arXiv subjects

Friederike Schmid

Publications and source records attributed to Friederike Schmid.

At least 109 records · Page 6Linked to original sources

arXiv2010

Polyelectrolyte Electrophoresis in Nanochannels: A Dissipative Particle Dynamics Simulation

We present mesoscopic DPD-simulations of polyelectrolyte electrophoresis in confined nanogeometries, for varying salt concentration and surface slip conditions. Special attention is given to the influence of electroosmotic flow (EOF) on the migration of the polyelectrolyte. The effective polyelectrolyte mobility is found to depend strongly on the boundary properties, i.e., the slip length and the width of the electric double layer. Analytic expressions for the electroosmotic mobility and the total mobility are derived which are in good agreement with the numerical results. The relevant quantity characterizing the effect of slippage is found to be the dimensionless quantity $κ\: δ_B$, where $δ_B$ is the slip length, and $κ^{-1}$ an effective electrostatic screening length at the channel boundaries.

cond-mat.soft↗

arXiv2009

Random copolymer adsorption: Morita approximation compared to exact numerical simulations

We study the adsorption of ideal random lattice copolymers with correlations in the sequences on homogeneous substrates with two different methods: An analytical solution of the problem based on the constrained annealed approximation introduced by Morita in 1964 and the generating functional (GF) technique, and direct numerical simulations of lattice chains averaged over many realizations of random sequences. Both methods allow to calculate the free energy and different conformational characteristics of the adsorbed chain. The comparison of the results for random copolymers with different degree of correlations and different types of nonadsorbing monomers (neutral or repelling from the surface) shows not only qualitative but a very good quantitative agreement, especially in the cases of Bernoullian and quasi-alternating random sequences.

cond-mat.soft↗

arXiv2009

Computing absolute free energies of disordered structures by molecular simulation

We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from a configuration which is representative for the state of interest. The method can be applied to lattice models (e.g., the Ising model) as well as off-lattice molecular models. We focus mainly on the more challenging off-lattice case. We propose a Monte Carlo algorithm, by which the thermodynamic integration path can be sampled efficiently. At the examples of the hard sphere liquid and a hard disk solid with a defect we discuss several properties of the approach.

cond-mat.stat-mech↗

arXiv2009

Mesoscopic simulations of the counterion-induced electroosmotic flow - a comparative study

We present mesoscopic simulations of the counterion-induced electroosmotic flow in different electrostatic coupling regimes. Two simulation methods are compared, Dissipative Particle Dynamics (DPD) and coupled Lattice-Boltzmann/Molecular Dynamics (LB/MD). A general mapping scheme to match DPD to LB/MD is developed. For the weak-coupling regime, analytic expressions for the flow profiles in the presence of partial-slip as well as no-slip boundary conditions are derived from the Poisson-Boltzmann and Stokes equations, which are in good agreement with the numerical results. The influence of electrofriction and partial slip on the flow profiles is discussed.

cond-mat.other↗

arXiv2009

Toy amphiphiles on the computer: What can we learn from generic models?

Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal properties of these classes. Here we review generic models for amphiphilic molecules and discuss applications in studies of self-assembling nanostructures and the local structure of bilayer membranes, i.e. their phases and their interactions with nanosized inclusions. Special attention is given to the comparison of simulations with elastic continuum models, which are, in some sense, generic models on a higher coarse-graining level. In many cases, it is possible to bridge quantitatively between generic particle models and continuum models, hence multiscale modeling works on principle. On the other side, generic simulations can help to interpret experiments by providing information that is not accessible otherwise.

cond-mat.soft↗

arXiv2008

Coarse-grained models of complex fluids at equilibrium and unter shear

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.

cond-mat.soft↗

arXiv2008

Fluctuating Interfaces in Liquid Crystals

We review and compare recent work on the properties of fluctuating interfaces between nematic and isotropic liquid-crystalline phases. Molecular dynamics and Monte Carlo simulations have been carried out for systems of ellipsoids and hard rods with aspect ratio 15:1, and the fluctuation spectrum of interface positions (the capillary wave spectrum) has been analyzed. In addition, the capillary wave spectrum has been calculated analytically within the Landau-de Gennes theory. The theory predicts that the interfacial fluctuations can be described in terms of a wave vector dependent interfacial tension, which is anisotropic at small wavelengths (stiff director regime) and becomes isotropic at large wavelengths (flexible director regime). After determining the elastic constants in the nematic phase, theory and simulation can be compared quantitatively. We obtain good agreement for the stiff director regime. The crossover to the flexible director regime is expected at wavelengths of the order of several thousand particle diameters, which was not accessible to our simulations.

cond-mat.soft↗

arXiv2008

Bistable anchoring of nematics on rough substrates

We analyze the interplay between wetting and anchoring of nematic liquid crystals on disordering, e.g., rough substrates in the framework of the Landau-de Gennes theory, in situations of competing homeotropic and planar easy axes on the substrate and the nematic-isotropic (NI) interface. The phase diagram for azimuthally symmetric substrates is calculated. We identify two regimes - a strongly coupled regime, where the wetting transition coincides with an anchoring transition, and a weakly coupled regime, where the two are separated. The anchoring transition is first order and switches between homeotropic and planar anchoring. The two competing orientations are metastable over a broad parameter range. Hence such surfaces can be used to generate bistable surfaces.

cond-mat.soft↗

arXiv2008

Screening of hydrodynamic interactions for polyelectrolytes in salt solution

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.

cond-mat.soft↗

arXiv2008

Influence of correlations on molecular recognition

The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealised coarse-grained lattice models. A general two-stage approach is utilised where an ensemble of probe molecules is designed first and the recognition ability of the probe ensemble is related to the free energy of association with both the target molecule and a different rival molecule in a second step. The influence of correlation effects are investigated using numerical Monte Carlo techniques and mean field methods. Correlations lead to different optimum characteristic lengths of the hydrophobic and polar patches for the mutual design of the two biomolecules on the one hand and their recognition ability in the presence of other molecules on the other hand.

physics.bio-ph↗

arXiv2008

Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers

We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: Direct interactions, lipid-induced depletion interactions, lipid bridging, lipid packing, and a smooth long-range contribution. The mechanisms leading to "hydrophobic mismatch" interactions are critically analyzed.

physics.bio-ph↗

arXiv2008

Tunable-slip boundaries for coarse-grained simulations of fluid flow

On the micro- and nanoscale, classical hydrodynamic boundary conditions such as the no-slip condition no longer apply. Instead, the flow profiles exhibit ``slip`` at the surface, which is characterized by a finite slip length (partial slip). We present a new, systematic way of implementing partial-slip boundary conditions with arbitrary slip length in coarse-grained computer simulations. The main idea is to represent the complex microscopic interface structure by a spatially varying effective viscous force. An analytical equation for the resulting slip length can be derived for planar and for curved surfaces. The comparison with computer simulations of a DPD (dissipative particle dynamics) fluid shows that this expression is valid from full-slip to no-slip.

physics.comp-ph↗

arXiv2008

Kinetically driven helix formation during the homopolymer collapse process

Using Langevin simulations, we find that simple 'generic' bead-and-spring homopolymer chains in a sufficiently bad solvent spontaneously develop helical order during the process of collapsing from an initially stretched conformation. The helix formation is initiated by the unstable modes of the straight chain, which drive the system towards a long-lived metastable transient state. The effect is most pronounced if hydrodynamic interactions are screened.

cond-mat.soft↗

arXiv2008

Spontaneous formation of complex micelles from homogeneous solution

We present an extensive computer simulation study of structure formation in amphiphilic block copolymer solutions after a quench from a homogeneous state. By using a mesoscopic field-based simulation method, we are able to access time scales in the range of a second. A phase diagram of final structures is mapped out as a function of the concentration and solvent-philicity of the copolymers. A rich spectrum of structures is observed, ranging from spherical and rodlike micelles and vesicles to toroidal and net-cage micelles. The dynamical pathways leading to these structures are analyzed in detail, and possible ways to control the structures are discussed briefly.

cond-mat.soft↗

arXiv2008

Coarse-grained lattice model for investigating the role of cooperativity in molecular recognition

Equilibrium aspects of molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First an ensemble of probe molecules is designed with respect to the target biomolecule. The recognition ability of the probe ensemble is then investigated by calculating the free energy of association. The influence of cooperative and anti-cooperative effects accompanying the association of the target and probe molecules is studied. Numerical findings are presented and compared to analytical results which can be obtained in the limit of dominating cooperativity and in the mean-field formulation of the models.

physics.bio-ph↗

arXiv2007

Structure of symmetric and asymmetric "ripple" phases in lipid bilayers

We reproduce the symmetric and asymmetric ``rippled'' $P_{β'}$ states of lipid membranes by Monte Carlo simulations of a coarse-grained molecular model for lipid-solvent mixtures. The structure and properties compare favorably with experiments. The asymmetric ripple state is characterized by a periodic array of fully interdigitated ``defect'' lines. The symmetric ripple state maintains a bilayer structure, but is otherwise structurally similar. The formation of both ripple states is driven by the propensity of lipid molecules with large head groups to exhibit splay.

physics.bio-ph↗

arXiv2006

A Coarse-Grained Lattice Model for Molecular Recognition

We present a simple model which allows to investigate equilibrium aspects of molecular recognition between rigid biomolecules on a generic level. Using a two-stage approach, which consists of a design and a testing step, the role of cooperativity and of varying bond strength in molecular recognition is investigated. Cooperativity is found to enhance selectivity. In complexes which require a high binding flexibility a small number of strong bonds seems to be favored compared to a situation with many but weak bonds.

physics.bio-ph↗

arXiv2006

A Thermostat for Molecular Dynamics of Complex Fluids

A thermostat of the Nose-Hoover type, based on relative velocities and a local definition of the temperature, is presented. The thermostat is momentum-conserving and Galilean-invariant, which should make it suitable for use in Dissipative Particle Dynamics simulations, as well as nonequilibrium molecular dynamics simulations.

cond-mat.stat-mech↗