Numerical modelling of non-ionic microgels: an overview

Microgels are complex macromolecules. These colloid-sized polymer networks possess internal degrees of freedom and, depending on the polymer(s) they are made of, can acquire a responsiveness to variations of the environment (temperature, pH, salt concentration, etc.). Besides being valuable for many practical applications, microgels are also extremely important to tackle fundamental physics problems. As a result, these last years have seen a rapid development of protocols for the synthesis of microgels, and more and more research has been devoted to the investigation of their bulk properties. However, from a numerical standpoint the picture is more fragmented, as the inherently multi-scale nature of microgels, whose bulk behaviour crucially depends on the microscopic details, cannot be handled at a single level of coarse-graining. Here we present an overview of the methods and models that have been proposed to describe non-ionic microgels at different length-scales, from the atomistic to the single-particle level. We especially focus on monomer-resolved models, as these have the right level of details to capture the most important properties of microgels, responsiveness and softness. We suggest that these microscopic descriptions, if realistic enough, can be employed as starting points to develop the more coarse-grained representations required to investigate the behaviour of bulk suspensions

Crystal-to-crystal transition of ultrasoft colloids under shear

Ultrasoft colloids typically do not spontaneously crystallize, but rather vitrify, at high concentrations. Combining in-situ rheo-SANS experiments and numerical simulations we show that shear facilitates crystallization of colloidal star polymers in the vicinity of their glass transition. With increasing shear rate well beyond rheological yielding, a transition is found from an initial bcc-dominated structure to an fcc-dominated one. This crystal-to-crystal transition is not accompanied by intermediate melting but occurs via a sudden reorganization of the crystal structure. Our results provide a new avenue to tailor colloidal crystallization and crystal-to-crystal transition at molecular level by coupling softness and shear

Tuning the rheological behavior of colloidal gels through competing interactions

We study colloidal gels formed by competing electrostatic repulsion and short-range attraction by means of extensive numerical simulations under external shear. We show that, upon varying the repulsion strength, the gel structure and its viscoelastic properties can be largely tuned. In particular, the gel fractal dimension can be either increased or decreased with respect to mechanical equilibrium conditions. Unexpectedly, gels with stronger repulsion, despite being mechanically stiffer, are found to be less viscous with respect to purely attractive ones. We provide a microscopic explanation of these findings in terms of the influence of an underlying phase separation. Our results allow for the design of colloidal gels with desired structure and viscoelastic response by means of additional electrostatic interactions, easily controllable in experiments

Aging effects manifested in the potential energy landscape of a model glass former

We present molecular dynamics simulations of a model glass-forming liquid (the binary Kob-Anderson Lennard-Jones model) and consider the distributions of inherent energies and metabasins during aging. In addition to the typical protocol of performing a temperature jump from a high temperature to a low destination temperature, we consider the temporal evolution of the distributions after an 'up-jump', i.e. from a low to a high temperature. In this case the distribution of megabasin energies exhibits a transient two-peak structure. Our results can qualitatively be rationalized in terms of a trap model with a Gaussian distribution of trap energies. The analysis is performed for different system sizes. A detailed comparison with the trap model is possible only for a small system because of major averging effects for larger systems.Comment: 16 pages, 14 figure

Charge affinity and solvent effects in numerical simulations of ionic microgels

Ionic microgel particles are intriguing systems in which the properties of thermo-responsive polymeric colloids are enriched by the presence of charged groups. In order to rationalize their properties and predict the behaviour of microgel suspensions, it is necessary to develop a coarse-graining strategy that starts from the accurate modelling of single particles. Here, we provide a numerical advancement of a recently-introduced model for charged co-polymerized microgels by improving the treatment of ionic groups in the polymer network. We investigate the thermoresponsive properties of the particles, in particular their swelling behaviour and structure, finding that, when charged groups are considered to be hydrophilic at all temperatures, highly charged microgels do not achieve a fully collapsed state, in favorable comparison to experiments. In addition, we explicitly include the solvent in the description and put forward a mapping between the solvophobic potential in the absence of the solvent and the monomer-solvent interactions in its presence, which is found to work very accurately for any charge fraction of the microgel. Our work paves the way for comparing single-particle properties and swelling behaviour of ionic microgels to experiments and to tackle the study of these charged soft particles at a liquid-liquid interface.Comment: 13 pages, 9 figure

Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction

Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing programme and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. The role of RIF1 in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing programme and nuclear architecture

Volume-energy correlations in the slow degrees of freedom of computer-simulated phospholipid membranes

Constant-pressure molecular-dynamics simulations of phospholipid membranes in the fluid phase reveal strong correlations between equilibrium fluctuations of volume and energy on the nanosecond time-scale. The existence of strong volume-energy correlations was previously deduced indirectly by Heimburg from experiments focusing on the phase transition between the fluid and the ordered gel phases. The correlations, which are reported here for three different membranes (DMPC, DMPS-Na, and DMPSH), have volume-energy correlation coefficients ranging from 0.81 to 0.89. The DMPC membrane was studied at two temperatures showing that the correlation coefficient increases as the phase transition is approached

Isomorphs in model molecular liquids

Isomorphs are curves in the phase diagram along which a number of static and dynamic quantities are invariant in reduced units. A liquid has good isomorphs if and only if it is strongly correlating, i.e., the equilibrium virial/potential energy fluctuations are more than 90% correlated in the NVT ensemble. This paper generalizes isomorphs to liquids composed of rigid molecules and study the isomorphs of two systems of small rigid molecules, the asymmetric dumbbell model and the Lewis-Wahnstrom OTP model. In particular, for both systems we find that the isochoric heat capacity, the excess entropy, the reduced molecular center-of-mass self part of the intermediate scattering function, the reduced molecular center-of-mass radial distribution function to a good approximation are invariant along an isomorph. In agreement with theory, we also find that an instantaneous change of temperature and density from an equilibrated state point to another isomorphic state point leads to no relaxation. The isomorphs of the Lewis-Wahnstrom OTP model were found to be more approximative than those of the asymmetric dumbbell model, which is consistent with the OTP model being less strongly correlating. For both models we find "master isomorphs", i.e., isomorphs have identical shape in the virial/potential energy phase diagram.Comment: 20 page

Pressure-energy correlations in liquids. II. Analysis and consequences

We present an analysis and discuss consequences of the strong correlations of the configurational parts of pressure and energy in their equilibrium fluctuations at fixed volume reported for simulations of several liquids in the companion paper [arXiv:0807.0550]. The analysis concentrates specifically on the single-component Lennard-Jones system. We demonstrate that the potential may be replaced, at fixed volume, by an effective power-law, but not because only short distance encounters dominate the fluctuations. Indeed, contributions to the fluctuations are associated with the whole first peak of the RDF, as we demonstrate by an analysis of the spatially resolved covariance matrix. The reason the effective power-law works so well depends on going beyond single-pair effects and on the constraint of fixed volume. In particular, a better approximation to the potential includes a linear term, which contributes to the mean values of potential energy and virial, but not to their fluctuations. We also study the T=0 limit of the crystalline phase, where the correlation coefficient becomes very close, but not equal, to unity. We then consider four consequences of strong pressure-energy correlations: (1) analyzing experimental data for supercritical Ar we find 96% correlation; (2) we discuss the significance acquired by the correlations for viscous van der Waals liquids approaching the glass transition: For strongly correlating viscous liquids knowledge of just one of the eight frequency-dependent thermoviscoelastic response functions basically implies knowledge of them all; (3) we re-interpret aging simulations of ortho-terphenyl carried out by Mossa {\it et al.} in 2002, showing their conclusions follow from the strongly correlating property; and (4) we discuss correlations in model biomembranes.Comment: Some changes corresponding to those made in the proof of the accepted articl