Related papers: Role of Polymer Loops in DNA Replication
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…
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…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the…
Nanoscale and microscale confinement of biopolymers naturally occurs in cells and has been recently achieved in artificial structures designed for nanotechnological applications. Here, we present an extensive theoretical investigation of…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
Recent theoretical studies found that mixtures of active and passive colloidal particles phase separate but only at very high activity ratio. The high value poses serious obstacles for experimental exploration of this phenomenon. Here we…
In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates…
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…