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.

Simulations of supercooled water under passive or active stimuli.

We use molecular dynamics simulations to study the behavior of supercooled water subject to different stimuli from a diluted azobenzene hydrophobic probe. When the molecular motor does not fold, it acts as a passive probe, modifying the structure of water around it, while when the motor is active, it induces elementary diffusion processes inside the medium acting mainly on the dynamics. We study two particular densities, the density of ambient water and a lower density around the ambient pressure ice density, chosen to favor high density liquid and low density liquid (LDL) water, respectively. We find that the passive probe induces ever an acceleration or a slowing down of the diffusion process around it depending on the density of water, while the active probe induces acceleration only. We find a crossover between the diffusion coefficients for the two densities near the passive probe, around T = 215 K. This dynamical crossover is associated with a modification of the structure of water near the probe. Structure calculations show a crossover of the proportion of LDL water around the same temperature, suggesting that it induces the observed dynamical crossover. In opposition with these results, the active stimuli increase diffusion for both densities and decrease the proportion of LDL water at low temperatures. However, we also find for the active stimuli a crossover of the LDL proportion between the two densities of study, showing remarkable similarities between active and passive stimulus results.

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.

Folding time dependence of the motions of a molecular motor in an amorphous medium.

We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time τ_{f}. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very slowly with τ_{f}, while for rapid foldings (regime II) the diffusion increases strongly with τ_{f}(D≈τ_{f}^{-2}), suggesting two different physical mechanisms. We find that in regime I the motor's displacement during the folding process is counteracted by a reverse displacement during the unfolding, while in regime II this counteraction is much weaker. We notice that regime I behavior is reminiscent of the scallop theorem that holds for larger motors in a continuous medium. We find that the difference in the efficiency of the motor's motion explains most of the observed difference between the two regimes. For fast foldings the motor trajectories differ significantly from the opposite trajectories induced by the following unfolding process, resulting in a more efficient global motion than for slow foldings. This result agrees with the fluctuation theorems expectation for time reversal mechanisms. In agreement with the fluctuation theorems we find that the motors are unexpectedly more efficient when they are generating more entropy, a result that can be used to increase dramatically the motor's motion.

Enhanced diffusion in finite-size simulations of a fragile diatomic glass former.

Using molecular dynamics simulations we investigate the finite-size dependence of the dynamical properties of a diatomic supercooled liquid. The simplicity of the molecule permits us to access the microsecond time scale. We find that the relaxation time decreases simultaneously with the strength of cooperative motions when the size of the system decreases. While the decrease of the cooperative motions is in agreement with previous studies, the decrease of the relaxation time opposes what has been reported to date in monatomic glass formers and in silica. This result suggests the presence of different competing physical mechanisms in the relaxation process. For very small box sizes the relaxation times behavior reverses itself and increases strongly when the box size decreases, thus leading to a nonmonotonic behavior. This result is in qualitative agreement with defect and facilitation theories.

The microscopic structure of cold aqueous methanol mixtures.

The evolution of the micro-segregated structure of aqueous methanol mixtures, in the temperature range 300 K-120 K, is studied with computer simulations, from the static structural point of view. The structural heterogeneity of water is reinforced at lower temperatures, as witnessed by a pre-peak in the oxygen-oxygen structure factor. Water tends to form predominantly chain-like clusters at lower temperatures and smaller concentrations. Methanol domains have essentially the same chain-like cluster structure as the pure liquid at high concentrations and becomes monomeric at smaller ones. Concentration fluctuations decrease with temperature, leading to quasi-ideal Kirkwood-Buff integrals, despite the enhanced molecular interactions, which we interpret as the signature of non-interacting segregated water and methanol clusters. This study throws a new light on the nature of the micro-heterogeneous structure of this mixture: the domain segregation is essentially based on the appearance of linear water clusters, unlike other alcohol aqueous mixtures, such as with propanol or butanol, where the water domains are more bulky.

How does the motion of the surrounding molecules depend on the shape of a folding molecular motor?

Azobenzene based molecules have the property of isomerizing when illuminated. In relation with that photoisomerization property, azobenzene containing materials are the subject of unexplained massive mass transport. In this work we use an idealised rectangular chromophore model to study the dependence of the isomerization induced transport on the chromophore's dimensions. Our results show the presence of a motor arm length threshold for induced transport, which corresponds to the host molecule's size. Above the threshold, the diffusive motions increase proportionally to the chromophore's length. Intriguingly, we find only a very small chromophore width dependence of the induced diffusive motions. Our very simplified motor reproduces relatively well the behavior observed using the real DR1 motor molecule, suggesting that the complex closing procedure and the detailed shape of the motor are not necessary to induce the molecular motions.

New Scenario of Dynamical Heterogeneity in Supercooled Liquid and Glassy States of 2D Monatomic System.

Via analysis of spatiotemporal arrangements of atoms based on their dynamics in supercooled liquid and glassy states of a 2D monatomic system with a double-well Lennard-Jones-Gauss (LJG) interaction potential, we find a new scenario of dynamical heterogeneity. Atoms with the same or very close mobility have a tendency to aggregate into clusters. The number of atoms with high mobility (and size of their clusters) increases with decreasing temperature passing over a maximum before decreasing down to zero. Position of the peak moves toward a lower temperature if mobility of atoms in clusters is lower together with an enhancement of height of the peak. In contrast, the number of atoms with very low mobility or solidlike atoms (and size of their clusters) has a tendency to increase with decreasing temperature and then it suddenly increases in the vicinity of the glass transition temperature leading to the formation of a glassy state. A sudden increase in the number of strongly correlated solidlike atoms in the vicinity of a glass transition temperature (Tg) may be an origin of a drastical increase in viscosity of the glass-forming systems approaching the glass transition. In fact, we find that the diffusion coefficient decays exponentially with a fraction of solidlike atoms exhibiting a sudden decrease in the vicinity of the glass transition region.