Related papers: Peeling and Sliding in Nucleosome Repositioning
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential, and a sideways constant…
We performed two-dimensional Molecular Dynamics simulations of cohesive disks under shear. The cohesion between the disks is added by the action of springs between very next neighbouring disks, modelling capillary forces. The geometry of…
We investigate the unfolding pathway of a cytosine-rich DNA hairpin structure via Molecular Dynamics simulations. Our results indicate a hidden complexity present in the unfolding process. W e show that this complex behavior arises due to…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
The flow of motor proteins on a filamental track is modelled within the the framework of lattice driven diffusive systems. Motors, considered as hopping particles, perform a highly biased asymmetric exclusion process when bound to the…
Sliding motion is evolution on a switching manifold of a discontinuous, piecewise-smooth system of ordinary differential equations. In this paper we quantitatively study the effects of small-amplitude, additive, white Gaussian noise on…
An in-situ neutron diffraction investigation of the annealing and healing of dislocations in the bulk Pd-D2 system was carried out. Lattice misfit between the alpha and beta hydride phases produces dislocations during the phase transition…
Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA).…
We consider a model of fragmentation of sheet by cracks that move with a velocity in preferred direction, but undergo random transverse displacements as they move. There is a non-zero probability of crack-splitting, and the split cracks…
We demonstrate a catalytic control method for speeding up the single-molecule DNA motor introduced by Li and Tan [Nano Lett. {\bf 2}, 315 (2002)]. A key rate-limiting barrier in the reaction part of the cycle is the tendency for the second…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Reprogramming is a process of transforming differentiated cells into pluripotent stem cells by inducing specific modifying factors in the cells. Reprogramming is a non-equilibrium process involving a collaboration at levels separated by…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
Sensitive and fast force measurements are performed on sheared granular layers undergoing stick-slip motion, along with simultaneous imaging. A full study has been done for spherical particles with a +-20% size distribution. Stick-slip…
In cells, cytoskeletal filament networks are responsible for cell movement, growth, and division. Filaments in the cytoskeleton are driven and organized by crosslinking molecular motors. In reconstituted cytoskeletal systems, motor activity…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
The notion of periodic two-scale convergence and the method of periodic unfolding are prominent and useful tools in multiscale modeling and analysis of PDEs with rapidly oscillating periodic coefficients. In this paper we are interested in…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…