Procedure to construct a multi-scale coarse-grained model of DNA-coated colloids from experimental data

We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying single-stranded DNA strands of length comparable to the colloids' size. We show that in this regime, the common theoretical approach of assuming pairwise additivity of the colloidal pair interactions leads to quantitatively and sometimes even qualitatively wrong predictions of the phase behaviour of DNA-grafted colloids. Comparing to experimental data, we find that our coarse-grained model correctly predicts the equilibrium structure and melting temperature of the formed solids. Due to limited experimental information on the persistence length of single-stranded DNA, some quantitative discrepancies are found in the prediction of spatial quantities. With the availability of better experimental data, the present approach provides a path for the rational design of DNA-functionalised building blocks that can self-assemble in complex, three-dimensional structures.Comment: 17 pages, 10 figures; to be published in Soft Matte

Blood Flow in silico: From Single Cells to Blood Rheology

This paper was presented at the 4th Micro and Nano Flows Conference (MNF2014), which was held at University College, London, UK. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute, ASME Press, LCN London Centre for Nanotechnology, UCL University College London, UCL Engineering, the International NanoScience Community, www.nanopaprika.eu.Mesoscale hydrodynamics simulations of red blood cells under flow have provided much new insight into their shapes and dynamics in microchannel flow. The presented results range from the behavior of single cells in confinement and the shape changes in sedimentation, to the clustering and arrangement of many cells in microchannels and the viscosity of red blood cell suspensions under shear flow. The interaction of red blood cells with other particles and cells, such as white blood cells, platelets, and drug carriers, shows an essential role of red blood cells in the margination of other blood components

Lane-formation vs. cluster-formation in two dimensional square-shoulder systems: A genetic algorithm approach

Introducing genetic algorithms as a reliable and efficient tool to find ordered equilibrium structures, we predict minimum energy configurations of the square shoulder system for different values of corona width $\lambda$. Varying systematically the pressure for different values of $\lambda$ we obtain complete sequences of minimum energy configurations which provide a deeper understanding of the system's strategies to arrange particles in an energetically optimized fashion, leading to the competing self-assembly scenarios of cluster-formation vs. lane-formation.Comment: 5 pages, 6 figure

Quantitative prediction of the phase diagram of DNA-functionalized nano-colloids

We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase behavior of DNA-functionalized nano-colloids without assuming pairwise additivity of the inter-colloidal interactions. Our simulations show that for nano-colloids, the assumption of pairwise additivity leads to substantial errors in the estimate of the free energy of the crystal phase. We compare our results with available experimental data and find that the simulations predict the correct structure of the solid phase and yield a very good estimate of the melting temperature. Current experimental estimates for the contour length and persistence length of single-stranded DNA sequences are subject to relatively large uncertainties. Using the best available estimates, we obtain predictions for the crystal lattice constants that are off by a few percent: this indicates that more accurate experimental data on ssDNA are needed to exploit the full power of our coarse-grained approach.Comment: 4 pages, 2 figures; accepted for publication in Phys. Rev. Let

Self-assembly of binary nanoparticle dispersions: from square arrays and stripe phases to colloidal corrals

The generation of nanoscale square and stripe patterns is of major technological importance since they are compatible with industry-standard electronic circuitry. Recently, a blend of diblock copolymer interacting via hydrogen-bonding was shown to self-assemble in square arrays. Motivated by those experiments we study, using Monte Carlo simulations, the pattern formation in a two-dimensional binary mixture of colloidal particles interacting via isotropic core-corona potentials. We find a rich variety of patterns that can be grouped mainly in aggregates that self-assemble in regular square lattices or in alternate strips. Other morphologies observed include colloidal corrals that are potentially useful as surface templating agents. This work shows the unexpected versatility of this simple model to produce a variety of patterns with high technological potential.Comment: 13 pages, 5 figures, submitte

Multiple glass transitions in star polymer mixtures: Insights from theory and simulations

The glass transition in binary mixtures of star polymers is studied by mode coupling theory and extensive molecular dynamics computer simulations. In particular, we have explored vitrification in the parameter space of size asymmetry $\delta$ and concentration $\rho_2$ of the small star polymers at fixed concentration of the large ones. Depending on the choice of parameters, three different glassy states are identified: a single glass of big polymers at low $\delta$ and low $\rho_2$, a double glass at high $\delta$ and low $\rho_2$, and a novel double glass at high $\rho_2$ and high $\delta$ which is characterized by a strong localization of the small particles. At low $\delta$ and high $\rho_2$ there is a competition between vitrification and phase separation. Centered in the $(\delta, \rho_2)$-plane, a liquid lake shows up revealing reentrant glass formation. We compare the behavior of the dynamical density correlators with the predictions of the theory and find remarkable agreement between the two.Comment: 15 figures, to be published in Macromolecule

Partial clustering prevents global crystallization in a binary 2D colloidal glass former

A mixture of two types of super-paramagnetic colloidal particles with long range dipolar interaction is confined by gravity to a flat interface of a hanging water droplet. The particles are observed by video microscopy and the dipolar interaction strength is controlled via an external magnetic field. The system is a model system to study the glass transition in 2D, and it exhibits partial clustering of the small particles. This clustering is strongly dependent on the relative concentration $\xi$ of big and small particles. However, changing the interaction strength $\Gamma$ reveals that the clustering does not depend on the interaction strength. The partial clustering scenario is quantified using Minkowski functionals and partial structure factors. Evidence that partial clustering prevents global crystallization is discussed