Roughness gradient induced spontaneous motion of droplets on hydrophobic surfaces: A lattice Boltzmann study

The effect of a step wise change in the pillar density on the dynamics of droplets is investigated via three-dimensional lattice Boltzmann simulations. For the same pillar density gradient but different pillar arrangements, both motion over the gradient zone as well as complete arrest are observed. In the moving case, the droplet velocity scales approximately linearly with the texture gradient. A simple model is provided reproducing the observed linear behavior. The model also predicts a linear dependence of droplet velocity on surface tension. This prediction is clearly confirmed via our computer simulations for a wide range of surface tensions.Comment: 6 pages, 8 figure

On The Critical Casimir Interaction Between Anisotropic Inclusions On A Membrane

Using a lattice model and a versatile thermodynamic integration scheme, we study the critical Casimir interactions between inclusions embedded in a two-dimensional critical binary mixtures. For single-domain inclusions we demonstrate that the interactions are very long range, and their magnitudes strongly depend on the affinity of the inclusions with the species in the binary mixtures, ranging from repulsive when two inclusions have opposing affinities to attractive when they have the same affinities. When one of the inclusions has no preference for either of the species, we find negligible critical Casimir interactions. For multiple-domain inclusions, mimicking the observations that membrane proteins often have several domains with varying affinities to the surrounding lipid species, the presence of domains with opposing affinities does not cancel the interactions altogether. Instead we can observe both attractive and repulsive interactions depending on their relative orientations. With increasing number of domains per inclusion, the range and magnitude of the effective interactions decrease in a similar fashion to those of electrostatic multipoles. Finally, clusters formed by multiple-domain inclusions can result in an effective affinity patterning due to the anisotropic character of the Casimir interactions between the building blocks

Exploring energy landscapes: metrics, pathways, and normal mode analysis for rigid-body molecules

We present new methodology for exploring the energy landscapes of molecular systems, using angle-axis variables for the rigid-body rotational coordinates. The key ingredient is a distance measure or metric tensor, which is invariant to global translation and rotation. The metric is used to formulate a generalized nudged elastic band method for calculating pathways, and a full prescription for normal-mode analysis is described. The methodology is tested by mapping the potential energy and free energy landscape of the water octamer, described by the TIP4P potential

Exploring energy landscapes: from molecular to mesoscopic systems

We review a comprehensive computational framework to survey the potential energy landscape for systems composed of rigid or partially rigid molecules. Illustrative case studies relevant to a wide range of molecular clusters and soft and condensed matter systems are discussed

Modeling ternary fluids in contact with elastic membranes

We present a thermodynamically consistent model of a ternary fluid interacting with elastic membranes. Following a free-energy modeling approach for the fluid phases, we derive the governing equations for the dynamics of the ternary fluid flow and membranes. We also provide the numerical framework for simulating such fluid-structure interaction problems. It is based on the lattice Boltzmann method for the ternary fluid (Eulerian description) and a finite difference representation of the membrane (Lagrangian description). The ternary fluid and membrane solvers are coupled through the immersed boundary method. For validation purposes, we consider the relaxation dynamics of a two-dimensional elastic capsule placed at a fluid-fluid interface. The capsule shapes, resulting from the balance of surface tension and elastic forces, are compared with equilibrium numerical solutions obtained by surface evolver. Furthermore, the Galilean invariance of the proposed model is proven. The proposed approach is versatile, allowing for the simulation of a wide range of geometries. To demonstrate this, we address the problem of a capillary bridge formed between two deformable capsules

Network of Minima of the Thomson Problem and Smale's 7th Problem

The Thomson problem, arrangement of identical charges on the surface of a sphere, has found many applications in physics, chemistry and biology. Here, we show that the energy landscape of the Thomson problem for N particles with N=132, 135, 138, 141, 144, 147, and 150 is single funneled, characteristic of a structure-seeking organization where the global minimum is easily accessible. Algorithmically, constructing starting points close to the global minimum of such a potential with spherical constraints is one of Smale’s 18 unsolved problems in mathematics for the 21st century because it is important in the solution of univariate and bivariate random polynomial equations. By analyzing the kinetic transition networks, we show that a randomly chosen minimum is, in fact, always “close” to the global minimum in terms of the number of transition states that separate them, a characteristic of small world networks

Multicomponent flow on curved surfaces: A vielbein lattice Boltzmann approach

We develop and implement a novel finite difference lattice Boltzmann scheme to study multicomponent flows on curved surfaces, coupling the continuity and Navier-Stokes equations with the Cahn-Hilliard equation to track the evolution of the binary fluid interfaces. The standard lattice Boltzmann method relies on regular Cartesian grids, which makes it generally unsuitable to study flow problems on curved surfaces. To alleviate this limitation, we use a vielbein formalism to write down the Boltzmann equation on an arbitrary geometry, and solve the evolution of the fluid distribution functions using a finite difference method. Focussing on the torus geometry as an example of a curved surface, we demonstrate drift motions of fluid droplets and stripes embedded on the surface of such geometries. Interestingly, they migrate in opposite directions: fluid droplets to the outer side while fluid stripes to the inner side of the torus. For the latter we demonstrate that the global minimum configuration is unique for small stripe widths, but it becomes bistable for large stripe widths. Our simulations are also in agreement with analytical predictions for the Laplace pressure of the fluid stripes, and their damped oscillatory motion as they approach equilibrium configurations, capturing the corresponding decay timescale and oscillation frequency. Finally, we simulate the coarsening dynamics of phase separating binary fluids in the hydrodynamics and diffusive regimes for tori of various shapes, and compare the results against those for a flat two-dimensional surface. Our finite difference lattice Boltzmann scheme can be extended to other surfaces and coupled to other dynamical equations, opening up a vast range of applications involving complex flows on curved geometries

A mesoscopic model for microscale hydrodynamics and interfacial phenomena: Slip, films, and contact angle hysteresis

We present a model based on the lattice Boltzmann equation that is suitable for the simulation of dynamic wetting. The model is capable of exhibiting fundamental interfacial phenomena such as weak adsorption of fluid on the solid substrate and the presence of a thin surface film within which a disjoining pressure acts. Dynamics in this surface film, tightly coupled with hydrodynamics in the fluid bulk, determine macroscopic properties of primary interest: the hydrodynamic slip; the equilibrium contact angle; and the static and dynamic hysteresis of the contact angles. The pseudo- potentials employed for fluid-solid interactions are composed of a repulsive core and an attractive tail that can be independently adjusted. This enables effective modification of the functional form of the disjoining pressure so that one can vary the static and dynamic hysteresis on surfaces that exhibit the same equilibrium contact angle. The modeled solid-fluid interface is diffuse, represented by a wall probability function which ultimately controls the momentum exchange between solid and fluid phases. This approach allows us to effectively vary the slip length for a given wettability (i.e. the static contact angle) of the solid substrate

Impalement transitions in droplets impacting microstructured superhydrophobic surfaces

Liquid droplets impacting a superhydrophobic surface decorated with micro-scale posts often bounce off the surface. However, by decreasing the impact velocity droplets may land on the surface in a fakir state, and by increasing it posts may impale droplets that are then stuck on the surface. We use a two-phase lattice-Boltzmann model to simulate droplet impact on superhydrophobic surfaces, and show that it may result in a fakir state also for reasonable high impact velocities. This happens more easily if the surface is made more hydrophobic or the post height is increased, thereby making the impaled state energetically less favourable.Comment: 8 pages, 4 figures, to appear in Europhysics Letter

Learning dynamical information from static protein and sequencing data

Many complex processes, from protein folding to neuronal network dynamics, can be described as stochastic exploration of a high-dimensional energy landscape. While efficient algorithms for cluster detection in high-dimensional spaces have been developed over the last two decades, considerably less is known about the reliable inference of state transition dynamics in such settings. Here, we introduce a flexible and robust numerical framework to infer Markovian transition networks directly from time-independent data sampled from stationary equilibrium distributions. We demonstrate the practical potential of the inference scheme by reconstructing the network dynamics for several protein folding transitions, gene-regulatory network motifs and HIV evolution pathways. The predicted network topologies and relative transition time scales agree well with direct estimates from time-dependent molecular dynamics data, stochastic simulations and phylogenetic trees, respectively. Owing to its generic structure, the framework introduced here will be applicable to high-throughput RNA and protein sequencing datasets and future cryo-electronmicroscopy data