Biochemistry & Pharmacology: Open Access

Biochemistry & Pharmacology: Open Access
Open Access

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Review Article - (2015) Volume 4, Issue 4

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An Optimization Model of Molecular Voronoi Cells in Computational Chemistry

Jiapu Zhang1,2*
1Molecular Model Discovery Laboratory, Department of Chemistry & Biotechnology, Faculty of Science, Engineering & Technology, Swinburne University of Technology, Hawthorn Campus, Hawthorn, Victoria 3122, Australia
2Graduate School of Sciences, Information Technology and Engineering & Centre of Informatics and Applied Optimisation, Faculty of Science, The Federation University of Australia, Mount Helen Campus, Mount Helen, Ballarat, Victoria 3353, Australia
*Corresponding Author: Jiapu Zhang, Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn Campus, Hawthorn, Victoria 3122, Australia, Tel: +61-3-9214-5596; +61-3-5327-6335 Email: ,

Abstract

In computational chemistry or crystallography, we always meet the problem that requires distributing N particles in one square unit with the minimal neighbor distance. Sometimes this problem is with special or complex constraints. This short article will build a molecular optimization model for the problem, and then will show one example of the application of this model

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Keywords: Computational chemistry, Crystal molecular structure, Optimization model, Optimized Voronoi cells distribution

Introduction

We consider the problem that requires distributing N (≥ 1) particles in one three- dimensional (3D) 2a × 2b × 2c box/cell/unit with the minimal neighborhood distance. Let us define that dij is the directdistance variable between particle i (1 ≤ i ≤ N) and particle j (1 ≤ i ≤ N, j ≠ i).

Direct-distance means particles i and j have a direct interaction relationship, for example, in computational chemistry, VanderWaals (vdW) contact [1,2], (or) solvent accessible surface area (ASA) contact (en.wikipedia.org/wiki/Accessible surface area), etc to each other. Denote (xi1, xi2, xi3) and (xj1, xj2, xj3) the coordinates of particles i and j, respectively. Then, for the convenience of practical computations [3,4], we can build an optimization model for the above problem.

(1)

(2)

(3)

This might be a problem of Voronoi diagram (en.wikipedia.org/wiki/Voronoi diagram) and the unit is called Voronoi cell. In computational chemistry, some crystals own special structures of the Voronoi cells; in such a case, we may add some additional constraints to Equation (3).

Clearly, the well-known Lennard-Jones Clusters problem [2] is one case of the above optimization problem Equations (1–3).

Example

We give a 2D Voronoi cells example Figure 1. We distribute 8 particles in one 2D square with the minimal neighborhood distance among them, with a constraint that each particle is only in one of the 8 Voronoi cells of the square. Figure 1(a) shows the initial solution that is given to the problem. Figure 1(b) and Figure 1(c) show the optimal (octagon) distribution of the 8 particles inner the square and onto the boundary of the square, respectively, after we solve the optimization problem Equations. (1-3) if in Equation. (3) “≤” is “≤” Figure 1(b) or “<” Figure 1(c).

biochemistry-pharmacology-optimization-model-distribute

Figure 1: The optimization model to distribute 8 particles into 8 Voronoi cells of a square unit: (a) initial distribution given, (b) optimal (octagon) distribution inner the square, and(c) Optimal (octagon) distribution onto the boundary of the square. The green dashed line denotes there is a direct relationship between the two particles they link (e.g. the two atoms have the vdW interactions).

Acknowlegements

This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant numbered VR0063 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government (Australia).

References

  1. Olechnovic K, et al. A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls. J Comput Chem.2014;35:672-681.
  2. Zhang JP. Thehybridideaofoptimizationmethodsappliedtotheenergy minimization of (prion) protein structures focusing on the ß2–a2 loop.Biochem Pharmacol(LosAngel) 2015
  3. Zhang JP, etal. A novel canonicaldualcomputationalapproachforprion AGAAAAGA amyloidfibrilmolecularmodeling.JTheorBiol.2011;284:149–157.
  4. Zhang JP. The LBFGS quasiNewtonian method for molecular modeling prion AGAAAAGA amyloid fib- rils. Nat Sci 4(12A) (Special Issue on Bioinformatics, Proteomics, Systems Biology and Their Impacts to Biomedicine). 2011;1:1097–1098.
Citation: Zhang J (2015) An Optimization Model of Molecular Voronoi Cells in Computational Chemistry. Biochem Pharmacol (Los Angel) 4:179.

Copyright: © 2015 Zhang J. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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