Tag Archives: Hui Zhang

Classical music makes protein songs easier listening

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Caption: This audio is oxytocin receptor protein music using the Fantasy Impromptu guided algorithm. Credit: Chen et al. / Heliyon

A September 29, 2021 news item on ScienceDaily describes new research into music as a means of communicating science,

In recent years, scientists have created music based on the structure of proteins as a creative way to better popularize science to the general public, but the resulting songs haven’t always been pleasant to the ear. In a study appearing September 29 [2021] in the journal Heliyon, researchers use the style of existing music genres to guide the structure of protein song to make it more musical. Using the style of Frédéric Chopin’s Fantaisie-Impromptu and other classical pieces as a guide, the researchers succeeded in converting proteins into song with greater musicality.

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Scientists (Peng Zhang, Postdoctoral Researcher in Computational Biology at The Rockefeller University, and Yuzong Chen, Professor of Pharmacy at National University of Singapore [NUS]) wrote a September 29, 2021 essay for The Conversation about their protein songs (Note: Links have been removed),

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There are many surprising analogies between proteins, the basic building blocks of life, and musical notation. These analogies can be used not only to help advance research, but also to make the complexity of proteins accessible to the public.

We’re computational biologists who believe that hearing the sound of life at the molecular level could help inspire people to learn more about biology and the computational sciences. While creating music based on proteins isn’t new, different musical styles and composition algorithms had yet to be explored. So we led a team of high school students and other scholars to figure out how to create classical music from proteins.

The musical analogies of proteins

Proteins are structured like folded chains. These chains are composed of small units of 20 possible amino acids, each labeled by a letter of the alphabet.

A protein chain can be represented as a string of these alphabetic letters, very much like a string of music notes in alphabetical notation.

Protein chains can also fold into wavy and curved patterns with ups, downs, turns and loops. Likewise, music consists of sound waves of higher and lower pitches, with changing tempos and repeating motifs.

Protein-to-music algorithms can thus map the structural and physiochemical features of a string of amino acids onto the musical features of a string of notes.

Enhancing the musicality of protein mapping

Protein-to-music mapping can be fine-tuned by basing it on the features of a specific music style. This enhances musicality, or the melodiousness of the song, when converting amino acid properties, such as sequence patterns and variations, into analogous musical properties, like pitch, note lengths and chords.

For our study, we specifically selected 19th-century Romantic period classical piano music, which includes composers like Chopin and Schubert, as a guide because it typically spans a wide range of notes with more complex features such as chromaticism, like playing both white and black keys on a piano in order of pitch, and chords. Music from this period also tends to have lighter and more graceful and emotive melodies. Songs are usually homophonic, meaning they follow a central melody with accompaniment. These features allowed us to test out a greater range of notes in our protein-to-music mapping algorithm. In this case, we chose to analyze features of Chopin’s “Fantaisie-Impromptu” to guide our development of the program.

If you have the time, I recommend reading the essay in its entirety and listening to the embedded audio files.

The September 29, 2021 Cell Press news release on EurekAlert repeats some of the same material but is worth reading on its own merits,

In recent years, scientists have created music based on the structure of proteins as a creative way to better popularize science to the general public, but the resulting songs haven’t always been pleasant to the ear. In a study appearing September 29 [2021] in the journal Heliyon, researchers use the style of existing music genres to guide the structure of protein song to make it more musical. Using the style of Frédéric Chopin’s Fantaisie-Impromptu and other classical pieces as a guide, the researchers succeeded in converting proteins into song with greater musicality.

Creating unique melodies from proteins is achieved by using a protein-to-music algorithm. This algorithm incorporates specific elements of proteins—like the size and position of amino acids—and maps them to various musical elements to create an auditory “blueprint” of the proteins’ structure.

“Existing protein music has mostly been designed by simple mapping of certain amino acid patterns to fundamental musical features such as pitches and note lengths, but they do not map well to more complex musical features such as rhythm and harmony,” says senior author Yu Zong Chen, a professor in the Department of Pharmacy at National University of Singapore. “By focusing on a music style, we can guide more complex mappings of combinations of amino acid patterns with various musical features.”

For their experiment, researchers analyzed the pitch, length, octaves, chords, dynamics, and main theme of four pieces from the mid-1800s Romantic era of classical music. These pieces, including Fantasie-Impromptu from Chopin and Wanderer Fantasy from Franz Schubert, were selected to represent the notable Fantasy-Impromptu genre that emerged during that time.

“We chose the specific music style of a Fantasy-Impromptu as it is characterized by freedom of expression, which we felt would complement how proteins regulate much of our bodily functions, including our moods,” says co-author Peng Zhang (@zhangpeng1202), a post-doctoral fellow at the Rockefeller University

Likewise, several of the proteins in the study were chosen for their similarities to the key attributes of the Fantasy-Impromptu style. Most of the 18 proteins tested regulate functions including human emotion, cognition, sensation, or performance which the authors say connect to the emotional and expressive of the genre.

Then, they mapped 104 structural, physicochemical, and binding amino acid properties of those proteins to the six musical features. “We screened the quantitative profile of each amino acid property against the quantized values of the different musical features to find the optimal mapped pairings. For example, we mapped the size of amino acid to note length, so that having a larger amino acid size corresponds to a shorter note length,” says Chen.

Across all the proteins tested, the researchers found that the musicality of the proteins was significantly improved. In particular, the protein receptor for oxytocin (OXTR) was judged to have one of the greatest increases in musicality when using the genre-guided algorithm, compared to an earlier version of the protein-to-music algorithm.

“The oxytocin receptor protein generated our favorite song,” says Zhang. “This protein sequence produced an identifiable main theme that repeats in rhythm throughout the piece, as well as some interesting motifs and patterns that recur independent of our algorithm. There were also some pleasant harmonic progressions; for example, many of the seventh chords naturally resolve.”

The authors do note, however, that while the guided algorithm increased the overall musicality of the protein songs, there is still much progress to be made before it resembles true human music.

“We believe a next step is to explore more music styles and more complex combinations of amino acid properties for enhanced musicality and novel music pieces. Another next step, a very important step, is to apply artificial intelligence to jointly learn complex amino acid properties and their combinations with respect to the features of various music styles for creating protein music of enhanced musicality,” says Chen.

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Research supported by the National Key R&D Program of China, the National Natural Science Foundation of China, and Singapore Academic Funds.

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

Protein Music of Enhanced Musicality by Music Style Guided Exploration of Diverse Amino Acid Properties by Nicole WanNi Tay, Fanxi Liu, Chaoxin Wang, Hui Zhang, Peng Zhang, Yu Zong Chen. Heliyon, 2021 DOI: https:// doi.org/10.1016/j.heliyon.2021.e07933 Published; September 29, 2021

This paper appears to be open access.

‘Stained glass nanotechnology’ for color displays

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From a Dec. 4, 2015 news item on ScienceDaily,

A new method for building “drawbridges” between metal nanoparticles may allow electronics makers to build full-color displays using light-scattering nanoparticles that are similar to the gold materials that medieval artisans used to create red stained-glass.

“Wouldn’t it be interesting if we could create stained-glass windows that changed colors at the flip of a switch?” said Christy Landes, associate professor of chemistry at Rice and the lead researcher on a new study about the drawbridge method that appears this week in the open-access journal Science Advances.

The research by Landes and other experts at Rice University’s Smalley-Curl Institute could allow engineers to use standard electrical switching techniques to construct color displays from pairs of nanoparticles that scatter different colors of light.

For centuries, stained-glass makers have tapped the light-scattering properties of tiny gold nanoparticles to produce glass with rich red tones. Similar types of materials could increasingly find use in modern electronics as manufacturers work to make smaller, faster and more energy-efficient components that operate at optical frequencies.

A Dec. 4, 2015 Rice University news release (also on EurekAlert), which originated the news item, describes the research in more detail,

Though metal nanoparticles scatter bright light, researchers have found it difficult to coax them to produce dramatically different colors, Landes said.

Rice’s new drawbridge method for color switching incorporates metal nanoparticles that absorb light energy and convert it into plasmons, waves of electrons that flow like a fluid across a particle’s surface. Each plasmon scatters and absorbs a characteristic frequency of light, and even minor changes in the wave-like sloshing of a plasmon shift that frequency. The greater the change in plasmonic frequency, the greater the difference between the colors observed.

“Engineers hoping to make a display from optically active nanoparticles need to be able to switch the color,” Landes said. “That type of switching has proven very difficult to achieve with nanoparticles. People have achieved moderate success using various plasmon-coupling schemes in particle assemblies. What we’ve shown though is variation of the coupling mechanism itself, which can be used to produce huge color changes both rapidly and reversibly.”

To demonstrate the method, Landes and study lead author Chad Byers, a graduate student in her lab, anchored pairs of gold nanoparticles to a glass surface covered with indium tin oxide (ITO), the same conductor that’s used in many smartphone screens. By sealing the particles in a chamber filled with a saltwater electrolyte and a silver electrode, Byers and Landes were able form a device with a complete circuit. They then showed they could apply a small voltage to the ITO to electroplate silver onto the surface of the gold particles. In that process, the particles were first coated with a thin layer of silver chloride. By later applying a negative voltage, the researchers caused a conductive silver “drawbridge” to form. Reversing the voltage caused the bridge to withdraw.

“The great thing about these chemical bridges is that we can create and eliminate them simply by applying or reversing a voltage,” Landes said. “This is the first method yet demonstrated to produce dramatic, reversible color changes for devices built from light-activated nanoparticles.”

This research has its roots in previous work (from the news release),

Byers said his research into the plasmonic behavior of gold dimers began about two years ago.

“We were pursuing the idea that we could make significant changes in optical properties of individual particles simply by altering charge density,” he said. “Theory predicts that colors can be changed just by adding or removing electrons, and we wanted to see if we could do that reversibly, simply by turning a voltage on or off.”

The experiments worked. The color shift was observed and reversible, but the change in the color was minute.

“It wasn’t going to get anybody excited about any sort of switchable display applications,” Landes said.

But she and Byers also noticed that their results differed from the theoretical predictions.

Landes said that was because the predictions were based upon using an inert electrode made of a metal like palladium that isn’t subject to oxidation. But silver is not inert. It reacts easily with oxygen in air or water to form a coat of unsightly silver oxide. This oxidizing layer can also form from silver chloride, and Landes said that is what was occurring when the silver counter electrode was used in Byers’ first experiments.

The scientists decided to embrace imperfection (from the news release),

“It was an imperfection that was throwing off our results, but rather than run away from it, we decided to use it to our advantage,” Landes said.

Rice plasmonics pioneer and study co-author Naomi Halas, director of the Smalley-Curl Institute, said the new research shows how plasmonic components could be used to produce electronically switchable color-displays.

“Gold nanoparticles are particularly attractive for display purposes,” said Halas, Rice’s Stanley C. Moore Professor of Electrical and Computer Engineering and professor of chemistry, bioengineering, physics and astronomy, and materials science and nanoengineering. “Depending upon their shape, they can produce a variety of specific colors. They are also extremely stable, and even though gold is expensive, very little is needed to produce an extremely bright color.”

In designing, testing and analyzing the follow-up experiments on dimers, Landes and Byers engaged with a brain trust of Rice plasmonics experts that included Halas, physicist and engineer Peter Nordlander, chemist Stephan Link, materials scientist Emilie Ringe and their students, as well as Paul Mulvaney of the University of Melbourne in Australia.

Together, the team confirmed the composition and spacing of the dimers and showed how metal drawbridges could be used to induce large color shifts based on voltage inputs.

Nordlander and Hui Zhang, the two theorists in the group, examined the device’s “plasmonic coupling,” the interacting dance that plasmons engage in when they are in close contact. For instance, plasmonic dimers are known to act as light-activated capacitors, and prior research has shown that connecting dimers with nanowire bridges brings about a new state of resonance known as a “charge-transfer plasmon,” which has its own distinct optical signature.

“The electrochemical bridging of the interparticle gap enables a fully reversible transition between two plasmonic coupling regimes, one capacitive and the other conductive,” Nordlander said. “The shift between these regimes is evident from the dynamic evolution of the charge transfer plasmon.”

Halas said the method provides plasmonic researchers with a valuable tool for precisely controlling the gaps between dimers and other multiparticle plasmonic configurations.

“In an applied sense, gap control is important for the development of active plasmonic devices like switches and modulators, but it is also an important tool for basic scientists who are conducting curiosity-driven research in the emerging field of quantum plasmonics.”

I’m glad the news release writer included the background work leading to this new research and to hint at the level of collaboration needed to achieve the scientists’ new understanding of color switching.

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

From tunable core-shell nanoparticles to plasmonic drawbridges: Active control of nanoparticle optical properties by Chad P. Byers, Hui Zhang, Dayne F. Swearer, Mustafa Yorulmaz, Benjamin S. Hoener, Da Huang, Anneli Hoggard, Wei-Shun Chang, Paul Mulvaney, Emilie Ringe, Naomi J. Halas, Peter Nordlander, Stephan Link, and Christy F. Landes. Science Advances  04 Dec 2015: Vol. 1, no. 11, e1500988 DOI: 10.1126/sciadv.1500988

In case you missed it in the news release, this is an open access paper.

Distinguishing between left-handed and right-handed molecules with nanocubes

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Learning to distinguish your left from your right isn’t all that easy for children. It’s also remarkably easy to lose the ability (temporarily) to make that distinction if you start experimenting with certain kinds of brain repatterning. However, the distinctions are important not only in daily life but in biology too according to a June 26, 2013 news item on Nanowerk,

In chemical reactions, left and right can make a big difference. A “left-handed” molecule of a particular chemical composition could be an effective drug, while its mirror-image “right-handed” counterpart could be completely inactive. That’s because, in biology, “left” and “right” molecular designs are crucial: Living organisms are made only from left-handed amino acids. So telling the two apart is important—but difficult.

Now, a team of scientists at the U.S. Department of Energy’s Brookhaven National Laboratory and Ohio University has developed a new, simpler way to discern molecular handedness, known as chirality.

The June 26, 2013 Brookhaven National Laboratory news release, which originated the news item, describes the new technique for distinguishing left- from right-handed molecules,

They used gold-and-silver cubic nanoparticles to amplify the difference in left- and right-handed molecules’ response to a particular kind of light. The study, described in the journal NanoLetters, provides the basis for a new way to probe the effects of handedness in molecular interactions with unprecedented sensitivity.

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The scientists knew that left- and right-handed chiral molecules would interact differently with “circularly polarized” light—where the direction of the electrical field rotates around the axis of the beam. This idea is similar to the way polarized sunglasses filter out reflected glare unlike ordinary lenses.

Other scientists have detected this difference, called “circular dichroism,” in organic molecules’ spectroscopic “fingerprints”—detailed maps of the wavelengths of light absorbed or reflected by the sample. But for most chiral biomolecules and many organic molecules, this “CD” signal is in the ultraviolet range of the electromagnetic spectrum, and the signal is often weak. The tests thus require significant amounts of material at impractically high concentrations.

The team was encouraged they might find a way to enhance the signal by recent experiments showing that coupling certain molecules with metallic nanoparticles could greatly increase their response to light. Theoretical work even suggested that these so-called plasmonic particles—which induce a collective oscillation of the material’s conductive electrons, leading to stronger absorption of a particular wavelength—could bump the signal into the visible light portion of the spectroscopic fingerprint, where it would be easier to measure.

The group experimented with different shapes and compositions of nanoparticles, and found that cubes with a gold center surrounded by a silver shell are not only able to show a chiral optical signal in the near-visible range, but even more striking, were effective signal amplifiers. For their test biomolecule, they used synthetic strands of DNA—a molecule they were familiar with using as “glue” for sticking nanoparticles together.

When DNA was attached to the silver-coated nanocubes, the signal was approximately 100 times stronger than it was for free DNA in the solution. That is, the cubic nanoparticles allowed the scientists to detect the optical signal from the chiral molecules (making them “visible”) at 100 times lower concentrations.

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The observed amplification of the circular dichroism signal is a consequence of the interaction between the plasmonic particles and the “exciton,” or energy absorbing, electrons within the DNA-nanocube complex, the scientists explained.

“This research could serve as a promising platform for ultrasensitive sensing of chiral molecules and their transformations in synthetic, biomedical, and pharmaceutical applications,” Lu [Fang Lu, the first author on the paper] said.

“In addition,” said Gang [Oleg Gang, a researcher at Brookhaven’s Center for Functional Nanomaterials and lead author on the paper], “our approach offers a way to fabricate, via self-assembly, discrete plasmonic nano-objects with a chiral optical response from structurally non-chiral nano-components. These chiral plasmonic objects could greatly enhance the design of metamaterials and nano-optics for applications in energy harvesting and optical telecommunications.”

I last mentioned chirality in the context of work being done with controlling the chirality of carbon nanotubes at Finland’s Aalto University in an April 30 , 2013 posting.

Here’s a link to and a citation for the paper published by the Brookhaven National Laboratory and Ohio University,

Discrete Nanocubes as Plasmonic Reporters of Molecular Chirality by Fang Lu, Ye Tian, Mingzhao Liu, Dong Su, Hui Zhang, Alexander O. Govorov, and Oleg Gang. Nano Lett., Article ASAP
DOI: 10.1021/nl401107g Publication Date (Web): June 18, 2013
Copyright © 2013 American Chemical Society

This paper is behind a paywall.