Collective dynamics of active dumbbells near a circular obstacle.

In this article, we present the collective dynamics of active dumbbells in the presence of a static circular obstacle using Brownian dynamics simulation. The active dumbbells aggregate on the surface of a circular obstacle beyond a critical radius. The aggregation is non-uniform along the circumference, and the aggregate size increases with the activity (Pe) and the curvature radius (Ro). The dense aggregate of active dumbbells displays persistent rotational motion with a certain angular speed, which linearly increases with activity. Furthermore, we show a strong polar ordering of the active dumbbells within the aggregate. The polar ordering exhibits long-range correlation, with the correlation length corresponding to the aggregate size. Additionally, we show that the residence time of an active dumbbell on the obstacle surface increases rapidly with area fraction due to many-body interactions that lead to a slowdown of the rotational diffusion. This article further considers the dynamical behavior of a tracer particle in the solution of active dumbbells. Interestingly, the speed of the passive tracer particle displays a crossover from monotonically decreasing to increasing with the size of the tracer particle upon increasing the dumbbells' speed. Furthermore, the effective diffusion of the tracer particle displays non-monotonic behavior with the area fraction; the initial increase in diffusivity is followed by a decrease for a larger area fraction.

Characteristic features of self-avoiding active Brownian polymers under linear shear flow.

We present Brownian dynamics simulation results of a flexible linear polymer with excluded-volume interactions under shear flow in the presence of active noise. The active noise strongly affects the polymer's conformational and dynamical properties, such as the stretching in the flow direction and compression in the gradient direction, shear-induced alignment, and shear viscosity. In the asymptotic limit of large activities and shear rates, the power-law scaling exponents of these quantities differ significantly from those of passive polymers. The chain's shear-induced stretching at a given shear rate is reduced by active noise, and it displays a non-monotonic behavior, where an initial polymer compression is followed by its stretching with increasing active force. The compression of the polymer in the gradient direction follows the relation ∼WiPe-3/4 as a function of the activity-dependent Weissenberg number WiPe, which differs from the scaling observed in passive systems ∼WiPe-1/2. The flow-induced alignment at large Péclet numbers Pe ≫ 1, where Pe is the Péclet number, and large shear rates WiPe ≫ 1 displays the scaling behavior WiPe-1/2, with an exponent differing from the passive value -1/3. Furthermore, the polymer's zero-shear viscosity displays a non-monotonic behavior, decreasing in an intermediate activity regime due to excluded-volume interactions and increasing again for large Pe. Shear thinning appears with increasing Weissenberg number with the power-laws WiPe-1/2 and WiPe-3/4 for passive and active polymers, respectively. In addition, our simulation results are compared with the results of an analytical approach, which predicts quantitatively similar behaviors for the various aforementioned physical quantities.

Compression of a confined semiflexible polymer under direct and oscillating fields.

The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is contrary to the previously reported stretching of the chain. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. In the case of a semiflexible polymer chain, the inhomogeneous hydrodynamic drag from the center to the periphery of the coil couples with the chain bending to cause a swirling movement of the chain segments, leading to structural intertwining and compaction. Contrarily, a flexible chain of the same length lacks such structural deformation and forms a well-established tadpole structure. While bending rigidity profoundly influences the chain's folding favorability, we also found that subject to the direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk where such compaction is absent. However, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. This field-induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures even for shorter chains, unlike other spontaneous knotting experiments where it happens exclusively for longer chains.

Explicit characterization of counterion dynamics around a flexible polyelectrolyte.

The article presents a comprehensive study of counterion dynamics around a generic linear polyelectrolyte chain with the help of coarse-grained computer simulations. The ion-chain coupling is discussed in the form of binding time, mean-square displacement (MSD) relative to the chain, local ion transport coefficient, and spatiotemporal correlations in the effective charge. We have shown that a counterion exhibits subdiffusive behavior 〈δR^{2}〉∼t^{δ}, δ≈0.9 w.r.t. chain's center of mass. The MSD of ions perpendicularly outward from the chain segment exhibits a smaller subdiffusive exponent compared to the one along the chain backbone. The effective diffusivity of ion is the lowest in chain's close proximity, extending up to the length-scale of radius of gyration R_{g}. Beyond R_{g} at larger distances, they attain diffusivity of free ion with a smooth cross-over from the adsorbed regime to the free ion regime. We have shown that the effective diffusivity drastically decreases for the multivalent ions, while the crossover length scale remains the same. Conversely, with increasing salt concentration the coupling-length scale reduces, while the diffusivity remains unaltered. The effective diffusivity of adsorbed-ion reveals an exponential reduction with electrostatic interaction strength. We further corroborate this from the binding time of ions on the chain, which also grows exponentially with the coupling strength of the ion-polymer duo. Moreover, the binding time of ions exhibits a weak dependence with salt concentration for the monovalent salt, while for multivalent salts the binding time decreases dramatically with concentration. Our work also elucidates fluctuations in the effective charge per site, where it exhibits strong negative correlations at short length-scales.

Migration of active filaments under Poiseuille flow in a microcapillary tube.

We present a comprehensive study of active filaments confined in a cylindrical channel under Poiseuille flow. The activity drives the filament towards the channel boundary, whereas external fluid flow migrates the filament away from the boundary. This migration further shifts towards the centre for higher flow strength. The migration behaviour of the filaments is presented in terms of the alignment order parameter that shows the alignment grows with shear and activity. Further, we have also addressed the role of length of filament on the migration behaviour, which suggests higher migration for larger filaments. Moreover, we discuss the polar ordering of filaments as a function of distance from the centre of channel that displays upstream motion near the boundary and downstream motion at the centre of the tube.

Phase separation of an active colloidal suspension via quorum-sensing.

We present the Brownian dynamics simulation of an active colloidal suspension in two dimensions, where the self-propulsion speed of a colloid is regulated according to the local density sensed by it. The role of concentration-dependent motility in the phase-separation of colloids and their dynamics is investigated in detail. Interestingly, the system phase separates at a very low packing fraction (Φ≈ 0.125) at higher self-propulsion speeds (Pe), into a dense phase coexisting with a homogeneous phase and attains a long-range crystalline order beyond the transition point. The transition point is quantified here from the local density profiles and local and global-bond order parameters. We have shown that the characteristics of the phase diagram are qualitatively akin to the active Brownian particle (ABP) model. Moreover, our investigation reveals that the density-dependent motility amplifies the slow-down of the directed speed, which facilitates phase-separation even at low packing fractions. The effective diffusivity shows a crossover from quadratic rise to a power-law behavior of exponent 3/2 with Pe in the phase-separated regime. Furthermore, we have shown that the effective diffusion decreases exponentially with packing fraction in the phase-separated regime, while it shows a linear decrease in the single phase regime.

Conformation and dynamics of a self-avoiding active flexible polymer.

We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially shrinks with active force, which starts swelling on further increase in force. The shrinkage followed by swelling is attributed purely to excluded-volume interactions among the monomers. In the swelling regime, the chain shows a crossover from the self-avoiding behavior to the Rouse behavior with scaling exponent ν_{a}≈1/2 for end-to-end distance. The nonmonotonicity in the structure is analyzed through various physical quantities; specifically, radial distribution function of monomers, scattering time, as well as various energy calculations. The chain relaxes faster than the Rouse chain in the intermediate force regime, with a crossover in variation of relaxation time at large active force as given by a power law τ_{r}∼Pe^{-4/3} (Pe is Péclet number).

Force driven transition of a globular polyelectrolyte.

We have systematically studied behavior of a flexible polyelectrolyte (PE) chain with explicit counterions, subjected to a constant force at the terminal ends. Our simulations reveal that in the hydrophobic regime, a PE globule abruptly opens to a coil state beyond a critical force Fc. At the transition point, the polymer shape shows large scale fluctuations that are quantified in terms of end-to-end distance Re. These fluctuations suggest that the system coexists in globule and coil states at the transition, which is also confirmed from the bimodal distribution of Re. Moreover, the critical force associated with the globule coil transition exhibits a nonmonotonic behavior, where surprisingly, Fc decreases with Bjerrum length lB in the limit of small lB, followed by an increase in the larger lB limit. Furthermore, this behavior is also validated from a theory adopted for the PE. From the free energy analysis, we have demonstrated that predominantly, the competition between the intrachain repulsive energy, counterion's translational entropy, and adsorption energy leads to the novel feature of nonmonotonic behavior of force.

Beating to rotational transition of a clamped active ribbon-like filament.

We present a detailed study of a clamped ribbon-like filament under a compressive active force using Brownian dynamics simulations. We show that a clamped ribbon-like filament is able to capture beating as well as rotational motion under the compressive force. The nature of oscillation is governed by the torsional rigidity of the filament. The frequency of oscillation is almost independent of the torsional rigidity. The beating of the filament gives a butterfly-shaped trajectory of the free-end monomer, whereas rotational motion yields a circular trajectory on a plane. The binormal correlation and the principal component analysis reveal the butterfly, elliptical, and circular trajectories of the free end monomer. We present a phase diagram for different kinds of motion in the parameter regime of compressive force and torsional rigidity.

Behavior of active filaments near solid-boundary under linear shear flow.

The steady-state behavior of a dilute suspension of self-propelled filaments confined between planar walls subjected to Couette-flow is reported herein. The effect of hydrodynamics has been taken into account using a mesoscale simulation approach. We present a detailed analysis of positional and angular probability distributions of filaments with varying propulsive force and shear-flow. The distribution of the centre-of-mass of the filament shows adsorption near the surfaces, which diminishes with the flow. The excess density of filaments decreases with Weissenberg number as Wi-ß with an exponent ß ≈ 0.8, in the intermediate shear range (1 < Wi < 30). The angular orientational moment also decreases near the wall as Wi-δ with δ ≈ 1/5; the variation in orientational moment near the wall is relatively slower than the bulk. It shows a strong dependence on the propulsive force near the wall, with variation on force as Pe-1/3 for large Pe ≥ 1. The active filament shows orientational preference with flow near the surfaces, which splits into upstream and downstream swimming. The population splitting from a unimodal (propulsive force dominated regime) to bimodal phase (shear dominated regime) is identified in the parameter space of propulsive force and shear flow.

Steady state sedimentation of ultrasoft colloids.

The structural and dynamical properties of ultra-soft colloids-star polymers-exposed to a uniform external force field are analyzed by applying the multiparticle collision dynamics technique, a hybrid coarse-grain mesoscale simulation approach, which captures thermal fluctuations and long-range hydrodynamic interactions. In the weak-field limit, the structure of the star polymer is nearly unchanged; however, in an intermediate regime, the radius of gyration decreases, in particular transverse to the sedimentation direction. In the limit of a strong field, the radius of gyration increases with field strength. Correspondingly, the sedimentation coefficient increases with increasing field strength, passes through a maximum, and decreases again at high field strengths. The maximum value depends on the functionality of the star polymer. High field strengths lead to symmetry breaking with trailing, strongly stretched polymer arms and a compact star-polymer body. In the weak-field-linear response regime, the sedimentation coefficient follows the scaling relation of a star polymer in terms of functionality and arm length.

Electrophoretic mobilities of counterions and a polymer in cylindrical pores.

We have simulated the transport properties of a uniformly charged flexible polymer chain and its counterions confined inside cylindrical nanopores under an external electric field. The hydrodynamic interaction is treated by describing the solvent molecules explicitly with the multiparticle collision dynamics method. The chain consisting of charged monomers and the counterions interact electrostatically with themselves and with the external electric field. We find rich behavior of the counterions around the polymer under confinement in the presence of the external electric field. The mobility of the counterions is heterogeneous depending on their location relative to the polymer. The adsorption isotherm of the counterions on the polymer depends nonlinearly on the electric field. As a result, the effective charge of the polymer exhibits a sigmoidal dependence on the electric field. This in turn leads to a nascent nonlinearity in the chain stretching and electrophoretic mobility of the polymer in terms of their dependence on the electric field. The product of the electric field and the effective polymer charge is found to be the key variable to unify our simulation data for various polymer lengths. Chain extension and the electrophoretic mobility show sigmoidal dependence on the electric field, with crossovers from the linear response regime to the nonlinear regime and then to the saturation regime. The mobility of adsorbed counterions is nonmonotonic with the electric field. For weaker and moderate fields, the adsorbed counterions move with the polymer and at higher fields they move opposite to the polymer's direction. We find that the effective charge and the mobility of the polymer decrease with a decrease in the pore radius.

Hydrodynamic correlations and diffusion coefficient of star polymers in solution.

The center-of-mass dynamics of star polymers in dilute solution is analyzed by hybrid mesoscale simulations. The fluid is modeled by the multiparticle collision dynamics approach, a particle-based hydrodynamic simulation technique, which is combined with molecular dynamics simulations for the polymers. Star polymers of various functionalities are considered. We determine the center-of-mass velocity correlation functions, the corresponding mean square displacements, and diffusion coefficients. The velocity correlation functions exhibit a functionality-dependent and structure-specific intermediate time regime, with a slow decay. It is followed by the long-time tail t(-3/2), which is solely determined by the fluid. Infinite-system-size diffusion coefficients are determined from the velocity correlation function by a combination of simulation and analytical results, as well as from the center-of-mass mean square displacement for various systems sizes and extrapolation. In terms of the hydrodynamic radius, the star polymer hydrodynamic diffusion coefficient exhibits the same universal system-size dependence as a spherical colloid. The functionality dependence of the ratio of hydrodynamic radii and the radii of gyration agrees well with experimental predictions.

Conformational and dynamical properties of ultra-soft colloids in semi-dilute solutions under shear flow.

We investigate structural and dynamical properties of ultra-soft colloids in dilute and semi-dilute solutions by hybrid mesoscale simulations under linear shear flow. In particular, the influence of functionality on these properties is addressed. Our study combines molecular dynamics simulations for the solute with the multiparticle collision dynamics approach for the coarse-grained solvent. The star polymers exhibit large conformational and orientational changes in shear flow, which we characterize by the radius of gyration tensor and the alignment angle. These quantities show a universal dependence on a concentration- and functionality-dependent Weissenberg number with slight deviations at high shear rates. Moreover, the star polymers display a rotational dynamics with a shear-rate- and concentration-dependent rotation frequency. We attribute the concentration dependence to the screening of hydrodynamic interactions in semi-dilute star-polymer solutions.

Nonequilibrium forces between dragged ultrasoft colloids.

The dynamical deformation of ultrasoft colloids as well as their dynamic frictional forces are numerically investigated, when one colloid is dragged past another at constant velocity. Hydrodynamic interactions are captured by a particle-based mesoscopic simulation method. At vanishing relative velocity, the equilibrium repulsive force-distance curve is obtained. At large drag velocities, in contrast, we find an apparent attractive force for departing colloids along the dragging direction. The deformation, in the close encounter of colloids, and the energy dissipation are examined as a function of the drag velocity and their separation.

Stromal-derived factor-1 delivered via hydrogel drug-delivery vehicle accelerates wound healing in vivo.

Topical treatment of superficial wounds has many advantages including decreased cost and increased ease of application compared with systemic treatments. Many of the advantages, however, are lost when it is necessary for repeated doses of topical medications to be given over an extended period of time. Therefore, a drug-delivery vehicle that delivers biologically appropriate doses in a sustained fashion would prove valuable. In this study, an alginate hydrogel scaffold impregnated with the angiogenic chemokine stromal-derived factor-1 was used to provide targeted, though short-term, delivery directly into the wound bed. Wounds were created on the dorsum of mice, and either a stromal-derived factor-1-impregnated or a saline-impregnated scaffold was applied. Wounds were explanted after 1, 3, 7 days, wound area was measured, and histology and immunohistochemistry for endothelial markers were performed. The remaining wound area in stromal-derived factor-1-treated wounds vs. controls was not significant 1 day after wounding (96.7 ± 0.1 vs. 97.5 ± 1.1%, p=0.317), but was significant after 3 days postwounding (46.7 ± 0.1 vs. 82.3 ± 2.4%, p=0.046) and 7 days postwounding (2.3 ± 1.3 vs. 32.0 ± 4.0%, p=0.049). Immunohistochemistry revealed a greater degree of endothelial cell invasion into the wound bed infiltration compared with controls. The results of this study suggest significant clinical promise for our hydrogel-delivery vehicle in the treatment of wounds.

Therapeutic metabolic inhibition: hydrogen sulfide significantly mitigates skeletal muscle ischemia reperfusion injury in vitro and in vivo.

BACKGROUND: Recent evidence suggests that hydrogen sulfide is capable of mitigating the degree of cellular damage associated with ischemia-reperfusion injury. The purpose of this study was to determine whether it is protective in skeletal muscle. METHODS: This study used both in vitro (cultured myotubes subjected to sequential anoxia and normoxia) and in vivo (mouse hind-limb ischemia followed by reperfusion) models in which hydrogen sulfide (0 to 1000 µM) was delivered before the onset of oxygen deficiency. Injury score and apoptotic index were determined by analysis of specimens stained with hematoxylin and eosin and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling, respectively. RESULTS: In vitro, hydrogen sulfide reduced the apoptotic index by as much as 99 percent (p=0.001), with optimal protection conferred by raising intravascular hydrogen sulfide to 10 µM. In vivo, 10 µM hydrogen sulfide delivered before 3 hours of hind-limb ischemia followed by 3 hours of reperfusion resulted in protection against ischemia-reperfusion injury-induced cellular changes, as evidenced by significant decreases in injury score and apoptotic index (by as much as 91 percent; p=0.001). These findings were consistent at 4 weeks after injury and reperfusion. CONCLUSION: These findings confirm that the preischemic delivery of hydrogen sulfide limits ischemia-reperfusion injury-induced cellular damage in myotubes and skeletal muscle and suggests that, when given in the appropriate dose, this molecule may have significant therapeutic applications in multiple clinical scenarios.

Low-dose radiation augments vasculogenesis signaling through HIF-1-dependent and -independent SDF-1 induction.

The inflammatory response to ionizing radiation (IR) includes a proangiogenic effect that could be counterproductive in cancer but can be exploited for treating impaired wound healing. We demonstrate for the first time that IR stimulates hypoxia-inducible factor-1α (HIF-1α) up-regulation in endothelial cells (ECs), a HIF-1α-independent up-regulation of stromal cell-derived factor-1 (SDF-1), as well as endothelial migration, all of which are essential for angiogenesis. 5 Gray IR-induced EC HIF-1α and SDF-1 expression was greater when combined with hypoxia suggesting an additive effect. While small interfering RNA silencing of HIF-1α mRNA and abolition of HIF-1α protein induction down-regulated SDF-1 induction by hypoxia alone, it had little effect on SDF-1 induction by IR, demonstrating an independent pathway. SDF-1-mediated EC migration in hypoxic and/or radiation-treated media showed IR induced strong SDF-1-dependent migration of ECs, augmented by hypoxia. IR activates a novel pathway stimulating EC migration directly through the expression of SDF-1 independent of HIF-1α induction. These observations might be exploited for stimulation of wound healing or controlling tumor angiogenesis.