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Characterization of void space in polydisperse sphere packings: Applications to hard-sphere packings and to protein structure analysis

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Abstract

The implementation of a method for the exact evaluation of the volume and surface area of cavities and free volumes in polydisperse sphere packings is described. The generalization of an algorithm for Voronoi tessellation by Tanemura et al. is presented, employing the radical plane construction, as a part of the method. We employ this method to calculate the equation of state for monodisperse and polydisperse hard-sphere fluids, crystals, and for the metastable amorphous branch up to random close packing or jamming densities. We compute the distribution of free volumes, and compare with previous results employing a heuristic definition of free volume. We show the efficacy of the method for analyzing protein structure, by computing various quantities such as the distribution of sizes of buried cavities and pockets, the scaling of solvent accessible area to the corresponding occupied volume, the composition of residues lining cavities, etc.

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Author notes

  1. Arun Lakshminarayanan

    Present address: eBay Inc, 2065 Hamilton Ave, San Jose, CA, 95125, USA

Authors and Affiliations

  1. Theoretical Sciences Unit, JNCASR, 560065, Jakkur, Banglore, India

    Moumita Maiti, Arun Lakshminarayanan & Srikanth Sastry

  2. TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, 500075, Narsingi, Hyderabad, India

    Srikanth Sastry

  3. Indian Institute of Technology, 721302, Kharagpur, West Bengal, India

    Arun Lakshminarayanan

Authors
  1. Moumita Maiti
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  2. Arun Lakshminarayanan
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  3. Srikanth Sastry
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Correspondence to Srikanth Sastry.

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Maiti, M., Lakshminarayanan, A. & Sastry, S. Characterization of void space in polydisperse sphere packings: Applications to hard-sphere packings and to protein structure analysis. Eur. Phys. J. E 36, 5 (2013). https://doi.org/10.1140/epje/i2013-13005-4

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  • DOI: https://doi.org/10.1140/epje/i2013-13005-4

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