Related papers: DNA Twist Elasticity: Mechanics and Thermal Fluctu…
DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
We present a method for solving the Worm Like Chain (WLC) model for twisting semiflexible polymers to any desired accuracy. We show that the WLC free energy is a periodic function of the applied twist with period 4 pi. We develop an analogy…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
We present a numerical solution of the Worm-Like Chain (WLC) model for semi-flexible polymers. We display graphs for the end-to-end distance distribution and the force-extension relation expected from the model. We predict the expected…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
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…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
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…
The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible…
We present an analytical study of bent twisted ribbons. We first describe the elastic response of a ribbon within a purely mechanical framework. We then study the role of thermal fluctuations in modifying its elastic response. We predict…
The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show…
We derive a reduced quasi-one-dimensional theory of geometrically frustrated elastic ribbons. Expressed in terms of geometric properties alone, it applies to ribbons over a wide range of scales, allowing the study of their elastic…
We characterize the fluctuation properties of a polymer chain under external tension and the fluctuation-induced forces between two ring molecules threaded around the chain. The problem is relevant in the context of fluctuation-induced…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We study the effects of thermal fluctuations on a small elastic ring. We derive analytical expressions for the correlation functions of the Euler angles, for the real space two--point correlation functions and for the probability…