Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop.

Several types of molecular machines move along biopolymers like chromatin. However, the details about the microscopic activity of these machines and how to distinguish their modes of action are not well understood. We propose that the activity of such machines can be classified by studying looped chromatin under shear flow. Our simulations show that a chromatin-like polymer with two types of activities-constant (type-I) or local curvature-dependent tangential forces (type-II)-exhibits very different behavior under shear flow. We show that one can distinguish both activities by measuring the nature of a globule-to-extended coil transition, tank treading, and tumbling dynamics.

Structure and dynamics of chemically active ring polymers: swelling to collapse.

The ring structures are common in many synthetic or natural systems and experience both local and long-range forces by chemical sensing. This work is an effort to investigate the structural and dynamical properties of a chemically active ring in an explicit solvent bath utilizing hybrid molecular dynamics (MD) and multiparticle collision dynamics (MPCD) simulation techniques. We show that by tuning the chemical properties of the ring, it can be converted from a chemo-attractant to a chemo-repellent, thereby changing the steady state to be either collapsed or swelled as compared to its passive limit. We quantify these observations by comparing the scaling laws, local structures and the dynamics of active and passive rings. Furthermore, we show the impact of varying numbers of active sites by calculating the contact probability of the collapse state that highlights diverse structures. We also analyze the dynamics of the ring by finding the relaxation time and the mean square displacement of the centre of mass. A faster relaxation with enhanced diffusion is observed for the active rings.

Enhanced self-propulsion of a sphere-dimer in viscoelastic fluid.

Micro-swimmers often have to encounter a medium that exhibits non-Newtonian behaviour. To understand the effect of complex environments on the propulsion dynamics of swimmers, here we have investigated a self-propelled sphere-dimer in a viscoelastic medium, using a coarse-grained hybrid mesoscopic simulation technique. We have shown that a viscoelastic fluid can result in the enhancement of swimming speed, as compared to the speed in a Newtonian fluid with the same viscosity. A non-linear response in the dimer velocity is seen for higher Péclet numbers in viscoelastic fluids. With help of various dynamical quantities, we have shown that the observed non-linear response of the directed velocity is associated with the micro-structural properties of the fluid. These include the alignment of the fluid elements and the density inhomogeneity around the moving dimer. The enhancement of self-propulsion velocity has been probed in detail, and the factors affecting the propulsion are identified.

Diffusiophoretically induced interactions between chemically active and inert particles.

In the presence of a chemically active particle, a nearby chemically inert particle can respond to a concentration gradient and move by diffusiophoresis. The nature of the motion is studied for two cases: first, a fixed reactive sphere and a moving inert sphere, and second, freely moving reactive and inert spheres. The continuum reaction-diffusion and Stokes equations are solved analytically for these systems and microscopic simulations of the dynamics are carried out. Although the relative velocities of the spheres are very similar in the two systems, the local and global structures of streamlines and the flow velocity fields are found to be quite different. For freely moving spheres, when the two spheres approach each other the flow generated by the inert sphere through diffusiophoresis drags the reactive sphere towards it. This leads to a self-assembled dimer motor that is able to propel itself in solution. The fluid flow field at the moment of dimer formation changes direction. The ratio of sphere sizes in the dimer influences the characteristics of the flow fields, and this feature suggests that active self-assembly of spherical colloidal particles may be manipulated by sphere-size changes in such reactive systems.

Spontaneous beating and synchronization of extensile active filament.

We simulate a semi-flexible active filament that exhibits spontaneous oscillations on clamping and show self-propulsion when left free. The activity on the filament relies on the nano-dimers distributed at regular intervals along the chain. With an emphasis on the spontaneous beating of a clamped filament, we demonstrate that the two competing forces necessary for oscillation are the elastic forces due to polymer rigidity and the active forces due to chemical activity. In addition, we also study the synchronization of two extensile filaments and the role played by non-local hydrodynamic interactions. We observe a phase lock scenario between the filaments during their synchronous motion.

Ring closure dynamics for a chemically active polymer.

The principles that underlie the motion of colloidal particles in concentration gradients and the propulsion of chemically-powered synthetic nanomotors are used to design active polymer chains. The active chains contain catalytic and noncatalytic monomers, or beads, at the ends or elsewhere along the polymer chain. A chemical reaction at the catalytic bead produces a self-generated concentration gradient and the noncatalytic bead responds to this gradient by a diffusiophoretic mechanism that causes these two beads to move towards each other. Because of this chemotactic response, the dynamical properties of these active polymer chains are very different from their inactive counterparts. In particular, we show that ring closure and loop formation are much more rapid than those for inactive chains, which rely primarily on diffusion to bring distant portions of the chain in close proximity. The mechanism presented in this paper can be extended to other chemical systems which rely on diffusion to bring reagents into contact for reactions to occur. This study suggests the possibility that synthetic systems could make use of chemically-powered active motion or chemotaxis to effectively carry out complex transport tasks in reaction dynamics, much like those that molecular motors perform in biological systems.

Particle-based mesoscopic model for phase separation in a binary fluid mixture.

A mesoscopic simulation model to study the phase separation in a binary fluid mixture in three dimensions (3D) is presented here by augmenting the existing particle-based multiparticle collision dynamics (MPCD) algorithm. The approach describes the nonideal equation of the fluid state by incorporating the excluded-volume interaction between the two components within the framework of stochastic collision, which depends on the local fluid composition and velocity. Calculating the nonideal contribution to the pressure both from simulation and analytics shows the model to be thermodynamically consistent. A phase diagram to explore the range of parameters that give rise to phase separation in the model is investigated. The interfacial width and phase growth obtained from the model agree with the literature for a wide range of temperatures and parameters.

Active particles in explicit solvent: Dynamics of clustering for alignment interaction.

We study the dynamics of clustering in systems containing active particles that are immersed in an explicit solvent. For this, we have adopted a hybrid simulation method, consisting of molecular dynamics and multiparticle collision dynamics. In our model, the overlap-avoiding passive interaction of an active particle with another active particle or a solvent particle has been taken care of via variants of the Lennard-Jones potential. Dynamic interactions among the active particles have been incorporated via a Vicsek-like alignment rule in self-propulsion that facilitates clustering. We quantify the effects of activity and importance of hydrodynamics on the dynamics of clustering via variations of relevant system parameters. Results are obtained for low overall density of active particles, for which the state point is close to the vapor branch of the coexistence curve, and thus the morphology consists of disconnected clusters. In such a situation, the mechanism of growth switches among particle diffusion, diffusive coalescence, and ballistic aggregation, depending upon the presence or absence of active and hydrodynamic interactions providing different kinds of mobilities to the clusters. Corresponding growth laws have been quantified and discussed in the context of appropriate theoretical pictures. Our results suggest that multiparticle collision dynamics is an effective method for the investigation of hydrodynamic phenomena in phase-separating active matter systems.

Dynamics of self-propelled nanomotors in chemically active media.

Synthetic chemically powered nanomotors often rely on the environment for their fuel supply. The propulsion properties of such motors can be altered if the environment in which they move is chemically active. The dynamical properties of sphere dimer motors, composed of linked catalytic and noncatalytic monomers, are investigated in active media. Chemical reactions occur at the catalytic monomer and the reactant or product of this reaction is involved in cubic autocatalytic or linear reactions that take place in the bulk phase environment. For these reactions, as the bulk phase reaction rates increase, the motor propulsion velocity decreases. For the cubic autocatalytic reaction, this net effect arises from a competition between a reduction of the nonequilibrium concentration gradient that leads to smaller velocity and the generation of fuel in the environment that tends to increase the motor propulsion. The role played by detailed balance in determining the form of the concentration gradient in the motor vicinity in the active medium is studied. Simulations are carried out using reactive multiparticle collision dynamics and compared with theoretical models to obtain further insight into sphere dimer dynamics in active media.

Dynamical phase of driven colloidal systems with short-range attraction and long-range repulsion.

We study the nonequilibrium dynamics of colloidal system with short-range depletion attraction and screened electrostatic repulsion on a disordered substrate. We find a growth-melting process of the clusters as the temperature is increased. By strengthening the screened electrostatic repulsion, a depinning transition from moving cluster to plastic flow is observed, which is characterized by a peak in threshold depinning force. The corresponding phase diagram is then mapped out. Due to the influences of disorder from substrate, the clusters are polarized by the strong external force, accompanied by the appearance of interesting orientational order parallel to the force and translational order perpendicular to the force. Under the condition of strong external force, the influences of density of pins and temperature are also studied.

Self-propelled nanodimer bound state pairs.

A pair of chemically powered self-propelled nanodimers can exist in a variety of bound and unbound states after undergoing a collision. In addition to independently moving unbound dimers, bound Brownian dimer pairs, whose center-of-mass exhibits diffusive motion, self-propelled moving dimer pairs with directed motion, and bound rotating dimer pairs, were observed. The bound pairs arise from a solvent depletion interaction, which depends on the nonequilibrium concentration field in the vicinity of dimers. The phase diagram reported in the paper shows regions in monomer interaction energy-diameter plane where these bound and unbound states are found. Particle-based simulations and analytical calculations are used to provide insight into the nature of interaction between dimers that gives rise to the observed bound states.

Coarsening through directed droplet coalescence in fluid-fluid phase separation.

Phase-separation dynamics of an asymmetric mixture of an isotropic dopant in a nematogenic fluid is presented. We show that, on steady cooling, the nucleating nematic drops move down the dopant concentration gradient, with a velocity that is dependent on the cooling rate and concentration gradient. This propulsion of the drops leads to a mechanism of droplet coarsening, where radius of a drop scales with time as R(t) approximately t. Various mechanisms for droplet propulsion are discussed.

Chemical micromotors self-assemble and self-propel by spontaneous symmetry breaking.

Self-propelling chemical motors have thus far required the fabrication of Janus particles with an asymmetric catalyst distribution. Here, we demonstrate that simple, isotropic colloids can spontaneously assemble to yield dimer motors that self-propel. In a mixture of isotropic titanium dioxide colloids with photo-chemical catalytic activity and passive silica colloids, light illumination causes diffusiophoretic attractions between the active and passive particles and leads to the formation of dimers. The dimers constitute a symmetry-broken motor, whose dynamics can be fully controlled by the illumination conditions. Computer simulations reproduce the dynamics of the colloids and are in good agreement with experiments. The current work presents a simple route to obtain large numbers of self-propelling chemical motors from a dispersion of spherically symmetric colloids through spontaneous symmetry breaking.

Coarse-grained simulations of an active filament propelled by a self-generated solute gradient.

A self-propelling semiflexible filament exhibits a variety of dynamical states depending on the flexibility and activity of the filament. Here we investigate the dynamics of such an active filament using a bead-spring model with the explicit hydrodynamic interactions. The activity in the filament is incorporated by inserting chemically active dimers at regular intervals along the chain. The chemical reactions at the catalytic bead of the dimer produces a self-generated concentration gradient and gives sufficient fuel to exhibit self-propulsion for the filament. Depending upon the rigidity and the configuration, the polymeric filament exhibits three distinct types of spontaneous motion, namely, rotational, snaking, and translational motion. The self-propulsion velocity of the filament for various rigidity and sizes has been calculated, and the factors affecting the propulsion are identified.

Autonomous movement of a chemically powered vesicle.

We investigate the diffusio-phoretic motion of a deformable vesicle. A vesicle is built from the linked catalytic and noncatalytic vertices that consumes fuel in the environment and utilize the resulting self-generated concentration gradient to exhibit propulsive motion. Under nonequilibrium conditions it is found that the self-propulsion velocity of the vesicle depends on its shape, which in turn is controlled by the bending rigidity of the membrane and solvent density around it. The self-propulsion velocity of the vesicle for different shapes has been calculated and the factors which affect the velocity are identified.

Collective dynamics of self-propelled sphere-dimer motors.

The collective dynamics of ensembles of chemically powered sphere dimer motors is investigated. Sphere dimers are self-propelled nanomotors built from linked catalytic and noncatalytic spheres. They consume fuel in the environment and utilize the resulting self-generated concentration gradients to produce directed motion along their internuclear axes. In collections of such motors, the individual motors interact through forces that arise from concentration gradients, hydrodynamic coupling, and direct intermolecular forces. Under nonequilibrium conditions it is found that the sphere dimer motors self-assemble into transient aggregates with distinctive structural correlations and exhibit swarming where the aggregates propagate through the system. The mean square displacement of a dimer motor in the ensemble displays short-time ballistic and long-time diffusive regimes and, for ensembles containing many motors, an increasingly prominent intermediate regime. The self-diffusion coefficient of a motor in a many-motor system behaves differently from that of an isolated motor, and the decay of orientational correlations is a nonmonotonic function of the number of motors. The results presented here illustrate the phenomena to be expected in applications, such as cargo transport, where many motors may act in consort.

Self-propulsion of nematic drops: novel phase separation dynamics in impurity-doped nematogens.

We report a novel phase separation dynamics, mediated by self-propelled motion of the nucleated drops, in a mixture of a nematogen and an isotropic dopant. We show that surface flow, induced by the gradient in the concentration of the dopant expelled by the growing drops, provides the driving force for the propulsion of nematic droplets. While the liquid crystal-isotropic transition is used here to demonstrate the phenomenon, self-propulsion should be observable in many other systems in which the dynamics of a conserved order parameter is coupled to a nonconserved order parameter.