• Brownian dynamics simulation of macromolecule diffusion in a protocell 

      Ando, Tadashi; Skolnick, Jeffrey (Georgia Institute of TechnologyWorld Scientific Publishing, 2011)
      The interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green ...
    • Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations 

      Ando, Tadashi; Chow, Edmond; Saad, Yousef; Skolnick, Jeffrey (Georgia Institute of TechnologyAmerican Institute of Physics, 2012-08)
      Hydrodynamic interactions play an important role in the dynamics of macromolecules. The most common way to take into account hydrodynamic effects in molecular simulations is in the context of a Brownian dynamics simulation. ...