Introduction: In the paper, static and dynamic of the confined semi-flexible polymer in nano-slit are investigated by molecular dynamic simulations. Free energy (F) and gyration radius are investigated as functions of polymer length (N) and confinement dimension (D) in self-crossing odijk regime. Odijk regime is an intense-confinement regime with confinement dimension , where w is the effective diameter of the chain. According to the Odijk theory, the force is scaled with . Our simulation results for large values of P have an excellent agreement with the Odijk theory. However, for small values of P, the behavior of the chain is in agreement with de Gennes theory for flexible chains. The threshold persistence length for this transition between the two regimes is also in agreement with these available theories. In Odijk theory, there is no relation between and D but gyration radius varies with P as . In simulation also independence of gyration radius to degree of confinement and the relation between and P is observed. The favorite dynamic parameter in this work is escape time of the chain from a nanopore, which is related to other parameters of the system like . In the case of large values of P, varies with D, according to theory. But in small values of P, the behavior is rather different. According to all of the simulations, by increasing D, the results of as a function of P become closer to the theoretical relation.
Methods: simulation molecular dynamic
Results: At the beginning of the simulation, the equilibrium time chain is given from the order of polymer length to the power of two, and the averages are made at four times this amount of time after the equilibrium of the chain.
Conclusion: It can be seen that the simulation results for static are in good agreement with the theory within the defined range for the Edic regimen. However, the simulation results for the time out of the limit are consistent with the theory only when the static length and size of the nanogap are large enough. In previous work, it has also been observed that, unlike static, polymer dynamics are more sensitive to the size of constraints.