Related papers: When Knots are Plectonemes
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…
A polymer chain confined in nano-scale geometry has been used to investigate the underlying mechanism of Nuclear Pore Complex (NPC), where transport of cargoes is directional. It was shown here that depending on the solvent quality (good or…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as…
We have used Langevin dynamics to simulate the forced translocation of linked polymer rings through a narrow pore. For fixed size (i.e. fixed number of monomers) the translocation time depends on the link type and on whether the rings are…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
Plasmonic nanopores are extensively investigated as single molecules detectors. The main limitations in plasmonic nanopore technology are the too fast translocation velocity of the molecule through the pore and the consequent very short…
Polymer translocation has long been a topic of interest in the field of biological physics given its relevance in both biological (protein and DNA/RNA translocation through nuclear and cell membranes) and technological processes (nanopore…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Flow-driven rotary motors drive functional processes in human society such as windmills and water wheels. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has…
We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory…
Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…
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…
Spontaneous formation of knots in long polymers at equilibrium is inevitable but becomes rare in sufficiently short chains. Here, we show that knotting and knot complexity increase by orders of magnitude in diblock polymers with a fraction…
We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across…
The requirement to boost the resolution of nanopore-based biosequencing devices necessitates the integration of novel biosensing techniques with reduced sensitivity to background noise. In this article, we probe the signatures of…