COVID-19 is one good example,” said Cha. “We can use this algorithm to efficiently design nanoparticles that have broad-spectrum antiviral activity against all variants.”

This breakthrough was enabled by the Blue Sky Initiative at the University of Michigan College of Engineering. It provided $1.5 million to support the interdisciplinary team carrying out the fundamental exploration of whether a machine learning approach could be effective when data on the biological activity of nanoparticles is so sparse.

“The core of the Blue Sky idea is exactly what this work covers: finding a way to represent proteins and nanoparticles in a unified approach to understand and design new classes of drugs that have multiple ways of working against bacteria,” said Angela Violi, an Arthur F. Thurnau Professor, a professor of mechanical engineering and leader of the nanobiotics Blue Sky project.

Emre led the building of a database of interactions between proteins that could help to predict nanoparticle and protein interaction. Cha then identified structural descriptors that would serve equally well for nanoparticles and proteins, working with collaborators at the University of Southern California, Los Angeles to develop a machine learning algorithm that combed through the database and used the patterns it found to predict how proteins and nanoparticles would interact with one another. Finally, the team compared these predictions for lock-and-key matches with the results from experiments and detailed simulations, finding that they closely matched.

Additional collaborators on the project include Ji-Young Kim, a postdoctoral researcher in chemical engineering at U-M, who helped calculate chirality in the proteins and nanoparticles. Paul Bogdan and Xiongye Xiao, a professor and PhD student, respectively, in electrical and computer engineering at USC [University of Southern California] contributed to the graph theory descriptors. Cha then worked with them to design and train the neural network, comparing different machine learning models. All authors helped analyze the data.

Here are links to and a citation for the research briefing and paper, respectively,

Universal descriptors to predict interactions of inorganic nanoparticles with proteins. Nature Computational Science (2022) [Research briefing] DOI: https://doi.org/10.1038/s43588-022-00230-3 Published: 28 April 2022

This paper is behind a paywall.

Unifying structural descriptors for biological and bioinspired nanoscale complexes by Minjeong Cha, Emine Sumeyra Turali Emre, Xiongye Xiao, Ji-Young Kim, Paul Bogdan, J. Scott VanEpps, Angela Violi & Nicholas A. Kotov. Nature Computational Science volume 2, pages 243–252 (2022) Issue Date: April 2022 DOI: https://doi.org/10.1038/s43588-022-00229-w Published: 28 April 2022

This paper appears to be open access.

Stronger than steel and spider silk: artificial, biodegradable, cellulose nanofibres

This is an artificial and biodegradable are two adjectives you don’t usually see united by the conjunction, and. However, it is worth noting that the artificial material is initially derived from a natural material, cellulose. Here’s more from a May 16, 2018 news item on ScienceDaily,

At DESY’s [Deutsches Elektronen-Synchrotron] X-ray light source PETRA III, a team led by Swedish researchers has produced the strongest bio-material that has ever been made. The artifical, but bio-degradable cellulose fibres are stronger than steel and even than dragline spider silk, which is usually considered the strongest bio-based material. The team headed by Daniel Söderberg from the KTH Royal Institute of Technology in Stockholm reports the work in the journal ACS Nano of the American Chemical Society.

A May 16, 2018 DESY press release (also on EurekAlert), which originated the news item, provides more detail,

The ultrastrong material is made of cellulose nanofibres (CNF), the essential building blocks of wood and other plant life. Using a novel production method, the researchers have successfully transferred the unique mechanical properties of these nanofibres to a macroscopic, lightweight material that could be used as an eco-friendly alternative for plastic in airplanes, cars, furniture and other products. “Our new material even has potential for biomedicine since cellulose is not rejected by your body”, explains Söderberg.

The scientists started with commercially available cellulose nanofibres that are just 2 to 5 nanometres in diameter and up to 700 nanometres long. A nanometre (nm) is a millionth of a millimetre. The nanofibres were suspended in water and fed into a small channel, just one millimetre wide and milled in steel. Through two pairs of perpendicular inflows additional deionized water and water with a low pH-value entered the channel from the sides, squeezing the stream of nanofibres together and accelerating it.

This process, called hydrodynamic focussing, helped to align the nanofibres in the right direction as well as their self-organisation into a well-packed macroscopic thread. No glue or any other component is needed, the nanofibres assemble into a tight thread held together by supramolecular forces between the nanofibres, for example electrostatic and Van der Waals forces.

With the bright X-rays from PETRA III the scientists could follow and optimise the process. “The X-rays allow us to analyse the detailed structure of the thread as it forms as well as the material structure and hierarchical order in the super strong fibres,” explains co-author Stephan Roth from DESY, head of the Micro- and Nanofocus X-ray Scattering Beamline P03 where the threads were spun. “We made threads up to 15 micrometres thick and several metres in length.”

Measurements showed a tensile stiffness of 86 gigapascals (GPa) for the material and a tensile strength of 1.57 GPa. “The bio-based nanocellulose fibres fabricated here are 8 times stiffer and have strengths higher than natural dragline spider silk fibres,” says Söderberg. “If you are looking for a bio-based material, there is nothing quite like it. And it is also stronger than steel and any other metal or alloy as well as glass fibres and most other synthetic materials.” The artificial cellulose fibres can be woven into a fabric to create materials for various applications. The researchers estimate that the production costs of the new material can compete with those of strong synthetic fabrics. “The new material can in principle be used to create bio-degradable components,” adds Roth.

The study describes a new method that mimics nature’s ability to accumulate cellulose nanofibres into almost perfect macroscale arrangements, like in wood. It opens the way for developing nanofibre material that can be used for larger structures while retaining the nanofibres’ tensile strength and ability to withstand mechanical load. “We can now transform the super performance from the nanoscale to the macroscale,” Söderberg underlines. “This discovery is made possible by understanding and controlling the key fundamental parameters essential for perfect nanostructuring, such as particle size, interactions, alignment, diffusion, network formation and assembly.” The process can also be used to control nanoscale assembly of carbon tubes and other nano-sized fibres.

(There are some terminology and spelling issues, which are described at the end of this post.)

Let’s get back to a material that rivals spider silk and steel for strength (for some reason that reminded me of an old carnival game where you’d test your strength by swinging a mallet down on a ‘teeter-totter-like’ board and sending a metal piece up a post to make a bell ring). From a May 16, 2018 DESY press release (also on EurekAlert), which originated the news item,

The ultrastrong material is made of cellulose nanofibres (CNF), the essential building blocks of wood and other plant life. Using a novel production method, the researchers have successfully transferred the unique mechanical properties of these nanofibres to a macroscopic, lightweight material that could be used as an eco-friendly alternative for plastic in airplanes, cars, furniture and other products. “Our new material even has potential for biomedicine since cellulose is not rejected by your body”, explains Söderberg.

The scientists started with commercially available cellulose nanofibres that are just 2 to 5 nanometres in diameter and up to 700 nanometres long. A nanometre (nm) is a millionth of a millimetre. The nanofibres were suspended in water and fed into a small channel, just one millimetre wide and milled in steel. Through two pairs of perpendicular inflows additional deionized water and water with a low pH-value entered the channel from the sides, squeezing the stream of nanofibres together and accelerating it.

This process, called hydrodynamic focussing, helped to align the nanofibres in the right direction as well as their self-organisation into a well-packed macroscopic thread. No glue or any other component is needed, the nanofibres assemble into a tight thread held together by supramolecular forces between the nanofibres, for example electrostatic and Van der Waals forces.

With the bright X-rays from PETRA III the scientists could follow and optimise the process. “The X-rays allow us to analyse the detailed structure of the thread as it forms as well as the material structure and hierarchical order in the super strong fibres,” explains co-author Stephan Roth from DESY, head of the Micro- and Nanofocus X-ray Scattering Beamline P03 where the threads were spun. “We made threads up to 15 micrometres thick and several metres in length.”

Measurements showed a tensile stiffness of 86 gigapascals (GPa) for the material and a tensile strength of 1.57 GPa. “The bio-based nanocellulose fibres fabricated here are 8 times stiffer and have strengths higher than natural dragline spider silk fibres,” says Söderberg. “If you are looking for a bio-based material, there is nothing quite like it. And it is also stronger than steel and any other metal or alloy as well as glass fibres and most other synthetic materials.” The artificial cellulose fibres can be woven into a fabric to create materials for various applications. The researchers estimate that the production costs of the new material can compete with those of strong synthetic fabrics. “The new material can in principle be used to create bio-degradable components,” adds Roth.

The study describes a new method that mimics nature’s ability to accumulate cellulose nanofibres into almost perfect macroscale arrangements, like in wood. It opens the way for developing nanofibre material that can be used for larger structures while retaining the nanofibres’ tensile strength and ability to withstand mechanical load. “We can now transform the super performance from the nanoscale to the macroscale,” Söderberg underlines. “This discovery is made possible by understanding and controlling the key fundamental parameters essential for perfect nanostructuring, such as particle size, interactions, alignment, diffusion, network formation and assembly.” The process can also be used to control nanoscale assembly of carbon tubes and other nano-sized fibres.

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

Multiscale Control of Nanocellulose Assembly: Transferring Remarkable Nanoscale Fibril Mechanics to Macroscale Fibers by Nitesh Mittal, Farhan Ansari, Krishne Gowda V, Christophe Brouzet, Pan Chen, Per Tomas Larsson, Stephan V. Roth, Fredrik Lundell, Lars Wågberg, Nicholas A. Kotov, and L. Daniel Söderberg. ACS Nano, Article ASAP DOI: 10.1021/acsnano.8b01084 Publication Date (Web): May 9, 2018

Copyright © 2018 American Chemical Society

This paper is open access and accompanied by this image illustrating the work,

Courtesy: American Chemical Society and the researchers [Note: The bottom two images of cellulose nanofibres, which are constittuents of an artificial cellulose fibre, appear to be from a scanning tunneling microsscope. Credit: Nitesh Mittal, KTH Stockholm

This news has excited interest at General Electric (GE) (its Wikipedia entry), which has highlighted the work in a May 25, 2018 posting (The 5 Coolest Things On Earth This Week) by Tomas Kellner on the GE Reports blog.

Terminology and spelling

I’ll start with spelling since that’s the easier of the two. In some parts of the world it’s spelled ‘fibres’ and in other parts of the world it’s spelled ‘fibers’. When I write the text in my post, it tends to reflect the spelling used in the news/press releases. In other words, I swing in whichever direction the wind is blowing.

For diehards only

As i understand the terminology situation, nanocellulose and cellulose nanomaterials are interchangeable generic terms. Further, cellulose nanofibres (CNF) seems to be another generic term and it encompasses both cellulose nanocrystals (CNC) and cellulose nanofibrils (CNF). Yes, there appear to be two CNFs. Making matters more interesting is the fact that cellulose nanocrystals were originally christened nanocrystalline cellulose (NCC). For anyone who follows the science and technology scene, it becomes obvious that competing terminologies are the order of the day. Eventually the dust settles and naming conventions are resolved. More or less.

Ordinarily I would reference the Nanocellulose Wikipedia entry in my attempts to clarify the issues but it seems that the writers for the entry have not caught up to the current naming convention for cellulose nanocrystals, still referring to the material as nanocrystalline cellulose. This means, I can’t trust the rest of the entry, which has only one CNF (cellulose nanofibres).

I have paid more attention to the NCC/CNC situation and am not as familiar with the CNF situation. Using, NCC/CNC as an example of a terminology issue, I believe it was first developed in Canada and it was Canadian researchers who were pushing their NCC terminology while the international community pushed back with CNC.

In the end, NCC became a brand name, which was trademarked by CelluForce, a Canadian company in the CNC market. From the CelluForce Products page on Cellulose Nanocrystals,

CNC are not all made equal. The CNC produced by CelluForce is called CelluForce NCCTM and has specific properties and are especially easy to disperse. CelluForce NCCTM is the base material that CelluForce uses in all its products. This base material can be modified and tailored to suit the specific needs in various applications.

These, days CNC is almost universally used but NCC (not as a trademark) is a term still employed on occasion (and, oddly, the researchers are not necessarily Canadian).

Should anyone have better information about terminology issues, please feel free to comment.

Kevlar-wrapped batteries on an airplane

Researchers at the University of Michigan are not trying to bulletproof lithium-ion batteries with kevlar. Rather, they’re trying prevent fires. From a Jan. 27, 2015 University of Michigan news release (also on EurekAlert),

New battery technology from the University of Michigan should be able to prevent the kind of fires that grounded Boeing 787 Dreamliners in 2013.

The innovation is an advanced barrier between the electrodes in a lithium-ion battery.

Made with nanofibers extracted from Kevlar, the tough material in bulletproof vests, the barrier stifles the growth of metal tendrils that can become unwanted pathways for electrical current.

A U-M team of researchers also founded Ann Arbor-based Elegus Technologies to bring this research from the lab to market. Mass production is expected to begin in the fourth quarter 2016.

“Unlike other ultra strong materials such as carbon nanotubes, Kevlar is an insulator,” said Nicholas Kotov, the Joseph B. and Florence V. Cejka Professor of Engineering. “This property is perfect for separators that need to prevent shorting between two electrodes.”

Lithium-ion batteries work by shuttling lithium ions from one electrode to the other. This creates a charge imbalance, and since electrons can’t go through the membrane between the electrodes, they go through a circuit instead and do something useful on the way.

But if the holes in the membrane are too big, the lithium atoms can build themselves into fern-like structures, called dendrites, which eventually poke through the membrane. If they reach the other electrode, the electrons have a path within the battery, shorting out the circuit. This is how the battery fires on the Boeing 787 are thought to have started.

“The fern shape is particularly difficult to stop because of its nanoscale tip,” said Siu On Tung, a graduate student in Kotov’s lab, as well as chief technology officer at Elegus. “It was very important that the fibers formed smaller pores than the tip size.”

While the widths of pores in other membranes are a few hundred nanometers, or a few hundred-thousandths of a centimeter, the pores in the membrane developed at U-M are 15-to-20 nanometers across. They are large enough to let individual lithium ions pass, but small enough to block the 20-to-50-nanometer tips of the fern-structures.

The researchers made the membrane by layering the fibers on top of each other in thin sheets. This method keeps the chain-like molecules in the plastic stretched out, which is important for good lithium-ion conductivity between the electrodes, Tung said.

“The special feature of this material is we can make it very thin, so we can get more energy into the same battery cell size, or we can shrink the cell size,” said Dan VanderLey, an engineer who helped found Elegus through U-M’s Master of Entrepreneurship program. “We’ve seen a lot of interest from people looking to make thinner products.”

Thirty companies have requested samples of the material.

Kevlar’s heat resistance could also lead to safer batteries as the membrane stands a better chance of surviving a fire than most membranes currently in use.

While the team is satisfied with the membrane’s ability to block the lithium dendrites, they are currently looking for ways to improve the flow of loose lithium ions so that batteries can charge and release their energy more quickly.

For anyone unfamiliar with the Boeing 787 Dreamliner fires, caused by lithium-ion batteries, these Boeing fires and others are mentioned in my May 29, 2013 post (Life-cycle assessment for electric vehicle lithium-ion batteries and nanotechnology is a risk analysis) scroll down about 50% of the way.

As for the research paper, here’s a link and a citation,

A dendrite-suppressing composite ion conductor from aramid nanofibres by Siu-On Tung, Szushen Ho, Ming Yang, Ruilin Zhang, & Nicholas A. Kotov. Nature Communications 6, Article number: 6152 doi:10.1038/ncomms7152 Published 27 January 2015

This paper is behind a paywall.

You can find out more about Elegus Technologies here.