Related papers: Chaperone driven polymer translocation through Nan…
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension…
We present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component,…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We investigate spreading of phase separated copolymer films, where domain walls and thickness steps influence polymer flow. We show that at early stages of spreading its rate is determined by slow activated flow at terrace steps (i.e.…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Routinely navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell's crucial components, such as neurotransmitters and organelles. They generate force and pull cargo,…
Many lamellar systems exhibit strongly anisotropic diffusion. When the diffusion across the lamellae is slow, an alternative mechanism for transverse transport becomes important. A tracer particle can propagate in the direction normal to…
The stress transfer mechanism from a polymer substrate to a nano-inclusion, such as a graphene flake, is of extreme interest for the production of effective nanocomposites. Previous work conducted mainly at the micron scale has shown that…
We investigate theoretically the transfer of excitation along a one dimensional chain of monomers for a situation in which initially the excitation is shared coherently by two monomers. We show that depending on the relative phase between…
Two distinct interactions of Pomerons should occur in dense multi-string events. Besides the usual triple Pomeron processes transitions to membraned cylinders can be expected to contribute in a significant way. They offer an efficient…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
Despite the spontaneity of some in vitro protein folding reactions, native folding in vivo often requires the participation of barrel-shaped multimeric complexes known as chaperonins. Although it has long been known that chaperonin…
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…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
We consider a laminar Blasius boundary-layer flow above a slightly heated horizontal plate and study the effect of polymer additives on the heat transport. We show that the action of the polymers can be understood as a space-dependent…
Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^\lambda$ at temperature of fastest folding.…
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…
An important indicator of membrane performance are free volume elements (FVEs): microporous void spaces created by the inefficient packing of bulky groups along the polymer chain. FVEs tend to degrade over time as polymer chains reorganize…
Ground state diffusion Monte Carlo is used to investigate the binding energies and carrier probability distributions of excitons, trions, and biexcitons in a variety of two-dimensional transition metal dichalcogenide materials. We compare…
Adsorption of polymers to surfaces is crucial for understanding many fundamental processes in nature. Recent experimental studies indicate that the adsorption dynamics is dominated by non-equilibrium effects. We investigate the adsorption…