Related papers: Multiple barriers in forced rupture of protein com…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
We use molecular dynamics to study the nucleation of cracks in a two dimensional material without pre-existing cracks. We study models with zero and non-zero shear modulus. In both situations the time required for crack formation obeys an…
A possible way to extract information about the reversible dissociation of a molecular adhesion bond from force fluctuations observed in force ramp experiments is discussed. For small loading rates the system undergoes a limited number of…
The static friction coefficient between two materials is considered to be a material constant. We present experiments demonstrating that the ratio of shear to normal force needed to move contacting blocks can, instead, vary systematically…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
This work is focused on the development of a dynamic criterion for the arching and bridging of spherical particles in a 3D suspension flow through a channel with plane walls. Elasticity of the particles and the channel walls are taken into…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
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…
We study the existence of distinct failure regimes in a model for fracture in fibrous materials. We simulate a bundle of parallel fibers under uniaxial static load and observe two different failure regimes: a catastrophic and a slowly…
We study the dynamical response of a harmonically trapped two-component few-fermion mixture to the external gaussian potential barrier moving across the system. The simultaneous role played by inter-particle interactions, rapidity of the…
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analyze both Markovian…
We study how the loading rate, specimen geometry and microstructural texture select the dynamics of a crack moving through an heterogeneous elastic material in the quasi-static approximation. We find a transition, fully controlled by two…
We consider a linearly elastic body consisting of two equal symmetrically arranged layers (or half-planes) connected by a structured interface as a prospective crack path. The interface is comprised by periodic discrete system of bonds. In…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. However, with increased spatiotemporal resolution of instruments…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
The behaviors of barrier characteristics and fusion cross sections are analyzed by changing neutron over wide range of colliding systems. For this purpose, we have extended our previous study (Eur. Phys. J. A \textbf{48}, 21 (2012), it is…