Related papers: Multiple barriers in forced rupture of protein com…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Fiber bundles with statistically distributed thresholds for breakdown of individual fibers are interesting models of the static and dynamics of failures in materials under stress. They can be analyzed to an extent that is not possible for…
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and…
Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state ``burnt-bridge'' models.…
A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are…
On the basis of energy conservation law an without utilizing Linear Fracture Mechanics (LFM) postulates the equation of a real-structure material elastic-plastic fracture has been derived. With the help of this equation the force and energy…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
Molecular-dynamics simulations of fracture in metallic glass-like systems are observed to undergo embrittlement due to a small change in interatomic potential. This change in fracture toughness, however, is not accompanied by a…
Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…
Dynamic fracture experiments were performed in PMMA over a wide range of velocities and reveal that the fracture energy exhibits an abrupt 3-folds increase from its value at crack initiation at a well-defined critical velocity, below the…
A formalism for semi-adiabatic cranking mass parameters is presented. For the fission process of 234U, the time-dependent pairing equations of motion were used to calculate the excitation energy and to extract values of the cranking…
Couplings between relative motion and internal structures are known to affect fusion barriers by dynamically modifying the densities of the colliding nuclei. The effect is expected to be stronger at energies near the barrier top, where…
The influence on the fusion process of coupling to collective degrees of freedom has been explored. The significant enhancement of the fusion cross section at sub-barrier energies was compared to predictions of one-dimensional barrier…
We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using…
One of the assumptions of Linear Elastic Fracture Mechanics is that the crack faces are traction-free or, at most, loaded by bounded tractions. The standard Irwin's crack closure integral, widely used for the computation of the Energy…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…