Cristiano De Michele

Self-Assembly of Bifunctional Patchy Particles with Anisotropic Shape into Polymers Chains: Theory, Simulations, and Experiments

Concentrated solutions of short blunt-ended DNA duplexes, as short as 6 base pairs, are known to order into the nematic liquid crystal phases. This self-assembly is due to the stacking interactions between duplex terminals that promotes their aggregation into polydisperse chains with a significant persistence length. Experiments show that liquid crystal phases form above a critical volume fraction depending on the duplex length. We introduce and investigate via numerical simulations, a coarse-grained model of DNA double-helical duplexes. Each duplex is represented as an hard quasi-cylinder whose bases are decorated with two identical reactive sites. The stacking interaction between terminal sites is modeled via a short-range square-well potential. We compare the numerical results with predictions based on a free energy functional and find satisfactory quantitative matching of the isotropic–nematic phase boundary and of the system structure. Comparison of numerical and theoretical results with experimental...

Anomalous dynamics of intruders in a crowded environment of mobile obstacles

Many natural and industrial processes rely on constrained transport, such as proteins moving through cells, particles confined in nanocomposite materials or gels, individuals in highly dense collectives and vehicular traffic conditions. These are examples of motion through crowded environments, in which the host matrix may retain some glass-like dynamics. Here we investigate constrained transport in a colloidal model system, in which dilute small spheres move in a slowly rearranging, glassy matrix of large spheres. Using confocal differential dynamic microscopy and simulations, here we discover a critical size asymmetry, at which anomalous collective transport of the small particles appears, manifested as a logarithmic decay of the density autocorrelation functions. We demonstrate that the matrix mobility is central for the observed anomalous behaviour. These results, crucially depending on size-induced dynamic asymmetry, are of relevance for a wide range of phenomena ranging from glassy systems to cell biology.

Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semiflexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on temperature and duplex length, such chains order into liquid crystal phases. Here, we investigate the self-assembly of such double-helical duplexes with a combined numerical and theoretical approach. We simulate the bulk system employing the coarse-grained DNA model recently proposed by Ouldridge et al. [J. Chem. Phys., 2011, 134, 08501]. Then we evaluate the input quantities for the theoretical framework directly from the DNA model. The resulting parameterfree theoretical predictions provide an accurate description of the simulation results in the isotropic phase and theoretical values for the isotropic‐nematic phase boundaries which are in line with experimental findings. In addition, the developed theoretical framework makes it possible to provide a route to estimate the stacking free energy.

Dynamics of uniaxial hard ellipsoids.

We study the dynamics of monodisperse hard ellipsoids via a new event-driven molecular dynamics algorithm as a function of volume fraction phi and aspect ratio X0. We evaluate the translational D(trans) and the rotational D(rot) diffusion coefficients and the associated isodiffusivity lines in the phi-X0 plane. We observe a decoupling of the translational and rotational dynamics which generates an almost perpendicular crossing of the D(trans) and D(rot) isodiffusivity lines. While the self-intermediate scattering function exhibits stretched relaxation, i.e., glassy dynamics, only for large phi and X(0) approximately 1, the second order orientational correlator C2(t) shows stretching only for large and small X0 values. We discuss these findings in the context of a possible prenematic order driven glass transition.

Routes to colloidal gel formation

We discuss features of simple inter-particle potentials which are able to generate low-packing fraction arrested states, i.e. gels, in the absence of a macroscopic phase separation phenomenon. We suggest that the ratio between surface and bulk free energy is crucial in favoring ideal gel states. Two possible models for gels, one based on the competition of short range attraction and long range repulsions and the other on local constraints disfavoring packed local structures are discussed.

Self-assembly of hard helices: a rich and unconventional polymorphism

Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit, from natural polynucleotides and polypeptides to synthetic helical polymers, and from bacterial flagella to colloidal helices. Here we present an extensive investigation of the phase diagram of hard helices using a variety of methods. Isobaric Monte Carlo numerical simulations are used to trace the phase diagram; on going from the low-density isotropic to the high-density compact phases a rich polymorphism is observed, exhibiting a special chiral screw-like nematic phase and a number of chiral and/or polar smectic phases. We present full characterization of the latter, showing that they have unconventional features, ascribable to the helical shape of the constituent particles. Equal area construction is used to locate the isotropic-to-nematic phase transition, and the results are compared with those stemming from an Onsager-like theory. Density functional theory is also used to study the nematic-to-screw-nematic phase transition; within the simplifying assumption of perfectly parallel helices, we compare different levels of approximation, that is second- and third-virial expansions and a Parsons-Lee correction.

The influence of bond rigidity and cluster diffusion on the self-diffusion of hard spheres with square well interaction.

Hard spheres interacting through a square well potential were simulated by using two different methods: Brownian cluster dynamics (BCD) and event driven Brownian dynamics (EDBD). The structure of the equilibrium states obtained by both methods was compared and found to be almost identical. Self-diffusion coefficients (D) were determined as a function of the interaction strength. The same values were found by using BCD or EDBD. Contrary to EDBD, BCD allows one to study the effect of bond rigidity and hydrodynamic interaction within the clusters. When the bonds are flexible, the effect of attraction on D is relatively weak compared to systems with rigid bonds. D increases first with increasing attraction strength, and then decreases for stronger interaction. Introducing intracluster hydrodynamic interaction weakly increases D for a given interaction strength. Introducing bond rigidity causes a strong decrease in D which no longer shows a maximum as function of the attraction strength.

Monte Carlo and event-driven dynamics of Brownian particles with orientational degrees of freedom

Recently, a simple scaling argument was introduced that allows us to map, with some precautions, Brownian and Monte Carlo dynamics for spherical particles. Here, we extend the scaling to study systems that have orientational degrees of freedom and carefully asses its validity over a wide region of temperature and density. Our work allows us to devise a Brownian Monte Carlo algorithm that produces, to a good approximation, physically meaningful trajectories with a minimum programming effort, although at the expense of some sampling efficiency.

Viscoelasticity and Stokes-Einstein relation in repulsive and attractive colloidal glasses

We report a numerical investigation of the viscoelastic behavior in models for steric repulsive and short-ranged attractive colloidal suspensions, along different paths in the attraction strength vs packing fraction plane. More specifically, we study the behavior of the viscosity (and its frequency dependence) on approaching the repulsive glass, the attractive glass, and in the reentrant region where viscosity shows a nonmonotonic behavior on increasing attraction strength. On approaching the glass lines, the increase of the viscosity is consistent with a power-law divergence with the same exponent and critical packing fraction previously obtained for the divergence of the density fluctuations. Based on mode-coupling calculations, we associate the increase of the viscosity with specific contributions from different length scales. We also show that the results are independent of the microscopic dynamics by comparing Newtonian and Brownian simulations for the same model. Finally, we evaluate the Stokes-Einstein relation approaching both glass transitions, finding a clear breakdown which is particularly strong for the case of the attractive glass.

Equilibration times in numerical simulation of structural glasses: Comparing parallel tempering and conventional molecular dynamics

Generation of equilibrium configurations is the major obstacle for numerical investigation of the slow dynamics in supercooled liquid states. The parallel tempering (PT) technique, originally proposed for the numerical equilibration of discrete spin-glass model configurations, has recently been applied in the study of supercooled structural glasses. We present an investigation of the ability of parallel tempering to properly sample the liquid configuration space at different temperatures, by mapping the PT dynamics into the dynamics of the closest local potential energy minima (inherent structures). Comparing the PT equilibration process with the standard molecular dynamics equilibration process we find that the PT does not increase the speed of equilibration of the (slow) configurational degrees of freedom.