Symmetry-breaking motility of penetrable objects in active fluids

We investigate how a symmetric penetrable object immersed in an active fluid becomes motile due to a negative drag acting in the direction of its velocity. While similar phenomena have been reported only for active fluids that possess polar or nematic order, we demonstrate that such motility can occur even in active fluids without any preexisting order. The emergence of object motility is characterized by both continuous and discontinuous transitions associated with the symmetry-breaking bifurcation of the object's steady-state velocity. Furthermore, we also discuss the relevance of the transitions to the nonmonotonic particle-size dependence of the object's diffusion coefficient.

Trapped tracer in a non-equilibrium bath: dynamics and energetics

We study the dynamics of a tracer that is elastically coupled to active particles being kept at two different temperatures, as a prototype of tracer dynamics in a non-equilibrium bath. Employing analytical techniques, we find the exact solution of the probability density function for the effective motion of the tracer. The analytical results are supported by numerical simulations. By combining the experimentally accessible quantities such as the response function and the power spectrum, we measure the non-equilibrium fluctuations in terms of the effective temperature. In addition, we compute the energy dissipation rate to find the precise effects of activity. Our study is relevant in understanding athermal fluctuations arising in cytoskeletal networks or inside a chromosome.

Structure and dynamics of an active polymer chain inside a nanochannel grafted with polymers

We use computer simulations to investigate the complex dynamics of a polymer, made of active Brownian particles, inside a channel grafted internally with passive polymer chains. Our simulations reveal that this probe-polymer, if passive, exhibits a compact structure when its interaction is repulsive with the grafted chains as it tends to stay within the hollow space created along the axis of the channel. On increasing the attractive interaction, the passive probe-polymer is pulled towards the grafted polymeric region and adopts an extended structure. By contrast, switching on the activity helps the probe-polymer to escape from the local traps caused by the sticky grafted chains. The interplay between the activity of the probe-polymer and its sticky interaction with the grafted chains results in shrinking, followed by swelling as the activity is increased. To elucidate the dynamics we compute the mean square displacement (MSD) of the center of mass of the probe-polymer, which increases monotonically with activity and displays superdiffusive behavior at an intermediate time and enhanced diffusion at a long time period. In addition, compared with the attractive interaction, the active probe-polymer shows faster dynamics when the interaction is repulsive to the grafted polymers. We believe that our current study will provide insights into the structural changes and dynamics of active polymers in heterogeneous media and will be useful in designing polymer-based drug delivery vehicles.

Dynamics of a spherical self-propelled tracer in a polymeric medium: interplay of self-propulsion, stickiness, and crowding

We employ computer simulations to study the dynamics of a self-propelled spherical tracer particle in a viscoelastic medium, made of a long polymer chain. Here, the interplay between viscoelasticity, stickiness, and activity (self-propulsion) brings additional complexity to the tracer dynamics. Our simulations show that on increasing the stickiness of the tracer particle to the polymer beads, the dynamics of the tracer particle slows down as it gets stuck to the polymer chain and moves along with it. But with increasing self-propulsion velocity, the dynamics gets enhanced. In the case of increasing stickiness as well as activity, the non-Gaussian parameter (NGP) exhibits non-monotonic behavior, which also shows up in the re-scaled self part of the van-Hove function. Non-Gaussianity results owing to the enhanced binding events and the sticky motion of the tracer along with the chain with increasing stickiness. On the other hand, with increasing activity, initially non-Gaussianity increases as the tracer moves through the heterogeneous polymeric environment but for higher activity, the tracer escapes resulting in a negative NGP. For higher values of stickiness, the trapping time distributions of the passive tracer particle broaden and have long tails. On the other hand, for a given stickiness with increasing self-propulsion force, the trapping time distributions become narrower and have short tails. We believe that our current simulation study will be helpful in elucidating the complex motion of activity-driven probes in viscoelastic media.

Measuring Structural Changes in Cytochrome c under Crowded Conditions Using In Vitro and In Silico Approaches

It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been exploited to discern their combined effect on the structural stability of proteins. These studies are more significant because their effect can mimicked with in vivo conditions, where the environment is heterogeneous. Effects of two crowders, polyethylene glycol (PEG 400 Da), and its monomer ethylene glycol (EG) alone and in mixture on the structural stability of cytochrome c (cyt c) were determined using various spectroscopic and bioinformatics tools. The main conclusions of our study are (i) the monomer EG has a kosmotropic effect on the protein (stabilizes the protein), and has no significant effect on the tertiary structure; (ii) PEG 400 destabilizes the structure as well as the stability of the protein; and (iii) EG counteracts the destabilizing effect of PEG 400. From this investigation, it seems evident that proteins may fold or unfold in the crowded environment of the cell where various interactions assist them to maintain their structure for their functions. Bioinformatics approaches were also used to support all of the in vitro observations. Cyt c is functional protein; if the structure of the protein is modulated due to change in the environment its nature of function will also change. Our research addresses the question by modulating the environment around the protein, and the macromolecule (protein) conformation dynamics and interaction study via in vitro and in silico approaches which indirectly compares with that of the environment in-cellular milieu, which is highly crowded.

Passive and active tracer dynamics in polymer solutions with isotropic-to-nematic phase transition

Macromolecular crowding plays a crucial role in determining the dynamics in a living cell. We adopt Langevin dynamics simulations to investigate the anomalous diffusion dynamics of passive and active particles in a solution of polymer chains with tunable stiffness. The solution's anisotropic feature is modulated by changing both the polymer stiffness and volume fraction, where isotropic-to-nematic phase transition is involved. Our results demonstrate the significant impact of polymer flexibility on the dynamics of both passive and active probes. The distinct diffusion mechanism for an active particle is clarified by the interplay between polymer stiffness, crowdedness and activity. Polymer stiffness leads to a global inhibition effect on passive particle diffusion. The diffusion coefficient exhibits an intriguing non-monotonic variation at increasing polymer stiffness, which is due to the fact that the alignment of polymer chains is beneficial for diffusion along the nematic direction but unfavorable for that in the direction perpendicular to it. In sharp contrast, polymer stiffness plays a dominant role in facilitating active particle diffusion. Self-propulsion of the particle can utilize stiffness-induced elastic interactions more efficiently, which promotes its mobility in both directions. Meanwhile, an active particle might have a stronger ability to take advantage of the polymer alignment, contributing substantially enhanced diffusivity. In addition, the diffusion coefficient of an active particle is subject to a tendency of degeneration against varying volume fraction. This counter-intuitive behavior is due to the contrasting factors that increasing crowdedness induces a lower particle speed but a longer persistent motion time.

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.

Tuning the selective permeability of polydisperse polymer networks

We study the permeability and selectivity ('permselectivity') of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations. In our work, permeability P is determined on the linear-response level using the solution-diffusion model, P = KDin, i.e., by calculating the equilibrium penetrant partition ratio K and penetrant diffusivity Din inside the membrane. We vary two key parameters, namely the network-network interaction, which controls the degree of swelling and collapse of the network, and the network-penetrant interaction, which tunes the selective penetrant uptake and microscopic energy landscape for diffusive transport. We find that the partitioning K covers four orders of magnitude and is a non-monotonic function of the parameters, well interpreted by a second-order virial expansion of the free energy of transferring one penetrant from a reservoir into the membrane. Moreover, we find that the penetrant diffusivity Din in the polydisperse networks, in contrast to highly ordered membrane structures, exhibits relatively simple exponential decays. We propose a semi-empirical scaling law for the penetrant diffusion that describes the simulation data for a wide range of densities and interaction parameters. The resulting permeability P turns out to follow the qualitative behavior (including maximization and minimization) of partitioning. However, partitioning and diffusion are typically anti-correlated, yielding large quantitative cancellations, controlled and fine-tuned by the network density and interactions, as rationalized by our scaling laws. We finally demonstrate that even small changes of network-penetrant interactions, e.g., by half a kBT, modify the permselectivity by almost one order of magnitude.

Aggregate morphology of active Brownian particles on porous, circular walls

We study the motility-induced aggregation of active Brownian particles (ABPs) on a porous, circular wall. We observe that the morphology of aggregated dense-phase on a static wall depends on the wall porosity, particle motility, and the radius of the circular wall. Our analysis reveals two morphologically distinct, dense aggregates; a connected dense cluster that spreads uniformly on the circular wall and a localized cluster that breaks the rotational symmetry of the system. These distinct morphological states are similar to the macroscopic structures observed in aggregates on planar, porous walls. We systematically analyze the parameter regimes where the different morphological states are observed. We further extend our analysis to motile circular rings. We show that the motile ring propels almost ballistically due to the force applied by the active particles when they form a localized cluster, whereas it moves diffusively when the active particles form a continuous cluster. This property demonstrates the possibility of extracting useful work from a system of ABPs, even without artificially breaking the rotational symmetry.

Anisotropic dynamics of a self-assembled colloidal chain in an active bath

Anisotropic macromolecules exposed to non-equilibrium (active) noise are very common in biological systems, and an accurate understanding of their anisotropic dynamics is therefore crucial. Here, we experimentally investigate the dynamics of isolated chains assembled from magnetic microparticles at a liquid-air interface and moving in an active bath consisting of motile E. coli bacteria. We investigate both the internal chain dynamics and the anisotropic center-of-mass dynamics through particle tracking. We find that both the internal and center-of-mass dynamics are greatly enhanced compared to the passive case, i.e., a system without bacteria, and that the center-of-mass diffusion coefficient D features a non-monotonic dependence as a function of the chain length. Furthermore, our results show that the relationship between the components of D parallel and perpendicular with respect to the direction of the applied magnetic field is preserved in the active bath compared to the passive case, with a higher diffusion in the parallel direction, in contrast to previous findings in the literature. We argue that this qualitative difference is due to subtle differences in the experimental geometry and conditions and the relative roles played by long-range hydrodynamic interactions and short-range collisions.

Non-monotonic dependence of polymer chain dynamics on active crowder size

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 R_g of the polymer chain depends on the size σ_c of active crowders. We find that R_g shows nontrivial non-monotonic dependence on σ_c: The chain first swells upon increasing σ_c, reaching a fully expanded state with maximum R_g, and then, R_g 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 σ_c. Our results demonstrate the important interplay between particle activity and size associated with polymer configurations in active crowding environments.

Collective forces in scalar active matter

Large-scale collective behavior in suspensions of active particles can be understood from the balance of statistical forces emerging beyond the direct microscopic particle interactions. Here we review some aspects of the collective forces that can arise in suspensions of self-propelled active Brownian particles: wall forces under confinement, interfacial forces, and forces on immersed bodies mediated by the suspension. Even for non-aligning active particles, these forces are intimately related to a non-uniform polarization of particle orientations induced by walls and bodies, or inhomogeneous density profiles. We conclude by pointing out future directions and promising areas for the application of collective forces in synthetic active matter, as well as their role in living active matter.

Crowding-Activity Coupling Effect on Conformational Change of a Semi-Flexible Polymer

The behavior of a polymer in a passive crowded medium or in a very dilute active bath has been well studied, while a polymer immersed in an environment featured by both crowding and activity remains an open problem. In this paper, a systematic Langevin simulation is performed to investigate the conformational change of a semi-flexible chain in a concentrated solution packed with spherical active crowders. A very novel shrinkage-to-swelling transition is observed for a polymer with small rigidity. The underlying phase diagram is constructed in the parameter space of active force and crowder size. Moreover, the variation of the polymer gyration radius demonstrates a non-monotonic dependence on the dynamical persistence length of the active particle. Lastly, the activity-crowding coupling effect in different crowder size baths is clarified. In the case of small crowders, activity strengthens the crowding-induced shrinkage to the chain. As crowder size increases, activity turns out to be a contrasting factor to crowding, resulting in a competitive shrinkage and swelling. In the large size situation, the swelling effect arising from activity eventually becomes dominant. The present study provides a deeper understanding of the unusual behavior of a semi-flexible polymer in an active and crowded medium, associated with the nontrivial activity-crowding coupling and the cooperative crowder size effect.

Tuning the Permeability of Dense Membranes by Shaping Nanoscale Potentials

Permeability is one of the most fundamental transport properties in soft matter physics, material engineering, and nanofluidics. Here, we report by means of Langevin simulations of ideal penetrants in a nanoscale membrane made of a fixed lattice of attractive interaction sites, how the permeability can be massively tuned, even minimized or maximized, by tailoring the potential energy landscape for the diffusing penetrants, depending on the membrane attraction, topology, and density. Supported by limiting scaling theories we demonstrate that the observed nonmonotonic behavior and the occurrence of extreme values of the permeability is far from trivial and triggered by a strong anticorrelation and substantial (orders of magnitude) cancellation between penetrant partitioning and diffusivity, especially within dense and highly attractive membranes.

Activity–crowding coupling effect on the diffusion dynamics of a self-propelled particle in polymer solutions

The anomalous diffusion dynamics of an active particle in polymer solutions is studied based on a Langevin Brownian dynamics simulation.

First evidence of formation of pre-molten globule state in myoglobin: A macromolecular crowding approach towards protein folding in vivo

Myoglobin is known to show formation of intermediate states under various environmental conditions, in spite of that, this is the first evidence of formation pre-molten globule (PMG) in myoglobin. Polyethylene glycol (PEG) of various molecular sizes shows assorted effects on different proteins. Out of too short and too long PEGs, only PEGs of optimal size interact with proteins leading to change in protein structure that form intermediate state. We are the first one to report the formation of PMG in a protein in the presence of a crowding agent. The PEG-induced intermediate state was characterized by various techniques like absorption, fluorescence, near- and far-UV circular dichroism spectroscopy, ANS binding, and dynamic light scattering measurements to be PMG. Isothermal titration calorimetry and docking studies were further carried out to delineate the mechanism of formation of PMG in myoglobin in physiological conditions. The intermediate formed due to interaction of PEG with myoglobin has physiological implications which are essential to unravel the mystery to solve the massively complicated problems involved in the proper folding of proteins in vivo. Further, outcomes from this study are expected to gain mechanistic insights on the native structure and functions of proteins under in vivo conditions.

Monte Carlo simulation on the dynamics of a semi-flexible polymer in the presence of nanoparticles

The dynamics of a semi-flexible polymer chain in the presence of periodically distributed nanoparticles is simulated by using off-lattice Monte Carlo simulations. For repulsive or weak attractive nanoparticles, the dynamics are slowed down monotonically by increasing the chain stiffness k_θ or decreasing the inter-particle distance d. For strong attractive nanoparticles, however, the dynamics show nonmonotonic behaviors with k_θ and d. An interesting result is that a stiff polymer may move faster than a flexible one. The underlying mechanism is that the nanoparticle's attraction is weakened by the chain stiffness. The nonmonotonic behavior of the polymer's dynamics with k_θ is explained by the competition between the weakening effect of the chain stiffness on the nanoparticle's attraction and the intrinsic effect of chain stiffness which reduces the dynamics of the polymer. In addition, the nonmonotonic behavior of the polymer's dynamics with d is explained by the competition between the nanoparticle-exchange motion of the polymer dominated at small d and the desorption-and-adsorption motion at large d. The excluded volume effect of the nanoparticles plays a more important role for stiffer polymers as the attraction of the nanoparticles is weakened by the chain stiffness.

Dynamics of networks in a viscoelastic and active environment

We investigate the dynamics of fractals and other networks in a viscoelastic and active environment. The viscoelastic dynamics is modeled based on the generalized Langevin equation, where the activity is introduced to it by means of the exponentially correlated noise. The intramolecular interactions are taken into account by the bead-spring picture. The microscopic connectivity (studied in the form of Vicsek fractals, of dual Sierpiński gaskets, of NT_D trees, and of a family of deterministic small-world networks) reveals itself in the multiscale monomeric dynamics, which shows vastly different behaviors in the active and passive baths. In particular, the dynamics under active forces leads to a swelling that is characterized through power laws which are not present in the passive case. In all cases, the dynamics reflects the broad scaling behavior of the density of states and not necessarily the maximal relaxation time of the structures in a passive bath, as it is exemplified on the NT_D trees.