相关论文: A generalized theory of semiflexible polymers
In many applications, linear models fit the data poorly. This article studies an appealing alternative, the generalized regression model. This model only assumes that there exists an unknown monotonically increasing link function connecting…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
We use the worm-like chain model to analytically calculate the linear response of a grafted semiflexible polymer to a uniform force field. The result is a function of the bending stiffness, the temperature, the total contour length, and the…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the…
Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influence the…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
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…
A quantitative theory of the buckling of a worm like chain based on a semi-classical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows to go beyond the…
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 present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
A nonlinear viscoelastic theory of nematodynamic type is developed for nematic liquid crystalline (LC) semi-flexible polymers. A measure of transient elastic strain due to the change in length of macromolecular strands under stress, and the…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
By means of computer simulations, we investigate the relaxation of the Rouse modes in a simple bead-spring model for non-entangled polymer blends. Two different models are used for the fast component, namely fully-flexible and semiflexible…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
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…
A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between…
Using a coarse-grained bead-spring model for semi-flexible macromolecules forming a polymer brush, structure and dynamics of the polymers is investigated, varying chain stiffness and grafting density. The anchoring condition for the grafted…
Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with…