Sonifying stochastic walks on biomolecular energy landscapes

Robert Arbon; Alex Jones; Lars Bratholm; Thomas Mitchell; David Glowacki

doi:10.21785/icad2018.000

Sonifying stochastic walks on biomolecular energy landscapes

Robert Arbon
, Alex Jones
, Lars Bratholm
, Thomas Mitchell
, David Glowacki

Research output: Chapter in Book/Report/Conference proceeding › Conference Contribution (Conference Proceeding)

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Abstract

Translating the complex, multi-dimensional data produced by simulations of biomolecules into an intelligible form is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams. This allows for concurrent visual display of the physical configuration of a biomolecule and auditory display of characteristics of the corresponding free energy landscape. The resulting sonification provides information about the relative free energy features of a given configuration including its stability.

Original language	English
Title of host publication	Complete proceedings of the 24th International Conference on Auditory Display (ICAD2018)
Subtitle of host publication	June 10-15, 2018, Michigan Technological University, Houghton, MI, USA.
Publisher	Georgia Institute of Technology
ISBN (Print)	0967090458
DOIs	https://doi.org/10.21785/icad2018.000
Publication status	Published - 10 Jun 2018

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Arbon, R., Jones, A., Bratholm, L., Mitchell, T., & Glowacki, D. (2018). Sonifying stochastic walks on biomolecular energy landscapes. In Complete proceedings of the 24th International Conference on Auditory Display (ICAD2018): June 10-15, 2018, Michigan Technological University, Houghton, MI, USA. Georgia Institute of Technology. https://doi.org/10.21785/icad2018.000

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abstract = "Translating the complex, multi-dimensional data produced by simulations of biomolecules into an intelligible form is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams. This allows for concurrent visual display of the physical configuration of a biomolecule and auditory display of characteristics of the corresponding free energy landscape. The resulting sonification provides information about the relative free energy features of a given configuration including its stability.",

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Sonifying stochastic walks on biomolecular energy landscapes. / Arbon, Robert; Jones, Alex; Bratholm, Lars et al.
Complete proceedings of the 24th International Conference on Auditory Display (ICAD2018): June 10-15, 2018, Michigan Technological University, Houghton, MI, USA.. Georgia Institute of Technology, 2018.

Research output: Chapter in Book/Report/Conference proceeding › Conference Contribution (Conference Proceeding)

TY - GEN

T1 - Sonifying stochastic walks on biomolecular energy landscapes

AU - Arbon, Robert

AU - Jones, Alex

AU - Bratholm, Lars

AU - Mitchell, Thomas

AU - Glowacki, David

PY - 2018/6/10

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N2 - Translating the complex, multi-dimensional data produced by simulations of biomolecules into an intelligible form is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams. This allows for concurrent visual display of the physical configuration of a biomolecule and auditory display of characteristics of the corresponding free energy landscape. The resulting sonification provides information about the relative free energy features of a given configuration including its stability.

AB - Translating the complex, multi-dimensional data produced by simulations of biomolecules into an intelligible form is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams. This allows for concurrent visual display of the physical configuration of a biomolecule and auditory display of characteristics of the corresponding free energy landscape. The resulting sonification provides information about the relative free energy features of a given configuration including its stability.

U2 - 10.21785/icad2018.000

DO - 10.21785/icad2018.000

M3 - Conference Contribution (Conference Proceeding)

SN - 0967090458

BT - Complete proceedings of the 24th International Conference on Auditory Display (ICAD2018)

PB - Georgia Institute of Technology

ER -

Sonifying stochastic walks on biomolecular energy landscapes

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