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We investigate with numerical simulations the molecular origin of viscosity in melts of flexible and semiflexible oligomer rings in comparison to corresponding systems with linear chains. The strong increase of viscosity with ring stiffness is linked to the formation of entangled clusters, which dissolve under shear. This shear-induced breakup and alignment of rings in the flow direction lead to pronounced shear-thinning and non-Newtonian behavior. In dispersions of linear chains, the viscosity can be associated with the (average) number of entanglements between chains, which also dissolve under shear. While blends of flexible and semiflexible rings are mixed at rest, the two species separate under flow. This phenomenon has potential applications in microfluidic devices to segregate ring polymers of similar mass and chemical composition by their bending rigidity.

Fluctuation-dissipation relations or "theorems" (FDTs) are fundamental for statistical physics and can be rigorously derived for equilibrium systems. Their applicability to non-equilibrium systems is, however, debated. Here, we simulate an active microrheology experiment, in which a spherical colloid is pulled with a constant external force through a fluid, creating near-equilibrium and far-from-equilibrium systems. We characterize the structural and dynamical properties of these systems, and reconstruct an effective generalized Langevin equation (GLE) for the colloid dynamics. Specifically, we test the validity of two FDTs: The first FDT relates the non-equilibrium response of a system to equilibrium correlation functions, and the second FDT relates the memory friction kernel in the GLE to the stochastic force. We find that the validity of the first FDT depends strongly on the strength of the external driving: it is fulfilled close to equilibrium and breaks down far from it. In contrast, we observe that the second FDT is always fulfilled. We provide a mathematical argument why this generally holds for memory kernels reconstructed from a deterministic Volterra equation for correlation functions, even for non-stationary non-equilibrium systems. Motivated by the Mori-Zwanzig formalism, we therefore suggest to impose an orthogonality constraint on the stochastic force, which is in fact equivalent to the validity of this Volterra equation. Such GLEs automatically satisfy the second FDT and are unique, which is desirable when using GLEs for coarse-grained modeling., Typos corrected in the Appendix

We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. By performing simulations of single chains in a shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations we identify by means of the Irving-Kirkwood formula the corresponding macroscopic stress tensor for a non-Newtonian polymer fluid. Shear-thinning effects in oligomer melts are also demonstrated by macroscopic simulations of a channel flow. The latter have been obtained by the discontinuous Galerkin method approximating macroscopic polymer flows. Our study confirms the influence of microscopic details in the molecular structure of short polymers such as chain flexibility on macroscopic polymer flows.

It is well-known that magnetic forces can induce a formation of densely packed strings of magnetic particles or even sheafs of several strings (spindles). Here we show that in a sufficiently strong magnetic field, more complex aggregates of particles, translating with a much faster speed than would be for a single particle or even a spindle, can be assembled at the water-air interface. Such a superfast flotilla is composed of many distant strings or spindles, playing a role of its vessels, and moves, practically, as a whole. We provide theoretical results to interpret the effect of a collective motion of such magnetic vessels. Our theory shows that, in contrast to an isolated chain or spindle, which velocity grows logarithmically with the number of magnetic particles, the speed of the interface flotilla becomes much higher, being proportional to the square root of their number. These results may guide the design of magnetic systems for extremely fast controlled delivery., Comment: 6 pages, 5 figures

Extensive molecular dynamics simulations reveal that the interactions between proteins and poly(ethylene glycol)(PEG) can be described in terms of the surface composition of the proteins. PEG molecules accumulate around non-polar residues while avoiding polar ones. A solvent-accessible-surface-area model of protein adsorption on PEGylated nanoparticles accurately fits a large set of data on the composition of the protein corona recently obtained by label-free proteomic mass spectrometry., Comment: submitted to Nanonscale on Sep. 5th 2016

This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated interactions, attraction between transmembrane proteins, and aggregation in biomembranes leading to large superstructures such as the light harvesting complex of green plants. After a general overview of theoretical considerations and continuum theory of lipid membranes we introduce different options for simulations of biomembrane systems, addressing questions such as: What can be learned from generic models? When is it expedient to go beyond them? And what are the merits and challenges for systematic coarse graining and quasi-atomistic coarse grained models that ensure a certain chemical specificity?

A mesoscopic colloid model is developed in which a spherical colloid is represented by many interacting sites on its surface. The hydrodynamic interactions with thermal fluctuations are taken accounts in full using Dissipative Particle Dynamics, and the electrostatic interactions are simulated using Particle-Particle-Particle Mesh method. This new model is applied to investigate the electrophoretic mobility of a charged colloid under an external electric field, and the influence of salt concentration and colloid charge are systematically studied. The simulation results show good agreement with predictions from the electrokinetic theory., 17 pages, 8 figures, submitted to the proceedings of High Performance Computing in Science & Engineering '13

We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived systematically from an underlying particle-based model by field theoretic methods. Particles in different representation regions can switch representations on the fly, controlled by a spatially varying tuning function. As a test case, the hybrid scheme is applied to simulate colloid-polymer composites with high resolution regions close to the colloids. The hybrid simulations are significantly faster than reference simulations of a pure particle-based model, and the results are in good agreement., 8 pages, 3 figures

This is a reply to a comment on the paper arXiv:1204.2075 "Are stress-free membranes really tensionless ?" (EPL 95,28008 (2011)).

We present a hybrid numerical method to introduce hydrodynamics in dynamic self-consistent field (SCF) studies of inhomogeneous polymer systems. It solves a set of coupled dynamical equations: The Navier-Stokes equations for the fluid flow, and SCF-based convection-diffusion equations for the evolution of the local monomer compositions. The Navier-Stokes equaitons are simulated by the lattice Boltzmann method and the dynamic self-consistent equations are solved by a finite difference scheme. Two applications are presented: First, we study microphase separation in symmetric and asymmetric block copolymer melts with various values of shear and bulk viscosities, comparing the results to those obtaiuned with purely diffusive dynamics. Second, we investigate the effect of hydrodynamics on vesicle formation in amphiphilic block copolymer solutions. In agreement with previous studies, hydrodynamic interactions are found to have little effect on the microphase separation at early times, buty they substantially accelerate the process of structure formation at later times. Furthermore, they also contribute to selecting the pathway of vesicle formation, favoring spherical intermediates over aspherical (disklike) ones.

The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not strictly attractive, but that can make adhesive contacts with other monomers. We find that the chain develop helical order during the process of collapsing from an initially stretched conformation. It seems in this case that the adhesive contacts help the polymer chain to stay trapped in the helix state., 6 pages, 5 figures

We study the stress distribution profiles and the height and thickness fluctuations of lipid membranes in the tilted gel state by Monte Carlo simulations of a generic coarse-grained model for lipid membranes, which reproduces many known properties of DPPC bilayers. The results are related to the corresponding properties of fluid membranes, and to theoretical predictions for crystalline and hexatic membranes. One striking observation is that the spontaneous curvature of the monolayers changes sign from the fluid to the gel phase. In the gel phase, the long-wavelength height fluctuations are suppressed, and the fluctuation spectrum is highly anisotropic. In the direction of tilt, it carries the signature of soft modes that are compatible with the wavelength of the ripple phase, which emerges in the transition region between the fluid and the gel state. In the direction perpendicular to the tilt, the thickness fluctuations are almost entirely suppressed, and the height fluctuations seem to be dominated by an interfacial energy, i.e., by out-of-layer fluctuations, up to length scales of tens of nanometers., to appear in Soft Matter

We present the results of mesoscopic dissipative particle dynamics (DPD) simulations of coupled electrohydrodynamic phenomena on the micro- and nanoscale. The effects of electroosmotic flow and slippage combined with polyelectrolyte electrophoresis are investigated in detail, taking full account of hydrodynamic and electrostatic interactions. Our numerical results are in excellent agreement with analytical calculations., Comment: 15 pages, 6 figures

Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different levels of coarse-graining can provide insight into generic structures and basic dynamical processes at equilibrium and non-equilibrium. In the first part of this lecture, some popular coarse-grained models for membranes and membrane systems are reviewed. Special focus is given to bead-spring models with different solvent representations, and to random-interface models. Selected examples of simulations at the molecular and the mesoscopic level are presented, and it is shown how simulations of molecular coarse-grained models can bridge between different levels. The second part addresses simulation methods for complex fluids under shear. After a brief introduction into the phenomenology (in particular for liquid crystals), different non-equilibrium molecular dynamics (NEMD) methods are introduced and compared to one another. Application examples include the behavior of liquid crystal interfaces and lamellar surfactant phases under shear. Finally, mesoscopic simulation approaches for liquid crystals under shear are briefly discussed., Lecture presented at the Summer School on "Computer Simulations in Condensed Matter: from Materials to Chemical Biology" in Erice, 2006

We provide numerical evidence that hydrodynamic interactions are screened for charged polymers in salt solution on time scales below the Zimm time. At very short times, a crossover to hydrodynamic behavior is observed. Our conclusions are drawn from extensive coarse-grained computer simulations of polyelectrolytes in explicit solvent and explicit salt, and discussed in terms of analytical arguments based on the Debye-Hueckel approximation., 4 pages, 4 figures, submitted to Physical Review Letters

We review various methods to investigate the statics and the dynamics of collective composition fluctuations in dense polymer mixtures within fluctuating-field approaches. The central idea of fluctuating-field theories is to rewrite the partition function of the interacting multi-chain systems in terms of integrals over auxiliary, often complex, fields, which are introduced by means of appropriate Hubbard-Stratonovich transformations. Thermodynamic averages like the average composition and the structure factor can be expressed exactly as averages of these fields. We discuss different analytical and numerical approaches to studying such a theory: The self-consistent field approach solves the integrals over the fluctuating fields in saddle-point approximation. Generalized random phase approximations allow to incorporate Gaussian fluctuations around the saddle point. Field theoretical polymer simulations are used to study the statistical mechanics of the full system with Complex Langevin or Monte Carlo methods. Unfortunately, they are hampered by the presence of a sign problem. In dense system, the latter can be avoided without losing essential physics by invoking a saddle point approximation for the complex field that couples to the total density. This leads to the external potential theory. We investigate the conditions under which this approximation is accurate. Finally, we discuss recent approaches to formulate realistic dynamical time evolution equations for such models. The methods are illustrated by two examples: A study of the fluctuation-induced formation of a polymeric microemulsion in a polymer-copolymer mixture, and a study of early-stage spinodal decomposition in a binary blend., preprint, to appear in Advances in Polymer Science

Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can bridge between atomic descriptions and phenomenological field theories. Here we focus on model systems for amphiphilic membranes. After a brief general introduction, we present selected simulation results on monolayers, bilayers, and bilayer stacks. First, we discuss internal phase transitions in membranes and show that idealized models reproduce the generic phase behavior. Then we consider membrane fluctuations and membrane defects. The simulation data is compared with mesoscopic theories, and effective phenomenological parameters can be extracted., in Computational Soft Matter: From Synthetic Polymers to Proteins, NIC-Lecture Notes, NIC Series Vol. 23, p. 323, N. Attig, K. Binder, H. Grubm\"uller, K. Kremer eds., Forschungszentrum J\"ulich (2004)

Computer simulations of amphiphilic systems are reviewed. Research areas cover a wide range of length and time scales, and a whole hierarchy of models and methods has been developed to address them all. They range from atomistically realistic models, idealized chain models, lattice spin models, to phenomenological models such as Ginzburg-Landau models and random interface models. Selected applications are discussed in order to illustrate the use of the models and the insights they can offer., Review article on computer simulations - Some minor corrections (Typos, Figure captions)