MOLECULAR SONIFICATION
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A fusion of DNA structure, its interaction with the biological environment, and musical composition. An invitation to hear the molecule of life through physical properties extracted from simulations and turned into audible signals.
WHAT IS SONIFICATION?
Sonification is a way of turning data into sound so we can understand it better. Instead of displaying information in graphs or tables, it is transformed into acoustic signals that we can hear. In this way, what would normally be a series of numbers or measurements becomes a “soundscape” that reflects how a phenomenon, experiment, or model behaves.
This process is not automatic; someone has to decide which data will be transformed and how they will sound. For example, a higher sensor reading can be turned into a higher pitch, or a sudden change in a measurement can be heard as a strike or a shift in rhythm.
In this way, sonification opens up a new path for exploring, interpreting, and communicating information by taking advantage of our natural ability to recognize patterns in what we hear.
https://accessibleoceans.whoi.edu/what-is-sonification/
One of the most useful applications is the Geiger counter. A Geiger counter is used to detect radiation, something our senses cannot perceive directly. Each radioactive particle that enters the detector is translated into an audible click, those familiar “crackling” sounds that become more frequent as the radiation grows more intense.
There are also more poetic examples of sonification, such as the approach developed by NASA to let us hear distant galaxies (nasa.gov/marshall):
Geiger counter: an iconic example of sonification. Thanks to this device, anyone, without needing to look at a screen or understand numbers, can immediately tell whether radiation is present, where it is coming from, and how intense it is.
EXAMPLES OF MOLECULAR SONIFICATION
Music from protein sequences, with musicality enhanced through a computer program that learns from Chopin. (Tay. Heliyon. 2021)
Conversion of amino acid sequences in proteins into classical music: a search for auditory patterns. (Takahashi. Genome Biology. 2007)
A musical approach to the interpretation of gene expression data using neuroblastoma cell lines. (Staege. Scientific Reports. 2015)
“Despite the filtering and rearrangement of the probe sets, the resulting melodies in the examples presented are quite abstract, and their evocative potential is difficult to predict. It seems likely that familiarity with such melodies would be achieved more quickly if dissonances from familiar melodies were heard.”
Musical patterns for comparative epigenomics. (Brocks. Clinical Epigenetics. 2015)
SNARE Dance: a musical interpretation of Atg9 transport to the tubulovesicular cluster. (Takahashi. Autophagy. 2012)
“After assigning instruments to each protein score, we went on to combine the individual scores into a final orchestration.”
Hydrogen-bond heterogeneity correlates with transition-state passage time in protein folding. (Scaletti. PNAS. 2024)
THE SCIENCE BEHIND IT
Molecular dynamics simulations are computer simulations that make it possible to observe how the molecules that make up life, such as proteins or DNA, move and change over time. They work by applying the laws of physics to each atom, allowing us to follow their trajectories as if we had a virtual microscope capable of seeing at the atomic level and in slow motion.
These simulations are extremely useful because they allow us to explore phenomena that are impossible to observe directly in the lab, such as exactly how a DNA sequence bends, folds, or becomes more rigid depending on the combination of letters (bases) that make it up.
Thanks to this approach, it has become clear that the physical properties of DNA—flexibility, rigidity, and tendency to bend—depend strongly on its sequence. A key role in this progress has been played, and continues to be played, by the Ascona B-DNA Consortium, an international collaboration of researchers that has been generating DNA simulations since the early 2000s, establishing standards and databases that are now essential references in the field.
DansLab has been part of the ABC Consortium since 2014 and was the most recent organizer of the ABC conference, held in April 2023 in Ascona, Switzerland (https://www.danslab.xyz/abc-2023).
Simulated DNA sequences (miniABC library, provided by the ABC Consortium). They contain 136 unique combinations made up of 4 letters:
Left: theoretical framework developed to calculate DNA–K+ interaction and K+ concentrations in the major groove.
Top: animation of a simulation. When the K+ ions turn green, they are interacting with the DNA grooves.
OUR APPROACH
Realizing that sonifications that are difficult or fatiguing to listen to will be less successful, some valiant attempts have been made to incorporate some elements of composition into the sound mappings. As music is designed to engage and hold the listener’s interest, surely a sonification that is more musical will be better than one that is not. Unfortunately, sonifications purportedly designed to be musical are often still fatiguing or unengaging. (...) Conversely, the goal of communicating essential information can be masked in the effort to achieve a stronger musical expression.
Vickers, P. (2017). Sonification and music, music and sonification. In: Cobussen, M., Meelberg, V., y Truax, B. (eds.), The Routledge Companion to Sounding Art, 135–144. Routledge, Oxford.
Trying to follow the balance between data and composition described by Vickers, we transformed the interaction between DNA and potassium cations (K+).
For all possible four-letter sequences, the interaction in the major and minor grooves of DNA was measured. The groove-interaction frequencies were multiplied by a factor to bring them into the human audible range. The resulting values were then rounded by mapping the frequencies to the nearest note in the tempered scale.
DNA MUSIC
As a pilot test, the 13 miniABC sequences were joined into a single long sequence of 234 letters (A, C, G, and T) and turned into music using piano and violin. The red notes represent DNA–K+ interactions in the minor groove, and the blue notes in the major groove. The black notes are part of the musical composition. Available on YouTube:
CREATORS
Nicolás Molla
Musician, composer, and music producer. He has created music for film, advertising, and social projects, and now works as an independent producer in his own studio (https://nicomolla.com/)
Pablo Dans
Researcher, teacher, and science communicator. International expert in nucleic acid structure (DNA and RNA) and in computational chemistry, molecular modeling, simulations, and structural bioinformatics.
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