相关论文: Molecular Dynamics Studies of Sequence-directed Cu…

Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…

The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…

A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…

Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…

For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…

In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…

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…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

Active networks made of biopolymers and motor proteins are valuable bioinspired systems that have been used in the last decades to study the cytoskeleton and its self-organization under mechanical stimulation. Different techniques are…

In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…

Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…

We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…

Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…

Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…

Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…

Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…

Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…

By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…

We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…