Theoretical investigations of asymmetric simple exclusion processes for interacting oligomers

Abstract

Motivated by biological transport phenomena that involve the motion of interacting molecular motors along linear filaments, we developed a theoretical framework to analyze the dynamics of interacting oligomers (extended size particles) on one-dimensional lattices. Our method extends the asymmetric simple exclusion processes for interacting monomers to particles of arbitrary size, and it utilizes cluster mean-field calculations supplemented by extensive Monte Carlo computer simulations. Interactions between particles are accounted for by a thermodynamically consistent method that views the formation and breaking bonds between particles as a chemical process. The dynamics of the system are analyzed for both periodic and open boundary conditions. It is found that the nature of the current-density relation depends on the strength of interactions, on the size of oligomers and on the way interactions influence particles transition rates. Stationary phase diagram is also fully evaluated, and it is shown how the dynamic properties depend on the interactions and on the sizes of the particles. To explain the dynamic behavior of the system particles density correlations are explicitly analyzed for dierent ranges of parameters. Theoretical calculations generally agree well with the results from the computer simulations, suggesting that our method correctly describes the main features of the molecular mechanisms of the transport of interacting oligomers.