Explanation of Musical Atlas: Project 1 | Listening to the Musical Atlas

PROJECT 2
(Composition 2)

By Gautam Malhotra (RU '96)

INTRODUCTION

"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 data.

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 consequence.

GENERAL SCHEME

• 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 chosen.
• 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 QuickTime^TM (version 2.5). All work was done on a Power Macintosh 7100/80, System 7.5.5 .

SIGNIFICANCE OF EACH MEASURE

Measure 1:

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 pitched).

• Z-DNA is represented by a timpani (a low booming drum).

These sounds are repeated to signal the beginning of every new measure and were chosen purely for aesthetic reasons.

Measure 2:

The 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.

	A-DNA	B-DNA	Z-DNA
Adenine	A	a1	a flat
Cytosine	c	c2	c1
Thymine	E	e1	e flat
Guanine	G	g1	g
Inosine	B	b1	b flat
Uracil	D	d1	d

Note: c¹ 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 3:

Exact repetition of measure 2.

Measure 4:

Syn/Anti configuration is represented by the choir voice.

• The pitch of the choir voice indicates high or low anti. (i.e. high pitch represents high anti and low pitch represents low anti.)
• If a base is in the syn configuration, the choir voice is silent.
• If a base is in the anti configuration a note is sounded. Therefore if all the bases are anti, the choir voice sustains a note; but if the strand alternates anti/syn, then the choir voice will alternate between sound and silence.

Measure 5:

Exact repetition of measure 4.

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.

Measure 8:

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.

Measure 9:

Exact repetition of measure 8.

Measure 10:

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.

Measure 11:

Exact repetition of measure 8.

Measure 12:

If present in the structure, mismatches are represented again. The Syn/Anti choir voice drops out.

Measure 13:

Exact repetition of measure 12.

Measure 14:

The complementary strand and any mismatches drop out.

Measure 15:

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 (see UDI030).
• 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

Acknowledgements
Thanks to Joanna de la Cruz for helpful discussion.

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