Related papers: Semiflexible Chains in Confined Spaces
We compute the free energy of confinement ${\cal{F}}$ for a wormlike chain (WLC), with persistence length $l_p$, that is confined to the surface of a cylinder of radius $R$ under an external tension $f$ using a mean field variational…
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…
Systems under external confinement and constraints often show interesting properties. In this thesis, we study some systems under external confinement. We begin by finding out the probability distribution of end-to-end separation of a Worm…
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…
Polymer models describing the statistics of biomolecules under confinement have applications to a wide range of single molecule experimental techniques and give insight into biologically relevant processes {\em{in vivo}}. In this paper, we…
We present an exact solution of the discrete wormlike chain (DWLC) model describing a single semiflexible polymer under arbitrary external force. Through exact closure relations between pair angular correlations and single-site angular…
The wormlike chain (WLC) model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for…
We present a simplified theory for semiflexible flagella under the action of a traveling-wave perturbation that emulates the organized active forces generated by molecular motors, capable of inducing beating patterns to the filament. By…
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is…
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…
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…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
We show that the mechanical properties of a worm-like-chain (WLC) polymer, of contour length $L$ and persistence length $\l$ such that $t=L/\l\sim{\cal O}(1)$, depend both on the ensemble and the constraint on end-orientations. In the…
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
We analyse the nature of the confinement of an infinitely long (and finite) linear semiflexible homo-polymer chain confined in between two geometrical constraints (A&B) under good solvent condition in two dimensions. The constraints are…
We present an analysis for the ring closure probability of semiflexible polymers within the pure bend Worm Like Chain (WLC) model. The ring closure probability predicted from our analysis can be tested against fluorescent actin cyclization…
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…
A multi-chain mean-field theory is developed and applied to a two-dimensional system of weakly coupled S=1/2 Heisenberg chains. The environment of a chain C_0 is modeled by a number of neighbor chains C_d, d = +/-1,...,+/-n, with the edge…
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…