Hydrodynamic screening of star polymers in shear flow

The mutual effects of the conformations of a star polymer in simple shear flow and the deformation of the solvent flow field are investigated by a hybrid mesoscale simulation technique. We characterize the flow field near the star polymer as a function of its functionality (arm number) f . A strong screening of the imposed flow is found inside the star polymer, which increases with increasing f . To elucidate the importance of hydrodynamic screening, we compare results for hydrodynamic and random solvents. The dependence of the polymer orientation angle on the Weissenberg number shows a power law behavior with super-universal exponent --independent of hydrodynamic and excluded-volume interactions. In contrast, the polymer rotation frequency changes qualitatively when hydrodynamic interactions are switched on.     

Noise effects in two different biological systems

We investigate the role of the colored noise in two biological systems: (i) adults of Nezara viridula (L.) (Heteroptera: Pentatomidae), and (ii) polymer translocation. In the first system we analyze, by directionality tests, the response of N. viridula individuals to subthreshold signals plus noise in their mating behaviour. The percentage of insects that react to the subthreshold signal shows a nonmonotonic behaviour, characterized by the presence of a maximum, as a function of the noise intensity. This is the signature of the non-dynamical stochastic resonance phenomenon. By using a “soft” threshold model we find that the maximum of the input-output cross correlation occurs in the same range of noise intensity values for which the behavioural activation of the insects has a maximum. Moreover this maximum value is lowered and shifted towards higher noise intensities, compared to the case of white noise. In the second biological system the noise driven translocation of short polymers in crowded solutions is analyzed. An improved version of the Rouse model for a flexible polymer is adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and the effects of a Lennard-Jones potential between all beads. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion in the presence of thermal fluctuations and a colored noise source. At low temperatures or for strong colored noise intensities the translocation process of the polymer chain is delayed. At low noise intensity, as the polymer length increases, we find a nonmonotonic behaviour for the mean first translocation time of the polymer centre of inertia. We show how colored noise influences the motion of short polymers, by inducing two different regimes of translocation in the dynamics of molecule transport.     

Molecular-dynamics simulations with explicit hydrodynamics II: On the collision of polymers with molecular obstacles

We present a study of the dynamics of single polymers colliding with molecular obstacles using Molecular-dynamics simulations. In concert with these simulations we present a generalized polymer-obstacle collision model which is applicable to a number of collision scenarios. The work focusses on three specific problems: i) a polymer driven by an external force colliding with a fixed microscopic post; ii) a polymer driven by a (plug-like) fluid flow colliding with a fixed microscopic post; and iii) a polymer driven by an external force colliding with a free polymer. In all three cases, we present a study of the length-dependent dynamics of the polymers involved. The simulation results are compared with calculations based on our generalized collision model. The generalized model yields analytical results in the first two instances (cases i) and ii)), while in the polymer-polymer collision example (case iii)) we obtain a series solution for the system dynamics. For the case of a polymer-polymer collision we find that a distinct V-shaped state exists as seen in experimental systems, though normally associated with collisions with multiple polymers. We suggest that this V-shaped state occurs due to an effective hydrodynamic counter flow generated by a net translational motion of the two-chain system.     

Influence of hydrodynamics on the dynamics of a homopolymer

We present an analytical approach of the dynamics of a polymer when it is quenched from a solvent into a good or bad solvent. The dynamics is studied by means of a Langevin equation, first in the absence of hydrodynamic effect, then taking into account the hydrodynamic interactions with the solvent. The variation of the radius of gyration is studied as a function of time. In both cases, for the first stage of collapse or swelling, the evolution is described by a power law with a characteristic time proportional to N ^4/3 (N), where N is the number of monomers, without (with) hydrodynamic interactions. At larger times, scaling laws are derived for the diffusive relaxation time. Received: 10 March 1998 / Received in final form: 15 September 1998 / Accepted: 25 September 1998     

Tethered polyelectrolytes under the action of an electrical field

For a polyelectrolyte undergoing electrophoretic motion, it is predicted (D. Long, J.L. Viovy, A. Ajdari, Phys. Rev. Lett. 76, 3858 (1996); D. Long, A. Ajdari, Electrophoresis 17, 1161 (1996)) that the mechanical force necessary to stall the molecule is substantially smaller than the sum of electrical forces applied on all monomers. In fact, it should be proportional to its hydrodynamic friction coefficient and therefore to the size of its conformation. In our work we examine this prediction using coarse-grained molecular-dynamics simulations in which we explicitly include the polymer, the solvent, the counterions and salt. The electrophoretic mobility of polyelectrolytes is evaluated, the mechanical force necessary to keep the molecules tethered is measured and the resulting anisotropic polymer conformations are observed and quantified. Our results corroborate Long et al.'s prediction.     

On coupling between the orientation and the shape of a vesicle under a shear flow

A simple 2D model of deformable vesicles tumbling in a shear under flow is introduced in order to account for the main qualitative features observed experimentally as shear rates are increased. The simplicity of the model allows for a full analytical tractability while retaining the essential physical ingredients. The model reveals that the main axes of the vesicle undergo oscillations which are coupled to the vesicle orientation in the flow. The model reproduces and sheds light on the main novel features reported in recent experiments [M. Mader et al., Eur. Phys. J. E. 19, 389 (2006)], namely that both coefficients A and B that enter the Keller-Skalak equation, dψ/dt = A+Bcos(2 ψ) (ψ is the vesicle orientation angle in the shear flow), undergo a collapse upon increasing shear rate.     

Fluid membranes in hydrodynamic flow fields: Formalism and an application to fluctuating quasispherical vesicles in shear flow

The dynamics of a single fluid bilayer membrane in an external hydrodynamic flow field is considered. The deterministic equation of motion for the configuration is derived taking into account both viscous dissipation in the surrounding liquid and local incompressibility of the membrane. For quasi-spherical vesicles in shear flow, thermal fluctuations can be incorporated in a Langevin-type equation of motion for the deformation amplitudes. The solution to this equation shows an overdamped oscillatory approach to a stationary tanktreading shape. Inclination angle and ellipticity of the contour are determined as a function of excess area and shear rate. Comparisons to numerical results and experiments are discussed. Received 20 August 1998     

Microscopic relationship between colloid–colloid interactions and the rheological behaviour of suspensions: a molecular dynamics-stochastic rotation dynamics investigation

ABSTRACT

We investigate the dependence of the shear viscosity of suspensions of spherical colloids as a function of the volume fraction of the suspension, the colloid–colloid interactions and the shear rate. We couple molecular dynamics to describe the motion of the colloids with stochastic rotation dynamics (MD–SRD) for the fluid environment by means of stochastic collisions, in order to incorporate hydrodynamics effects leading to non-newtonian responses. The shear viscosity is computed using non-equilibrium simulations by imposing explicit velocity gradients. The impact of the colloid–colloid interactions is examined by modelling the inter-colloid pair potential with a repulsive power law, that allows interpolating different degrees of colloidal softness. The general rheological behaviour of our suspensions can be described with a Krieger–Dougherty like equation, which must be corrected to account for the variations in the maximum packing fraction and non-equilibrium effects arising from the flux of momentum imposed to the suspension, which appear when varying the softness of the inter-colloidal interactions. We further show evidence for non-newtonian behaviour at high Péclet numbers, characterised both by shear thinning and shear thickening, and thus demonstrate these effects can be successfully captured using MD–SRD methods.     

Dynamics of a tethered polymer in shear flow

The dynamics of a single polymer tethered to a solid surface in a shear flow was observed using fluorescently labeled DNA chains. Dramatic shear enhanced temporal fluctuations in the chain extension were observed. The rate of these fluctuations initially decreased for increasing shear rate gamma; and increased above a critical gamma;. Simulations revealed that these anomalous dynamics arise from a continual recirculating motion of the chain or cyclic dynamics. These dynamics arise from a coupling of the chain velocity in the flow direction to thermally driven fluctuations of the chain in the shear gradient direction.     

Shear viscosity of pseudo hard-spheres

We present molecular dynamics simulations of pseudo hard sphere fluid (generalized WCA potential with exponents (50, 49) proposed by Jover et al. [J. Chem. Phys 137, (2012)] using GROMACS package. The equation of state and radial distribution functions at contact are obtained from simulations and compared to the available theory of true hard spheres (HS) and available data on pseudo hard spheres. The comparison shows agreements with data by Jover et al. and the Carnahan–Starling equation of HS. The shear viscosity is obtained from the simulations and compared to the Enskog expression and previous HS simulations. It is demonstrated that the PHS potential reproduces the HS shear viscosity accurately.     

Rowers coupled hydrodynamically. Modeling possible mechanisms for the cooperation of cilia

We introduce a model system of stochastic entities, called rowers which include some essentials of the behavior of real cilia. We introduce and discuss the problem of symmetry breaking for these objects and its connection with the onset of macroscopic, directed flow in the fluid. We perform a mean field-like calculation showing that hydrodynamic interaction may provide for the symmetry breaking mechanism and the onset of fluid flow. Finally, we discuss the problem of the metachronal wave in a stochastic context through an analytical calculation based on a path integral representation of our model equation. Received 12 June 2001 and Received in final form 9 January 2002     

Molecular Dynamics simulation of a polymer chain translocating through a nanoscopic pore

The detection of linear polymers translocating through a nanoscopic pore is a promising idea for the development of new DNA analysis techniques. However, the physics of constrained macromolecules and the fluid that surrounds them at the nanoscopic scale is still not well understood. In fact, many theoretical models of polymer translocation neglect both excluded-volume and hydrodynamic effects. We use Molecular Dynamics simulations with explicit solvent to study the impact of hydrodynamic interactions on the translocation time of a polymer. The translocation time τ that we examine is the unbiased (no charge on the chain and no driving force) escape time of a polymer that is initially placed halfway through a pore perforated in a monolayer wall. In particular, we look at the effect of increasing the pore radius when only a small number of fluid particles can be located in the pore as the polymer undergoes translocation, and we compare our results to the theoretical predictions of Chuang et al. (Phys. Rev. E 65, 011802 (2001)). We observe that the scaling of the translocation time varies from τ ∼ N ^11/5 to τ ∼ N ^9/5 as the pore size increases (N is the number of monomers that goes up to 31 monomers). However, the scaling of the polymer relaxation time remains consistent with the 9/5 power law for all pore radii.     

Stationary nonequilibrium states in boundary-driven Hamiltonian systems: Shear flow

We investigate stationary nonequilibrium states of systems of particles moving according to Hamiltonian dynamics with specified potentials. The systems are driven away from equilibrium by Maxwell-demon reflection rules at the walls. These deterministic rules conserve energy but not phase space volume, and the resulting global dynamics may or may not be time reversible (or even invertible). Using rules designed to simulate moving walls, we can obtain a stationary shear flow. Assuming that for macroscopic systems this flow satisfies the Navier-Stokes equations, we compare the hydrodynamic entropy production with the average rate of phase-space volume compression. We find that they are equalwhen the velocity distribution of particles incident on the walls is a local Maxwellian. An argument for a general equality of this kind, based on the assumption of local thermodynamic equilibrium, is given. Molecular dynamic simulations of hard disks in a channel produce a steady shear flow with the predicted behavior.     

Influence of the nematic order on the rheology and conformation of stretched comb-like liquid crystalline polymers

We have studied the rheology and the conformation of stretched comb-like liquid-crystalline polymers. Both the influence of the comb-like structure and the specific effect of the nematic interaction on the dynamics are investigated. For this purpose, two isomers of a comb-like polymetacrylate polymer, of well-defined molecular weights, were synthesized: one displays a nematic phase over a wide range of temperature, the other one has only an isotropic phase. Even with high degrees of polymerization N, between 40 and 1000, the polymer chains studied were not entangled. The stress-strain curves during the stretching and relaxation processes show differences between the isotropic and nematic comb-like polymers. They suggest that, in the nematic phase, the chain dynamics is more cooperative than for a usual linear polymer. Small-angle neutron scattering has been used in order to determine the evolution of the chain conformation after stretching, as a function of the duration of relaxation t _r. The conformation can be described with two parameters only: , the global deformation of the polymer chain, and p, the number of statistical units of locally relaxed sub-chains. For the comb-like polymer, the chain deformation is pseudo-affine: is always smaller than (the deformation ratio of the whole sample). In the isotropic phase, has a constant value, while pincreases as tr. This latter behavior is not that expected for non-entangled chains, in which p varies as t _r ^1/2 (Rouse model). In the nematic phase, decreases as a stretched exponential function of t _r, while p remains constant. The dynamics of the comb-like polymers is discussed in terms of living clusters from which junctions are produced by interactions between side chains. The nematic interaction increases the lifetime of these junctions and, strikingly, the relaxation is the same at all scales of the whole polymer chain. Received 5 May 1999 and Received in final form 18 October 1999     

Dynamics of viscous vesicles in shear flow

The dynamics of giant lipid vesicles under shear flow is experimentally investigated. Consistent with previous theoretical and numerical studies, two flow regimes are identified depending on the viscosity ratio between the interior and the exterior of the vesicle, and its reduced volume or excess surface. At low viscosity ratios, a tank-treading motion of the membrane takes place, the vesicle assuming a constant orientation with respect to the flow direction. At higher viscosity ratios, a tumbling motion is observed in which the whole vesicle rotates with a periodically modulated velocity. When the shear rate increases, this tumbling motion becomes increasingly sensitive to vesicle deformation due to the elongational component of the flow and significant deviations from simpler models are observed. A good characterization of these various flow regimes is essential for the validation of analytical and numerical models, and to relate microscopic dynamics to macroscopic rheology of suspensions of deformable particles, such as blood.     

Stretching dynamics of semiflexible polymers

We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the propagation speed of the backbone tension which is induced in response to stretching. Here, we employ a newly developed unified theory to systematically substantiate, restrict, and extend these approaches. Introducing the practically relevant scenario of a chain equilibrated under some prestretching force f _pre that is suddenly exposed to a different external force f _ext at the ends, we give a concise physical explanation of the underlying relaxation processes by means of an intuitive blob picture. We discuss the corresponding intermediate asymptotics, derive results for experimentally relevant observables, and support our conclusions by numerical solutions of the coarse-grained equations of motion for the tension.     

Dynamical properties of the slithering-snake algorithm: A numerical test of the activated-reptation hypothesis

Correlations in the motion of reptating polymers in a melt are investigated by means of Monte Carlo simulations of the three-dimensional slithering-snake version of the bond-fluctuation model. Surprisingly, the slithering-snake dynamics becomes inconsistent with classical reptation predictions at high chain overlap (created either by chain length N or by the volume fraction φ of occupied lattice sites), where the relaxation times increase much faster than expected. This is due to the anomalous curvilinear diffusion in a finite time window whose upper bound (N) is set by the density of chain ends φ/N. Density fluctuations created by passing chain ends allow a reference polymer to break out of the local cage of immobile obstacles created by neighboring chains. The dynamics of dense solutions of “snakes” at t ≪ is identical to that of a benchmark system where all chains but one are frozen. We demonstrate that the subdiffusive dynamical regime is caused by the slow creeping of a chain out of its correlation hole. Our results are in good qualitative agreement with the activated-reptation scheme proposed recently by Semenov and Rubinstein (Eur. Phys. J. B, 1 (1998) 87). Additionally, we briefly comment on the relevance of local relaxation pathways within a slithering-snake scheme. Our preliminary results suggest that a judicious choice of the ratio of local to slithering-snake moves is crucial to equilibrate a melt of long chains efficiently. Received: 18 December 2002 / Accepted: 3 April 2003 / Published online: 12 May 2003 RID="a" ID="a"e-mail: jwittmer@dpm.univ-lyon1.fr RID="b" ID="b"Current address: University of Illinois at Urbana-Champaign.     

Viscosity and normal stress forces of Lennard-Jones chains using reverse non-equilibrium molecular dynamics

Reverse non-equilibrium molecular dynamics was applied for the calculation of the viscosity for different chain lengths. Each chain consisted of m tangent spherical sites, where m was 1, 2, 4, 8 or 16, respectively. From these results, shear thinning was observed at high shear rates. The normal stress forces were also estimated via the calculation of the total stress tensor, and they were related to the shear thinning effect depending on the length of the chain. Furthermore, a power law equation was used to fit the rheological curves of each chain, making possible the calculation of the viscoelasticity as a function of the sites involved in the chains.     

Diffusion of a Test Chain in a Quenched Background of Semidilute Polymers

Based on a recently established formalism [U. Ebert, J. Stat. Phys. 82:183 (1996)], we analyze the diffusive motion of a long polymer in a quenched random medium. The medium is modeled by a frozen semidilute polymer system. In the framework of standard renormalization group (RG) theory we present a systematic perturbative approach to handle such a many-chain system. In contrast to the work cited above, here we deal with long-range correlated disorder and find an attractive RG fixed point. Unlike in polymer statics, the semidilute limit here yields new nontrivial power laws for dynamic quantities. The exponents are intermediate between the Rouse and reptation results. An explicit one-loop calculation for the center-of-mass motion is given.     

A Monte-Carlo study of equilibrium polymers in a shear flow

We use an off-lattice microscopic model for solutions of equilibrium polymers (EP) in a lamellar shear flow generated by means of a self-consistent external field between parallel hard walls. The individual conformations of the chains are found to elongate in flow direction and shrink perpendicular to it while the average polymer length decreases with increasing shear rate. The Molecular Weight Distribution of the chain lengths retains largely its exponential form in dense solutions whereas in dilute solutions it changes from a power-exponential Schwartz distribution to a purely exponential one upon an increase of the shear rate. With growing shear rate the system becomes increasingly inhomogeneous so that a characteristic variation of the total monomer density, the diffusion coefficient, and the center-of-mass distribution of polymer chains of different contour length with the velocity of flow is observed. At higher temperature, as the average chain length decreases significantly, the system is shown to undergo an order-disorder transition into a state of nematic liquid crystalline order with an easy direction parallel to the hard walls. The influence of shear flow on this state is briefly examined. Received 22 October 1998 and Received in final form 12 April 1999