We present a study of the DNA translocation of the bacteriophage phi 29 packaging molecular motor. From the experimental available information we present a model system based in an stochastic fashing potential, which reproduces the experimental obser
vations such as: detailed trajectories, steps and substeps, spatial correlation, and velocity. Moreover the model allows the evaluation of power and efficiency of this motor. We have found that the maximum power regime does not correspond with that of the maximum efficiency. These informations can stimulate further experiments.
We analyze theoretically the problem of cargo transport along microtubules by motors of two species with opposite polarities. We consider two different one-dimensional models previously developed in the literature. On the one hand, a quite widespread
model which assumes equal force sharing, here referred to as mean field model (MFM). On the other hand, a stochastic model (SM) which considers individual motor-cargo links. We find that in generic situations the MFM predicts larger cargo mean velocity, smaller mean run time and less frequent
The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerizati
on reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.
A simple flashing ratchet model in two dimensions is proposed to simulate the hand-over-hand motion of two head molecular motors like kinesin. Extensive Langevin simulations of the model are performed. Good qualitative agreement with the expected beh
avior is observed. We discuss different regimes of motion and efficiency depending of model parameters.
