Related papers: Polymer Translocation in Crowded Environments
The cavitation flow of linear-polymer solutions around a cylinder is studied by performing a large-scale molecular dynamics simulation. The addition of polymer chains remarkably suppresses the cavitation. The polymers are stretched into a…
This paper studies the features of a homopolymer translocating through a flexible pore. The channel is modeled as a monolayer tube composed by monomers with two elastic parameters: spring-like two body interaction and bending three body…
Using Langevin dynamics simulations, we investigate the dynamics of a flexible polymer translocation into a confined area under a driving force through a nanopore. We choose an ellipsoidal shape for the confinement and consider the…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
Extensive molecular dynamics simulations were conducted to explore the conformational phase diagram of a neutral polymer in the presence of attractive crowders of varying sizes. For weakly self-attractive polymers, larger crowders induce a…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
Polymers adopt extended coil and compact globule states according to the balance between entropy and interaction energies. The transition of a polymer between an extended coil state and compact globule state can be induced by changing…
We propose a method for the theoretical investigation of polymer translocation through composite pore structures possessing arbitrarily specified geometries. Translocation through each constituent part of the composite is treated as being…
Translocation of a polymer out of curved surface or membrane is studied via mean first passage time approach. Membrane curvature gives rise to a constraint on polymer conformation, which effectively drives the polymer to the outside of…
We elucidate the structural transitions in a helical off-lattice homopolymer induced by crowding agents, as function of the number of monomers ($N$) and volume fraction ($\phi_c$) of crowding particles. At $\phi_c = 0$, the homopolymer…
We discuss the temporal distribution of dynamic processes in driven polymer transport inherent to flexible chains due to stochastic tension propagation. The stochasticity originates from the disordered initial configuration of an…
Under high cylindrical confinement, segments of ring polymers can be localized along the long axis of the cylinder by introducing internal loops within the ring polymer. The emergent organization of the polymer segments occurs because of…
We employ 3D Langevin Dynamics simulations to study the dynamics of polymer chains translocating through a nanopore in presence of asymmetric solvent conditions. Initially a large fraction ($>$ 50%) of the chain is placed at the…
Packing and crowding are used in biology as mechanisms to (self-)regulate internal molecular or cellular processes based on collective signalling. Here, we study how the transition kinetics of an internal switch of responsive macromolecules…
Conformations of a crowded neutral semiflexible polymer under confinement near an attractive wall are studied via coarse-grained simulations. We study the effects of the interplay of the length of the polymer, bending rigidity, and the…
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the…
The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate…
The effect of ambient disorders and sequence heterogeneities on the reptation of a long polymer is studied with the aid of a disordered tube model. The dynamics of a random heteropolymer is found to be much slower than that of a homopolymer…
Hydrodynamic forces may significantly affect the motion of polymers. In sheet-like cavities, such as the cell's cytoplasm and microfluidic channels, the hydrodynamic forces are long-range. It is therefore expected that that hydrodynamic…
We consider the flow-driven translocation of single polymer chains through nanochannels. Using analytical calculations based on the de Gennes blob model and mesoscopic numerical simulations, we estimate the threshold flux for the…