Related papers: The effect of undulations on Spontaneous Braid for…
Adhesion bonds between membranes and surfaces are attracted to each other via effective interactions whose origin the entropy loss due to the reduction in the amplitude of the membrane thermal fluctuations in the vicinity of the adhesion…
We consider the problem of an inextensible but flexible fiber advected by a steady chaotic flow, and ask the simple question whether the fiber can spontaneously knot itself. Using a 1D Cosserat model, a simple local viscous drag model and…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
From the per unit length free energy for DNA under tension, we have calculated an effective contour length dependent persistence length for short DNA. This effective persistence length results from the enhanced fluctuations in short DNA. It…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
Magnetic beads attract each other forming chains. We pushed such chains into an inclined Hele-Shaw cell and discovered that they spontaneously form self-similar patterns. Depending on the angle of inclination of the cell, two completely…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR…
We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
The dependence of electron transfer rates and yields in bridged molecular systems on the bridge length, and the dependence of the zero-bias conduction of molecular wires on wire length are discussed. Both phenomena are controlled by…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Natural slender structures, such as plant leaves, petals, and tendrils, often exhibit complex three-dimensional (3D) morphologies-including twisting, helical coiling, and saddle-bending-driven by differential growth. The resulting internal…
We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…