We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)]10.1063/1.3552946 originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software.

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse-graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

Microgels are colloidal-scale particles individually made of cross-linked polymer networks that can swell and deswell in response to external stimuli, such as changes to temperature or pH. Despite a large amount of experimental activities on microgels, a proper theoretical description based on individual particle properties is still missing due to the complexity of the particles. To go one step further, here we propose a novel methodology to assemble realistic microgel particles in silico. We exploit the self-assembly of a binary mixture composed of tetravalent (cross-linkers) and bivalent (monomer beads) patchy particles under spherical confinement in order to produce fully bonded networks. The resulting structure is then used to generate the initial microgel configuration, which is subsequently simulated with a bead–spring model complemented by a temperature-induced hydrophobic attraction. To validate our assembly protocol, we focus on a small microgel test case and show that we can reproduce the experimental swelling curve by appropriately tuning the confining sphere radius, something that would not be possible with less sophisticated assembly methodologies, e.g., in the case of networks generated from an underlying crystal structure. We further investigate the structure (in reciprocal and real space) and the swelling curves of microgels as a function of temperature, finding that our results are well described by the widely used fuzzy sphere model. This is a first step toward a realistic modeling of microgel particles, which will pave the way for a careful assessment of their elastic properties and effective interactions.

Thermoresponsive microgels find widespread use as colloidal model systems, because their temperature-dependent size allows facile tuning of their volume fraction in situ. However, an interaction potential unifying their behavior across the entire phase diagram is sorely lacking. Here we investigate microgel suspensions in the fluid regime at different volume fractions and temperatures, and in the presence of another population of small microgels, combining confocal microscopy experiments and numerical simulations. We find that effective interactions between microgels are clearly temperature dependent. In addition, microgel mixtures possess an enhanced stability compared to hard colloid mixtures - a property not predicted by a simple Hertzian model. Based on numerical calculations we propose a multi-Hertzian model, which reproduces the experimental behavior for all studied conditions. Our findings highlight that effective interactions between microgels are much more complex than usually assumed, displaying a crucial dependence on temperature and on the internal core-corona architecture of the particles.

Soft particles display highly versatile properties with respect to hard colloids, even more so at fluid-fluid interfaces. In particular, microgels, consisting of a crosslinked polymer network, are able to deform and flatten upon adsorption at the interface due to the balance between surface tension and internal elasticity. Despite the existence of experimental results, a detailed theoretical understanding of this phenomenon is still lacking due to the absence of appropriate microscopic models. In this work, we propose an advanced modelling of microgels at a flat water-oil interface. The model builds on a realistic description of the internal polymeric architecture and single-particle properties of the network and is able to reproduce the experimentally observed shape of the microgel at the interface. Complementing molecular dynamics simulations with in-situ cryo-electron microscopy experiments and Atomic Force Microscopy imaging after Langmuir-Blodgett deposition, we compare the morphology of the microgels for different values of the crosslinking ratios. Our model allows for a systematic microscopic investigation of soft particles at fluid interfaces, which is essential to develop predictive power for the use of microgels in a broad range of applications, including the stabilization of smart emulsions and the versatile patterning of surfaces.