Related papers: Polymer translocation under a pulling force: scali…
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. We have created a method for…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
The translocation of a short DNA fragment through a nanopore is addressed when the perforated membrane contains an embedded electrode. Accurate numerical solutions of the coupled Poisson, Nernst-Planck, and Stokes equations for a realistic,…
We present an analysis of a partially directed walk model of a polymer which at one end is tethered to a sticky surface and at the other end is subjected to a pulling force at fixed angle away from the point of tethering. Using the kernel…
We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent, using an innovative multi-scale methodology which treats the biopolymer at the microscopic scale as combined with a…
We investigate the impact of dielectric boundary forces on the translocation process of charged rigid DNA segments through solid neutral nanopores. We assess the electrostatic contribution to the translocation free energy barrier of a model…
The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…
We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to…
We investigate the dynamics of pore-driven polymer translocation by theoretical analysis and molecular dynamics (MD) simulations. Using the tension propagation theory within the constant flux approximation we derive an explicit equation of…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
We consider elongated cylindrical particles, modeling e.g. DNA fragments or nano-rods, while translocating under the action of an externally applied voltage through a solid state nanopore. Particular emphasis is put on the concomitant…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…