Related papers: Chaperone driven polymer translocation through Nan…
By tracking small particles in the bulk of an intensely turbulent flow, we show that even a very small concentration of long-chain polymers disrupts the usual turbulent energy cascade. The polymers affect scales much larger than their…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
We suggest a governing equation which describes the process of polymer chain translocation through a narrow pore and reconciles the seemingly contradictory features of such dynamics: (i) a Gaussian probability distribution of the…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…
We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…
Motivated by identifying the origin of the bias dependence of tension propagation we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here the motion of flexible…
We use a combination of computer simulations and iso-flux tension propagation (IFTP) theory to investigate translocation dynamics of a flexible linear polymer through a nanopore into an environment composed of repulsive active rods in 2D.…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
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…
Ionic transport in nano- to sub-nano-scale pores is highly dependent on translocation barriers and potential wells. These features in the free-energy landscape are primarily the result of ion dehydration and electrostatic interactions. For…
The transfer of electrons and holes along DNA dimers, trimers and polymers is described at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. The temporal and…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here, we describe first the protein structure networks of molecular chaperones, then characterize chaperone containing…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Processes on different length scales affect the dynamics of chain molecules. In this work, we focus on structures on the scale of a monomer and investigate polyolefins, i.e. hydrocarbon chains with different small scale architectures. We…
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
The Pomeron Regge trajectory underlies the dynamics dependence of hadronic total cross sections and diffractive reactions at high energies. The physics of the Pomeron is closely related to the gluon distribution function and the gluon…
The threading of a polymer chain through a small pore is a classic problem in polymer dynamics and underlies nanopore sensing technology. However important experimental aspects of the polymer motion in a solid-state nanopore, such as an…
Most proteins must remain soluble in the cytosol in order to perform their biological functions. To protect against undesired protein aggregation, living cells maintain a population of molecular chaperones that ensure the solubility of the…
Graphene nanopore based sensor devices are exhibiting the great potential for the detection of DNA. To understand the fundamental aspects of DNA translocating through a graphene nanopore, in this work, molecular dynamics (MD) simulations…