Related papers: Exploring DNA translocation through a nanopore via…
We investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation…
The biotransport of the intravascular nanoparticle (NP) is influenced by both the complex cellular flow environment and the NP characteristics. Being able to computationally simulate such intricate transport phenomenon with high efficiency…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…
We present a very simple model for the study of charge transport in a molecule patterned on B-DNA. In this model we use a discrete non-linear Schr\"{o}dinger equation to describe electrons propagating along the sugar-phosphate backbone of…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
We present the detailed analysis of the diffusive transport of spatially inhomogeneous fluid mixtures and the interplay between structural and dynamical properties varying on the atomic scale. The present treatment is based on different…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Force-driven translocation of a macromolecule through a nanopore is investigated by taking into account the monomer-pore friction as well as the "crowding" of monomers on the {\it trans} - side of the membrane which counterbalance the…
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…
Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K.…
In recent years polymer translocation, i.e., transport of polymeric molecules through nanometer-sized pores and channels embedded in membranes, has witnessed strong advances. It is now possible to observe single-molecule polymer dynamics…
We report a Lattice-Boltzmann scheme that accounts for adsorption and desorption in the calculation of mesoscale dynamical properties of tracers in media of arbitrary complexity. Lattice Boltzmann simulations made it possible to solve…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Our study aims at a better control and understanding of the transfer of a complex [DNA supercoiled plasmid - dodecyltrimethylammonium surfactant] layer from a liquid-vapour water interface onto a silicon surface without any additional…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…