We develop a refined macroscopic model of supercoiled DNA with Brownian dynamics (BD) simulation protocols. DNA is modeled as a homogeneous elastic circle moving in solvent. Simulations on the 100-ms time scale for 300-6000 bp supercoiled DNA reproduce equilibrium conformational properties and offer adequate information for analyzing local and global dynamics of supercoiled DNA. We systematically study the kinetics of site juxtaposition, the process in which two or more sites distant in sequence move into spatial proximity at various salt concentrations and superhelical densities.
(For detailed information, see the article "Dynamics of Site Juxtaposition in Supercoiled DNA", J. Huang, T. Schlick, and A. Vologodskii, Proc. Natl. Acad. Sci., 98:968-973, January 2001).