First principles calculations of the thermodynamic stability of Ba, Zr, and O vacancies in BaZrO3

The temperature dependence of the stability of bulk BaZrO3 (BZO) and of the vacancies in this material are investigated by considering phonon contributions to the free energy. The stability diagram of BZO is determined for different chemical environments. With increasing temperature the stability region becomes smaller which is particularly caused by the strong temperature dependence of the chemical potential of gaseous oxygen. The free formation energy of Ba, Zr, and O vacancies in BZO is calculated for all possible charge states and for different atomic reservoirs. While the free formation energy of Zr vacancies is strongly influenced by temperature a weaker dependence is found for Ba and O vacancies. This also has an effect on the charge transition levels at different temperatures. The present results demonstrate that O poor reservoir conditions and a Fermi level close to the valence band maximum favour a high concentration of doubly positively charged O vacancies which is a prerequisite to get a large number of protonic defects and good proton conductivity. In such a chemical environment the number of Ba and Zr vacancies is low so that Ba and Zr deficiencies are not an important issue and BZO remains sufficiently stable.

Model for bidirectional movement of cytoplasmic dynein

Cytoplasmic dynein exhibits a directional processive movement on microtubule filaments and is known to move in steps of varying length based on the number of ATP molecules bound to it and the load that it carries. It is experimentally observed that dynein takes occasional backward steps and the frequency of such backward steps increases as the load approaches the stall force. Using a stochastic process model, we investigate the bidirectional movement of single head of a dynein motor. The probability for backward step is implemented based on fluctuation theorem of non-equilibrium statistical mechanics. We find that the movement of dynein motor is characterized with negative velocity implying backward motion beyond stall force. We observe that the motor moves backward for super stall forces by hydrolyzing the ATP exactly the same way as it does while moving forward for sub-stall forces. Movement of dynein is also simulated using a kinetic Monte Carlo method and the simulated velocities are in good agreement with velocities obtained using a stochastic rate equation model.

Steady state dynamics of a moving model cell

Crawling cell motility results due to treadmilling of a polymerized actin network at the leading edge. Steady state dynamics of a moving cell are governed by actin concentration profiles across the cell. Branching of new filaments implicating Arp2/3 and capping of existing filaments with capZ or Gelsolin are central to the robust functioning of the actin network. Using computer simulations, steady state concentration profiles of globular actin (G actin) and filamentous actin (F actin) are computed. The profiles are in agreement with experimentally observed ones. Simulations unveil that there is an optimal capping and branching rate for which the velocity of the model cell is maximum. Our simulations also indicate that the capping of actin filaments results in an increase in nucleation of new filaments by Arp2/3-induced branching and is in agreement with a recently observed monomer gating model. We observe that Arp2/3 and capping protein exhibit a functional antagonism with respect to the actin network treadmilling.

Shape and motility of a model cell: A computational study

We have investigated the shape, size, and motility of a minimal model of an adherent biological cell using the Monte Carlo method. The cell is modeled as a two dimensional ring polymer on the square lattice enclosing continuously polymerizing and depolymerizing actin networks. Our lattice model is an approximate representation of a real cell at a resolution of one actin molecule, 5 nm. The polymerization kinetics for the actin network are controlled by appropriate reaction probabilities which correspond to the correct experimental reaction rates. Using the simulation data we establish various scaling laws relating the size of the model cell to the concentration of polymerized and unpolymerized actin molecules and the length of the enclosing membrane. The computed drift velocities, which characterize the motility of the cell, exhibit a maximum at a certain fraction of polymerized actin which agrees with physiological fractions observed in experiments. The appearance of the maximum is related to the competition between the polymerization-induced protrusion of the membrane and the concomitant suppression of membrane fluctuations.