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Scientific highlights 2014


Swirls and Vortices in Suspensions of Self-Propelled Brownian Spheres


A. Wysocki, R.G. Winkler, and G. Gompper,
SoftComp partner: FZJ-Gompper
EPL 105, 48004 (2014)



Assemblies of intrinsically active objects represent an exceptional class of non-equilibrium systems. Examples range from the macroscopic scale of human crowds to the microscopic scale of cells and motile microorganisms. A generic phenomenon in such systems is the emergence of self-organized large-scale dynamical patterns like vortices, swarms, networks, or self-sustained turbulence. This intriguing dynamics is a consequence of the complex interplay of self-propulsion, internal or external noise, and many-body interactions.

The understanding of the collective behavior requires the characterization of the underlying physical interaction mechanisms. Alignment induced by particle interactions, e.g., collisions between elongated objects or hydrodynamic interactions, is well known to lead to clustering and collective motion. In contrast, we study suspensions of self-propelled Brownian spheres in three spatial dimensions, which lack any alignment mechanism. Our simulations reveal a phase separation into a dilute and a dense phase, above a certain density and strength of self-propulsion. The packing fraction of the dense phase approaches random close packing at high activity, yet the system remains fluid. Although no alignment mechanism exists, we find long-lived cooperative motion of particles in the dense regime, which is due to an interface-induced sorting process.





Self-propelled Brownian spheres display phase separation and collective swirl-like motion on large length scales. Red (blue) color indicates large (small) displacements in a fixed time interval.



Wrapping of Nanoparticles by Lipid-Bilayer Membranes

S. Dasgupta, T. Auth, and G. Gompper,
SoftComp partner: FZJ-Gompper
Nano Lett. 14, 687 (2014)



Membrane budding and particle uptake is important for the communication of cells with their environment, e.g. for endocytosis, phagocytosis, and parasite or virus entry. Also, various potential applications of nanoparticles in complex materials require a better understanding of their cellular toxicity. Furthermore, nanoparticles can be used for targeted drug delivery, for cancer therapy, and as membrane makers for biomedical studies.

We study passive endocytosis of nanoparticles with sizes between ten and few hundred nanometers that are wrapped by lipid bilayer membranes. Upon wrapping, the membrane deformation energy increases while the adhesion energy due to the attractive interaction between particle and membrane decreases. Numerical calculations with triangulated surfaces allow the calculation of deformation energies for various particle shapes.

We characterise nanoparticle wrapping analogously to thermodynamic phase transitions. While for spherical nanoparticles partially-wrapped states are found only for membranes with tension, cube-like, rod-like, and ellipsoidal nanoparticles show shallow and deep partially-wrapped states also without tension. Here, shape matters! Not only the aspect ratio, but also the local curvature distribution on the nanoparticle surface controls binding and wrapping. This is the first and a necessary step for the
interaction of nanoparticles with biological cells.





Nanocubes are wrapped by membranes in a multi-step process with two stable partially-wrapped states. For the deep-wrapped states five faces are wrapped,
whereas for the shallow-wrapped state only one face adheres to the membrane (not shown).



Structure and Dynamics of Intrinsically Disordered Proteins

A. Stadler, L. Stingaciu, A. Radulescu, O. Holderer, M. Monkenbusch, R. Biehl, and D. Richter,
SoftComp partner: FZJ-Richter
JACS 136 (2014) 6987−6994



Intrinsically disordered proteins (IDP) are a specific class of proteins, which lack a well defined and fully folded three-dimensional structure. The expected structural and dynamic properties of IDP reach from very soft structures, over folded elements connected by extended and flexible loops, to fully disordered polypeptide chains. The biological role of IDP is believed to be highly conformational adaptive, which would be important for association with their biological binding partners, or to respond rapidly to different environmental conditions.

We investigated myelin basic protein (MBP) as a biophysical model system for IDP. MBP can bind lipid molecules and in that form stabilizes the myelin sheath around nerve cells. In solution and without lipid molecules the protein is largely unstructured and intrinsically disordered. In our study we demonstrated that conformational motions on the nanosecond time scale in IDP can be investigated using neutron spin-echo spectroscopy in combination with small angle scattering of X-rays and neutrons.

The intrinsically disordered MBP was found to be very flexible on the nanosecond time scale. Normal mode analysis of the structural ensemble indicates that the observed motions are essentially governed by low frequency collective stretching and bending motions, where the termini were found to be especially flexible. The large-scale conformational motions increase the accessible protein surface, which facilitates the interaction with binding partners. In an alternative approach we investigated, if models from polymer theory are suitable for the interpretation of the observed motions. The motions of MBP were found to be significantly slower than compared to the ideal behavior of Gaussian polymer chains in solution.





Left figure: Structural model of MBP with calculated first non-trivial normal mode. The displacement vectors indicate that the end regions are rather flexible, while the structured core remains rigid. Right figure: Neutron spin-echo spectra of MBP measured on J-NSE. The solid lines are fits to the data using the structural model shown on the left.



Molecular Scale Dynamics of Large Ring Polymers

S. Gooßen, A. R. Brás, M. Krutyeva, W. Pyckhout-Hintzen, A. Wischnewski, D. Richter,
SoftComp partner: FZJ-Richter
PRL 113 (2014) 168302



The fundamental concepts that successfully describe the dynamics of polymers like the tube model including contour length fluctuations and constraint release processes or the hierarchical relaxation in branched systems – to name the most important ones – are heavily determined by the influence of chain ends. Therefore, from a topological point of view among all polymer architectures, polymer rings are inimitable since rings are closed structures without ends. Recent progress on the synthesis of highly pure ring polymers in the multi-gram scale finally enabled the investigation of ring polymers in the melt by neutron spin echo (NSE) spectroscopy. The dynamics of polyethylene oxide (PEO) rings with molecular weights up to ten times the entanglement mass of the linear counterpart exhibited a completely different behavior as compared to linear and branched systems. The dynamics is characterized by a fast Rouse relaxation of loops and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.





Left figure: NSE data for a 20 kg/mol PEO ring. Dashed black lines represent a fit to the data only considering internal loop dynamics (Rouse relaxation). Deviations to the data can solely be resolved by taking into account slower dynamics (loop migration) as can be seen by the colored fit lines. Right figure: Schematic mean square displacement displaying the time dependence of these dynamics processes and the sum of them (global loop motion).



Unravelling the multilayer growth of the fullerene C60 in real-time: growth phenomena at the boundary between atomic, molecular and colloidal systems

S. Bommel, N. Kleppmann, C. Weber, H. Spranger, P. Schäfer, J. Novak, S. V. Roth, F. Schreiber, S. H. L. Klapp, S. Kowarik
SoftComp partner: Univ. Tübingen
to appear in Nature Communications



Self-assembly of molecular building blocks into functional nanomaterials is increasingly used in devices, but the non-equilibrium processes of molecular film growth on a nanoscopic level are not yet fully understood and hard to predict. In this study real-time x-ray scattering experiments performed at the MiNaXS beamline at PETRA III (DESY) combined with kinetic Monte-Carlo (KMC) simulations shed light on growth phenomena of fullerene C60, that is for a building block size ranging between the atomic scale and colloidal scales. The main result of our study is the quantification of the energy landscape for the basic growth processes of diffusion within a layer, diffusion across a step edge and binding to islands of fullerene C60 (see Figure 1a). This growth study bridges the gap between the growth of small atomic and large colloidal systems, by showing that the molecular step-edge crossing process is similar to atoms, but unlike colloidal growth. In contrast, the lateral surface diffusion lengths and diffusion times of a C60 molecule - see Figure 1b for an exemplary trajectory - resemble colloidal epitaxy. In conclusion, our work enables quantitative predictions of the growth mode and interface morphology of C60 and thereby helps in a systematic understanding of growth of molecular and soft materials.



a) Surface processes during C60 growth and b) simulated C60 trajectory in the 4th monolayer (ML) showing long diffusion times and the effect of the step edge barrier preventing jumps into the lower layer.


Monodisperse Gold Nanotriangles: Size Control, Large-Scale Self-Assembly, and Performance in Surface-Enhanced Raman Scattering

L. Scarabelli, M. Coronado-Puchau, J.J. Giner-Casares, J. Langer, L.M. Liz-Marzán
SoftComp partner: CIC BiomaGUNE
ACS Nano 8 (2014) 5833–584



Au nanotriangles display interesting nanoplasmonic features with potential application in various fields. However, such applications have been hindered by the lack of efficient synthetic methods yielding sufficient size and shape monodispersity, as well as by insufficient morphological stability. We present here a synthesis and purification protocol that efficiently addresses these issues. The size of the nanotriangles can be tuned within a wide range by simply changing the experimental parameters. The obtained monodispersity leads to extended self-assembly, not only on electron microscopy grids but also at the air–liquid interface, allowing transfer onto centimeter-size substrates. These extended monolayers show promising performance as surface-enhanced Raman scattering substrates, as demonstrated for thiophenol detection.





Left: TEM images of Au NTs. Right: SERS performance of Au NTs in solution. SERS spectra of benzenethiol (BT)excited at 785 nm.


Nickel Nanoparticle-Doped Paper as a Bioactive Scaffold for Targeted and Robust Immobilization of Functional Proteins

G. Bodelón, S. Mourdikoudis, L. Yate, I. Pastoriza-Santos, J. Pérez-Juste, L.M. Liz-Marzán
SoftComp partner: CIC BiomaGUNE
ACS Nano 8 (2014) 6221–6231



Cellulose-based materials are widely used in analytical chemistry as platforms for chromatographic and immunodiagnostic techniques. Due to its countless advantages (e.g., mechanical properties, three-dimensional structure, large surface to volume area, biocompatibility and biodegradability, and high industrial availability), paper has been rediscovered as a valuable substrate for sensors. Polymeric materials such as cellulosic paper present high protein capture ability, resulting in a large increase of detection signal and improved assay sensitivity. However, cellulose is a rather nonreactive material for direct chemical coupling. Aiming at developing an efficient method for controlled conjugation of cellulose-based materials with proteins, we devised and fabricated a hybrid scaffold based on the adsorption and in situ self-assembly of surface-oxidized Ni nanoparticles on filter paper, which serve as “docking sites” for the selective immobilization of proteins containing polyhistidine tags (His-tag). We demonstrate that the interaction between the nickel substrate and the His-tagged protein G is remarkably resilient toward chemicals at concentrations that quickly disrupt standard Ni-NTA and Ni-IDA complexes, so that this system can be used for applications in which a robust attachment is desired. The bioconjugation with His-tagged protein G allowed the binding of anti-Salmonella antibodies that mediated the immuno-capture of live and motile Salmonella bacteria. The versatility and biocompatibility of the nickel substrate were further demonstrated by enzymatic reactions.





Schematic representation of the bioactive scaffold preparation composed of (I) nickel NPs on filter paper, (II) targeted immobilization of the polyhistidine-tagged protein G (pG-6xHis), and (III) protein G-mediated capture of antibodies. Protein G is represented by the protein G B1 domain (PDB: 1GB1, orange) bearing a 6xHis at its C-terminus (red). The antibody is an IgG2a immunoglobulin (PDB: 1IGT, green).


Pen-on-Paper Approach Toward the Design of Universal Surface Enhanced Raman Scattering Substrates

L. Polavarapu, A. La Porta, S.M. Novikov, M. Coronado-Puchau, L.M. Liz-Marzán
SoftComp partner: CIC BiomaGUNE
Small 10, (20149 3065 - 3071



The translation of a technology from the laboratory into the real world should meet the demand of economic viability and operational simplicity. Inspired by recent advances in conductive ink pens for electronic devices on paper, we present a “pen-on-paper” approach for making surface enhanced Raman scattering (SERS) substrates. Through this approach, no professional training is required to create SERS arrays on paper using an ordinary fountain pen filled with plasmonic inks comprising metal nanoparticles of arbitrary shape and size. We demonstrate the use of plasmonic inks made of gold nanospheres, silver nanospheres and gold nanorods, to write SERS arrays that can be used with various excitation wavelengths. The strong SERS activity of these features allowed us to reach detection limits down to 10 attomoles of dye molecules in a sample volume of 10 μL, depending on the excitation wavelength, dye molecule and type of nanoparticles. Furthermore, such simple substrates were applied to pesticide detection down to 20 ppb. This universal approach offers portable, cost effective fabrication of efficient SERS substrates at the point of care. This approach should bring SERS closer to the real world through ink cartridges to be fixed to a pen to create plasmonic sensors at will.





Photograph of a fountain pen loaded with a plasmonic nanoparticle ink and writing SERS substrates on paper.


Microcellular foams made from gliadin

S. Quester, M. Dahesh, and R. Strey
SoftComp partner: Univ. Cologne
Colloid Polym Sci (2014) 292:2385–2389



In Cologne we have generated closed-cell microcellular foams with thin membranes of only a few nanometers from gliadin, an abundantly available wheat storage protein, provided by Montpellier. A genuine SoftComp collaboration. The extraction procedure of gliadin from wheat gluten, which involves only the natural solvents water and ethanol, respectively, results in a fine dispersion of mostly spherical, submicron gliadin particles assumed to be composed of millions of protein molecules. A dense packing of these particles was hydrated and subjected to an atmosphere of carbon dioxide or nitrogen in a high-pressure cell at 250 bar. Subsequent heating to temperatures close to but still below 100 °C followed by a sudden expansion and simultaneous cooling resulted in closed-cell microcellular foam. The spherical gliadin templates along with the resulting foam have been analyzed by SEM pictures. The size distribution of the primary particles show diameters peaked around 0.5 μm, the final foam cell size peaks around 1.2 μm at a porosity of 80%. These are clearly the smallest foams ever obtained from gliadin. Interestingly, the cell walls of these microcellular foams are remarkably thin with wall thicknesses in the lower nanometer range, thus nourishing the hope to be able to reach gliadin nanofoam. The procedure is simple and low cost, possibly lending itself to a technical realization.





SEM-picture of the fracture face of the foam resulting from foaming procedure of hydrated gliadin (wH2O = 33 wt%) which was soaked with fluid CO2 at room temperature, heated to 95 °C while the pressure was adjusted to 250 bar for 30 minutes followed by a sudden expansion while slowly cooling to 25 °C (scale bar is 100 μm, respectively 1 μm).


Highly cooperative stress relaxation in two-dimensional soft colloidal crystals

B. van der Meer, W. Qi, R. Fokkink, J. van der Gucht, M. Dijkstra and J. Sprakel
SoftComp partner: Univ. Wageningen
PNAS, 111 (2014) 43



The creation, annihilation, and diffusion of defects in crystal lattices play an important role during crystal melting and deformation. Although it is well understood how defects form and react when crystals are subjected to external stresses, it remains unclear how crystals cope with internal stresses. A team of researchers from both Wageningen and Utrecht University, lead by dr. Joris Sprakel of Wageningen University, shed new light onto this question using colloidal crystals as an experimental model for crystalline solids. They created a highly localised mechanical perturbation in a two-dimensional colloidal crystal using optical tweezers, and studied the response of the solid in detail with optical microscopy. Their study revealed something surprising: even though the perturbation is localised to a single lattice site, the crystal responds by exhibiting a collective dance of colloidal particles, which can span many lattices spacings. These collective reorganisations induced by a point perturbation manifest as string- or loop-like swapping of particles, as if the colloids partake in a game of musical chairs. Even more surprising is their finding that, when the solid gets sufficiently soft, these same heterogeneous dynamics can emerge in a solid in which local excitation is caused by thermal fluctuations alone. A single, sufficiently large, thermal fluctuation, can cause a chain reaction of irreversible displacement in which several hundreds of particles are displaced from their original sites. These collective actions provide a new mechanism with which internal stresses can relaxed in crystalline solids, and may provide a clue into the origins of plasticity in crystals approaching their melting transition.




Color-coded reconstruction of an experiment on a two-dimensional colloidal crystal of charged particles (top) and corresponding Voronoi tessellation showing defects in red and blue. The red particle is driven by an optical tweezer to perform a sinusoidal oscillation, creating a vacancy-interstitial pair which migrate apart thereby nucleating a string-like collective reorganisation of the crystal (yellow particles). This reorganisation persists until either end of the the string meets another vacancy or interstitial and annihilates.


Drug Delivery by Micro- and Nanoparticles in Blood Flow

K. Müller, D. A. Fedosov, and G. Gompper
SoftComp partner: FZJ-Gompper
Sci. Rep. 4 (2014) 4871, DOI: 10.1038/srep04871



A promising strategy for early detection and efficient treatment of diseases, such as cancer, is the use of targeted carriers. After injection into the blood, ideal carriers would migrate to the wall, in a process called “margination”, in order to be able to scan the blood vessel for indications of the disease. After recognizing affected tissue, the carriers would adhere to the wall, and imaging agents and/or drugs would be released and transported into the tissue.

We investigate the carrier margination in blood flow depending on particle size and shape, and the flow parameters like flow rate and hematocrit (volume fraction of red blood cells). We employ a mesoscopic particle-based hydrodynamics simulation technique, combined with a triangulated-network model for red blood cells (RBCs) and carriers. Due to a lift force — the hydrodynamic interaction of particles with the vessel wall —, the deformable RBCs migrate away from the wall and a RBC-free layer close to the wall develops, into which the less deformable carriers can marginate. Margination is found to improve with decreasing channel size, increasing hematocrit, and with increasing shear rate. Furthermore, micron-sized particles are preferable over nano-sized particles, and ellipsoids are more efficient than spheres. These predictions are supported by recent experiments on particle margination and adhesion.




Snapshots of carrier distribution in micro-vessels for two different hematocrits (20% [top] and 40% [bottom]).
The spherical carriers are colored according to their radial position given in micrometers. The RBCs are
colored in red.
Last modified: 07/04/2014