Explanation of Musical Atlas: Project
1 | Listening
to the Musical Atlas
By Gautam Malhotra (RU '96)
"Seeing" things on the molecular level
is obviously impossible with the naked eye, as even the electron
microscope provides limited visibility of molecules. Therefore,
other ways of "looking" at structures have been developed.
Since the majority of us have difficulty visualizing molecular structure
by glancing at tables of numbers, a familiar adage can be altered
to "a picture is worth a lot of data." Thus drawings and
models are a necessary tool for understanding and interpreting scientific
However, perceptions of reality are not limited
only to vision but to four other senses. The concept of "hearing"
DNA through music as seen in Dr. David Deamer's DNA Suite (1983),
motivated Joanna de la Cruz (Rutgers University '98 of the NDB)
to further develop aural representations of molecular structures
to aid in "hearing" things which could not be "seen."
De la Cruz created compositions based around DNA sequences to provide
a unique representation of B-DNA sequence.
The algorithm presented here builds on Deamer's
and de la Cruz's ideas in a number of ways. First, the new algorithm
represents more aspects of the DNA structure (conformation, mismatches,
modifications, nicks, uracil, inosine, etc). Secondly, it uses more
than one timbre or tone color to aid in representation (i.e. the
main sequence is represented by a piano while the complementary
sequence is represented by a string section). The primary goal of
this project was to use music to identify structures. Thus the representational
value of each musical idea was more important than its aesthetic
- Each piece of DNA
music consists of 15 measures.
- Measure length is
determined by the number of bases in the DNA strand. (Each base
is equal to one beat.) For example, a strand which is 10 base
pairs long will have 10-beat measures, while a 4 base pair strand
will be represented by 4 beats per measure, and so on.
- In the time signature
there are (# of nitrogenous bases) beats per measure with the
eighth note getting the beat. The eighth note was arbitrarily
- The sequence is repeated
in each measure.
- All MIDI composing
and recording was done using LOGIC Audio PPC (version 2.5) and
sounds were synthetically generated by QuickTimeTM
(version 2.5). All work was done on a Power Macintosh 7100/80,
System 7.5.5 .
SIGNIFICANCE OF EACH MEASURE
A number of equally spaced percussive clicks
are sounded to represent the number of nitrogenous bases in the
DNA strand. For example, if there are a total of 6 successive
clicks, then there are 6 bases in the strand of DNA (and consequently
the time signature is 6/8). The first sound establishes whether
you are listening to A-, B-, or Z-DNA.
A-DNA is represented by a ride cymbal.
B-DNA is represented by a triangle (high
Z-DNA is represented by a timpani (a low
These sounds are repeated to signal the beginning
of every new measure and were chosen purely for aesthetic reasons.
melody, or main strand, is introduced by the piano and is repeated
until the end of the piece. Notes are equidistant since the nitrogenous
bases themselves are structurally an equal distance apart. Thus
spaces in the melody can reveal missing bases and extra notes
can represent hairpin loops and overhangs. Notational representation
of bases is shown below.
is "middle c." c2 is one octave above "middle
c" and c is one octave below it. Capitalized letters are
in the octave directly below c.
A-DNA is represented by a low range of pitches
which correspond to low anti conformation. B-DNA's high range
represents high anti conformation. Z-DNA has pitches between
A-DNA & B-DNA ranges, which represent sequence only.
A-DNA & B-DNA are both right handed helices
which are being represented in the major mode. Z-DNA is a left
handed helix and is therefore represented by the natural minor
mode. This explains why the notes A, B and E in Z-DNA have been
flatted. (Note: the keys of C major and c minor were chosen
for convenience and clarity of identification.) Thus the left/right
handedness of a strand can be identified by listening to the
mode of each piece.
Measure 6 & 7:
The strings introduce the complementary strand
using the algorithm described below. This introduction develops
for two measures. The complementary strand's melody will always
sound an octave below that of the main strand. Syn/Anti choir
voice drops out.
Full sequence of the complementary strand is
established using the same principles for pitch and duration as
were used for the main strand. The syn/Anti choir voice re-enters.
If mismatches are present in the structure,
they are represented in this measure by a layer of Orchestra Hits
at the precise locations of the mismatches. (Orchestra Hits is
a combination of strings, timpanis, brass, and woodwinds which
achieves a loud staccato snap.) This measure will sound the same
as measure 9 for structures without mismatches.
If present in the structure, mismatches are
represented again. The Syn/Anti choir voice drops out.
Muted triangle sound indicates the end of the
piece. Anything sounded after this is structurally meaningless.
(However, for the sake of simplicity these pieces consistently
end with single note cadences.)
REPRESENTING THE COMPLEMENTARY STRAND
The complementary strand, which is represented
by the String Section sound, is preceded by a 2 measure melodic
introduction. This melody is the result of an algorithm which
was used purely for aesthetic purposes to relieve some of the
monotony of the music. It does not signify structure.
Measure 6 contains two notes. The first note
is just the first note of the complementary strand.
The second note is the note found halfway
down the sequence. So for example, if the sixth note of a 10-base
sequence is C, then the second note of measure of 6 is C.
Measure 7 contains four notes. Two of them
are the same as in measure 6. The other two are the final note
of the sequece and the note just before halfway.
REPRESENTING SPECIAL DNA FEATURES
- Overhangs are represented by a rest (a space
or silence) in the complementary strand at the site of the overhang
- Flipped-out Bases are preceded by a quick
grace note (see UDI047).
- Uracil and Inosine are treated as mismatches
(see BDL075 & ZDH030).
TABLE OF SOUND-STRUCTURE RELATIONSHIPS
BRIEF MEASURE BY MEASURE SYNOPSIS
Thanks to Joanna de la Cruz for helpful
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