Dynamic regimes of fluids simulated by multiparticle-collision dynamics

From local to hydrodynamic friction in Brownian motion: A multiparticle collision dynamics simulation study

The friction and diffusion coefficients of rigid spherical colloidal particles dissolved in a fluid are determined from velocity and force autocorrelation functions by mesoscale hydrodynamic simulations. Colloids with both slip and no-slip boundary conditions are considered, which are embedded in fluids modeled by multiparticle collision dynamics with and without angular momentum conservation. For no-slip boundary conditions, hydrodynamics yields the well-known Stokes law, while for slip boundary conditions the lack of angular momentum conservation leads to a reduction of the hydrodynamic friction coefficient compared to the classical result. The colloid diffusion coefficient is determined by integration of the velocity autocorrelation function, where the numerical result at shorter times is combined with the theoretical hydrodynamic expression for longer times. The suitability of this approach is confirmed by simulations of sedimenting colloids. In general, we find only minor deviations from the Stokes-Einstein relation, which even disappear for larger colloids. Importantly, for colloids with slip boundary conditions, our simulation results contradict the frequently assumed additivity of local and hydrodynamic diffusion coefficients.

Catalytic microrotor driven by geometrical asymmetry

An asymmetric gear with homogeneous surface properties is, here, presented as a prototype to fabricate catalytic microrotors. The driving torque arises from the diffusiophoretic effect induced by the concentration gradients generated by catalytic chemical reactions at the gear surface. This torque produces a spontaneous and unidirectional rotation of the asymmetric gear. By means of mesoscopic simulations, we prove and characterize this scenario. The gear rotational velocity is determined by the gear-solvent interactions, the gear geometry, the solvent viscosity, and the catalytic reaction ratio. Our work presents a simple way to design self-propelled microrotors, alternative to existing catalytic bi-component, or thermophoretic ones.

Modelling the mechanics and hydrodynamics of swimming E. coli

The swimming properties of an E. coli-type model bacterium are investigated by mesoscale hydrodynamic simulations, combining molecular dynamics simulations of the bacterium with the multiparticle particle collision dynamics method for the embedding fluid. The bacterium is composed of a spherocylindrical body with attached helical flagella, built up from discrete particles for an efficient coupling with the fluid. We measure the hydrodynamic friction coefficients of the bacterium and find quantitative agreement with experimental results of swimming E. coli. The flow field of the bacterium shows a force-dipole-like pattern in the swimming plane and two vortices perpendicular to its swimming direction arising from counterrotation of the cell body and the flagella. By comparison with the flow field of a force dipole and rotlet dipole, we extract the force-dipole and rotlet-dipole strengths for the bacterium and find that counterrotation of the cell body and the flagella is essential for describing the near-field hydrodynamics of the bacterium.

Effects of hydrodynamic interactions on the crystallization of passive and active colloidal systems

Effects of hydrodynamic interactions (HI) on the crystallization of a two-dimensional suspension of colloidal particles have been investigated, by applying a multiscale simulation method combining multiparticle collision dynamics for solvent particles with standard molecular dynamics for the colloids. For a passive system, we find that HI slightly shifts the freezing point to a smaller density, while the equilibrium structure remains nearly unchanged for a given global order parameter. For an active system, however, HI can significantly shift the freezing density to a higher value and the freezing transition becomes more continuous compared to its passive counterpart. This HI-induced shift becomes more remarkable with increasing propelling force. In addition, HI may also enhance the structural heterogeneities in an active system. For both passive and active systems, it is shown that HI can accelerate the relaxation process to their final steady state.

Effects of excluded volume and hydrodynamic interaction on the deformation, orientation and motion of ring polymers in shear flow

A ring polymer is a classical model to explore the behaviors of biomacromolecules. Compared with its linear counterpart in shear flow, the ring polymer should be more sensitive to excluded volume and hydrodynamic interaction attributed to the absence of chain ends. We carried out multiparticle collision dynamics combined with molecular dynamics simulation to study the effects of excluded volume and hydrodynamic interaction on the behaviors of ring polymers in shear flow. The results show that in the absence of the strong excluded volume interaction, the ring polymer prefers a two-strand linear conformation with high deformation and orientation in the flow-gradient plane, and the tank-treading motion is nearly negligible. Ring polymers without excluded volume show no significant difference from linear polymers in the scaling exponents for the deformation, orientation and tumbling motion. We also observed that the hydrodynamic interaction could efficiently slow down the relaxation of ring polymers while the scaling exponents against the Weissenberg number have rarely been affected.

Effect of angular momentum conservation on hydrodynamic simulations of colloids

In contrast to most real fluids, angular momentum is not a locally conserved quantity in some mesoscopic simulation methods. Here we quantify the importance of this conservation in the flow fields associated with different colloidal systems. The flow field is analytically calculated with and without angular momentum conservation for the multiparticle collision dynamics (MPC) method, and simulations are performed to verify the predictions. The flow field generated around a colloidal particle moving under an external force with slip boundary conditions depends on the conservation of angular momentum, and the amplitude of the friction force is substantially affected. Interestingly, no dependence on the angular momentum conservation is found for the flow fields generated around colloids under the influence of phoretic forces. Moreover, circular Couette flow between a no-slip and a slip cylinder is investigated, which allows us to validate one of the two existing expressions for the MPC stress tensor.

Finite-size scaling study of shear viscosity anomaly at liquid-liquid criticality

We study the equilibrium dynamics of a symmetrical binary Lennard-Jones fluid mixture near its consolute criticality. Molecular dynamics simulation results for the shear viscosity, η, from a microcanonical ensemble are compared with those from a canonical ensemble with various thermostats. It is observed that the Nosé-Hoover thermostat is a good candidate for this purpose, and is therefore adopted for the quantification of the critical singularity of η, to avoid the temperature fluctuations (or even drifts) that are often encountered in microcanonical simulations. Via a finite-size scaling analysis of our simulation data we have been able to confirm that the shear viscosity exhibits a weak critical singularity in agreement with the theoretical predictions.

Bulk viscosity of multiparticle collision dynamics fluids

We determine the viscosity parameters of the multiparticle collision dynamics (MPC) approach, a particle-based mesoscale hydrodynamic simulation method for fluids. We perform analytical calculations and verify our results by simulations. The stochastic rotation dynamics and the Andersen thermostat variant of MPC are considered, both with and without angular momentum conservation. As an important result, we find a nonzero bulk viscosity for every MPC version. The explicit calculation shows that the bulk viscosity is determined solely by the collisional interactions of MPC.

Thermostat for nonequilibrium multiparticle-collision-dynamics simulations

Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for complex fluid, is widely employed in nonequilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization of the fluid is often required for certain MPC variants. We investigate the influence of three thermostats on the nonequilibrium properties of a MPC fluid under shear or in Poiseuille flow. In all cases, the local velocities are scaled by a factor, which is either determined via a local simple scaling approach (LSS), a Monte Carlo-like procedure (MCS), or by the Maxwell-Boltzmann distribution of kinetic energy (MBS). We find that the various scaling schemes leave the flow profile unchanged and maintain the local temperature well. The fluid viscosities extracted from the various simulations are in close agreement. Moreover, the numerically determined viscosities are in remarkably good agreement with the respective theoretically predicted values. At equilibrium, the calculation of the dynamic structure factor reveals that the MBS method closely resembles an isothermal ensemble, whereas the MCS procedure exhibits signatures of an adiabatic system at larger collision-time steps. Since the velocity distribution of the LSS approach is non-Gaussian, we recommend to apply the MBS thermostat, which has been shown to produce the correct velocity distribution even under nonequilibrium conditions.

A microscale thermophoretic turbine driven by external diffusive heat flux

We propose a theoretical prototype of a micro-scale turbine externally driven by diffusive heat flux without the need for macroscopic particle flux, which is in sharp contrast to conventional turbines. The prototypes are described analytically and validated by computer simulations. Our results indicate that a micro-scale turbine composed of anisotropic blades can rotate unidirectionally in an external temperature gradient due to the anisotropic thermophoresis effect. The rotational direction and speed depend on the temperature gradient, the geometry and the thermophoretic properties of the turbine. The proposed thermophoretic turbines can be experimentally realized and implemented on micro-devices such as computer-chips to recover waste heat or to facilitate cooling.

Hydrodynamic simulations of self-phoretic microswimmers

A mesoscopic hydrodynamic model to simulate synthetic self-propelled Janus particles which is thermophoretically or diffusiophoretically driven is here developed. We first propose a model for a passive colloidal sphere which reproduces the correct rotational dynamics together with strong phoretic effect. This colloid solution model employs a multiparticle collision dynamics description of the solvent, and combines stick boundary conditions with colloid-solvent potential interactions. Asymmetric and specific colloidal surface is introduced to produce the properties of self-phoretic Janus particles. A comparative study of Janus and microdimer phoretic swimmers is performed in terms of their swimming velocities and induced flow behavior. Self-phoretic microdimers display long range hydrodynamic interactions with a decay of 1/r(2), which is similar to the decay of gradient fields generated by self-phoretic particle, and can be characterized as pullers or pushers. In contrast, Janus particles are characterized by short range hydrodynamic interactions with a decay of 1/r(3) and behave as neutral swimmers.

Hydrodynamics of discrete-particle models of spherical colloids: a multiparticle collision dynamics simulation study

We investigate the hydrodynamic properties of a spherical colloid model, which is composed of a shell of point particles by hybrid mesoscale simulations, which combine molecular dynamics simulations for the sphere with the multiparticle collision dynamics approach for the fluid. Results are presented for the center-of-mass and angular velocity correlation functions. The simulation results are compared with theoretical results for a rigid colloid obtained as a solution of the Stokes equation with no-slip boundary conditions. Similarly, analytical results of a point-particle model are presented, which account for the finite size of the simulated system. The simulation results agree well with both approaches on appropriative time scales; specifically, the long-time correlations are quantitatively reproduced. Moreover, a procedure is proposed to obtain the infinite-system-size diffusion coefficient based on a combination of simulation results and analytical predictions. In addition, we present the velocity field in the vicinity of the colloid and demonstrate its close agreement with the theoretical prediction. Our studies show that a point-particle model of a sphere is very well suited to describe the hydrodynamic properties of spherical colloids, with a significantly reduced numerical effort.

A self-propelled thermophoretic microgear

An asymmetric microgear will spontaneously and unidirectionally rotate if it is heated in a cool surrounding solvent. The resulting temperature gradient along the edges of the gear teeth translates in a directed thermophoretic force, which will exert a net torque on the gear. By means of computer simulations, the validity of this scenario is proved. The rotational direction and speed are dependent on gear–solvent interactions, and can be analytically related to system parameters like the thermal diffusion factor, the solvent viscosity, or the temperature difference. This microgear provides a simple way to extract net work from non-isothermal solutions, and can become a valuable tool in microfluids.

Modeling steady-state dynamics of macromolecules in exponential-stretching flow using multiscale molecular-dynamics-multiparticle-collision simulations

We introduce a method to obtain steady-state uniaxial exponential-stretching flow of a fluid (akin to extensional flow) in the incompressible limit, which enables us to study the response of suspended macromolecules to the flow by computer simulations. The flow field in this flow is defined by v(x) = εx, where v(x) is the velocity of the fluid and ε is the stretch flow gradient. To eliminate the effect of confining boundaries, we produce the flow in a channel of uniform square cross section with periodic boundary conditions in directions perpendicular to the flow, but simultaneously maintain uniform density of fluid along the length of the tube. In experiments a perfect elongational flow is obtained only along the axis of symmetry in a four-roll geometry or a filament-stretching rheometer. We can reproduce flow conditions very similar to extensional flow near the axis of symmetry by exponential-stretching flow; we do this by adding the right amounts of fluid along the length of the flow in our simulations. The fluid particles added along the length of the tube are the same fluid particles which exit the channel due to the flow; thus mass conservation is maintained in our model by default. We also suggest a scheme for possible realization of exponential-stretching flow in experiments. To establish our method as a useful tool to study various soft matter systems in extensional flow, we embed (i) spherical colloids with excluded volume interactions (modeled by the Weeks-Chandler potential) as well as (ii) a bead-spring model of star polymers in the fluid to study their responses to the exponential-stretched flow and show that the responses of macromolecules in the two flows are very similar. We demonstrate that the variation of number density of the suspended colloids along the direction of flow is in tune with our expectations. We also conclude from our study of the deformation of star polymers with different numbers of arms f that the critical flow gradient ε(c) at which the star undergoes the coil-to-stretch transition is independent of f for f = 2,5,10, and 20.

Dynamics of solutes with hydrodynamic interactions: comparison between Brownian dynamics and stochastic rotation dynamics simulations

The dynamics of particles in solution or suspension is influenced by thermal fluctuations and hydrodynamic interactions. Several mesoscale methods exist to account for these solvent-induced effects such as Brownian dynamics with hydrodynamic interactions and hybrid molecular dynamics-stochastic rotation dynamics methods. Here we compare two ways of coupling solutes to the solvent with stochastic rotation dynamics (SRD) to Brownian dynamics with and without explicit hydrodynamic interactions. In the first SRD scheme [SRD with collisional coupling (CC)] the solutes participate in the collisional step with the solvent and in the second scheme [SRD with central force coupling (CFC)] the solutes interact through direct forces with the solvent, generating slip boundary conditions. We compare the transport coefficients of neutral and charged solutes in a model system obtained by these simulation schemes. Brownian dynamics without hydrodynamic interactions is used as a reference to quantify the influence of hydrodynamics on the transport coefficients as modeled by the different methods. We show that, in the dilute range, the SRD CFC method provides results similar to those of Brownian dynamics with hydrodynamic interactions for the diffusion coefficients and for the electrical conductivity. The SRD CC scheme predicts diffusion coefficients close to those obtained by Brownian dynamic simulations without hydrodynamic interactions, but accounts for part of the influence of hydrodynamics on the electrical conductivity.

Synchronization, slippage, and unbundling of driven helical flagella

Peritrichous bacteria exploit bundles of helical flagella for propulsion and chemotaxis. Here, changes in the swimming direction (tumbling) are induced by a change of the rotational frequency of some flagella. Employing coarse-grained modeling and simulations, we investigate the dynamical properties of helical flagella bundles driven by mismatched motor torques. Over a broad range of distances between the flagella anchors and applied torque differences, we find a stable bundled state, which is important for a robust directional motion of a bacterium. With increasing torque difference, a phase lag in the flagellar rotations develops, followed by slippage and ultimately unbundling, which sensitively depends on the anchoring distance of neighboring flagella. In the slippage and drift states, the different rotation frequencies of the flagella generate a tilting torque on the bacterial body, which implies a change of the swimming direction as observed experimentally.

Hydrodynamic mechanisms of spinodal decomposition in confined colloid-polymer mixtures: a multiparticle collision dynamics study

A multiscale model for a colloid-polymer mixture is developed. The colloids are described as point particles interacting with each other and with the polymers with strongly repulsive potentials, while polymers interact with each other with a softer potential. The fluid in the suspension is taken into account by the multiparticle collision dynamics method (MPC). Considering a slit geometry where the suspension is confined between parallel repulsive walls, different possibilities for the hydrodynamic boundary conditions (b.c.) at the walls (slip versus stick) are treated. Quenching experiments are considered, where the system volume is suddenly reduced (keeping the density of the solvent fluid constant, while the colloid and polymer particle numbers are kept constant) and thus an initially homogeneous system is quenched deeply into the miscibility gap, where it is unstable. For various relative concentrations of colloids and polymers, the time evolution of the growing colloid-rich and polymer-rich domains are studied by molecular dynamics simulation, taking hydrodynamic effects mediated by the solvent into account via MPC. It is found that the domain size [script-l](d)(t) grows with time t as [script-l](d)(t) [proportionality] t(1/3) for stick and (at late stages) as [script-l](d)(t) [proportionality] t(2/3) for slip b.c., while break-up of percolating structures can cause a transient "arrest" of growth. While these findings apply for films that are 5-10 colloid diameters wide, for ultrathin films (1.5 colloid diameters wide) a regime with [script-l](d)(t) [proportionality] t(1/2) is also identified for rather shallow quenches.

No-slip boundary conditions and forced flow in multiparticle collision dynamics

Multiparticle collision dynamics (MPCD) is a particle-based fluid simulation technique that is becoming increasingly popular for mesoscale fluid modeling. However, some confusion and conflicting results persist in literature regarding several important methodological details, in particular the enforcement of the no-slip condition and thermostatting in forced flow. These issues persist in simple flows past stationary boundaries, which we exclusively focus on here. We discuss the parametrization of MPCD fluids and its consequences for fluid-solid boundaries in great detail, and show that the method of virtual particles proposed by Lamura et al. and adopted by many others is required only for parameter choices that lead to viscosities dominated by collisional contributions. We test several implementations of the virtual particle method and discuss how to completely eliminate slip at stationary boundaries. We also show that stochastic boundary reflection rules are inherently problematic for forced flow and suggest a possible remedy. Finally, we discuss the most robust way to achieve forced flow and evaluate several thermostatting methods in the process. All discussion is limited to solid objects that do not move as a result of collisions with MPCD particles (i.e., walls). However, the results can be extended to solutes that experience forces and torques due to interactions with MPCD particles (e.g., colloids). The detailed analysis presented for this simple case provides the level of rigor and accuracy to the MPCD method required for the study of more complex systems.

Hydrodynamic correlations in multiparticle collision dynamics fluids

The emergent fluctuating hydrodynamics of the multiparticle collision dynamics (MPC) approach, a particle-based mesoscale simulation technique for fluid dynamics, is analyzed theoretically and numerically. We focus on the stochastic rotation dynamics implementation of the MPC method. The fluid is characterized by its longitudinal and transverse velocity correlation functions in Fourier space and velocity autocorrelation functions in real space. Particular attention is paid to the role of sound, which leads to piecewise negative correlation functions. Moreover, finite system-size effects are addressed with an emphasis on the role of sound. Analytical expressions are provided for the transverse and longitudinal velocity correlations, which are derived from the linearized Landau-Lifshitz Navier-Stokes equation adopted for an isothermal MPC fluid. The comparison of the analytical results with simulations shows excellent agreement above a minimal length scale. The simulations indicate a breakdown in hydrodynamics on length scales smaller than this minimal length. This demonstrates that we have an excellent analytical description and understanding of the MPC method and its limitations in terms of time and length scales.

Hybrid molecular dynamics simulations of living filaments

We propose a hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled adenosine diphosphate-actin filaments in the absence of adenosine triphosphate (ATP) hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.

Drift velocity in non-isothermal inhomogeneous systems

Drift velocity and driving force are not directly proportional in the case of inhomogeneous suspensions, where a space dependent mobility induces an additional contribution to the drift velocity. Similarly, particle flux and drift velocity are related not only by the gradient of density but also by an additional contribution given by the gradient of the self-diffusion coefficient. We provide quantitative support to this scenario in a non-equilibrium system by means of computer simulations with a temperature gradient. Moreover, our simulation results demonstrate that the temperature gradient-induced mass transport coefficient, namely thermal diffusion coefficient, is not directly proportional to the drift velocity so that the well-accepted relation of proportionality is just an approximation.

Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.

Thermophoresis of colloids by mesoscale simulations

The motion of a colloid induced by a temperature gradient is simulated by means of multiparticle collision dynamics, a mesoscale simulation technique. Two algorithms to quantify the thermophoretic behavior are employed and contrasted. The validity of the methods is verified as a function of the temperature gradient, system size, and algorithm parameters. The variation of the solvent-colloid interaction from attractive to purely repulsive interestingly results in the change of the colloid behavior from thermophobic to thermophilic.

Non-equilibrium relaxation and tumbling times of polymers in semidilute solution

The end-over-end tumbling dynamics of individual polymers in dilute and semidilute solutions is studied under shear flow by large-scale mesoscale hydrodynamic simulations. End-to-end vector relaxation times are determined along the flow, gradient, and vorticity directions. Along the flow and gradient directions, the correlation functions decay exponentially with sinusoidal modulations at short times. In dilute solution, the decay times of the various directions are very similar. However, in semidilute solutions, the relaxation behaviors are rather different along the various directions, with the longest relaxation time in the vorticity direction and the shortest time in the flow direction. The various relaxation times exhibit a power-law shear-rate dependence with the exponent  - 2/3 at high shear rates. Quantitatively, the relaxation times are equal to the tumbling times extracted from cross-correlation functions of fluctuations of radius-of-gyration components along the flow and gradient direction.

Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics

The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer beads that is less than unity. In both solvent regimes the oligomer is found to extend in the direction of flow. Under the ideal solvent conditions, torsional twisting of the chain and aperiodic cyclical dynamics are observed for the end of the oligomer. Under poor solvent conditions, a metastable helix forms in the end of the chain despite the lack of any attractive potential between beads in the oligomeric chain. The formation of the helix is postulated to be the result of a solvent induced chain collapse that has been confined to a single dimension by a strong flow field.

Simulations of thermophoretic nanoswimmers

We consider a nanodimer in solution with asymmetric thermal properties that shows self-propelled motion. One monomer of the nanodimer can be heated to a fixed temperature producing a radially symmetric temperature gradient. The thermophoretic properties of the second monomer produce then a propulsion against or toward the heated particle, such that the nanodimer becomes a puller or pusher nanoswimmer. We combine our simulation measurements with a theoretical analysis that satisfactorily characterizes the self-propelled velocity with the temperature gradient, and the thermophoretic properties of the bead.

Hydrodynamics and the fluctuation theorem

The fluctuation theorem is a pivotal result of statistical physics. It quantifies the probability of observing fluctuations which are in violation of the second law of thermodynamics. More specifically, it quantifies the ratio of the probabilities of observing entropy-producing and entropy-consuming fluctuations measured over a finite volume and time span in terms of the rate of entropy production in the system, the measurement volume, and time. We study the fluctuation theorem in computer simulations of planar shear flow. The simulations are performed by employing the method of multiparticle collision dynamics, which captures both thermal fluctuations and hydrodynamic interactions. The main outcome of our analysis is that the fluctuation theorem is verified at any averaging time provided that the measurement volume exhibits a specific dependence on a hydrodynamic time scale.

Semiflexible polymer conformation, distribution and migration in microcapillary flows

The flow behavior of a semiflexible polymer in microchannels is studied using multiparticle collision dynamics, a particle-based hydrodynamic simulation technique. Conformations, distributions, and radial cross-streamline migration are investigated for various bending rigidities, with persistence lengths L(p) in the range 0.5 ≤ L(p)/L(r) ≤ 30. The flow behavior is governed by the competition between a hydrodynamic lift force and steric repulsion from the wall, which lead to migration away from the wall, and a locally varying flow induced orientation, which drives the polymer away from the channel center and towards the wall. The different dependences of these effects on the polymer bending rigidity and the flow velocity results in a complex dynamical behavior. However, a generic effect is the appearance of a maximum in the monomer and the center-of-mass distributions, which occurs at the channel center for small flow velocities, but moves off-center at higher velocities.

Helicopter rotation and smectic-isotropic coexistence of strongly attractive rods

Hydrodynamic simulations of strongly attractive rodlike colloids are performed with and without shear flow. In the absence of flow, the isotropic-nematic coexistence becomes isotropic-smectic A, and the interfacial properties clearly vary with increasing attraction strength. In the presence of shear flow, a new collective rotation appears in which the director rotates in the vorticity-flow plane in a similar fashion to the movement of the rotor of a helicopter.

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.

Dynamics of chemically powered nanodimer motors subject to an external force

The chemically powered self-propelled directed motions of nanodimer motors confined in a rectangular channel and subject to an applied external conservative force are investigated using hybrid molecular dynamics/multiparticle collision dynamics. The influence of factors, such as dimer sizes, chemical reaction type, and the nature of the interaction potentials between dimer monomers and solvent molecules, on the propulsion force and friction constant are examined. The stall force, for which the nanodimer has zero net velocity, and the thermodynamic efficiency of the motor are calculated. Both irreversible and reversible chemical reactions are considered. The simulation results are compared to theoretical predictions which are able to capture the major features of the self-propelled motion.

Hydrodynamics of confined colloidal fluids in two dimensions

We apply a hybrid molecular dynamics and mesoscopic simulation technique to study the dynamics of two-dimensional colloidal disks in confined geometries. We calculate the velocity autocorrelation functions and observe the predicted t;{-1} long-time hydrodynamic tail that characterizes unconfined fluids, as well as more complex oscillating behavior and negative tails for strongly confined geometries. Because the t;{-1} tail of the velocity autocorrelation function is cut off for longer times in finite systems, the related diffusion coefficient does not diverge but instead depends logarithmically on the overall size of the system. The Langevin equation gives a poor approximation to the velocity autocorrelation function at both short and long times.