Related papers: Polymer Translocation in Crowded Environments
Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive…
Force-driven translocation of a macromolecule through a nanopore is investigated by taking into account the monomer-pore friction as well as the "crowding" of monomers on the {\it trans} - side of the membrane which counterbalance the…
We construct a new statistical physical model of polymer translocation through a pore in a membrane treated as the diffusion process across a free energy barrier. We determine the translocation time in terms of chain flexibility yielding an…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…
The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded…
The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through…
We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore…
Using Langevin dynamics simulations in three dimensions (3D), we investigate the dynamics of polymer translocation into the regions between two parallel plane walls with separation $R$ under a driving force $F$, respectively. Compared with…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
Using two dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter $R$ through a nanopore under a driving force $F$. Due to the crowding effect induced by the…
We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced…
The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
Many biological channels perform highly selective transport without direct input of metabolic energy and without transitions from a 'closed' to an 'open' state during transport. Mechanisms of selectivity of such channels serve as an…