Induced cooperative motions in a medium driven at the nanoscale: searching for an optimum excitation period

Dynamic phase transition induced by active molecules in a supercooled liquid

The purpose of this work is to use active particles to investigate the effect of facilitation on supercooled liquids. To this end we examine the behavior of a model supercooled liquid that is doped with a mixture of active particles and slowed particles. To simulate the facilitation mechanism, the activated particles are subjected to a force that follows the mobility of their most mobile neighboring molecule, while the slowed particles experience a friction force. Upon activation, we observe a fluidization of the entire medium along with a significant increase in dynamic heterogeneity. This effect is reminiscent of the fluidization observed experimentally when introducing molecular motors into soft materials. Interestingly, when the characteristic time τ_{μ}, used to define the mobility in the facilitation mechanism, matches the physical time t^{*} that characterizes the spontaneous cooperativity of the material, we observe a phase transition accompanied by structural aggregation of the active molecules. This transition is characterized by a sharp increase in fluidization and dynamic heterogeneity.

Orientation of motion of a flat folding nano-swimmer in soft matter

It is well established that anisotropic molecules do have a preferential direction of motion at short time scales that is washed out at larger times by Brownian noise. Anisotropic molecular motors are able to move at lower temperatures when Brownian noise is smaller suggesting the possibility of oriented motion for larger time scales. We use molecular dynamics simulations to investigate that possibility, calculating the displacements of a simple flat folding molecular nano-swimmer embedded in soft matter. We find actually that the motor displacement is oriented in the direction of its length. We note that the observed orientation of the displacement explains the experimental polarization effect in surface relief gratings formation in agreement with the caterpillar model for azobenzene SRG formation mechanism. That result also suggests a simple route for the creation of molecular motors with oriented displacements.

Breakdown of the Stokes-Einstein Relation in Supercooled Water/Methanol Binary Mixtures: Explanation Using the Translational Jump-Diffusion Approach

A recent experiment has directly checked the validity of the Stokes-Einstein (SE) relation for pure water, pure methanol, and their binary mixtures of three different compositions at different temperatures. The effect of composition on the nature of breakdown of the SE relation is interesting. While in the majority of the systems, an increasing SE breakdown is observed with decreasing temperature, the breakdown is already significant at higher temperatures for the equimolar mixture. Violations of the SE relation in pure supercooled water at different temperatures and pressures have been previously explained using the translational jump-diffusion (TJD) approach, which provides a fundamental molecular basis, by directly connecting the SE breakdown with jump-diffusion of the molecules. We have used the same TJD approach for explaining the SE breakdown for the methanol/water binary mixtures of compositions studied in the experiment over a wide range of temperatures between 220 K and 300 K. We have understood that the jump-diffusion is the key responsible factor for the SE breakdown. The maximum jump-diffusion contribution gives rise to the early SE breakdown observed for the equimolar mixture observed in the experiment. This study, therefore, provides molecular insight into the SE breakdown for the supercooled water/methanol binary mixture, as found in the experiment.

Breakdown of the scallop theorem for an asymmetrical folding molecular motor in soft matter

We use molecular dynamic simulations to investigate the motion of a folding molecular motor inside soft matter. Purcell's scallop theorem forbids the displacement of the motor due to time symmetrical hydrodynamic laws at low Reynolds numbers whatever the asymmetry of the folding and unfolding rates. However, the fluctuation theorems imply a violation of the time symmetry of the motor's trajectories due to the entropy generated by the motor, suggesting a breakdown of the scallop theorem at the nanoscale. To clarify this picture, we study the predicted violation of time reversibility of the motor's trajectories, using two reverse asymmetric folding mechanisms. We actually observe this violation of time reversibility of the motor's trajectories. We also observe the previously reported fluidization of the medium induced by the motor's folding, but find that this induced diffusion is not enough to explain the increase of the motor's displacement. As a result, the motor is not carried by the medium in our system but moves by its own, in violation of the scallop theorem. The observed violation of the scallop theorem opens a route to create very simple molecular motors moving in soft matter environments.

Temperature dependence of the violation of Purcell's theorem experienced by a folding molecular motor

We investigate the violation of Purcell's scallop theorem experienced by a mono-molecular motor, successively folding and unfolding inside a soft matter environment due to an external stimulus. We find a breakdown of the Purcell theorem due to fluctuations, that permits the molecular motor's efficient motion. The diffusion of the motor, its efficiency and its elementary displacement strongly depend on the characteristic time of the folding, but only slightly on the temperature. The increase of the motor's efficiency when the folding characteristic time τ decreases agrees with the fluctuation theorem expectation as the entropy generated inside the medium increases. The constant efficiency with respect to temperature is more difficult to understand as it suggests a generated entropy independent of temperature. In contrast with these results, the diffusion of the medium induced by the motor's folding strongly depends on the temperature, but doesn't depend on the characteristic time of the folding. That result suggests that the medium's diffusion is not due to the motor's displacement. We find that cooperative motions known as dynamic heterogeneity depend significantly on both temperature and folding time, leading in some conditions to a decoupling between dynamic heterogeneity and the medium's diffusion. Eventually, we find that the cooperative motions induced by the folding are larger when the motor cannot move.

Optimizing the motion of a folding molecular motor in soft matter

We use molecular dynamics simulations to investigate the displacement of a periodically folding molecular motor in a viscous environment. Our aim is to find significant parameters to optimize the displacement of the motor. We find that the choice of a massy host or of small host molecules significantly increase the motor displacements. While in the same environment, the motor moves with hopping solid-like motions while the host moves with diffusive liquid-like motions, a result that originates from the motor's larger size. Due to hopping motions, there are thresholds on the force necessary for the motor to reach stable positions in the medium. These force thresholds result in a threshold in the size of the motor to induce a significant displacement, that is followed by plateaus in the motor displacement.