Organization of two kinesins in a two-dimensional microtubule network.

In intracellular active transport, molecular motors are responsible for moving biological cargo along networks of microtubules that serve as scaffolds. Cargo dynamics can be modified by different features of microtubule networks such as geometry, density, orientation modifications. Also, the dynamical behaviour of the molecular motors is determined by the microtubule network and by the individual and/or collective action of the motors.

Polymer translocation driven by longitudinal and transversal time-dependent end-pulling forces.

In this article, we simulate the translocation of a semiflexible homopolymer through an extended pore, driven by both a constant and a time-dependent end-pulled force, employing a model introduced in previous studies. The time dependence is simplistically modeled as a cosine function, and we distinguish between two scenarios for the driving--longitudinal force and transversal force-depending on the relative orientation of the force, parallel or perpendicular, respectively, with respect to the pore axis. Besides some key differences between the two drivings, the mean translocation times present a large minimum region as a function of the frequency of the force that is typical of the resonant activation effect.

Elastic traits of the extensible discrete wormlike chain model.

Polymer models play the special role of elucidating the elementary features describing the physics of long molecules and become essential to interpret the measurements of their magnitudes. In this work the end-to-end distance of an extensible discrete wormlike chain polymer as a function of the applied force has been calculated both numerically and analytically, the latter as an effective approximation. The numerical evaluation uses the transfer matrix formalism to obtain an exact calculation of the partition function, while the analytic derivations generalize the simple phenomenological formulas largely used up to now.

Thermal versus mechanical unfolding in a model protein.

Force spectroscopy techniques are often used to learn about the free energy landscape of single biomolecules, typically by recovering free energy quantities that, extrapolated to zero force, are compared to those measured in bulk experiments. However, it is not always clear how the information obtained from a mechanically perturbed system can be related to the information obtained using other denaturants since tensioned molecules unfold and refold along a reaction coordinate imposed by the force, which is not likely to be meaningful in its absence. Here, we explore this dichotomy by investigating the unfolding landscape of a model protein, which is unfolded first mechanically through typical force spectroscopy-like protocols and next thermally.

Mesoscopic model for DNA G-quadruplex unfolding.

Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been reported to date by all-atom simulations, which cannot dissect the major physical interactions responsible for their cohesion. Here, we propose a mesoscopic model to describe both the mechanical and thermal stability of DNA G-quadruplexes, where each nucleotide of the structure, as well as each central cation located at the inner channel, is mapped onto a single bead.