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The conformations and dynamics of semiflexible filaments subject to a homogeneous external (gravitational) field, e.g., in a centrifuge, are studied numerically and analytically. The competition between hydrodynamic drag and bending elasticity generates new shapes and dynamical features. We show that the shape of a semiflexible filament undergoes instabilities as the external field increases. We identify two transitions that correspond to the excitation of higher bending modes. In particular, for strong fields the filament stabilizes in a non-planar shape, resulting in a sideways drift or in helical trajectories. For two interacting filaments, we find the same transitions, with the important consequence that the new non-planar shapes have an effective hydrodynamic repulsion, in contrast to the planar shapes which attract themselves even when their osculating planes are rotated with respect to each other. For the case of planar filaments, we show analytically and numerically that the relative velocity is not necessarily due to a different drag of the individual filaments, but to the hydrodynamic interactions induced by their shape asymmetry., Comment: 9 pages, 7 figures in Soft Matter (2015)

Numerical simulations of vesicle suspensions are performed in two dimensions to study their dynamical and rheological properties. An hybrid method is adopted, which combines a mesoscopic approach for the solvent with a curvature-elasticity model for the membrane. Shear flow is induced by two counter-sliding parallel walls, which generate a linear flow profile. The flow behavior is studied for various vesicle concentrations and viscosity ratios between the internal and the external fluid. Both the intrinsic viscosity and the thickness of depletion layers near the walls are found to increase with increasing viscosity ratio., Comment: To be published in the DynaCaps 2014 Conference Proceedings (Procedia IUTAM)

In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to quantify the relationship between individual motors plus filaments to organisation and dynamics on molecular and supra-molecular length scales. Here we present results of extensive numerical simulations of active gels where the motors and filaments are confined between two infinite parallel plates. Thermal fluctuations and excluded-volume interactions between filaments are included. A systematic variation of rates for motor motion, attachment and detachment, including a differential detachment rate from filament ends, reveals a range of non-equilibrium behaviour. Strong motor binding produces structured filament aggregates that we refer to as asters, bundles or layers, whose stability depends on motor speed and differential end-detachment. The gross features of the dependence of the observed structures on the motor rate and the filament concentration can be captured by a simple one-filament model. Loosely bound aggregates exhibit super-diffusive mass transport, where filament translocation scales with lag time with non-unique exponents that depend on motor kinetics. An empirical data collapse of filament speed as a function of motor speed and end-detachment is found, suggesting a dimensional reduction of the relevant parameter space. We conclude by discussing the perspectives of microscopic modelling in the field of active gels., Comment: 11 pages, 13 figures. Extended parameter range and clarification. To appear in Phys. Rev. E

The dynamics and rheology of suspensions of fluid vesicles or red blood cells is investigated by a combination of molecular dynamics and mesoscale hydrodynamics simulations in two dimensions. The vesicle suspension is confined between two no-slip walls, which are driven externally to generate a shear flow with shear rate $\dot\gamma$. The flow behavior is studied as a function of $\dot\gamma$, the volume fraction of vesicles, and the viscosity contrast between inside and outside fluids. Results are obtained for the encounter and interactions of two vesicles, the intrinsic viscosity of the suspension, and the cell-free layer near the walls., Comment: In press in EPL

Binary mixtures of amphiphiles in solution can self-assemble into a wide range of structures when the two species individually form aggregates of different curvatures. In this paper, we focus on small, spherically-symmetric aggregates in a solution of sphere-forming amphiphile mixed with a smaller amount of lamella-forming amphiphile. Using a coarse-grained mean-field model (self-consistent field theory, or SCFT), we scan the parameter space of this system and find a range of morphologies as the interaction strength, architecture and mixing ratio of the amphiphiles are varied. When the two species are quite similar in architecture, or when only a small amount of lamella-former is added, we find simple spherical micelles with cores formed from a mixture of the hydrophobic blocks of the two amphiphiles. For more strongly mismatched amphiphiles and higher lamella-former concentrations, we instead find small vesicles and more complex micelles. In these latter structures, the lamella-forming species is encapsulated by the sphere-forming one. For certain interaction strengths and lamella-former architectures, the amount of lamella-forming copolymer encapsulated may be large, and the implications of this for the solubilization of hydrophobic chemicals are considered. The mechanisms behind the formation of the above structures are discussed, with a particular emphasis on the sorting of amphiphiles according to their preferred curvature., Comment: 32 pages, 14 figures, double-spaced preprint format, submitted to Macromolecules

The tumbling dynamics of individual polymers in semidilute solution is studied by large-scale non-equilibrium mesoscale hydrodynamic simulations. We find that the tumbling time is equal to the non-equilibrium relaxation time of the polymer end-to-end distance along the flow direction and strongly depends on concentration. In addition, the normalized tumbling frequency as well as the widths of the alignment distribution functions for a given concentration-dependent Weissenberg number exhibit a weak concentration dependence in the cross-over regime from a dilute to a semidilute solution. For semidilute solutions a universal behavior is obtained. This is a consequence of screening of hydrodynamic interactions at polymer concentrations exceeding the overlap concentration.

Binary mixtures of amphiphiles in solution can self-assemble into a wide range of structures when the two species individually form aggregates of different curvatures. A specific example of this is seen in solutions of lipid mixtures where the two species form lamellar structures and spherical micelles respectively. Here, vesicles connected by thread-like micelles can form in a narrow concentration range of the sphere-forming lipid. We present a self-consistent field theory (SCFT) study of these structures. Firstly, we show that the addition of sphere-forming lipid to a solution of lamella-former can lower the free energy of cylindrical, thread-like micelles and hence encourage their formation. Next, we demonstrate the coupling between composition and curvature; specifically, that increasing the concentration of sphere-former in a system of two bilayers connected by a thread leads to a transfer of amphiphile to the thread. We further show that the two species are segregated within the structure, with the concentration of sphere-former being significantly higher in the thread. Finally, the addition of larger amounts of sphere-former is found to destabilize the junctions linking the bilayers to the cylindrical micelle, leading to a breakdown of the connected structures. The degree of segregation of the amphiphiles and the amount of sphere-former required to destabilize the junctions is shown to be sensitive to the length of the hydrophilic block of the sphere-forming amphiphiles., Comment: 16 pages plus 10 figures; preprint format; submitted to Langmuir

In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD). The method consists of alternating streaming and collision steps in an ensemble of point particles. The multi-particle collisions are performed by grouping particles in collision cells, and mass, momentum, and energy are locally conserved. This simulation technique captures both full hydrodynamic interactions and thermal fluctuations. The first part of the review begins with a description of several widely used MPC algorithms and then discusses important features of the original SRD algorithm and frequently used variations. Two complementary approaches for deriving the hydrodynamic equations and evaluating the transport coefficients are reviewed. It is then shown how MPC algorithms can be generalized to model non-ideal fluids, and binary mixtures with a consolute point. The importance of angular-momentum conservation for systems like phase-separated liquids with different viscosities is discussed. The second part of the review describes a number of recent applications of MPC algorithms to study colloid and polymer dynamics, the behavior of vesicles and cells in hydrodynamic flows, and the dynamics of viscoelastic fluids.

The non-equilibrium structural and dynamical properties of flexible polymers confined in a square microchannel and exposed to a Poiseuille flow are investigated by mesoscale simulations. The chain length and the flow strength are systematically varied. Two transport regimes are identified, corresponding to weak and strong confinement. For strong confinement, the transport properties are independent of polymer length. The analysis of the long-time tumbling dynamics of short polymers yields non-periodic motion with a sublinear dependence on the flow strength. We find distinct differences for conformational as well as dynamical properties from results obtained for simple shear flow.

We investigate the hydrodynamic properties of a fluid simulated with a mesoscopic solvent model. Two distinct regimes are identified, the `particle regime' in which the dynamics is gas-like, and the `collective regime' where the dynamics is fluid-like. This behavior can be characterized by the Schmidt number, which measures the ratio between viscous and diffusive transport. Analytical expressions for the tracer diffusion coefficient, which have been derived on the basis of a molecular-chaos assumption, are found to describe the simulation data very well in the particle regime, but important deviations are found in the collective regime. These deviations are due to hydrodynamic correlations. The model is then extended in order to investigate self-diffusion in colloidal dispersions. We study first the transport properties of heavy point-like particles in the mesoscopic solvent, as a function of their mass and number density. Second, we introduce excluded-volume interactions among the colloidal particles and determine the dependence of the diffusion coefficient on the colloidal volume fraction for different solvent mean-free paths. In the collective regime, the results are found to be in good agreement with previous theoretical predictions based on Stokes hydrodynamics and the Smoluchowski equation., Comment: 15 pages, 15 figures

The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions and depths of these minima are regulated by the counterion density in the bulk. Using two-dimensional lattice sum and free energy perturbation theories, the coexisting phases for DNA bundles are calculated. A DNA-condensation and redissolution transition and a stable mesocrystal with an intermediate lattice constant for high counterion concentration are obtained., Comment: 26 pages, 10 figures

Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and the persistence length of the helical polymer are much larger than the diameter of the cylinder. In case (i) we calculate the free energy of confinement and interpret it in terms of a worm-like chain in a pore with an effective diameter that depends on the parameters of the helix. In case (ii) we consider the possibility that one end of the helical polymer escapes from the rod and wanders away. The average numbers of turns at which the helix escapes or intersects the rod are measured in the simulations, as a function of the pitch $p_0$. The behavior for large and small $p_0$ is explained with simple scaling arguments., Comment: 5 figures

The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum in the potential at short distances which then disappears in favor of a shallower minimum at larger separations. The resulting phase diagram includes a DNA-condensation and redissolution transition and a stable mesocrystal with an intermediate lattice constant for high counterion concentration., Comment: 4 pages, 4 figures

The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model are used and the shape of the DNA molecules is accurately modelled using different geometrical shapes. We find that multivalent ions induce a significant attraction between the DNA molecules whose strength can be tuned by the averaged valency of the ions. The physical origin of the attraction is traced back either to electrostatics or to entropic contributions. For multivalent counter- and monovalent salt ions, we find a salt-induced stabilization effect: the force is first attractive but gets repulsive for increasing salt concentration. Furthermore, we show that the multivalent-ion-induced attraction does not necessarily correlate with DNA overcharging., Comment: 51 pages and 13 figures

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove., Comment: 34 pages with 14 figures

Amphiphiles are molecules which have both hydrophilic and hydrophobic parts. In water- and/or oil-like solvent, they self-assemble into extended sheet-like structures due to the hydrophobic effect. The free energy of an amphiphilic system can be written as a functional of its interfacial geometry, and phase diagrams can be calculated by comparing the free energies following from different geometries. Here we focus on bicontinuous structures, where one highly convoluted interface spans the whole sample and thereby divides it into two separate labyrinths. The main models for surfaces of this class are triply periodic minimal surfaces, their constant mean curvature and parallel surface companions, and random surfaces. We discuss the geometrical properties of each of these types of surfaces and how they translate into the experimentally observed phase behavior of amphiphilic systems., Comment: Review, 50 pages, Latex, 7 PS figures included, 7 large PS figures left out. appeared in: Morphology of Condensed Matter: Physics and Geometry of Spatially Complex Systems, eds. K. R. Mecke and D. Stoyan, Springer Lecture Notes in Physics vol. 600, pp. 107-151 (2002)

A particle-based model for mesoscopic fluid dynamics is used to simulate steady and unsteady flows around a circular and a square cylinder in a two-dimensional channel for a range of Reynolds number between 10 and 130. Numerical results for the recirculation length, the drag coefficient, and the Strouhal number are reported and compared with previous experimental measurements and computational fluid dynamics data. The good agreement demonstrates the potential of this method for the investigation of complex flows., Comment: 6 pages, separated figures in .jpg format, to be published in Europhysics Letters

The conformational properties of a semi-flexible polymer chain, anchored at one end in a uniform force field, are studied in a simple two-dimensional model. Recursion relations are derived for the partition function and then iterated numerically. We calculate the angular fluctuations of the polymer about the direction of the force field and the average polymer configuration as functions of the bending rigidity, chain length, chain orientation at the anchoring point, and field strength., Comment: to be published in Phys. Rev. E

Inverse bicontinuous cubic phases are ubiquitous in lipid-water mixtures and consist of a lipid bilayer forming a cubic minimal surface, thereby dividing space into two cubic networks of water channels. For small hydrocarbon chain lengths, the monolayers can be modeled as parallel surfaces to a minimal midsurface. The bending energy of the cubic phases is determined by the distribution of Gaussian curvature over the minimal midsurfaces which we calculate for seven different structures (G, D, P, I-WP, C(P), S and F-RD). We show that the free-energy densities of the structures G, D and P are considerably lower than those of the other investigated structures due to their narrow distribution of Gaussian curvature. The Bonnet transformation between G, D, and P implies that these phases coexist along a triple line, which also includes an excess water phase. Our model includes thermal membrane undulations. Our qualitative predictions remain unchanged when higher order terms in the curvature energy are included. Calculated phase diagrams agree well with the experimental results for 2:1 lauric acid/dilauroyl phosphatidylcholine and water., Comment: Revtex, 23 pages with 9 postscript figures included, to appear in Langmuir

We investigate the stability of seven inverse bicontinuous cubic phases ($G$, $D$, $P$, $C(P)$, $S$, $I-WP$, $F-RD$) in lipid-water mixtures based on a curvature model of membranes. Lipid monolayers are described by parallel surfaces to triply periodic minimal surfaces. The phase behavior is determined by the distribution of the Gaussian curvature on the minimal surface and the porosity of each structure. Only $G$, $D$ and $P$ are found to be stable, and to coexist along a triple line. The calculated phase diagram agrees very well with experimental results for 2:1 lauric acid/DLPC., Comment: Revtex, 4 pages with 3 EPS-figures included

We study the phase behavior of ternary amphiphilic systems in the framework of a curvature model with non-vanishing spontaneous curvature. The amphiphilic monolayers can arrange in different ways to form micellar, hexagonal, lamellar and various bicontinuous cubic phases. For the latter case we consider both single structures (one monolayer) and double structures (two monolayers). Their interfaces are modeled by the triply periodic surfaces of constant mean curvature of the families G, D, P, C(P), I-WP and F-RD. The stability of the different bicontinuous cubic phases can be explained by the way in which their universal geometrical properties conspire with the concentration constraints. For vanishing saddle-splay modulus $\bar \kappa$, almost every phase considered has some region of stability in the Gibbs triangle. Although bicontinuous cubic phases are suppressed by sufficiently negative values of the saddle-splay modulus $\bar \kappa$, we find that they can exist for considerably lower values than obtained previously. The most stable bicontinuous cubic phases with decreasing $\bar \kappa < 0$ are the single and double gyroid structures since they combine favorable topological properties with extreme volume fractions., Comment: Revtex, 23 pages with 10 Postscript files included, to appear in J. Chem. Phys. 112 (6) (February 2000)

The Fourier approach and theories of space groups and color symmetries are used to systematically generate and compare bicontinuous cubic structures in the framework of a Ginzburg-Landau model for ternary amphiphilic systems. Both single and double structures are investigated; they correspond to systems with one or two monolayers in a unit cell, respectively. We show how and why single structures can be made to approach triply periodic minimal surfaces very closely, and give improved nodal approximations for G, D, I-WP and P surfaces. We demonstrate that the relative stability of the single structures can be calculated from the geometrical properties of their interfaces only. The single gyroid G turns out to be the most stable bicontinuous cubic phase since it has the smallest porosity. The representations are used to calculate distributions of the Gaussian curvature and 2H-NMR bandshapes for C(P), C(D), S, C(Y) and F-RD surfaces., Comment: Revtex, 24 pages with 13 EPS-figures included, to appear in Phys. Rev. E 59(5) (May 1999)

A lattice-Boltzmann model for the study of the dynamics of oil-water-surfactant mixtures is constructed. The model, which is based on a Ginzburg-Landau theory of amphiphilic systems with a single, scalar order parameter, is then used to calculate the spectrum of undulation modes of an oil-water interface and the spontaneous emulsification of oil and water after a quench from two-phase coexistence into the lamellar phase. A comparison with some analytical results shows that the model provides an accurate description of the static and dynamic behavior of amphiphilic systems., Comment: 6 pages, 2 figures, europhysics-letter style

We study the dependence of the phase behavior of ternary amphiphilic systems on composition and temperature. Our analysis is based on a curvature elastic model of the surfactant film with sufficiently large spontaneous curvature and sufficiently negative saddle-splay modulus that the stable phases are the lamellar phase and a droplet microemulsion. In addition to the curvature energy, we consider the contributions to the free energy of the long-ranged van der Waals interaction and of the undulation modes. We find that for bending rigidities of order k_B T, the lamellar phase extends further and further into the water apex of the phase diagram as the phase inversion temperature is approached, in good agreement with experimental results., Comment: LaTeX2e, 11 pages with references and 2 eps figures included, submitted to Europhys. Lett

The dynamic structure factor $G({\bf k},\omega)$ is studied in a time-dependent Ginzburg-Landau model for microemulsion and sponge phases in thermal equilibrium by field-theoretic perturbation methods. In bulk contrast, we find that for sufficiently small viscosity $\eta$, the structure factor develops a peak at non-zero frequency $\omega$, for fixed wavenumber $k$ with $k_0 < k {< \atop \sim} q$. Here, $2\pi/q$ is the typical domain size of oil- and water-regions in a microemulsion, and $k_0 \sim \eta q^2$. This implies that the intermediate scattering function, $G({\bf k}, t)$, {\it oscillates} in time. We give a simple explanation, based on the Navier-Stokes equation, for these temporal oscillations by considering the flow through a tube of radius $R \simeq \pi/q$, with a radius-dependent tension., Comment: 24 pages, LaTex, 11 Figures on request; J. Phys. II France 4 (1994) to be published

A simple Ginzburg-Landau theory with a single, scalar order parameter is used to study the microscopic structure of microemulsions and sponge phases. The scattering intensity in both film and bulk contrast, as well as averages of the internal area $S$, the Euler characteristic $\chi_E$, and the mean curvature squared $$, are calculated by Monte Carlo methods. The results are compared with results obtained from a variational approach in combination with the theory of Gaussian random fields and level surfaces. The results for the location of the transition from the microemulsion to oil/water coexistence, for the scattering intensity in bulk contrast, and for the dimensionless ratio $\chi_E V^2/S^3$ (where $V$ is the volume) are found to be in good quantitative agreement. However, the variational approach fails to give a peak in the scattering intensity in film contrast at finite wavevector, a peak which is observed both in the Monte Carlo simulations and in experiment. Also, the variational approach fails to produce a transition from the microemulsion to the lamellar phase., Comment: 23 pages (LaTeX) + 15 figures appended, figures 10-13 upon request, LMU-WAG-940530

The conformation and scaling properties of self-avoiding fluid vesicles with zero extrinsic bending rigidity subject to an internal pressure increment $\Delta p>0$ are studied using Monte Carlo methods and scaling arguments. With increasing pressure, there is a first-order transition from a collapsed branched polymer phase to an extended inflated phase. The scaling behavior of the radius of gyration, the asphericities, and several other quantities characterizing the average shape of a vesicle are studied in detail. In the inflated phase, continuously variable fractal shapes are found to be controlled by the scaling variable $x=\Delta p N^{3\nu/2}$ (or equivalently, $y = {}/ N^{3\nu/2}$), where $N$ is the number of monomers in the vesicle and $V$ the enclosed volume. The scaling behavior in the inflated phase is described by a new exponent $\nu=0.787\pm 0.02$., Comment: 18 pages