Scientists have turned the structure of the coronavirus into music
Thursday, April 23, 2020
Our third journal club is online! Feel free to join the discussion remotely in the comments below. One of our participants in Project CHROMA suggested the following research that combines science and music to study the coronavirus:
Vineeth Venugopal (2020) “Scientists have turned the structure of the coronavirus into music,” Science 10.1126/science.abc0657.
Researchers at MIT have created a musical representation of the amino acid sequence and structure of the COVID-19 spike protein (based on protein data bank entry 6VSB published by Wrapp et al. 2020) using a technique known as sonification.
The team led by Markus Buehler transposed the vibrational frequencies of the 20 natural amino acids to an audible spectrum in order to assign a musical note to each amino acid, thus creating a 20-tone “amino acid scale.” To create the COVID-19 spike protein musical score, the notes were played on a Japanese koto. The volume and duration of each note were defined by the secondary and higher-order folded structure of the protein. Heat-induced molecular vibrations were represented by unique sounds as well. A neural network was then used to generate music compositions that captured the relationships between amino acid sequence and protein structure.
It’s apparently faster using this technique rather than traditional molecular dynamics modeling to search for sites where antibodies or drugs could bind on the viral protein — researchers simply have to compare the musical scores of the sonified structures.
This musical technique is also a great way to communicate the significance of protein sequences and their folded structure to the public!
Read more about this sonification method developed by the research team:
Chi-Hua Yu, Zhao Qin, Francisco J Martin-Martinez, and Markus J Buehler (2019) “A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence,” ACS Nano, 13(7): 7471-7482.
Playing unfamiliar music to patients could improve music therapy outcomes.
Music can promote brain healing, but scientists are still trying to understand which types of music work best for each patient.
When Melia Bonomo wants to kick back and relax, she turns to music and the gentle melodies of pop star Ed Sheeran. Like many people, the physicist feels her mood lift with certain tunes, a change doctors exploit to improve the health of patients with cognitive impairments. But some patients are unresponsive to music therapy. And it remains unclear exactly what restorative changes music actually induces in the brain. New results from Bonomo, a graduate student at Rice University, Texas, and her colleagues suggest that clues to both of these problems lie in how the brain responds to a listener’s favorite tune. Bonomo was set to share her findings in a session on the physics of the brain at the March Meeting of the American Physical Society earlier last month. (The meeting was canceled due to concerns about the new coronavirus disease, COVID-19, but Physics is reporting on some of the results that would have been presented.)
“Music therapy doesn’t work for everybody,” says Bonomo, who collaborated with researchers at Houston Methodist Hospital’s Center for Performing Arts Medicine. “We wanted to see if we could better understand why that is from how a person’s brain processes music.”
In the study, Bonomo and her colleagues used functional magnetic resonance imaging (fMRI) to monitor the neuronal activity of 25 people as they listened to six audio excerpts. Each person’s set list included their favorite song, a Bach concerto, and an old newscast by Walter Cronkite. The team then translated the resulting fMRI images into network-like maps, with one map for each excerpt per person. To make these maps, the researchers divided the brain into 84 regions and drew a connecting line between two regions if they had similar patterns of activity during an audio excerpt.
Bonomo looked first at the brain maps of participants listening to their favorite songs. Within these networks, she noticed that some regions were more strongly connected with each other than others, forming a “community.” She then found that the networks fell into two categories: those where there were many connections between different communities and those where there were fewer. And interestingly, the category for a participant’s map was predictive of how they would respond to the other five sound clips.
She and her colleagues found that when a participant’s “favorite-song” network had many intercommunity connections but few intracommunity ones, the distribution of connections changed significantly for each of the other excerpts. But when the opposite was true, these connections tended to stay in place, unless the participant was listening to the most unfamiliar sound clips. (For the people in the study, the least known excerpts were a melody from a Japanese opera and a passage of foreign language speech.)
The fact that networks with more isolated communities are harder to disrupt is well known in network theory, explains Bonomo. Seeing this effect in the brain’s response to music tells us that, for some, forming new neuronal connections—something the brain needs to do to compensate for an injury, for example—may require a bigger auditory stimulus. That could have implications for music therapy, where clinicians select music to foster neuronal connections and help the brain heal. Typically, therapists select popular melodies, such as the classical music of Bach or Beethoven, to stimulate a recovery. But the new study suggests that those pieces might not be the right ones to play for everyone, says Bonomo. Instead, unfamiliar music might be the best bet. Bonomo and her colleagues are currently testing this hypothesis in a study of people with mild cognitive impairment.
Although Bonomo’s work went unpresented at the March Meeting, she did share it on Twitter. Inspired by fellow physicist Douglas Holmes of Boston University, she condensed her planned talk into ten slides that she tweeted out under the hashtag #APS10slides10tweets. She hopes that the tweets will scroll across the screens of others studying how music impacts the brain. While she doesn’t know yet if that has happened, she said that sending the tweets “was a cool way to publicly share a snapshot of my research.”
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Systematically Improving Espresso: Insights from Mathematical Modeling and Experiment
Thursday, March 19, 2020
Our second journal club was moved online! Feel free to join the discussion remotely in the comments below. Josh Hill from the department of Physics & Astronomy suggested the following paper that combines science and the culinary arts:
Michael Cameron, Dechen Morisco, Daniel Hofstetter, Erol Uman, Justin Wilkinson, Zachary Kennedy, Sean Fontenot, William Lee, Christopher Hendon, and Jamie M. Foster (2020) “Systematically Improving Espresso: Insights from Mathematical Modeling and Experiment,” Matter2(3):631-648.
The coffee industry is huge! In the U.S. alone, it provided 1.5 million jobs and accounted for 1.6% of the gross domestic profit in 2015. Espresso is the trickiest coffee beverage format in terms of maintaining a consistent yield and desirable flavor. The goal of this project was to develop a mathematical model of espresso extraction in order to optimize the espresso parameters at play for a reduction of the variation in taste and waste!
These espresso parameters are:
grind setting
coffee mass
water pressure and temperature
beverage volume
The model determined that variation in espresso drinks was not due to human variation, but rather due to non-uniform flow during espresso extraction related to coffee grind size. The team determined a critical minimum grind size that would homogenize the flow, increase extraction yield, and reduce drink variability. Interestingly, the extraction yield had a non-linear dependence on grind setting — this was attributed to a competing relationship between a finer grind leading to an increase in flow but also an increase in grind aggregation leading to partial clogging conditions that affect the flow.
Typically, 20g of dry coffee mass is used to make a single 40g espresso shot. However, the research team demonstrated that a barista can achieve highly reproducible espresso with the same 40g extraction yield by reducing the coffee mass to 15gand using a counter-intuitively coarser grind!
The mass reduction suggestions were implemented at a local cafe in Eugene, Oregon. Espresso drinks were prepared with 15g of specialty-grade coffee, rather than 20g. Firstly, there was a reduced order-to-delivery time since the shot brewing time was 14s rather than 20-30s. Secondly, the research team calculated that the cafe had saved $0.13 per drink given the lower coffee dry mass being used. This amounted to an increase in profit of $3,620 per year!
To summarize: The multi-scale mathematical model of espresso extraction enabled an understanding of the origin of the variation in espresso drinks. The research team made suggestions to minimize drink variation and dry coffee waste: (1) reduce the dry coffee mass used and (2) increase the grind size. Espresso yield and taste were both preserved, while the shot brewing time became faster.
These novel, model-based brewing protocols will contribute to creating a more sustainable coffee-consuming future!