Related papers: Slow nucleic acid unzipping kinetics from sequence…
Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there are between six and eight unfolding transitions in the…
Microphase separation is common in active biological systems as exemplified by the separation of RNA and DNA-rich phases in the cell nucleus driven by the transcriptional activity of polymerase enzymes acting similarly to amphiphiles in a…
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…
This review focuses on the force-induced unzipping transition of double-stranded DNA. It begins with a brief history of DNA melting, which emerged alongside the growth of the field of molecular biology, juxtaposed with the advancements in…
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…
We study slow dynamics of particles moving in a matrix of immobile obstacles using molecular dynamics simulations. The glass transition point decreases drastically as the obstacle density increases. At higher obstacle densities, the…
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
Active matter can flow and yield under conditions where passive matter jams and slows down, as self-propulsion significantly modulates particle escape from local cages. How activity microscopically reshapes the caging environment to produce…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…