Tag Archives: Kate McAlpine

Nanobiotics and a new machine learning model

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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.

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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.

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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.

Geek rap, Björk, and science communication

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I came across a June 29, 2011 article in Physics Today [online] by Steve Corneliussen about ‘geek’ rap. From the Corneliussen article,

Science rap is no flash in the pan according to Dennis Overbye, the high-visibility New York Times science writer. This week he proclaimed that “‘geek rap’ … is becoming one of the most popular and vital forms of science communication.” Immediately he added: “Few exegeses of the Large Hadron Collider match Alpinekat’s ‘Large Hadron Rap’ for punch and rhythm, and Stephen Hawking’s robot voice and puckish wit have spawned a host of imitators, like M C Hawking, rapping about black holes and entropy.”

Poetry and/or music, in combination with science is not new. Take a few more recent examples, James Clerk Maxwell, in addition to his scientific accomplishments in the 19th century, was also a poet and Tom Lehrer (pianist and mathematician) set the Periodic Table of Chemical Elements to music (The Elements) in the 1950s.

One can stretch back further to De rerum natura, an epic poem about physics and Epicurean philosophy written by Lucretius in the first century BCE (before the common era). From the Wikipedia essay on De rerum natura,

The poem, written in dactylic hexameter, is divided into six books, and explores Epicurean physics through richly poetic language and metaphors. Lucretius presents the principles of atomism; the nature of the mind and soul; explanations of sensation and thought; the development of the world and its phenomena; and explains a variety of celestial and terrestrial phenomena. The universe described in the poem operates according to these physical principles, guided by fortuna, “chance,” and not the divine intervention of the traditional Roman deities.

It’s good to see that rappers are keeping the traditions alive and reinterpreting them for modern audiences. Dennis Overbye, the New York Times science writer mentioned in the Corneliussen article, recently highlighted Baba Brinkman, a Vancouver-based rapper, (mentioned here a few times a list of those posts follows), who’s currently  performing his Rap Guide to Evolution at an off Broadway theatre. From Overbye’s June 27, 2011 article of Brinkman’s show,

Don’t sleep with mean people.

That’s a lesson some of us learn painfully, if at all, in regard to our personal happiness. That there could be a cosmic evolutionary angle to this thought had never occurred to me until I heard Baba Brinkman, a rap artist and Chaucer scholar, say it the other night. Think of it as the ultimate example of thinking globally and acting very, very locally. We are all in the process of recreating our species in our most intimate acts:

Don’t sleep with mean people, that’s the anthem

Please! Think about your granddaughters and grandsons

Don’t sleep with mean people, pretty or handsome

Mean people hold the gene pool for ransom.

…

Writing on NYTimes.com last year, Olivia Judson, the biologist and author, called the evolution rap show “one of the most astonishing, and brilliant, lectures on evolution I’ve ever seen.” On a humid night last week the crowd spilled out of the playhouse and down the streets of SoHo after the show, chatting about the technical and social aspects of natural selection.

Björk has taken her own approach to science, music, and, in her case, song with her new show Biophilia. From the July 1, 2011 article by David Robson for The New Scientist’s Culture Lab blog,

As the lights dimmed and we waited for Björk to mount the stage of the Victorian market hall, the last thing I expected to hear was a recording of the dulcet tones of David Attenborough, waxing lyrical about nature, music and technology.

Perhaps I shouldn’t have been surprised, though. The show does, after all, take its name, Biophilia, from Edward O. Wilson’s theory about the instinctive bond between humankind and nature, which he claims is a necessary consequence of our evolutionary origins. And the Icelandic singer has made it clear that she is a life-long fan of the British naturalist. “When I was a kid, my rock star was David Attenborough,” she recently told Rolling Stone. “I’ve always been interested in science.”

And boy, did she manage to pack a dizzying amount of it into the show. There were songs about plate tectonics, galaxy formation, crystallisation, DNA and heredity, equilibrium, gravity and dark matter. Then there were the novel instruments, including four harps driven by 10-foot pendulums and a gigantic Tesla coil that sparked in time to the music. We’re told that the structures of her compositions, too, were inspired by scientific ideas – the beats to some of the songs were based on prime number sequences, for example.

While Baba’s rap is peer-reviewed, Björk’s work is aimed a little differently. As David Bruggeman (Pasco Phronesis) explains in his July 3, 2011 posting,

They [reviews of Biophilia] suggest that Björk is not even thinking of encroaching on Baba Brinkman or They Might Be Giants science music turf anytime soon.  While she shares their enthusiasm for science, expressing that enthusiasm, rather than explaining the concepts underneath it, seems to be the main science emphasis of the work.

Here’s a demonstration of the Tesla coil synth prior to a Biophilia performance in Campfield (ETA July 5, 2011: This is where Bjork premiered Biophilia June 27, 2011 at the Manchester International Festival, more details in July 5, 2011 note added after this  post),

There are more Biophilia-related video clips but this was one of the shorter ones.

As for the Baba Brinkman posts I mentioned earlier, here are the most relevant ones from the earliest to the latest,

Darwin theme: Rap about Darwin & evolutionary biology and Darwinism in quantum dots

Rapping science

Interview with Baba Brinkman who performs his Rap Guide to Evolution in Vancouver on Feb. 20, 2011

Performance, feedback, revision: Baba Brinkman’s Feb.20.11 performance

Baba Brinkman launches his new Lit Fuse record label website and a Vancouver debut performance of his Chaucer/Gilgamesh/Beowulf adaptation

2011 World Science Festival and a couple of Canucks

Prince Charles, evolution and Baba Brinkman

Here’s very recent news (from a July 4, 2011 email) about Baba’s CD,

First thing’s [sic] first, I have a new CD out! The Rap Guide to Evolution: Revised is a brand new 14-track album produced by Mr. Simmonds. It started out as a “remix” of the original RGE CD from a few years ago but soon took on a life of its own with all new music, new collaborations, and most of the lyrics re-written (performance, feedback, revision), plus three completely new tracks. We’ve been working on this album all year long and finally finished it last week. Click here to listen to the evolution of the rap guide, and download it Radiohead-style (pay what you like).

I like the fact that there’s a range of approaches to science communication, poetry, and music. I think there’s room for everybody.

ETA July 5, 2011: There’s a July 4, 2011 article by Simon Reynolds of The Guardian that offers a little more information about Biophilia and Björk (from the article),

Originally formulated by scientist Edward O Wilson, the biophilia hypothesis suggests that human beings have an innate affinity with the natural world – plants, animals or even the weather. Yet it’s not biophilia but good old-fashioned fandom that has drawn a small band of Björk obsessives to queue outside Manchester’s Campfield Market Hall since 10am this morning. Not that there’s anything old-fashioned about the woman they are here to see. Biophilia is the Icelandic singer’s new project – the word means “love of living things” – and promises to push the envelope so far you’ll need the Hubble telescope to see it.

A collection of journalists have already had a preview at a press conference in the Museum of Science and Industry over the road. Björk is absent, preparing for tonight’s live show, her first in the UK for over three years, which will open the Manchester international festival. Instead, artist and app developer Scott Snibbe, musicologist Nikki Dibben and project co-ordinator James Merry talk through Biophilia’s many layers. There will be an album in September, with an app to go with each of the 10 songs. There will be an education project, designed to teach children about nature, music and technology – some local kids will embark on it next week. There will be a documentary. And then there will be tonight’s show, performed in the round to a 2,000-strong crowd including journalists representing publications from New Scientist to the New York Times, as well as the diehard fans waiting outside.

There you have it.

Blood, memristors, cyborgs plus brain-controlled computers, prosthetics, and art

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The memristor, a circuit element that quite interests me [April 7, 2010 posting], seems to be moving from being a purely electrical engineering term to one that’s used metaphorically to describe biological processes in a way that is transforming my understanding of machine/human (and other animal) interfaces from a science fiction concept to reality.

March 2, 2011 Kate McAlpine wrote an article for the New Scientist which suggested that skin has memristive properties while noting that the same has been said of the brain. From Sweat ducts make skin a memristor,

Synapses, junctions between neurons in the brain, display electrical behaviour that depends on past activity and are said to behave like memristors. This has raised the prospect of using memristors as the basis of an artificial brain.

Now, by re-examining data from the early 1980s on the electrical conductivity of human skin in response to various voltages, Gorm Johnsen and his colleagues at the University of Oslo in Norway have uncovered a more prosaic example of memristive behaviour in nature.

They found that when a negative electrical potential is applied to skin on various parts of the arm, creating a current, that stretch of skin exhibits a low resistance to a subsequent current flowing through the skin. But if the first potential is positive relative to the skin, then a subsequent potential produces a current that meets with a much higher resistance. In other words, the skin has a memory of previous currents. The finding is due to be published in Physical Review E.
The researchers attribute skin’s memristor behaviour to sweat pores.

More recently, there’s been some excitement about a research team in India that’s working with blood so they can eventually create a ‘liquid memristor’. Rachel Courtland wrote a brief item on the ‘blood memristor’ on April 1, 2011 for the IEEE Tech Talk blog,

S.P. Kosta of the Education Campus Changa in Gujarat, India and colleagues have published a paper in the International Journal of Medical Engineering and Informatics showing that human blood changes its electrical resistance depending on how much voltage is applied. It also seems to retain memory of this resistance for at least five minutes.

The team says that makes human blood a memristor: the fourth in the family of fundamental circuit elements that includes the resistor, the capacitor, and the inductor. Proposed in 1971, the memristor’s existence wasn’t proven until 2008, when HP senior fellow Stanley Williams and colleagues demonstrated a memristor device made of doped titanium dioxide.

There was also a March 30, 2011 news item about the Indian research titled, Blood simple circuitry for cyborgs, on Nanowerk, which provided this information,

They [the research team] constructed the laboratory-based biological memristor using a 10 ml test tube filled with human blood held at 37 Celsius into which two electrodes are inserted; appropriate measuring instrumentation was attached. The experimental memristor shows that resistance varies with applied voltage polarity and magnitude and this memory effect is sustained for at least five minutes in the device.

Having demonstrated memristor behavior in blood, the next step was to test that the same behavior would be observed in a device through which blood is flowing. This step was also successful. The next stage will be to develop a micro-channel version of the flow memristor device and to integrate several to carry out particular logic functions. This research is still a long way from an electronic to biological interface, but bodes well for the development of such devices in the future.

Kit Eaton in an April 4, 2011 article (Electronics Made from Human Blood Cells Suggest Cyborg Interfaces, Spark Nightmares) on the Fast Company website gives more details about possible future applications,

Ultimately, the fact that a biological system could be used to interact with a hard semiconductor system could revolutionize biomechanics. That’s because wiring devices like cochlear implants, nerve-triggered artificial limbs and artificial eyeballs into the body at the moment involves a terribly difficult integration of metal wiring–with all the associated risk of infection and rejection. Plus it’s really a very promising first step toward making a cyborg. Countdown to military interest in this tech in 5…4…3…

It should be noted that the team in India is working towards applications in neuroprosthetics. As for the Norwegian team with their ‘sweat duct/skin memristor’, the article did not specify what types of applications, if any, their work might lead to.

As evidenced by the research covered in these news items, the memristor seems to be drifting or, more accurately, developing a second identity/ghost identity as the term is applied to biological processes.

The body as a machine is a notion that’s been around for a while as has the notion of combining the two. The first notion is a metaphor while the second is a staple in science fiction which, in a minor way, has found a home in the real life practice of body hacking where someone implants a magnetic or computer chip into their body (my May 27, 2010 posting). So the memristor becoming a metaphor for certain biological processes doesn’t seem something new but rather the next step in a process that’s well on its way.

Two students at Ryerson University (Toronto, Canada) recently announced that they had developed a brain-controlled prosthetic. From the March 30, 2011 news item on Nanowerk,

Two Ryerson University undergraduate biomedical engineering students are changing the world of medical prosthetics with a newly developed prosthetic arm that is controlled by brain signals. The Artificial Muscle-Operated (AMO) Arm not only enables amputees more range of movement as compared to other prosthetic arms but it allows amputees to avoid invasive surgeries and could potentially save hundreds of thousands of dollars. The AMO Arm is controlled by the user’s brain signals and is powered by ‘artificial muscles’ – simple pneumatic pumps and valves – to create movements. In contrast, traditional prosthetic limbs – which typically offer more limited movements – rely on intricate and expensive electrical and mechanical components.

Developed by third-year student Thiago Caires and second-year student Michal Prywata, the AMO Arm is controlled by the brain and uses compressed air as the main source of power. The digital device makes use of signals in the brain that continue to fire even after a limb is amputated. Users wear a head-set that senses a signal – for example, the thought “up” – and sends it wirelessly to a miniature computer in the arm. The computer then compares the signal to others in a database. The resulting information is sent to the pneumatic system, which in turn, activates the arm to create the correct movement. Simulating the expansion and contraction of real muscles, the system makes use of compressed air from a small, refillable tank in the user’s pocket.

I think what they mean is that the components are not traditionally electrical and mechanical but in fact informed by emerging technologies and the science that supports them. After all, the computer must run on some kind of electricity and brain activity (wireless signals from the brain will be controlling the prosthetic) is often described as electrical. The result is that the human and the machine are effectively made one since the prosthetic arm is controlled as if it were ‘biological’ arm.

On another part of the spectrum, Iraqui artist Wafaa Bilal made headlines recently when he had a camera implanted into the back of his head creating a third eye. Designed to be a one year project, the artist had to remove the camera when he developed an infection at the site of one of the metal posts used to anchor the camera to his head. From the Feb. 11, 2011 BBC news item,

An artist who had a camera implanted into the back of his head has been forced to remove it after his body rejected part of the device.

Iraqi-born Wafaa Bilal had surgery last week to remove one of three posts holding the camera in place as it posed a risk of infection.

The camera had been taking a photo every minute as part of a year-long project.

Wafaa Bilal and camera (image downloaded from BBC website)

(The artist would like to try it again but, in the meantime, has slung the camera around his neck as a substitute.)

In Bilal’s case, the body is being significantly altered as the machine (camera) is implanted in a place (back of head) where no animal has them located.

What I’m getting at with all of this is that at the same time we seem to be expanding the memristor’s meaning from a term used to describe a concept in electrical engineering to include biological processes, we are exploring new ways of integrating machinery into our bodies. In effect our relationships to our bodies and machines are changing and that change can be traced in the language we use to describe ourselves.