Related papers: Ring DNA confers enhanced bulk elasticity and rest…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination…
Mixtures of polyethylene glycol (PEG) and dextran (Dex) represent a widely used class of aqueous two-phase systems (ATPS), with applications ranging from the purification of various biomolecules such as nucleic acids to the synthesis of…
This review summarizes recent progress in investigating polymer systems by using Differential dynamic microscopy (DDM), a rapidly emerging approach that transforms a commercial microscope by combining real-space information with the…
In Keplerian accretion disks, turbulence and magnetic fields may be jointly excited through a subcritical dynamo process involving the magnetorotational instability (MRI). High-resolution simulations exhibit a tendency towards statistical…
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…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
We investigate by means of a number of different dynamical Monte Carlo simulation methods the self-assembly of equilibrium polymers in dilute, semidilute and concentrated solutions under good-solvent conditions. In our simulations, both…
Despite the significance of the high flexibility exhibited by short DNAs, there remains an incomplete understanding of their anomalous persistence length. In this study, we propose a novel approach wherein each fundamental characteristic of…
In bacteria, regulatory proteins search for a specific DNA binding target via "facilitated diffusion": a series of rounds of 3D diffusion in the cytoplasm, and 1D linear diffusion along the DNA contour. Using large scale Brownian dynamics…
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
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…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…