Dynamic regimes of fluids simulated by multiparticle-collision dynamics

Dynamics of polymers in coarse-grained nematic solvents

Polymers are a primary building block in many biomaterials, often interacting with anisotropic backgrounds. While previous studies have considered polymer dynamics within nematic solvents, rarely are the effects of anisotropic viscosity and polymer elongation differentiated. Here, we study polymers embedded in nematic liquid crystals with isotropic viscosity via numerical simulations to explicitly investigate the effect of nematicity on macromolecular conformation and how conformation alone can produce anisotropic dynamics. We employ a hybrid multi-particle collision dynamics and molecular dynamics technique that captures nematic orientation, thermal fluctuations and hydrodynamic interactions. The coupling of the polymer segments to the director field of the surrounding nematic elongates the polymer, producing anisotropic diffusion even in nematic solvents with isotropic viscosity. For intermediate coupling, the competition between background anisotropy and macromolecular entropy leads to hairpins - sudden kinks along the backbone of the polymer. Experiments of DNA embedded in a solution of rod-like fd viruses qualitatively support the role of hairpins in establishing characteristic conformational features that govern polymer dynamics. Hairpin diffusion along the backbone exponentially slows as coupling increases. Better understanding two-way coupling between polymers and their surroundings could allow the creation of more biomimetic composite materials.

Supercoiled ring polymers under shear flow

We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account of the hydrodynamic interactions, accompanied, in parallel, by simulations in which these are switched off. The combination of bending and torsional rigidities inherent in these polymers, in conjunction with hydrodynamics, has a profound impact on their flow properties. In contrast to their flexible counterparts, which dramatically deform and inflate under shear [Liebetreu et al., Commun. Mater. 2020, 1, 4], supercoiled rings undergo only weak changes in their overall shape and they display both a reduced propensity to tumbling (at fixed Weissenberg number) and a much stronger orientational resistance with respect to their flexible counterparts. In the presence of hydrodynamic interactions, the coupling of the polymer to solvent flow is capable of bringing about a topological transformation of writhe to twist at strong shear upon conservation of the overall linking number.

Effects of Linking Topology on the Shear Response of Connected Ring Polymers: Catenanes and Bonded Rings Flow Differently

We perform computer simulations of mechanically linked (poly[2]catenanes, PC) and chemically bonded (bonded rings, BR) pairs of self-avoiding ring polymers in steady shear. We find that BRs develop a novel motif, termed gradient tumbling, rotating around the gradient axis. For the PCs the rings are stretched and display another new pattern, termed slip tumbling. The dynamics of BRs is continuous and oscillatory, whereas that of PCs is intermittent between slip-tumbling attempts. Our findings demonstrate the interplay between topology and hydrodynamics in dilute solutions of connected polymers.

Influence of shape on heteroaggregation of model microplastics: a simulation study

Microplastics are a growing threat, especially in aqueous habitats. For assessing the influence on the ecosystem and possible solution strategies, it is necessary to investigate the "fate" of microplastics in the environment. Microplastics are typically surrounded by natural organic matter, which can cause aggregation via favorable interactions. However, the effect of shape and flow conditions on heteroaggregation is not well understood. We perform molecular dynamics simulations of different microplastic particle shapes with smaller spherical organic matter. We find that mostly smooth particles formed compact structures with large number of neighbors with weak connection strength and higher fractal dimension. Microplastics with sharper edges and corners aggregated into more fractal structures with fewer neighbors, but with stronger connections. We investigated the behavior of aggregates under shear flow. The critical shear rate at which the aggregates break up is much larger for spherical and rounded cube microplastics, the compact aggregate structure outweighs their weaker connection strength. The rounded cube aggregate exhibited unexpectedly high resistance against breakup under shear. We attribute this to being fairly compact due to weaker, flexible neighbor connections, which are still strong enough to prevent particles to break off during shear flow. Irrespective of stronger connections between neighbouring microplastics, fractal aggregates of cubes break up at lower shear rates. We find that cube aggregates reduced their radius of gyration significantly, indicating restructuring during shear, while most neighbor connections were kept intact. Sphere aggregates, however, kept their overall size while undergoing local rearrangements, breaking a significant portion of their neighbor interactions.

Hydrodynamic Anisotropy of Depletion in Nonequilibrium

Active colloids in a bath of inert particles of smaller size cause anisotropic depletion. The active hydrodynamics of this nonequilibrium phenomenon, which is fundamentally different from its equilibrium counterpart and passive particles in an active bath, remains scarcely understood. Here we combine mesoscale hydrodynamic simulation as well as theoretical analysis to examine the physical origin for the active depletion around a self-propelled noninteractive colloid. Our results elucidate that the variable hydrodynamic effect critically governs the microstructure of the depletion zone. Three characteristic states of anisotropic depletion are identified, depending on the strength and stress of activity. This yields a state diagram of depletion in the two-parameter space, captured by developing a theoretical model with the continuum kinetic theory and leading to a mechanistic interpretation of the hydrodynamic anisotropy of depletion. Furthermore, we demonstrate that such depletion in nonequilibrium results in various clusters with ordered organization of squirmers, which follows a distinct principle contrary to that of the entropy scenario of depletion in equilibrium. The findings might be of immediate interest to tune the hydrodynamics-mediated anisotropic interactions and active nonequilibrium organizations in the self-propulsion systems.

Multi-particle collision dynamics for a coarse-grained model of soft colloids applied to ring polymers

The simulation of polymer solutions often requires the development of methods that accurately include hydrodynamic interactions. Resolution on the atomistic scale is too computationally expensive to cover mesoscopic time and length scales on which the interesting polymer phenomena are observed. Therefore, coarse-graining methods have to be applied. In this work, the solvent is simulated using the well-established multi-particle collision dynamics scheme, and for the polymer, different coarse-graining methods are employed and compared against the monomer resolved Kremer-Grest model by their resulting diffusion coefficients. This research builds on previous work [Ruiz-Franco et al., J. Chem. Phys. 151, 074902 (2019)], in which star polymers and linear chains in a solvent were simulated and two different coarse-graining methods were developed, in order to increase computational efficiency. The present work extends this approach to ring polymers and seeks to refine one of the authors' proposed model: the penetrable soft colloid model. It was found that both proposed models are not well suited to ring polymers; however, the introduction of a factor to the PSC model delivers satisfying results for the diffusion behavior by regulating the interaction intensity with the solvent.

Confined Electrolytes Show Bulk Dynamics Modulated by Hydrodynamic Couplings with the Walls

We use numerical simulations at the mesoscopic scale, namely, multiparticle collision dynamics (MPCD), to investigate the properties of electrolyte solutions in a charged slit pore. The solution is described within the primitive model of electrolytes, where ions are charged hard spheres embedded in a dielectric medium. Hydrodynamic couplings between ions and with the charged walls are precisely accounted for by the MPCD algorithm. We show that the dynamic properties of ions in this situation strongly differ from the behavior at infinite dilution (ideal case), contrary to what is usually assumed in the usual Poisson-Nernst-Planck description of this kind of systems. As a consequence of confinement, the diffusion coefficients of ions unexpectedly increase with the average ionic density in the systems. This is due to a decrease of the proportion of ions that are slowed down by the wall. Moreover, nonequilibrium simulations are used to estimate the electrical conductivity of these confined electrolytes. We show that the simulation results can be accounted for quantitatively by combining bulk descriptions of the electrical conductivity of electrolytes with a simple description of the hydrodynamics of ions in a slit pore.

Clustering of self-thermophilic asymmetric dimers: the relevance of hydrodynamics

Self-thermophilic dimers are characterized by a net phoretic attraction which, in combination with hydrodynamic interactions, results in the formation of crystalline-like aggregates. To distinguish the effect of the different contributions is frequently an important challenge. We present a simulation investigation done in parallel in the presence and the absence of hydrodynamic interactions for the case of asymmetric self-thermophoretic dimers. In the absence of hydrodynamics, the clusters have the standard heads-in configurations. In contrast, in the presence of hydrodynamics, clusters with heads-in conformation are being formed, in which dimers with their propulsion velocity pointing out of the cluster are assembled and stabilized by strong hydrodynamic osmotic flows. Significant variation in the material properties is to be expected from such differences in the collective behavior, whose understanding and control is of great relevance for the development of new synthetic active materials.

Hydrodynamic effects on the liquid-hexatic transition of active colloids

We study numerically the role of hydrodynamics in the liquid-hexatic transition of active colloids at intermediate activity, where motility induced phase separation (MIPS) does not occur. We show that in the case of active Brownian particles (ABP), the critical density of the transition decreases upon increasing the particle's mass, enhancing ordering, while self-propulsion has the opposite effect in the activity regime considered. Active hydrodynamic particles (AHP), instead, undergo the liquid-hexatic transition at higher values of packing fraction [Formula: see text] than the corresponding ABP, suggesting that hydrodynamics have the net effect of disordering the system. At increasing densities, close to the hexatic-liquid transition, we found in the case of AHP the appearance of self-sustained organized motion with clusters of particles moving coherently.

Electroosmotic Flow Induced Lift Forces on Polymer Chains in Nanochannels

A major objective of research in nanofluidics is to achieve better selectivity in manipulating the fluxes of nano-objects and in particular of biopolymers. Numerical simulations allow one to better understand the physical mechanisms at play in such situations. We performed hybrid mesoscale simulations to investigate the properties of polymers under flows in slit pores at the nanoscale. We use multiparticle collision dynamics, an algorithm that includes hydrodynamics and thermal fluctuations, to investigate the properties of fully flexible and stiff polymers under several types of flow, showing that Poiseuille flows and electroosmotic flows can lead to quantitatively and qualitatively different behaviors of the chain. In particular, a counterintuitive phenomenon occurs in the presence of an electroosmotic flow: When the monomers are attracted by the solid surfaces through van der Waals forces, shear-induced forces lead to a stronger repulsion of the polymers from these surfaces. Such focusing of the chain in the middle of the channel increases its flowing velocity, a phenomenon that may be exploited to separate different types of polymers.

Multiparticle Collision Dynamics for Ferrofluids

Detailed studies of the intriguing field-dependent dynamics and transport properties of confined flowing ferrofluids require efficient mesoscopic simulation methods that account for fluctuating ferrohydrodynamics. Here, we propose such a new mesoscopic model for the dynamics and flow of ferrofluids, where we couple the multi-particle collision dynamics method as a solver for the fluctuating hydrodynamics equations to the stochastic magnetization dynamics of suspended magnetic nanoparticles. This hybrid model is validated by reproducing the magnetoviscous effect in Poiseuille flow, obtaining the rotational viscosity in quantitative agreement with theoretical predictions. We also illustrate the new method for the benchmark problem of flow around a square cylinder. Interestingly, we observe that the length of the recirculation region is increased whereas the drag coefficient is decreased in ferrofluids when an external magnetic field is applied, compared with the field-free case at the same effective Reynolds number. The presence of thermal fluctuations and the flexibility of this particle-based mesoscopic method provides a promising tool to investigate a broad range of flow phenomena of magnetic fluids and could also serve as an efficient way to simulate solvent effects when colloidal particles are immersed in ferrofluids.

Self-phoretic Brownian dynamics simulations

A realistic and effective model to simulate phoretic Brownian dynamics swimmers based on the general form of the thermophoretic force is here presented. The collective behavior of self-phoretic dimers is investigated with this model and compared with two simpler versions, allowing the understanding of the subtle interplay of steric interactions, propulsion, and phoretic effects. The phoretic Brownian dynamics method has control parameters which can be tuned to closely map the properties of experiments or simulations with explicit solvent, in particular those performed with multiparticle collision dynamics. The combination of the phoretic Brownian method and multiparticle collision dynamics is a powerful tool to precisely identify the importance of hydrodynamic interactions in systems of self-phoretic swimmers.

Diffusion and sedimentation in colloidal suspensions using multiparticle collision dynamics with a discrete particle model

We study self-diffusion and sedimentation in colloidal suspensions of nearly hard spheres using the multiparticle collision dynamics simulation method for the solvent with a discrete mesh model for the colloidal particles (MD+MPCD). We cover colloid volume fractions from 0.01 to 0.40 and compare the MD+MPCD simulations to experimental data and Brownian dynamics simulations with free-draining hydrodynamics (BD) as well as pairwise far-field hydrodynamics described using the Rotne-Prager-Yamakawa mobility tensor (BD+RPY). The dynamics in MD+MPCD suggest that the colloidal particles are only partially coupled to the solvent at short times. However, the long-time self-diffusion coefficient in MD+MPCD is comparable to that in experiments, and the sedimentation coefficient in MD+MPCD is in good agreement with that in experiments and BD+RPY, suggesting that MD+MPCD gives a reasonable description of hydrodynamic interactions in colloidal suspensions. The discrete-particle MD+MPCD approach is convenient and readily extended to more complex shapes, and we determine the long-time self-diffusion coefficient in suspensions of nearly hard cubes to demonstrate its generality.

Simulating wet active polymers by multiparticle collision dynamics

The conformational and dynamical properties of active Brownian polymers embedded in a fluid depend on the nature of the driving mechanism, e.g., self-propulsion or external actuation of the monomers. Implementations of self-propelled and actuated active Brownian polymers in a multiparticle collision (MPC) dynamics fluid are presented, which capture the distinct differences between the two driving mechanisms. The active force-free nature of self-propelled monomers requires adaptations of the MPC simulation scheme, with its streaming and collision steps, where the monomer self-propulsion velocity has to be omitted in the collision step. Comparison of MPC simulation results for active polymers in dilute solution with results of Brownian dynamics simulations accounting for hydrodynamics via the Rotne-Prager-Yamakawa tensor confirm the suitability of the implementation. The polymer conformational and dynamical properties are analyzed by the static and dynamic structure factor, and the scaling behavior of the latter with respect to the wave number and time dependence are discussed. The dynamic structure factor displays various activity-induced temporal regimes, depending on the considered wave number, which reflect the persistent diffusive motion of the whole polymer at small wave numbers, and the activity-enhanced internal dynamics at large wave numbers. The obtained simulation results are compared with theoretical predictions.

Preference Parameters for the Calculation of Thermal Conductivity by Multiparticle Collision Dynamics

Calculation of the thermal conductivity of nanofluids by molecular dynamics (MD) is very common. Regrettably, general MD can only be employed to simulate small systems due to the huge computation workload. Instead, the computation workload can be considerably reduced due to the coarse-grained fluid when multiparticle collision dynamics (MPCD) is employed. Hence, such a method can be utilized to simulate a larger system. However, the selection of relevant parameters of MPCD noticeably influences the calculation results. To this end, parameterization investigations for various bin sizes, number densities, time-steps, rotation angles and temperatures are carried out, and the influence of these parameters on the calculation of thermal conductivity are analyzed. Finally, the calculations of thermal conductivity for liquid argon, water and Cu-water nanofluid are performed, and the errors compared to the theoretical values are 3.4%, 1.5% and 1.2%, respectively. This proves that the method proposed in the present work for calculating the thermal conductivity of nanofluids is applicable.

Hydrodynamics of immiscible binary fluids with viscosity contrast: a multiparticle collision dynamics approach

We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids A and B of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the time-dependent shear stress functions are in excellent agreement with our continuum hydrodynamics results for the composite fluid. The wave-vector dependent transverse velocity auto-correlation functions (TVAF) in the bulk-fluid regions of the layers decay exponentially, and agree with those of single-phase isotropic MPC fluids. In addition, we determine the hydrodynamic mobilities of an embedded colloidal sphere moving steadily parallel or transverse to a fluid-fluid interface, as functions of the distance from the interface. The obtained mobilities are in good agreement with hydrodynamic force multipoles calculations, for a no-slip sphere moving under creeping flow conditions near a clean, ideally flat interface. The proposed MPC fluid-layer model can be straightforwardly implemented, and it is computationally very efficient. Yet, owing to the spatial discretization inherent to the MPC method, the model can not reproduce all hydrodynamic features of an ideally flat interface between immiscible fluids.

Multi-ciliated microswimmers-metachronal coordination and helical swimming

The dynamics and motion of multi-ciliated microswimmers with a spherical body and a small number N (with [Formula: see text]) of cilia with length comparable to the body radius, is investigated by mesoscale hydrodynamics simulations. A metachronal wave is imposed for the cilia beat, for which the wave vector has both a longitudinal and a latitudinal component. The dynamics and motion is characterized by the swimming velocity, its variation over the beat cycle, the spinning velocity around the main body axis, as well as the parameters of the helical trajectory. Our simulation results show that the microswimmer motion strongly depends on the latitudinal wave number and the longitudinal phase lag. The microswimmers are found to swim smoothly and usually spin around their own axis. Chirality of the metachronal beat pattern generically generates helical trajectories. In most cases, the helices are thin and stretched, i.e., the helix radius is about an order of magnitude smaller than the pitch. The rotational diffusion of the microswimmer is significantly smaller than the passive rotational diffusion of the body alone, which indicates that the extended cilia contribute strongly to the hydrodynamic radius. The swimming velocity is found to increase with the cilia number N with a slightly sublinear power law, consistent with the behavior expected from the dependence of the transport velocity of planar cilia arrays on the cilia separation.

Multiparticle collision dynamics simulations of a squirmer in a nematic fluid

We study the dynamics of a squirmer in a nematic liquid crystal using the multiparticle collision dynamics (MPCD) method. A recently developed nematic MPCD method [Phys. Rev. E 99, 063319 (2019)] which employs a tensor order parameter to describe the spatial and temporal variations of the nematic order is used to simulate the suspending anisotropic fluid. Considering both nematodynamic effects (anisotropic viscosity and elasticity) and thermal fluctuations, in the present study, we couple the nematic MPCD algorithm with a molecular dynamics (MD) scheme for the squirmer. A unique feature of the proposed method is that the nematic order, the fluid, and the squirmer are all represented in a particle-based framework. To test the applicability of this nematic MPCD-MD method, we simulate the dynamics of a spherical squirmer with homeotropic surface anchoring conditions in a bulk domain. The importance of anisotropic viscosity and elasticity on the squirmer's speed and orientation is studied for different values of self-propulsion strength and squirmer type (pusher, puller or neutral). In sharp contrast to Newtonian fluids, the speed of the squirmer in a nematic fluid depends on the squirmer type. Interestingly, the speed of a strong pusher is smaller in the nematic fluid than for the Newtonian case. The orientational dynamics of the squirmer in the nematic fluid also shows a non-trivial dependence on the squirmer type. Our results compare well with existing experimental and numerical data. The full particle-based framework could be easily extended to model the dynamics of multiple squirmers in anisotropic fluids.

Collective behavior of thermophoretic dimeric active colloids in three-dimensional bulk

Colloids driven by phoresis constitute one of the main avenues for the design of synthetic microswimmers. For these swimmers, the specific form of the phoretic and hydrodynamic interactions dramatically influences their dynamics. Explicit solvent simulations allow the investigation of the different behaviors of dimeric Janus active colloids. The phoretic character is modified from thermophilic to thermophobic, and this, together with the relative size of the beads, strongly influences the resulting solvent velocity fields. Hydrodynamic flows can change from puller-type to pusher-type, although the actual flows significantly differ from these standard flows. Such hydrodynamic interactions combined with phoretic interactions between dimers result in several interesting phenomena in three-dimensional bulk conditions. Thermophilic dimeric swimmers are attracted to each other and form large and stable aggregates. Repulsive phoretic interactions among thermophobic dimeric swimmers hinder such clustering and lead, together with long- and short-ranged attractive hydrodynamic interactions, to short-lived, aligned swarming structures.

Clusterization of self-propelled particles in a two-component system

We consider a mixture of active solute molecules in a suspension of passive solvent particles comprising a thermal bath. The solute molecules are considered to be extended objects with two chemically distinct heads, one head of which having chemical affinity towards the solvent particles. The coupled Langevin equations for the solvent particles along with the equations governing the dynamics of active molecules are numerically simulated to show how the active molecules self-assemble to form clusters which remain in dynamic equilibrium with the free solute molecules. We observe an interesting crossover at an intermediate time in the variation of the order parameter with time when the temperature of the bath is changed signifying the differential behavior of clusterization below and above the crossover time associated with a transition between a thermodynamic and a quasithermodynamic regime. Enthalpy-entropy compensation in the formation of clusters below the crossover is demonstrated.

Enhanced Rotational Motion of Spherical Squirmer in Polymer Solutions

The rotational diffusive motion of a self-propelled, attractive spherical colloid immersed in a solution of self-avoiding polymers is studied by mesoscale hydrodynamic simulations. A drastic enhancement of the rotational diffusion by more than an order of magnitude in the presence of activity is obtained. The amplification is a consequence of two effects, a decrease of the amount of adsorbed polymers by active motion and an asymmetric encounter with polymers on the squirmer surface, which yields an additional torque and random noise for the rotational motion. Our simulations suggest a way to control the rotational dynamics of squirmer-type microswimmers by the degree of polymer adsorption and system heterogeneity.

Hydrodynamic correlations of viscoelastic fluids by multiparticle collision dynamics simulations

The emergent fluctuating hydrodynamics of a viscoelastic fluid modeled by the multiparticle collision dynamics (MPC) approach is studied. The fluid is composed of flexible, Gaussian phantom polymers that interact by local momentum-conserving stochastic MPCs. For comparison, the analytical solution of the linearized Navier-Stokes equation is calculated, where viscoelasticity is taken into account by a time-dependent shear relaxation modulus. The fluid properties are characterized by the transverse velocity autocorrelation function in Fourier space as well as in real space. Various polymer lengths are considered-from dumbbells to (near-)continuous polymers. Viscoelasticity affects the fluid properties and leads to strong correlations, which overall decay exponentially in Fourier space. In real space, the center-of-mass velocity autocorrelation function of individual polymers exhibits a long-time tail, independent of the polymer length, which decays as t^-3/2, similar to a Newtonian fluid, in the asymptotic limit t → ∞. Moreover, for long polymers, an additional power-law decay appears at time scales shorter than the longest polymer relaxation time with the same time dependence, but negative correlations, and the polymer length dependence L^-1/2. Good agreement is found between the analytical and simulation results.

Weak Shape Anisotropy Leads to a Nonmonotonic Contribution to Crowding, Impacting Protein Dynamics under Physiologically Relevant Conditions

The effect of a nonspherical particle shape on the dynamics in crowded solutions presents a significant challenge for a comprehensive understanding of interaction and structural relaxation in biological and soft matter. We report that small deviations from a spherical shape induce a nonmonotonic contribution to the crowding effect on the short-time cage diffusion compared with spherical systems, using molecular dynamics simulations with mesoscale hydrodynamics of a multiparticle collision dynamics fluid in semidilute systems with volume fractions smaller than 0.35. We show that the nonmonotonic effect due to anisotropy is caused by the combination of a reduced relative mobility over the entire concentration range and a looser and less homogeneous cage packing of nonspherical particles. Our finding stresses that nonsphericity induces new complexity, which cannot be accounted for in effective sphere models, and is of great interest in applications such as formulations as well as for the fundamental understanding of soft matter in general and crowding effects in living cells in particular.

On the effect of the thermostat in non-equilibrium molecular dynamics simulations

The numerical investigation of the statics and dynamics of systems in non-equilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium systems can be successfully adapted to out-of-equilibrium cases. This is especially true for thermostats. Indeed, even though thermostats developed to work under equilibrium conditions sometimes display good agreement with rheology experiments, their performance rapidly degrades beyond weak dissipation and small shear rates. Here we focus on gauging the relative performances of three thermostats, Langevin, dissipative particle dynamics, and Bussi-Donadio-Parrinello under varying parameters and external conditions. We compare their effectiveness by looking at different observables and clearly demonstrate that choosing the right thermostat (and its parameters) requires a careful evaluation of, at least, temperature, density and velocity profiles. We also show that small modifications of the Langevin and DPD thermostats greatly enhance their performance in a wide range of parameters.

Flow Behavior of Chain and Star Polymers and Their Mixtures

Star-shaped polymers show a continuous change of properties from flexible linear chains to soft colloids, as the number of arms is increased. To investigate the effect of macromolecular architecture on the flow properties, we employ computer simulations of single chain and star polymers as well as of their mixtures under Poiseuille flow. Hydrodynamic interactions are incorporated through the multi-particle collision dynamics (MPCD) technique, while a bead-spring model is used to describe the polymers. For the ultradilute systems at rest, the polymers are distributed uniformly in the slit channel, with a weak dependence on their number of arms. Once flow is applied, however, we find that the stars migrate much more strongly towards the channel center as the number of arms is increased. In the star-chain mixtures, we find a flow-induced separation between stars and chains, with the stars located in the channel center and the chains closer to the walls. In order to identify the origin of this flow-induced partitioning, we conduct additional simulations without hydrodynamic interactions, and find that the observed cross-stream migration originates from a combination of wall-induced hydrodynamic lift forces and viscoelastic effects. The results from our study give valuable insights for designing microfluidic devices for separating polymers based on their architecture.

Guidance and Self-Sorting of Active Swimmers: 3D Periodic Arrays Increase Persistence Length of Human Sperm Selecting for the Fittest

Male infertility is a reproductive disease, and existing clinical solutions for this condition often involve long and cumbersome sperm sorting methods, including preprocessing and centrifugation-based steps. These methods also fall short when sorting for sperm free of reactive oxygen species, DNA damage, and epigenetic aberrations. Although several microfluidic platforms exist, they suffer from structural complexities, i.e., pumps or chemoattractants, setting insurmountable barriers to clinical adoption. Inspired by the natural filter-like capabilities of the female reproductive tract for sperm selection, a model-driven design, featuring pillar arrays that efficiently and noninvasively isolate highly motile and morphologically normal sperm, with lower epigenetic global methylation, from raw semen, is presented. The Simple Periodic ARray for Trapping And isolatioN (SPARTAN) created here modulates the directional persistence of sperm, increasing the spatial separation between progressive and nonprogressive motile sperm populations within an unprecedentedly short 10 min assay time. With over 99% motility of sorted sperm, a 5-fold improvement in morphology, 3-fold increase in nuclear maturity, and 2-4-fold enhancement in DNA integrity, SPARTAN offers to standardize sperm selection while eliminating operator-to-operator variations, centrifugation, and flow. SPARTAN can also be applied in other areas, including conservation ecology, breeding of farm animals, and design of flagellar microrobots for diagnostics.

The effect of hydrodynamic interactions on nanoparticle diffusion in polymer solutions: a multiparticle collision dynamics study

The diffusion of nanoparticles (NPs) in polymer solutions is studied by a combination of a mesoscale simulation method, multiparticle collision dynamics (MPCD), and molecular dynamics (MD) simulations. We investigate the long-time diffusion coefficient D as well as the subdiffusive behavior in the intermediate time region. The dependencies of both D and subdiffusion factor α on NP size and polymer concentration, respectively, are explicitly calculated. Particular attention is paid to the role of hydrodynamic interaction (HI) in the NP diffusion dynamics. Our simulation results show that the long-time diffusion coefficients satisfy perfectly the scaling relation found by experimental observations. Meanwhile, the subdiffusive factor decreases with the increase in polymer concentration but is of little relevance to the NP size. By parallel simulations with and without HI, we reveal that HI will generally enhance D, while the enhancement effect is non-monotonous with increasing polymer concentration, and it becomes most pronounced at semidilute concentrations. With the aid of a scaling law based on the diffusive activation energy model, we understand that HI affects diffusion through decreasing the diffusive activation energy on the one hand while increasing the effective diffusion size on the other. In addition, HI will certainly influence the subdiffusive behavior of the NP, leading to a larger subdiffusion exponent.

Anisotropic thermophoresis

Colloidal migration in a temperature gradient is referred to as thermophoresis. In contrast to particles with a spherical shape, we show that elongated colloids may have a thermophoretic response that varies with the colloid orientation. Remarkably, this can translate into a non-vanishing thermophoretic force in the direction perpendicular to the temperature gradient. Opposite to the friction force, the thermophoretic force of a rod oriented with the temperature gradient can be larger or smaller than when oriented perpendicular to it. The precise anisotropic thermophoretic behavior clearly depends on the colloidal rod aspect ratio, and also on its surface details, which provides an interesting tunability to the devices constructed based on this principle. By means of mesoscale hydrodynamic simulations, we characterize this effect for different types of rod-like colloids.

Refined energy-conserving dissipative particle dynamics model with temperature-dependent properties and its application in solidification problem

It has been observed previously that the physical behaviors of Schmidt number (Sc) and Prandtl number (Pr) of an energy-conserving dissipative particle dynamics (eDPD) fluid can be reproduced by the temperature-dependent weight function appearing in the dissipative force term. In this paper, we proposed a simple and systematic method to develop the temperature-dependent weight function in order to better reproduce the physical fluid properties. The method was then used to study a variety of phase-change problems involving solidification. The concept of the "mushy" eDPD particle was introduced in order to better capture the temperature profile in the vicinity of the solid-liquid interface, particularly for the case involving high thermal conductivity ratio. Meanwhile, a way to implement the constant temperature boundary condition at the wall was presented. The numerical solutions of one- and two-dimensional solidification problems were then compared with the analytical solutions and/or experimental results and the agreements were promising.

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics

We have extended an existing hybrid MD-SCF simulation technique that employs a coarsening step to enhance the computational efficiency of evaluating non-bonded particle interactions. This technique is conceptually equivalent to the single chain in mean-field (SCMF) method in polymer physics, in the sense that non-bonded interactions are derived from the non-ideal chemical potential in self-consistent field (SCF) theory, after a particle-to-field projection. In contrast to SCMF, however, MD-SCF evolves particle coordinates by the usual Newton's equation of motion. Since collisions are seriously affected by the softening of non-bonded interactions that originates from their evaluation at the coarser continuum level, we have devised a way to reinsert the effect of collisions on the structural evolution. Merging MD-SCF with multi-particle collision dynamics (MPCD), we mimic particle collisions at the level of computational cells and at the same time properly account for the momentum transfer that is important for a realistic system evolution. The resulting hybrid MD-SCF/MPCD method was validated for a particular coarse-grained model of phospholipids in aqueous solution, against reference full-particle simulations and the original MD-SCF model. We additionally implemented and tested an alternative and more isotropic finite difference gradient. Our results show that efficiency is improved by merging MD-SCF with MPCD, as properly accounting for hydrodynamic interactions considerably speeds up the phase separation dynamics, with negligible additional computational costs compared to efficient MD-SCF. This new method enables realistic simulations of large-scale systems that are needed to investigate the applications of self-assembled structures of lipids in nanotechnologies.

Self-assembly of colloidal micelles in microfluidic channels

The self-assembly of amphiphilic Janus colloids in microfluidic channels is studied using hybrid molecular dynamics simulations with fully resolved hydrodynamic interactions incorporated through the multi-particle collision dynamics algorithm. The simulations are conducted at a density and temperature where the Janus particles spontaneously self-assemble into spherical micelles to minimize the interface between the solvophobic caps and the surrounding solvent. In confined systems, this contact area can also be reduced by aggregation at the channel walls. Indeed, a sizable fraction of free particles and small clusters with three and four members are found at the walls when the microfluidic channel is made up of a comparably solvophobic material as the Janus colloids. When the applied Poiseuille flow is sufficiently strong, the colloidal micelles break up into smaller fragments and isolated particles. However, at intermediate flow rates the shear-induced dissociation and reorganization of aggregates lead to a net growth of the micelles with a sizable amount of particles in icosahedral clusters with 13 particles. Furthermore, the parabolic velocity profile of the flow causes a highly non-uniform cluster size distribution between the channel walls, where the aggregation number decreases close to the walls.

Tunable slow dynamics in a new class of soft colloids

By means of extensive simulations, we investigate concentrated solutions of globular single-chain nanoparticles (SCNPs), an emergent class of synthetic soft nano-objects. By increasing the concentration, the SCNPs show flattening, and even reentrant behaviour, in the density dependence of their structural and dynamic correlations, as well as a soft caging regime and weak dynamic heterogeneity. The latter is confirmed by validation of the Stokes-Einstein relation up to concentrations far beyond the overlap density. Therefore SCNPs arise as a new class of soft colloids, exhibiting slow dynamics and actualizing in a real system the structural and dynamic anomalies proposed by models of ultrasoft particles. Quantitative differences in the dynamic behaviour depend on the SCNP deformability, which can be tuned through the degree of internal cross-linking.

Thermoosmotic microfluidics

Microchannels with asymmetrically ratcheted walls are here shown to behave as effective and versatile microfluidic pumps if locally heated. When the boundary walls have different temperatures, the confined liquid experiences a temperature gradient along the sawtooth edges, which can induce a thermoosmotic flow. A mesoscale molecular simulation approach is here employed to investigate the flows which are contrasted using an analytical approach. Microchannels can be composed by one or two ratcheted walls which can be straight or cylindrical. Varying the channel geometry can not only change the overall fluid flux, but also vary the flow patters from shear to capillary type, or even to extensional type flows. This scheme does not require multiphase fluids or any movable channel parts, although they are possible to be implemented. The proposed principle is then very versatile to locally manipulate complex fluids, and a promising tool to recover waste heat, to facilitate cooling of microchips, and to manufacture portable lab-on-a-chip devices.

Bacterial swarmer cells in confinement: a mesoscale hydrodynamic simulation study

A wide spectrum of Peritrichous bacteria undergo considerable physiological changes when they are inoculated onto nutrition-rich surfaces and exhibit a rapid and collective migration denoted as swarming. Thereby, the length of such swarmer cells and their number of flagella increases substantially. In this article, we investigated the properties of individual E. coli-type swarmer cells confined between two parallel walls via mesoscale hydrodynamic simulations, combining molecular dynamics simulations of the swarmer cell with the multiparticle particle collision dynamics approach for the embedding fluid. E. coli-type swarmer cells are three-times longer than their planktonic counter parts, but their flagella density is comparable. By varying the wall separation, we analyze the confinement effect on the flagella arrangement, on the distribution of cells in the gap between the walls, and on the cell dynamics. We find only a weak dependence of confinement on the bundle structure and dynamics. The distribution of cells in the gap changes from a geometry-dominated behavior for very narrow to fluid-dominated behavior for wider gaps, where cells are preferentially located in the gap center for narrower gaps and stay preferentially next to one of the walls for wider gaps. Dynamically, the cells exhibit a wide spectrum of migration behaviors, depending on their flagella bundle arrangement, and ranges from straight swimming to wall rolling.

Comparison of different coupling schemes between counterions and charged nanoparticles in multiparticle collision dynamics

We applied the multiparticle collision dynamics (MPC) simulation technique to highly asymmetric electrolytes in solution, i.e., charged nanoparticles and their counterions in a solvent. These systems belong to a domain of solute size which ranges between the electrolyte and the colloidal domains, where most analytical theories are expected to fail, and efficient simulation techniques are still missing. MPC is a mesoscopic simulation method which mimics hydrodynamics properties of a fluid, includes thermal fluctuations, and can be coupled to a molecular dynamics of solutes. We took advantage of the size asymmetry between nanoparticles and counterions to treat the coupling between solutes and the solvent bath within the MPC method. Counterions were coupled to the solvent bath during the collision step and nanoparticles either through a direct interaction force or with stochastic rotation rules which mimic stick boundary conditions. Moreover, we adapted the simulation procedure to address the issue of the strong electrostatic interactions between solutes of opposite charges. We show that the short-ranged repulsion between counterions and nanoparticles can be modeled by stochastic reflection rules. This simulation scheme is very efficient from a computational point of view. We have also computed the transport coefficients for various densities. The diffusion of counterions was found in one case to increase slightly with the volume fraction of nanoparticles. The deviation of the electric conductivity from the ideal behavior (solutes at infinite dilution without any direct interactions) is found to be strong.