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Faculty Selected Works of Chung Wong
Article
Brownian Dynamics Simulations of Ion Atmospheres Around Polyalanine and B‐Dna: Effects of Biomolecular Dielectric
Biopolymers (2003)
  • David S. Cerutti, University of California, San Diego
  • Chung F. Wong, University of California, San Diego
  • J. Andrew McCammon, University of California, San Diego
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Abstract
We have extended an earlier Brownian dynamics simulation algorithm for simulating the structural dynamics of ions around biomolecules to accommodate dielectric inhomogeneity. The electrostatic environment of a biomolecule immersed in water was obtained by numerically solving the Poisson equation with the biomolecule treated as a low dielectric region and the solvent treated as a high dielectric region. Instead of using the mean-field type approximations of ion interactions as in the Poisson-Boltzmann model, the ions were treated explicitly by allowing them to evolve dynamically under the electrostatic field of the biomolecule. This model thus accounts for ion-ion correlations and the finite-size effects of the ions. For a 13-residue alpha-helical polyalanine and a 12-base-pair bp B-form DNA, we found that the choice of the dielectric constant of the biomolecule has much larger effects on the mean ionic structure around the biomolecule than on the fluctuational and dynamical properties of the ions surrounding the biomolecule.
Disciplines
Publication Date
November 1, 2003
DOI
10.1002/bip.10498
Citation Information
David S. Cerutti, Chung F. Wong and J. Andrew McCammon. "Brownian Dynamics Simulations of Ion Atmospheres Around Polyalanine and B‐Dna: Effects of Biomolecular Dielectric" Biopolymers Vol. 70 Iss. 3 (2003) p. 391 - 402
Available at: http://works.bepress.com/chung-wong/41/