Monte Carlo study of external noise influence on polymer translocation

The translocation of biopolymers into or across membranes is one of the most important biological process in nature, and is central in processes such as: (i) protein translocation from the cytosol into and across the endoplasmatic reticulum membrane; (ii) DNA and RNA translocations across nuclear pores; (iii) virus (bacteriophages) injection through the pores of a membrane to fight bacteria resistant to antibiotic therapies; (iv) gene therapy and controlled drug delivery. Previous studies demonstrated that the translocation time can be influenced by several factors, such as different geometrical and physical characteristics of the pore-channel structure, thermal fluctuations, always present in a biological system because of its continuous interaction with environment, and presence of any other external forces which can perturb the dynamics of the polymeric chain. In this work a Monte Carlo algorithm is employed to explore the effects of external noise on the dynamics of a flexible linear chain molecule crossing a nanochannel in the presence of a static or oscillating driving electric field acting on the monomers of the chain. The polymer chain is modeled using the two-dimensional “bond fluctuation model”. In analogy with the stochastic behavior of a Brownian particle, the polymer dynamics is generated by random monomer jumps, which originate from the thermal fluctuations affecting the polymer due to its interaction with environmental variables such as temperature. In addition, we consider that the polymer dynamics is influenced not only by a white Gaussian noise whose origin is connected with the thermal fluctuations, but also by the presence of noise sources characterized by different statistical properties. Within this context we model the dynamics of the polymeric chain by considering that the polymer moves through the channel so that the monomers of the chain interact with the walls by a discrete quasi-Lennard-Jones potential. Moreover, the interactions between adjacent monomers is modeled by a spring potential, and between non-adjacent beads through a Lennard-Jones potential. Finally, in view of providing a more realistic description of the polymer dynamics, the chain is provided with a suitable stiffness obtained by including a bending recoil torque in the model, with a rest angle equal to zero between two consecutive bonds. In our study we concentrate on the Mean First Translocation Time (MFTT) of the polymer centre of inertia through the channel and analyze how this time is influenced by the presence of an external noise source, for different values of the strength and frequency of the driving field, varying the length of the chain and the dimension of the channel.