Related papers: Elastic lever arm model for myosin V
Multi-degree of freedom robots are playing very important role in different applications of automation. They are providing much more accuracy in carrying out a typical procedure as compared to the manual work done by human. In recent years…
Motivated by recent experimental results for the step sizes of dynein motor proteins, we develope a cellular automata model for intra-cellular traffic of dynein motors incorporating special features of the hindrance-dependent step size of…
We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics…
We propose a class of microstructurally informed models for the linear elastic mechanical behavior of cross-linked polymer networks such as the actin cytoskeleton. Salient features of the models include the possibility to represent…
We present a variational treatment of the ground state of the 2-leg t-J ladder, which combines the dimer and the hard-core boson models into one effective model. This model allows us to study the local structure of the hole pairs as a…
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…
We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
We present a simple model for the underlying structure of protein-protein pairwise interaction graphs that is based on the way in which proteins attach to each other in experiments such as yeast two-hybrid assays. We show that data on the…
Muscle contraction is a prototypical multiscale chemomechanical process in which ATP hydrolysis at the molecular level drives force generation and mechanical work at larger scales. A long-standing challenge is to connect microscopic…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
A system consisting of a doubly clamped beam with an attached body (slider) free to move along the beam has been studied recently by multiple research groups. Under harmonic base excitation, the system has the capacity to passively adapt…
Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor…
Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is…
Voltage-driven memristive switching has been reported in molecular junctions, yet its microscopic origin often remains elusive. Here, we study three rigid OPE-like derivatives that lack an obvious internal switching pathway using…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
We propose a dynamic mechanism of a molecular machine for energy conversion, by considering a simple model describing the dynamics of two components, the head and the chain. After injection of energy to the head region, the energy is stored…
Molecular motors belonging to the kinesin and myosin super family hydrolyze ATP by cycling through a sequence of chemical states. These cytoplasmic motors are dimers made up of two linked identical monomeric globular proteins. Fueled by the…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. For that purpose, we have performed a version of steered molecular dynamics (SMD) calculations. The…