Saber Naderi (TU Eindhoven)
Conformational changes in the structure of a charged model virus coat protein in the presence of DNA
In the process of DNA encapsulation by virus coat proteins, protein-DNA interactions play a crucial role. These interactions are believed to lead to conformational changes in the coat protein structure, a form of allostery that ultimately results in a full coverage of the DNA. In our work, we investigate these conformational changes by means of molecular dynamics simulations focusing on a model protein that has a beta-sheet structure with positively charged residues on the turn regions that act as a DNA binding domain. First, we study the structure of the proteins and protein aggregates in the absence of the DNA. We find that charges destabilise the beta-sheet and that stacks of beta-sheets are also unstable. Next, we look at these structures in the presence of the DNA, and find that in the presence of DNA both individual proteins and stack of proteins are stable under appropriate conditions of ionic strength. Our simulations lend support to the idea that the attractive Coulomb interactions between protein and DNA can induce a conformational change in proteins.
Joost de Graaf (Utrecht)
Poisson-Boltzmann Theory and Monte Carlo Simulations for Charged Janus Dipoles
We study the ionic screening of charged spherical Janus particles using primitive-model Monte Carlo simulations and compare these results to the predictions of nonlinear Poisson-Boltzmann theory. Our results allow us to probe the range of validity of the Poisson-Boltzmann approximation. For homogeneously charged spheres this range of validity corresponds well to the range that was predicted by field theoretical studies of homogeneously charged flat surfaces. We find similar ranges for colloids with a Janus-type charge distribution. The techniques and parameters we introduce show great promise for future studies of an even wider class of charged-patterned particles.
Tim Krüger (TU Eindhoven)
Interplay of inertia and deformability: lateral motion of deformable particles in channel flow
The lateral motion of deformable particles in a planar Poiseuille flow has not been entirely understood. On the one hand, it is known that the deformability of particles (expressed by the capillary number, Ca, the ratio of viscous fluid and elastic particle stresses) promotes a migration towards the centerplane of the flow in the absence of inertia (zero Reynolds number, Re = 0). On the other hand, inertia effects are responsible for an outward migration of rigid particles (Ca = 0) close to the centerplane. We present 3D simulation results for systems with both finite Ca and Re and discuss the interplay of inertia and deformability effects.
Hamed Mortazavi (TU Eindhoven)
Rheology of associative micellar solutions
Strain stiffening is a unique property of biological materials which has been observed only in associative biopolymer networks. In this work a viscoelastic model of a hydrogel: a water soluble micellar network cross-linked by flexible biopolymers is studied. It is shown how cross-links in the network quantitatively affect the shear stiffening of the hydrogel. Also the morphology of the micellar network is studied to characterize its impact on the modulus.
Esther Vermolen (Shell)
Badr Kaoui (TU Eindhoven)
How does confinement affect the dynamics of a viscous vesicle?
We studied numerically the interplay between the wall confinement effect and the vesicle viscosity contrast (the ratio between the inner- and outer-fluid viscosities). We find that the vesicle dynamical states (tank-treading and tumbling) are altered by confinement. Moreover, we find that the tank-treading-to-tumbling transition threshold is delayed by confinement.
Artem Bakulin (Amolf)
Microscopic Structure Influencing Macroscopic Splash at High Weber Number
The dynamics of water drop impact at high impinging velocity onto superhydrophobic substrate is experimentally investigated. The solid substrate---comprised of regular and hydrophobic micropillars---is transparent, thereby facilitating close-up, top-or-bottom-view, high-speed imaging. With a sufficient impact velocity, instead of a completely-bouncing ``Fakir" droplet, wetting splashing can occur, with an entrapped air bubble at the centre surrounded by a wetted area as well as an emission of satellite droplets during the advancing phase of spreading lamella. A large portion of the lamella travels upon air and subsequently recoils due to surface tension, forming a partial rebound on the central wet spot. We present and discuss quantitative results of the entrapped air bubble, the central wetted area, and the maximal spreading lamella as the impact velocity is increased. We further vary the lattice periodicity of the micro-patterns and find its profound influence on the macroscopic flow. More specifically, directional splashing can emerge, emitting secondary droplets in certain directions which are associated with the lattice. Directional splashing can be suppressed to a gentle spreading by decreasing the periodicity of the lattice and, furthermore, can be tuned to a completely-wetting splashing in the diagonal directions of the lattice by a larger periodicity, offering opportunities to control the wetting process. Finally, the elimination of directional splashing by reducing air pressure, P, suggests that the underlying air is squeezed outwards by the falling droplet upon the solid boundary whereby the air flow is affected, leading to different splashing behavior.
Ceyda Sanli (Twente)
Dense heteregenous flow of floaters
When a monolayer of granular, floating at an air-liquid interface, is agitated by a capillary wave groups of granulars are observed to move together. Size of the groups is consists of a few grains for low packing fraction and they breaks-up into small pieces very quickly. However, when the packing fraction increases, both the group size and the break-up time increases. By characterizing the time dependent morphological deformations of the groups, i.e. the area and the aspect ratio, we can easily estimate typical length and time scales of the groups. Such kind of cluster formation resembles formation of granular eddies in dense chute flow, and further understanding and analysis are required to learn more about rheology of dense granulars.
Francois Boyer (Twente)
Drop impact of non-Newtonian fluids
Drop impact dynamics on solid surfaces is a classical subject of interfacial hydrodynamics, which occurs in many industrial and environmental situations. So far, most of the studies have concerned Newtonian fluids. Complex fluids (polymer dispersions, particle suspensions, gels, emulsions, ...) are however of considerable interest for a wide range of applications. From a fundamental point of view, how the non-Newtonian features of a complex liquid change (drastically in some cases) the drop impact dynamics is a challenging open problem. Newly observed phenomena will then be presented.
Stephan Ulrich (Leiden)
Influence of Network Topology on Material Failure
Any material will break, if exposed to a sufficiently large stress. In this talk, the material is simplified as a network of particles. These particles are randomly connected with bonds which break, if exceeding a critical force. I present results on how the network topology influences the failure patterns, meaning the manifestation and dynamics of breaking bonds. For applications the important question is, if a macroscopic and system spanning crack emerges (which means that the material falls apart), or if the failure is localized to distinct spots, randomly distributed throughout the network (which means that the material may still be intact).
Thomas Beuman (Leiden)
Stochastic geometry of non-Gaussian fields
Gaussian random fields pervade various areas of physics and have distinctive and well understood stochastic properties. Here we study the stochastic geometry of a random surface, whose height is given by a nonlinear function of a Gaussian field. We find that, as a result of the non-Gaussianity, the density of maxima and minima no longer match and calculate the relative imbalance between the two. We perform similar calculations for the density of umbilical points, which are topological defects of the lines of curvature. Our results apply to the analysis of speckle patterns generated by nonlinear random waves and more generally to detect and quantify non-Gaussianities present in any scalar field that can be represented as a smooth two-dimensional surface.
Panayiotis Voudouris (TU Eindhoven)
Shear thinning of soft particle suspensions
Suspensions of soft deformable particles are encountered in a wide range of food and biological materials. Examples are biological cells, micelles, vesicles or microgel particles. While the behavior of suspenions of hard spheres - the classical model system of colloid science - is reasonably well understood, a full understanding of these soft particle suspensions remains elusive. While at low concnentrations the rheology, structure and dynamics closely resembles that of hard spheres, this is not the case for high concentrations, where significant differences are observed. Because soft particles can change both their shape as well as their volume, they can be packed to much higher concentrations than hard particles. For the same reason, for soft particles the suspension viscosity is less sensitive to volume fraction than for hard particles. However, the relation between single particle properties and macroscopic mechanical properties still remains poorly understood in these materials. Here we examine the surprising shear thinning behavior that is observed in soft particle suspensions as a function of particle softness. We use poly-N-isopropylacrylamide (p-NIPAM) particles as a model system to study this effect in detail. We use a microfluidic flow-focussing device to make aqueous drops containing NIPAM monomer, crosslinker, catalyst and a photoinitiator. Subsequently, we form uniformly sized p-NIPAM particles by polymerization inside these drops. These soft spheres show significant shear thinning even at very large Peclet numbers, where this would not be observed for hard particles. The degree of shear thinning is directly related to the single particle elastic properties, which we characterize by the recently developed Capillary Micromechanics technique.
Bas van Ravensteijn (Utrecht)
Phase Behavior of Faceted Polyhedral Particles.
With the advent of experimental techniques to synthesize various anisotropic polyhedral particles, of nano and micro meter size, the interests in the colloidal self assembly of faceted polyhedral particles have been rejuvenated. The shape anisotropy of colloids play a key role in determining the self-assembled structures. We study the phase behavior of such experimentally producible hard polyhedral particles using Monte Carlo simulations. Point symmetric hard polyhedral particles undergo an entropic phase transition from a liquid to a periodic crystal phase upon increasing the pressure. Recent computational studies have shown that various asymmetric particles undergo an entropic phase transition from liquid phase to a quasi crystalline phase with increasing pressure. Here we present the phase behavior hard colloids with truncated cubic shape
Daniel Florea (TU Eindhoven)
Microrheology of ultra soft microgels particle suspension
For ultra soft microgels, the suspension remains liquid irrespective of concentration in normal rheological experiments. With a normal oscillatory rheometer we get the average response of the material which does not shed any light of why the samples still behave liquid like. By the use of the microrheology experiments, local rheological properties are computed and these results emphasize the rich phenomenology that is brought about when the particles are deformable and compressible.
Benny van Zuiden (Leiden)
Curved surface crystal melting
We are studying the melting of curved surface crystals. Previous studies, at low temperatures and weak curvature, indicate spatial in-homogeneities and dislocations due to curvature. Currently, we are writing a molecular dynamics simulation that will enable us to simulate at arbitrary temperature with arbitrary smooth curvatures, where we expect to find a lot of new interesting physics, such as spatial in-homogeneous melting.
Douglas Ashton (Utrecht)
Colloidal cubes with depletion
Cube shaped colloids can now be synthesised and are driven to self assemble in square arrays through the depletion interaction. We perform explicit-polymer Monte Carlo simulations to predict where square structures are stable and to study the barriers to self assembly.