We construct a phenomenological Landau-de Gennes theory for hard colloidal rods by performing an order parameter expansion of the chemical-potential dependent grand potential. By fitting the coefficients to known results of Onsager theory, we are not only able to describe the isotropic-nematic phase transition as function of density, including the well-known density jump, but also the isotropic-nematic planar interface. The resulting theory is applied in calculations of the isotropic core size in a radial hedgehog defect, the density dependence of linear defects of hard rods in square confinement, and the formation of a nematic droplet in an isotropic background.

We experimentally and theoretically studied the self-assembly kinetics of linear virus-like particles (VLPs) consisting of double-stranded DNA and virus-like coat proteins. The polynucleotide acts as a self-assembly template for our proteins with engineered attractive protein-DNA and protein-protein interactions that imitate the physicochemical functionality of virus coat proteins. Inspired by our experimental observations, where we found that VLPs grow from one point onward, our model presumes a nucleation step before subsequent sequential cooperative binding from one of the ends of the polynucleotide. By numerically solving the pertinent reaction rate equations, we investigated the assembly dynamics as a function of the ratio between the number of available binding sites and proteins in the solution, i.e., the stoichiometry of the molecular building blocks. Depending on the stoichiometry, we found monotonic or nonmonotonic assembly kinetics. If the proteins in the solution vastly outnumber the binding sites on all of the polynucleotides, then the assembly kinetics were strictly monotonic and the assembled fraction increases steadily with time. However, if the concentration of proteins and binding sites is equal, then we found an overshoot in the concentration of fully covered polynucleotides. We compared our model with length distributions of two types of VLPs measured by atomic force microscopy imaging and found satisfactory agreement, suggesting that a relatively simple model may be useful in describing the assembly kinetics of chemically complex systems. We furthermore re-evaluated data by Hernandez-Garcia et al. (Nat. Nanotechnol. 2014, 9, 698-702) to include the effect of a finite protein concentration previously ignored. By fitting our model to the experimental data, we were able to pinpoint the sum of the protein-protein and protein-DNA interaction free energies, the binding rate of a protein to the DNA, and the nucleation free energy associated with switching a protein from the solution to the bound conformation. The values that we found for the VLPs are comparable to virus capsid binding energies of linear and spherical viruses.

Soft living tissues like cartilage can be considered as biphasic materials comprised of a fibrous complex biopolymer network and a viscous background liquid. Here, we show by a combination of experiment and theoretical analysis that both the hydraulic permeability and the elastic properties of (bio)polymer networks can be determined with simple ramp compression experiments in a commercial rheometer. In our approximate closed-form solution of the poroelastic equations of motion, we find the normal force response during compression as a combination of network stress and fluid pressure. Choosing fibrin as a biopolymer model system with controllable pore size, measurements of the full time-dependent normal force during compression are found to be in excellent agreement with the theoretical calculations. The inferred elastic response of large-pore (µm) fibrin networks depends on the strain rate, suggesting a strong interplay between network elasticity and fluid flow. Phenomenologically extending the calculated normal force into the regime of nonlinear elasticity, we find strain-stiffening of small-pore (sub-µm) fibrin networks to occur at an onset average tangential stress at the gel-plate interface that depends on the polymer concentration in a power-law fashion. The inferred permeability of small-pore fibrin networks scales approximately inverse squared with the fibrin concentration, implying with a microscopic cubic lattice model that the thickness of the fibrin fibers decreases with protein concentration. Our theoretical model provides a new method to obtain the hydraulic permeability and the elastic properties of biopolymer networks and hydrogels with simple compression experiments, and paves the way to study the relation between fluid flow and elasticity in biopolymer networks during dynamical compression.Soft biopolymer networks have essential functions in living cells 1,2 , the extracellular matrix 3,4 and the process of blood coagulation 5,6 . Their mechanical properties are determined by the network's hydraulic permeability and (visco)elastic properties.The permeability of biopolymer networks determines mass transport in soft tissues 7-9 , the dynamic behaviour of cells 10,11 * These authors contributed equally to this work.

Please check the document version of this publication:• A submitted manuscript is the author's version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website.• The final author version and the galley proof are versions of the publication after peer review.• The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publicationCitation for published version (APA): Sleeboom, J. J. F., Voudouris, P., Punter, M. T. J. J. M., Aangenendt, F. J., Florea, D., van der Schoot, P. P. A. M., & Wyss, H. M. (2017). Compression and reswelling of microgel particles after an osmotic shock. Physical Review Letters, 119(9), [098001].

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We show that forced syneresis in model low fat mayonnaise, a colloid polymer mixture, can be described as a gravity-driven porous flow through the densely packed emulsion, explainable with a model based on Darcy's law.

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