Related papers: First-principles calculation of DNA looping in tet…
We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the…
The modelling of DNA mechanics under external constraints is discussed. Two analytical models are widely known, but disagree for instance on the value of the torsional modulus. The origin of this embarassing situation is located in the…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
We consider the single-file dynamics of $N$ identical random walkers moving with diffusivity $D$ in one dimension (walkers bounce off each other when attempting to overtake). Additionally, we require that the separation between neighboring…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…
We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting…
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Using Langevin dynamics simulations, we study elastic response of single semiflexible polyelectrolytes to an external force pulling on the chain ends, to mimic the stretching of DNA molecules by optical tweezers. The linear chains are…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
Monte Carlo dynamics of the lattice 48 monomers toy protein is interpreted as a random walk in an abstract (discrete) space of conformations. To test the geometry of this space, we examine the return probability $P(T)$, which is the…