Related papers: Multiple barriers in forced rupture of protein com…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Dynamic force spectroscopy of single molecules is described by a model which predicts a distribution of rupture forces, the corresponding mean rupture force and variance, all amenable to experimental tests. The distribution has a pronounced…
Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained. To describe the complexity of the underlying energy…
In this paper, a computational model in (2+1)-dimensions which simulates the rupture process of a fibrous material submitted to a constant force $F$, is analyzed. The roughness exponent $\zeta$ at the boundary that separates two failure…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
The relationship between the threshold energy for a deep sub-barrier fusion hindrance phenomenon and the energy at which the regime of interaction changes (the turning-off of the nuclear forces and friction) in the sub-barrier capture…
We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the stochastic properties of the unbinding/rebinding events and analyze their mean number and their…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
We investigate dynamic fracture of heterogeneous materials experimentally by measuring displacement fields as a rupture propagates through a periodic array of obstacles of controlled fracture energy. Our measurements demonstrate the…
Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…
Single-file transport, arising in quasi one-dimensional geometries where particles cannot pass each other, is characterized by the anomalous dynamics of a probe, notably its response to an external force. In these systems, the motion of…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
The thermal decay of linear chains from a metastable state is investigated. A crossover from rigid to elastic decay occurs when the number of particles, the single particle energy barrier or the coupling strength between the particles is…
We study experimentally the slow growth of a single crack in a fibrous material and observe stepwise growth dynamics. We model the material as a lattice where the crack is pinned by elastic traps and grows due to thermally activated stress…