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Audibilization: Data Analysis by Ear

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posted on 08.04.2014, 00:00 by Andrew P. Jallouk, Peter T. Cummings
As molecular dynamics simulations continue to grow in size and complexity, new techniques are needed to rapidly identify regions of data likely to benefit from further analysis. Audibilization, the conversion of data to sound, facilitates this task by taking advantage of the user’s innate ability to identify anomalies in patterns of sound. Audibilization also complements visualization of a molecular simulation by allowing the user to easily correlate changes in numerical quantities with changes in the overall structure of the molecular system. Here we present three examples highlighting the utility of audibilization in the analysis of three different molecular simulations. First, we present a simulation of liquid water in which the lengths of the O–H bonds are calculated at each time step and audibilized. Interestingly, we find that anomalies in the pattern of bond vibration are due to intermolecular interactions but do not correlate with the formation of hydrogen bonds. Next, we present a simulation of the rupture of a gold nanowire. Here we audibilize the nanowire potential energy and illustrate that sharp changes in this value coincide with important structural events such as the formation of monatomic chains and dislocations. Finally, we present a simulation of single-stranded DNA passing through a nanogap. Here the bond angle is audibilized and used to illustrate the conformational changes of each base as it passes through the nanogap. This simulation also illustrates the use of more advanced audibilization techniques such as the multiplexing of audibilized signals and the weighting of certain segments of data relative to others.