Related papers: Knot-controlled ejection of a polymer from a virus…
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…
Motivated by recent advances in single molecule manipulation techniques that enabled several groups to tie knots in individual polymer strands and to monitor their dynamics, we have used computer simulations to study "friction knots"…
This paper visualizes a knot reduction algorithm
We investigate the ejection dynamics of a ring polymer out of a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. The ejection dynamics for ring polymers shows two regimes like for…
Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with…
We probe the character of knotting in open, confined polymers, assigning knot types to open curves by identifying their projections as virtual knots. In this sense, virtual knots are transitional, lying in between classical knot types,…
The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
HH objects are characterized by a complex knotty morphology detected mainly along the axis of protostellar jets in a wide range of bands. Evidence of interactions between knots formed in different epochs have been found, suggesting that…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
We employ computer simulations and thermodynamic integration to analyse the effects of bending rigidity and slit confinement on the free energy cost of tying knots, $\Delta F_{\rm knotting}$, on polymer chains under tension. A…
We study the control parameters that govern the dynamics of in vitro DNA ejection in bacteriophage lambda. Past work has demonstrated that bacteriophage DNA is highly pressurized; this pressure has been hypothesized to help drive DNA…