Sanne Abeln (Amolf)
Steric stabilization prevents peptide aggregation
Natively unstructured or disordered regions appear to be abundant in Eukaryotic proteins. Many such regions have been found alongside small linear binding motifs. We report a Monte Carlo study that aims to elucidate the role of disordered regions next to binding motifs. Our simulations show that flanking disordered regions may prevent aggregation of such linear motifs. The coarse-grained simulations show that small hydrophobic peptides without disordered flanks tend to aggregate under conditions where peptides embedded in unstructured peptide sequences are stable as monomers or as part of small micelle-like clusters. Our simulations also confirm a previously reported effect of coupled folding and binding; namely that the presence of disordered domains tends to decouple the binding specificity and binding strength of binding motifs. However, the disordered flanking regions have only a small effect on the folding and binding of the linear motif.
Mounir Aytouna (UvA Amsterdam)
Symmetric and asymmetric droplet pinch-off
We present a study of pinch-off dynamics droplets of Newtonian fluid, using a fast camera. The progressive thinning of a fluid filament is driven by capillary forces, which are countered by inertia, and/or viscosity. If viscosity is the dominant resisting force, the pinch-off is symmetric on the other hand, if inertia also becomes important, the breakup is asymmetric. We show that, contrary to what is expected from theory, if one externally imposes symmetry by studying the break up of a symmetric capillary bridge, one can have a symmetric breakup, whereas for the same fluid a drop pinches off in a symmetric fashion.
Mel Bacabac (Amolf)
Elastic behaviour of 3D biomimetic gel-cell complexes
Cells in vivo are typically embedded in an extracellular matrix (ECM). Recently, increasing evidence underlines the importance of the ECM in terms of its biochemical and structural support for tissue function. We will nvestigate the rheological properties of biomimetic systems composed of cells in reconstituted biopolymers, fibrin and collagen. Macroscopic rheometry complemented with the use of optical tweezers to measure the contributions of individual biopolymer fibers and cellular traction forces to overall network viscoelastic properties.
Jan-Willem Beenakker (Amolf)
Microtubule dynamics in active actin-myosin gels
In cells, microtubule dynamic instability is influenced by the actin cortex in they are embedded. To mimic this system in vitro, we grow microtubules in an active actin-myosin gel and follow their tips dynamics.
Markus Bier (Utrecht University)
Van Hove correlation functions of fluids of rodlike particles
The self and distinct van Hove correlation functions of a fluid of rodlike particles in the nematic and the smectic A phase are calculated by means of dynamic density functional theory. A comparison with recent measurements exhibits qualitative agreement.
Astridde de Wijn (University of Nijmegen)
Viscosity of dense mixtures of hydrocarbons
There is a need for reliable and internally consistent methods for prediction of viscosity of a wide range of fluid mixtures. Methods based purely on theoretical approaches are not accurate enough for industrial applications. It is therefore desirable to make use of the large body of accurate experimental work already completed on pure fluids. The VW method makes use of Enskog rigid-sphere theory in a self-consistent manner to interpolate between the viscosities of the pure components. It successfully predicts the viscosity of mixtures of similar-sized and shaped molecules, but fails for more asymmetric mixtures. In this work, we extend Enskog theory to include effects of molecular shape on the viscosity and incorporate this into the VW method. Molecules are described as chains of equal-sized, tangentially-joined rigid spheres. Correlation between spheres is included through the excluded volume and screening effects between neighbouring segments of the chains. We demonstrate that our extended Enskog theory
Eelco Eggen (Utrecht University)
What is a multipole expansion ?
In the description of the electrostatics of an arbitrary charge distribution, the multipole expansion is well established by an expansion of the Coulomb potential in spherical harmonics. What about the screened Coulomb (or Yukawa) potential?
Burak Eral (University of Twente)
Confinement induced flow and layering forces in concentrated colloidal suspensions
Concentrated colloidal suspensions under confinement appear in recently emerging technologies such as micro fluidic synthesis of anisotropic colloids and several Lab on a chip applications. Unwanted wall-particle interaction and channel clogging are the principle obstacles in development of such technologies. Despite the recent developments in control of flow and manipulation of colloids in micro fluidic devices; lack of control over structure formation under confinement in the vicinity of walls is the fundamental problem underlying mentioned obstacles. In this short presentation, we are representing a force sensor so called confinement apparatus integrated with Confocal Scanning Laser Microscopy (CSLM). Confinement apparatus is a double cantilever design with strain gauges for force measurements. Integration of confinement apparatus with Confocal Scanning Laser Microscopy allowed us to observe Quasi-Static dynamics of concentrated colloidal suspensions in real time and measure confining forces simultaneously
Thomas Hermans (TU Eindhovent)
Controlling aggregation: Dynamic patchiness
Self-assembly of structures in water is often directed by the balance between electrostatic interactions (long range) and hydrophobic patches (short range). The distribution of these patches on the surface of the components, the so-called patchiness, is crucial to the way of assembly, and can be either: random, ordered or uniform. Here we show that the degree of random patchiness of a hydrophobic dendrimer can be controlled using guest-host chemistry i.e. the guest and host together act as a supramolecular amphiphile. This enables thermodynamic or kinetically trapped supramolecular structures in water, depending on guest-host ratio during the non-covalent synthesis and on the concentration. We stress the importance of combining static and dynamic analysis techniques for these kind of supramolecular structures.
Asmae Khaldoun (UvA Amsterdam)
Landslides kill dozens of people every year, and cause large economical damage. Different mechanisms for the onset and development of slides have been reported; however especially for clayey soils their extreme instability (‘quickness’) remains poorly understood. Here we report laboratory experiments on natural quicklay samples that reveal a spectacular liquefaction of the material under flow that explains the instability. ‘Laboratory landslide’ experiments in addition show that, contrary to what is expected, a higher water content does not lead to more unstable soils. For high clay content, the liquefaction occurs in a very thin layer of the material, the rest of the clay moving as a solid block; this explains the large distances over which quickclay landslides travel. We reproduce the flow behaviour of the natural samples mixing different clays, water and salt, allowing us to assess the impact on the quickness of the different constituents of the clay.
Andriy Kyrylyuk (Utrecht University)
Random Packing of Non-Spherical Granular Materials and Colloids
A striking and non-intuitive behavior of non-spherical granular packings is revealed. The non-spherical particles demonstrate the existence of a maximum in the packing density upon a slight deviation from spherical shape, which is proved experimentally in our group. In the present study we investigate the universality in the behavior of near-spheres and the dependence of the position and value of the maximum in the packing density on the system parameters. We examine the random packing of rod-sphere mixtures by mechanical contraction computer simulation. We find that independently of the mixture composition particles pack more efficiently as the rod aspect ratio is perturbed slightly from unity and the maximum density is reached at the rod aspect ratio of approximately 1.4. The maximum in the packing density is also observed in bidisperse rod mixtures when one component in the mixture is slightly perturbed from spherical shape. Finally, we consider the universality in packing of polydisperse near-spherical particles.
Oksana Manyuhina (University of Nijmegeno)
Minimal surfaces in soft matter: statistical physics meets differential geometry
We study topological changes in liquid crystals and self-assembled vesicles due to external constraints. We show that the minimal surfaces, with vanishing bending energy, is a natural way to describe these soft materials.
Nefeli Georguelia (Amolf)
F-actin self-assembly in microfabricated chambers
Actin is one of the protein components of the cytoskeleton, responsible for cell shape. To investigate the role of cellular confinement in actin network structure, we use an in-vitro approach. Actin is introduced into solid, microfabricated chambers of various shapes and of sizes above and below the actin persistence length.
Duc Nguyen (UvA Amsterdam)
Controlled growth of hard-sphere colloidal crystal
We use colloidal hydrogel particles to study crystal growth on the atomic scale. By applying a temperature gradient we are able to control the growth of large single crystal. We can visualize nucleation and solidification at the interface in three dimensions by using confocal microscopy. Studying the crystal-fluid interface gives us insight into the mechanism of solidification.
Ronald Otten (TU Eindhoven)
Capillary rise of an isotropic-nematic interface: surface tension vs elasticity
A theoretical study is presented on a sharp horizontal interface between coexisting isotropic and nematic phases in a dispersion of anisotropic particles. The nematic wets a solid vertical wall and the interface profile, which is determined by a competition between surface tension and elasticity, is computed in case of both weak and strong surface anchoring. In the former case the director field is uniform and the capillary rise height depends non-trivially on the angle of this field. In the latter case the field is curved and the profiles decay non-monotonously.
Philipp Schapotschnikow (TU Delft)
Interactions between capped nanocystals
Marieke Schor (UvA Amsterdam)
From B-sheet to B-roll
Stimulus-responsive, self-assembling polymers have high value applications in various fields of nanotechnology. Block co-polymers composed of a silk-based block flanked by either collagen-like or PEG blocks are known to form fibres from solution in response to changes in the pH. Although the solution structure of the silk-based block should provide insight into the process of fibre formation, so far only a solid state structure has been proposed. We propose a solution structure based on experimental data and molecular modelling. Furthermore parallel tempering (PT) simulations show transition of this structure into a structure similar to the solid state one.
Steven Slotterback (University of Maryland)
Particle motion during the compaction of granular matter
We track particle motions in a granular material subjected to compaction using a laser scattering based imaging method where compaction is achieved through thermal cycling. Particle displacements in this jammed fluid correlate strongly with rearrangments of the Voronoi cells defining the local spatial partitioning about the particles, similar to previous observations of Rahman on cooled liquids. Our observations provide further evidence of commonalities between particle dynamics in granular matter close to jamming and supercooled liquids.
Marina Soares e Silva (Amolf)
Dynamics of active actin-myosin networks probed by microtubule bending
The cytoskeleton mediates various active cellular processes such as migration and division. Non-thermal random fluctuations in the actomyosin cytoskeleton have been suggested as a possible mechanism of modulation of the cell elasticity without changes in density or polymerization of actin filaments.To elucidate the role and mechanical action of myosin in these processes, we study a three-component in vitro model system. Actin filaments, myosin filaments and fluorescently labelled microtubules are assembled together in order to quantitatively determine the amplitude of microtubule bending fluctuations visualized by fluorescence microscopy. At low myosin motor densities we observe local motor-induced stress fluctuations that lead to small microtubule bends. At high motor densities the motors cause network contraction. We subsequently quantify network motor-driven stresses by Fourier analyzing the shape of the embedded microtubules.
Leon van Dijk (TU Eindhoven)
Fluorescence Spectra of Self-Assembling Helical Supramolecular Aggregates: a Theoretical Study
The reversible assembly of helical supramolecular polymers in solution is governed by the interplay between mass action and the competition between weakly bound states and strong helically bound states of the building blocks. The highly cooperative transition from free monomers at high temperatures to long helical aggregates at low temperatures can be monitored with fluorescence measurements. In order to provide the interpretation of fluorescence data with a theoretical basis, we present a model that combines a statistical theory of equilibrium polymerization with a quantum-mechanical theory for the excitations. The theoretical predictions are compared to fluorescence spectra of chiral oligo(p-phenylene-vinylene) molecules dodecane solution and we find them to qualitatively describe the red-shift of the main fluorescence peak and its decreasing intensity upon aggregation.
Jacobus van Meel (Amolf)
Crystal nucleation from cold vapor
We report Monte Carlo simulations to study the pathway of crystal nucleation of simple atomic materials at temperatures below the triple point. Two distinct routes for crystal nucleation are observed: close to the triple point, surface melting can occur and a high-density liquid droplet nucleates before the crystal forms. The formation of the crystal phase involves a second nucleation step inside this droplet. At lower temperatures, we observe direct of ordered phases. At first, small clusters with icosahedral symmetry emerge. These constitute the cores for larger twinned crystal clusters with predominantly fcc order. At intermediate temperatures, the two nucleation routes compete.
Ana Vila Verde (Amolf)
Investigating aggregation of bile salts through coarse-grained molecular dynamics models and replica exchange
Bile salts exist in the digestive tract and are key to the digestion of fats by humans and other species. Bile salt molecules consist of a rigid steroid backbone - with a hydrophobic and a hydrophilic face - and a very short flexible tail. They are surfactant molecules and aggregate into micelles when dissolved in water. Because of the unusual geometry of bile salt molecules, we cannot assume that their aggregation behavior and mechanism are similar to those observed for more standard surfactants (flexible molecules with a short hydrophilic head and a long hydrophobic tail). For example, aggregation has unusually low cooperativity as indicated by the low number of bile salt molecules (ranging from 2 to 20) in the smaller micelles. Outstanding issues in our understanding of bile salt aggregation are the mechanism by which bile micelles grow (Ostwald ripening or fusion), their shape (spherical or cylindrical) and the orientation of the bile salt molecules in the micelle. Here we present a coarse-grained model of bile salts glyco- and taurochenode- oxycholate which we use to investigate these issues. We investigate the dependence of micelle size, shape and molecular arrangement on temperature, concentration of NaCl and of bile salt using replica exchange molecular dynamics simulations in temperature space, which allow for enhanced sampling of our system. The micellar growth mechanism during the early stages of micellization is investigated through molecular dynamics. Our results agree with literature reports on similar systems and give insight into the molecular level micellar growth mechanisms and arrangement of bile salt molecules in the micelle.