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Configuration dynamics of flexible polymer chains is of ubiquitous importance in many biological processes. Here, we investigate a polymer chain immersed in a bath of size-changed active particles in two dimensional space using Langevin dynamics simulations. Particular attention is paid to how the radius of gyration Rg of the polymer chain depends on the size σc of active crowders. We find that Rg shows nontrivial non-monotonic dependence on σc: The chain first swells upon increasing σc, reaching a fully expanded state with maximum Rg, and then, Rg decreases until the chain collapses to a compact coil state if the crowder is large enough. Interestingly, the chain may oscillate between a collapse state and a stretched state at moderate crowder size. Analysis shows that it is the competition between two effects of active particles, one stretching the chain from inside due to persistence motion and the other compressing the chain from outside, that leads to the non-monotonic dependence. Besides, the diffusion of the polymer chain also shows nontrivial non-monotonic dependence on σc. Our results demonstrate the important interplay between particle activity and size associated with polymer configurations in active crowding environments.

We investigate configuration dynamics of a flexible polymer chain in a bath of active particles with dynamic chirality, i.e., particles rotate with a deterministic angular velocity $\omega$ besides self-propulsion,by Langevin dynamics simulations in two dimensional space. Particular attentions are paid to how the gyration radius $R_{g}$ changes with the propulsion velocity $v_{0}$,angular velocity $\omega$ and chain length. We find that in a chiral bath with a typical nonzero $\omega$, the chain first collapses into a small compact cluster and swells again with increasing $v_{0}$, in quite contrast to the case for a normal achiral bath $(\omega=0)$ wherein a flexible chain swells with increasing $v_{0}$. More interestingly, the polymer can even form a closed ring if the chain length is large enough,which may oscillate with the cluster if $v_{0}$ is large. Consequently, the gyration radius $R_{g}$ shows nontrivial non-monotonic dependences on $v_{0}$, i.e., it undergoes a minimum for relatively short chains, and two minima with a maximum in between for longer chains. Our analysis shows that such interesting phenomena are mainly due to the competition between two roles played by the chiral active bath: while the persistence motion due to particle activity tends to stretch the chain, the circular motion of the particle may lead to an effective osmotic pressure that tends to collapse the chain. In addition, the size of the circular motion $R_{0}=v_{0}/\omega$ shows an important role in that the compact clusters and closed-rings are both observed at nearly the same values of $R_{0}$ for different $\omega$.

Formation of highly ordered structures usually needs to overcome a high free-energy barrier that is greatly beyond the ability of thermodynamic fluctuation, such that the system would be easily trapped into a state with many defects and the annealing process of which often occurs on unreachable long time-scales. Here we report a fascinating example theoretically that active core corona particles can successfully self-assemble into a large-scaled and highly ordered stripe or trimer lattice, which is hardly achieved in a non-driven equilibrium system. Besides, such an activity-induced ordered structure shows an interesting self-healing feature of defects. In addition, there exists an optimal level of activity that most favorably enhance the formation of ordered self-assembly structures. Since core corona particles act as important units for self-assembly in real practice, we believe our study opens a new design-strategy for highly ordered materials., 8 pages, 6 figures

Polymer translocation through nanopores into a crowded environment is of ubiquitous importance in many biological processes. Here we investigate polymer translocation through a nanopore into an active bath of self-propelled particles in two-dimensional space using Langevin dynamics simulations. Interestingly, we find that the mean translocation time τ can show a bell-shape dependence on the particle activity Fa at a fixed volume fraction ϕ, indicating that the translocation process may become slower for small activity compared to the case of the passive media, and only when the particle activity becomes large enough can the translocation process be accelerated. In addition, we also find that τ can show a minimum as a function of ϕ if the particle activity is large enough, implying that an intermediate volume fraction of active particles is most favorable for the polymer translocation. Detailed analysis reveals that such nontrivial behaviors result from the two-fold effect of active bath: one that active particles tend to accumulate near the pore, providing an extra pressure hindering the translocation, and the other that they also aggregate along the polymer chain, generating an effective pulling force accelerating the translocation. Such results demonstrate that active bath plays rather subtle roles on the polymer translocation process.

We study the dynamic separation process of two identical polymers confined in a cylinder, allowing both ends of the polymer chains to be free, based on a three dimensional (3D) free energy landscape combined with direct molecular dynamics (MD) simulations. The landscape suggests that the probability distribution curves of induction time (segregation time) reduced by corresponding average values would collapse into a single one under the so-called blob constraint, i.e., κ ≡ ND-1/ν is a constant, where N is the number of monomers in a chain, D is the channel diameter, and ν ≃ 3/5. Such a collapse behavior is well demonstrated by direct MD simulations and further by Brownian dynamics simulations of an effective particle on the 3D landscape. Interestingly, Brownian dynamics shows that the average induction time t¯in or segregation time t¯se decreases monotonically with κ in a power-law dependence if the diffusion coefficient D is fixed, suggesting a distinct mechanism of the induction process which is neither diffusion nor barrier-crossing, in accordance with trajectory analysis by using MD simulations. In addition, we find that both t¯in and t¯se show good power-law dependencies on the polymer length N under the blob constraint.

The dynamics of point-like Brownian particles in a periodic confined channel with oscillating boundaries has been studied. Directional transport (DT) behavior, characterized by net displacement along the horizontal direction, is observed even without external force which is necessary for the conventional DT where the boundaries are static. For typical parameter values, the average velocity Vt of DT reaches a maximum with the variation of the noise intensity D, being alike to the phenomenon of stochastic resonance. Interestingly, we find that Vt shows nontrivial dependences on the particle gravity G depending on the noise level. When the noise is large, Vt increases monotonically with G indicating that heavier particle moves faster, while for small noise, Vt shows a bell-shape dependence on G, suggesting that a particle with an intermediate weight may move the fastest. Such results were not observed for DT in a channel with static boundaries. To understand these findings, we have adopted an effective one-dimensional coarsening description, which facilitates us to introduce an effective entropic force along the horizontal direction. The average force is apparently nonzero due to the oscillatory boundary, hence leading to the net transport, and it shows similar dependences as Vt on the noise intensity D and particle gravity G. The dependences of the DT behavior on other parameters describing the oscillatory channel have also been investigated, showing that DT is more pronounced for larger oscillation amplitude and frequency, and asymmetric geometry within a channel period and phase difference between neighboring periods are both necessary for the occurrence of DT.

Epitaxial growth via chemical vapor deposition is considered to be the most promising way towards synthesizing large area graphene with high quality. However, it remains a big theoretical challenge to reveal growth kinetics with atomically energetic and large-scale spatial information included. Here, we propose a minimal kinetic Monte Carlo model to address such an issue on an active catalyst surface with graphene/substrate lattice mismatch, which facilitates us to perform large scale simulations of the growth kinetics over two dimensional surface with growth fronts of complex shapes. A geometry-determined large-scale growth mechanism is revealed, where the rate-dominating event is found to be $C_{1}$-attachment for concave growth front segments and $C_{5}$-attachment for others. This growth mechanism leads to an interesting time-resolved growth behavior which is well consistent with that observed in a recent scanning tunneling microscopy experiment., 5 pages, 3 figures

We have studied the dynamics of Brownian particles in a confined geometry of dumbbell-shape with periodically oscillating walls. Entropic stochastic resonance (ESR) behavior, characterizing by a maximum value of the coherent factor Q at some optimal level of noise, is observed even without external periodic force in the horizontal direction, which is necessary for conventional ESR where the wall is static and the particle is subjected to the force. Interestingly, the ESR can be remarkably enhanced by the particle gravity G, in contrast to the conventional case. In addition, Q decreases (increases) with G in the small (large) noise limit, respectively, while it non-monotonically changes with G for moderate noise levels. We have applied an effective 1D coarsening description to illustrate such a nontrivial dependence on G, by investigating the property of the 1D effective potential of entropic nature and paying special attention to the excess part resulting from the boundary oscillation. Dependences of the ESR strength with other related parameters are also discussed.