Tag Archives: National Key R&D Program of China

Classical music makes protein songs easier listening

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.

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),

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.


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.

Oxygen-deficient nanotitania (titanium dioxide nanoparticles) for whiter teeth without the damage

A September 8, 2021 news item on phys.org announces research that could make the process of whitening teeth safer,

Most people would like to flash a smile of pearly whites, but over time teeth can become stained by foods, beverages and some medications. Unfortunately, the high levels of hydrogen peroxide in dentists’ bleaching treatments can damage enamel and cause tooth sensitivity and gum irritation. Now, researchers reporting in ACS Applied Materials & Interfaces have developed a gel that, when exposed to near infrared (NIR) light, safely whitens teeth without the burn.

Caption: A new bleaching gel whitened tooth samples by six shades, using a low level of hydrogen peroxide (12%). Credit: Adapted from ACS Applied Materials & Interfaces 2021, DOI: 10.1021/acsami.1c06774

A September 8, 2021Amercian Chemical Society (ACS) news release (also on EurekAlert), which originated the news item, provides more detail,

The growing demand for selfie-ready smiles has made tooth whitening one of the most popular dental procedures. Treatments at a dentist’s office are effective, but they use high-concentration hydrogen peroxide (30–40%). Home bleaching products contain less peroxide (6–12%), but they usually require weeks of treatment and don’t work as well. When a bleaching gel is applied to teeth, hydrogen peroxide and peroxide-derived reactive oxygen species (mainly the hydroxyl radical) degrade pigments in stains. The hydroxyl radical is much better at doing this than hydrogen peroxide itself, so researchers have tried to improve the bleaching capacity of low-concentration hydrogen peroxide by boosting the generation of powerful hydroxyl radicals. Because previous approaches have had limitations, Xingyu Hu, Li Xie, Weidong Tian and colleagues wanted to develop a safe, effective whitening gel containing a catalyst that, when exposed to NIR light, would convert low levels of hydrogen peroxide into abundant hydroxyl radicals.

The researchers made oxygen-deficient titania nanoparticles that catalyzed hydroxyl radical production from hydrogen peroxide. Exposing the nanoparticles to NIR light increased their catalytic activity, allowing them to completely bleach tooth samples stained with orange dye, tea or red dye within 2 hours. Then, the researchers made a gel containing the nanoparticles, a carbomer gel and 12% hydrogen peroxide. They applied it to naturally stained tooth samples and treated them with NIR light for an hour. The gel bleached teeth just as well as a popular tooth whitening gel containing 40% hydrogen peroxide, with less damage to enamel. The nanoparticle system is highly promising for tooth bleaching and could also be extended to other biomedical applications, such as developing antibacterial materials, the researchers say.

The authors acknowledge funding from the National Natural Science Foundation of China, the National Key R&D Program of China and the Key Technologies R&D Program of Sichuan Province.

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

Photothermal-Enhanced Fenton-like Catalytic Activity of Oxygen-Deficient Nanotitania for Efficient and Safe Tooth Whitening by Xingyu Hu, Li Xie, Zhaoyu Xu, Suru Liu, Xinzhi Tan, Ruojing Qian, Ruitao Zhang, Mingyan Jiang, Wenjia Xie, and Weidong Tian. ACS Appl. Mater. Interfaces 2021, 13, 30, 35315–35327 Publication Date: July 22, 2021 DOI: https://doi.org/10.1021/acsami.1c06774 Copyright © 2021 American Chemical Society

This paper is behind a paywall.

Cerium-containing nanoparticles in microneedle patches for hair regrowth (a treatment for baldness?)

It’s still being tested but according to an August 11, 2021 news item on ScienceDaily, this is a promising treatment for baldness,

Although some people say that baldness is the “new sexy,” for those losing their hair, it can be distressing. An array of over-the-counter remedies are available, but most of them don’t focus on the primary causes: oxidative stress and insufficient circulation. Now, researchers reporting in ACS Nano have designed a preliminary microneedle patch containing cerium nanoparticles to combat both problems, regrowing hair in a mouse model faster than a leading treatment.

An August 11, 2021 American Chemical Society (ACS) news release (also on EurekAlert) provides more detail (Note: Links have been removed),

The most common hair loss condition is called androgenic alopecia, also known as male- or female- pattern baldness. Hair loss is permanent for people with the condition because there aren’t enough blood vessels surrounding the follicles to deliver nutrients, cytokines and other essential molecules. In addition, an accumulation of reactive oxygen species in the scalp can trigger the untimely death of the cells that form and grow new hair. Previously, Fangyuan Li, Jianqing Gao and colleagues determined that cerium-containing nanoparticles can mimic enzymes that remove excess reactive oxygen species, which reduced oxidative stress in liver injuries, wounds and Alzheimer’s disease. However, these nanoparticles cannot cross the outermost layer of skin. So, the researchers wanted to design a minimally invasive way to deliver cerium-containing nanoparticles near hair roots deep under the skin to promote hair regrowth.

As a first step, the researchers coated cerium nanoparticles with a biodegradable polyethylene glycol-lipid compound. Then they made the dissolvable microneedle patch by pouring a mixture of hyaluronic acid — a substance that is naturally abundant in human skin — and cerium-containing nanoparticles into a mold. The team tested control patches and the cerium-containing ones on male mice with bald spots formed by a hair removal cream. Both applications stimulated the formation of new blood vessels around the mice’s hair follicles. However, those treated with the nanoparticle patch showed faster signs of hair undergoing a transition in the root, such as earlier skin pigmentation and higher levels of a compound found only at the onset of new hair development. These mice also had fewer oxidative stress compounds in their skin. Finally, the researchers found that the cerium-containing microneedle patches resulted in faster mouse hair regrowth with similar coverage, density and diameter compared with a leading topical treatment and could be applied less frequently. Microneedle patches that introduce cerium nanoparticles into the skin are a promising strategy to reverse balding for androgenetic alopecia patients, the researchers say.

The authors acknowledge funding from the Ten-thousand Talents Program of Zhejiang Province, National Key R&D Program of China, National Natural Science Foundation of China, One Belt and One Road International Cooperation Project from the Key Research and Development Program of Zhejiang Province, Fundamental Research Funds for the Central Universities and Zhejiang Provincial Natural Science Foundation of China.

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

Ceria Nanozyme-Integrated Microneedles Reshape the Perifollicular Microenvironment for Androgenetic Alopecia Treatment by Anran Yuan, Fan Xia, Qiong Bian, Haibin Wu, Yueting Gu, Tao Wang, Ruxuan Wang, Lingling Huang, Qiaoling Huang, Yuefeng Rao, Daishun Ling, Fangyuan Li, and Jianqing Gao. ACS Nano 2021, XXXX, XXX, XXX-XXX DOI: https://doi.org/10.1021/acsnano.1c05272 Publication Date:July 19, 2021 © 2021 American Chemical Society

This paper is behind a paywall.

Manipulating light at the nanoscale with kiragami-inspired technique

At left, different patterns of slices through a thin metal foil, are made by a focused ion beam. These patterns cause the metal to fold up into predetermined shapes, which can be used for such purposes as modifying a beam of light. Courtesy of the researchers

Nanokiragami (or nano-kiragami) is a fully fledged field of research? That was news to me as was much else in a July 6, 2018 news item on ScienceDaily,

Nanokirigami has taken off as a field of research in the last few years; the approach is based on the ancient arts of origami (making 3-D shapes by folding paper) and kirigami (which allows cutting as well as folding) but applied to flat materials at the nanoscale, measured in billionths of a meter.

Now, researchers at MIT [Massachusetts Institute of Technology] and in China have for the first time applied this approach to the creation of nanodevices to manipulate light, potentially opening up new possibilities for research and, ultimately, the creation of new light-based communications, detection, or computational devices.

A July 6, 2018 MIT news release (also on EurekAlert), which originated the news item, adds detail,

The findings are described today [July 6, 2018] in the journal Science Advances, in a paper by MIT professor of mechanical engineering Nicholas X Fang and five others. Using methods based on standard microchip manufacturing technology, Fang and his team used a focused ion beam to make a precise pattern of slits in a metal foil just a few tens of nanometers thick. The process causes the foil to bend and twist itself into a complex three-dimensional shape capable of selectively filtering out light with a particular polarization.

Previous attempts to create functional kirigami devices have used more complicated fabrication methods that require a series of folding steps and have been primarily aimed at mechanical rather than optical functions, Fang says. The new nanodevices, by contrast, can be formed in a single folding step and could be used to perform a number of different optical functions.

For these initial proof-of-concept devices, the team produced a nanomechanical equivalent of specialized dichroic filters that can filter out circularly polarized light that is either “right-handed” or “left-handed.” To do so, they created a pattern just a few hundred nanometers across in the thin metal foil; the result resembles pinwheel blades, with a twist in one direction that selects the corresponding twist of light.

The twisting and bending of the foil happens because of stresses introduced by the same ion beam that slices through the metal. When using ion beams with low dosages, many vacancies are created, and some of the ions end up lodged in the crystal lattice of the metal, pushing the lattice out of shape and creating strong stresses that induce the bending.

“We cut the material with an ion beam instead of scissors, by writing the focused ion beam across this metal sheet with a prescribed pattern,” Fang says. “So you end up with this metal ribbon that is wrinkling up” in the precisely planned pattern.

“It’s a very nice connection of the two fields, mechanics and optics,” Fang says. The team used helical patterns to separate out the clockwise and counterclockwise polarized portions of a light beam, which may represent “a brand new direction” for nanokirigami research, he says.

The technique is straightforward enough that, with the equations the team developed, researchers should now be able to calculate backward from a desired set of optical characteristics and produce the needed pattern of slits and folds to produce just that effect, Fang says.

“It allows a prediction based on optical functionalities” to create patterns that achieve the desired result, he adds. “Previously, people were always trying to cut by intuition” to create kirigami patterns for a particular desired outcome.

The research is still at an early stage, Fang points out, so more research will be needed on possible applications. But these devices are orders of magnitude smaller than conventional counterparts that perform the same optical functions, so these advances could lead to more complex optical chips for sensing, computation, or communications systems or biomedical devices, the team says.

For example, Fang says, devices to measure glucose levels often use measurements of light polarity, because glucose molecules exist in both right- and left-handed forms which interact differently with light. “When you pass light through the solution, you can see the concentration of one version of the molecule, as opposed to the mixture of both,” Fang explains, and this method could allow for much smaller, more efficient detectors.

Circular polarization is also a method used to allow multiple laser beams to travel through a fiber-optic cable without interfering with each other. “People have been looking for such a system for laser optical communications systems” to separate the beams in devices called optical isolaters, Fang says. “We have shown that it’s possible to make them in nanometer sizes.”

The team also included MIT graduate student Huifeng Du; Zhiguang Liu, Jiafang Li (project supervisor), and Ling Lu at the Chinese Academy of Sciences in Beijing; and Zhi-Yuan Li at the South China University of Technology. The work was supported by the National Key R&D Program of China, the National Natural Science Foundation of China, and the U.S Air Force Office of Scientific Research.

The researchers have also provided some GIFs,


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

Nano-kirigami with giant optical chirality by Zhiguang Liu, Huifeng Du, Jiafang Li, Ling Lu, Zhi-Yuan Li, and Nicholas X. Fang. Science Advances 06 Jul 2018: Vol. 4, no. 7, eaat4436 DOI: 10.1126/sciadv.aat4436

This paper is open access.