Conductance/conduction molecular system simulations

Lee et al. [21] conducted molecular dynamics simulations of the flow of a com-positionally symmetric diblock copolymer into the galleries between two siUcate sheets whose surfaces were modified by grafted surfactant chains. In these simulations they assumed that block copolymers and surfactants were represented by chains of soft spheres connected by an finitely extensible nonlinear elastic potential, non-Hookean dumbbells [22], which had been employed earlier in the simulations of the dynamics of polymer blends and block copolymers by Grest et al. [23] and Murat et al. [24]. To describe the interactions among the four components, namely the surfaces, the surfactant, and two blocks, Lee et al. [21] employed a Lennard-Jones potential having the energy parameters which are associated with the type of interactions often employed for lattice systems such as in the Flory-Huggins theory. 

The theory for various molecular dynamics simulation algorithms for the calculation of transport coefficients of liquid crystals is presented. We show in particular how the thermal conductivity and the viscosity are obtained. The viscosity of a nematic liquid crystal has seven independent components because of the lower symmetry. We present numerical results for various phases of the Gay-Berne fluid even though the theory is completely general and applicable to more realistic model systems. 

Indeed, all ingredients for a complete thermodynamic characterization of the system are available in molecular dynamics simulations atomic resolution, protein flexibility, membrane fluctuations, explicit solvent, and ionic motion. Because the free energy profile controls ion conduction, along with nonequilibrium parameters like the diffusion coefficient, one can expect to fully understand the permeation (and selectivity) processes from it. Furthermore, because one can explore the energetics of molecular configurations in response to external stimuli, free energy calculations can in principle supply information about gating mechanisms or, at least, could be used to confirm hypotheses derived from indirect experimental observations. 

---