Interpenetrating gels in binary suspensions of DNA nanostars.

We experimentally investigate the equilibrium gel formation in a binary mixture of DNA nanostars. The binding rules, encoded in the DNA sequence of the nanostar binding ends, are such that each component is able to form only intra-species bonds. Reducing the excluded volume by properly designing the DNA nanostars, we show that two interpenetrating unconnected gels form in the sample on cooling, each of the two forms at a temperature controlled by the selected binding DNA sequence. The dynamic light scattering correlation functions show a non-common three-step relaxation process due to the splitting of the slow relaxation into two distinct decays, each of them reflecting the relaxation dynamics of one of the two networks.

Building up DNA, bit by bit: a simple description of chain assembly.

We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well reproduced by a simple theory that treats the association of particles into ideal (i.e., non-interacting) clusters as a reversible chemical reaction. The reaction constants can be predicted either from SantaLucia's theory or from Wertheim's thermodynamic perturbation theory of association for spherical patchy particles. Our results suggest that theories incorporating very limited molecular detail may be useful for predicting the broad equilibrium features of copolymerisation.

Particle transport constraints via Bayesian spectral fitting of multiple atomic lines.

Optimized operation of fusion devices demands detailed understanding of plasma transport, a problem that must be addressed with advances in both measurement and data analysis techniques. In this work, we adopt Bayesian inference methods to determine experimental particle transport, leveraging opportunities from high-resolution He-like ion spectra in a tokamak plasma. The Bayesian spectral fitting code is used to analyze resonance (w), forbidden (z), intercombination (x, y), and satellite (k, j) lines of He-like Ca following laser blow-off injections on Alcator C-Mod. This offers powerful transport constraints since these lines depend differently on electron temperature and density, but also differ in their relation to Li-like, He-like, and H-like ion densities, often the dominant Ca charge states over most of the C-Mod plasma radius. Using synthetic diagnostics based on the AURORA package, we demonstrate improved effectiveness of impurity transport inferences when spectroscopic data from a progressively larger number of lines are included.

Patchy particles at a hard wall: Orientation-dependent bonding.

The well-known and widely used Wertheim thermodynamic perturbation theory (TPT) of associating fluids averages over the orientational dependence of the bonding interactions. For this reason, density functional theories based on the otherwise very successful TPT have been unable to describe the structure of patchy particle fluids at hard walls, when the coupling of positional and orientational degrees of freedom becomes important at low temperatures [N. Gnan et al., J. Chem. Phys. 137, 084704 (2012)]. As a first attempt at remedying this, we propose to introduce into the theory an additional, nonbonding, anisotropic interparticle potential that enforces end-to-end alignment of two-patch particles. Within the simplest mean-field approximation, this additional potential does not change the thermodynamics of the bulk system and hence preserves its phase diagram but has the qualitatively correct effect on the order parameter and density profiles at a hard wall, as determined from computer simulation.

All-DNA System Close to the Percolation Threshold.

We characterize via small-angle neutron scattering the structural properties of a mixture of all-DNA particles with functionalities 4 (A) and 2 (B) constrained by design to reside close to the percolation threshold. DNA base sequences are selected such that A particles can only bind with B ones and that at the studied temperature (10 °C) all AB bonds are formed and long-lived, originating highly polydisperse persistent equilibrium clusters. The concentration dependence of the scattered intensity and its wavevector dependence is exploited to determine the fractal dimension and the size distribution of the clusters, which are found to be consistent with the critical exponents of the 3-D percolation universality class. The value of DNA nanoparticles as nanometric patchy colloids with well-defined functionality, bonding selectivity, and exquisite control of the interaction strength is demonstrated.

Explaining Cold-Pulse Dynamics in Tokamak Plasmas Using Local Turbulent Transport Models.

A long-standing enigma in plasma transport has been resolved by modeling of cold-pulse experiments conducted on the Alcator C-Mod tokamak. Controlled edge cooling of fusion plasmas triggers core electron heating on time scales faster than an energy confinement time, which has long been interpreted as strong evidence of nonlocal transport. This Letter shows that the steady-state profiles, the cold-pulse rise time, and disappearance at higher density as measured in these experiments are successfully captured by a recent local quasilinear turbulent transport model, demonstrating that the existence of nonlocal transport phenomena is not necessary for explaining the behavior and time scales of cold-pulse experiments in tokamak plasmas.

Binding branched and linear DNA structures: From isolated clusters to fully bonded gels.

The proper design of DNA sequences allows for the formation of well-defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well-defined valence, namely, tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T. We report dynamic light scattering experiments in a window of Ts ranging from 10 °C to 55 °C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T, when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel, and as a cluster fluid depending on the selected r.

Structure and elasticity of composite nanoparticle/polymer nanoshells (hybridosomes®).

Our group recently introduced a new process to synthesize nanoparticle shells of about 100 nm, named "hybridosomes®". Here, the structure and mechanical properties of hybridosomes® made from iron oxide nanoparticles and poly(acrylic acid) are characterized using TEM, AFM and an osmotic compression technique. For the latter, the size distribution of the hybridosomes is monitored by nanoparticle tracking analysis (NTA) in the presence of poly(ethylene glycol)s of different molecular weights. It is found that the size of the hybridosomes® can be tuned from ca. 80 nm to over 110 nm by adjusting the amount of nanoparticles and that their shell consists of a single layer of nanoparticles, with a porous structure. The size of the pores is estimated from osmotic compression experiments at ca. 4000 g mol-1. The mechanical properties are measured both at the ensemble level using size measurements under osmotic pressure and at the single nanoparticle level by atomic force microscopy nanoindentation. Both osmotic and AFM experiments are analyzed in the framework of the continuum elastic theory of thin shells and yield a value of Young's modulus of the order of MPa.

Experimental Verification of the Role of Electron Pressure in Fast Magnetic Reconnection with a Guide Field.

We report detailed laboratory observations of the structure of a reconnection current sheet in a two-fluid plasma regime with a guide magnetic field. We observe and quantitatively analyze the quadrupolar electron pressure variation in the ion-diffusion region, as originally predicted by extended magnetohydrodynamics simulations. The projection of the electron pressure gradient parallel to the magnetic field contributes significantly to balancing the parallel electric field, and the resulting cross-field electron jets in the reconnection layer are diamagnetic in origin. These results demonstrate how parallel and perpendicular force balance are coupled in guide field reconnection and confirm basic theoretical models of the importance of electron pressure gradients for obtaining fast magnetic reconnection.

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars.

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.

How fluorescent labelling alters the solution behaviour of proteins.

A complete understanding of the role of molecular anisotropy in directing the self assembly of colloids and proteins remains a challenge for soft matter science and biophysics. For proteins in particular, the complexity of the surface at a molecular level poses a challenge for any theoretical and numerical description. A soft matter approach, based on patchy models, has been useful in describing protein phase behaviour. In this work we examine how chemical modification of the protein surface, by addition of a fluorophore, affects the physical properties of protein solutions. By using a carefully controlled experimental protein model (human gamma-D crystallin) and numerical simulations, we demonstrate that protein solution behaviour defined by anisotropic surface effects can be captured by a custom patchy particle model. In particular, the chemical modification is found to be equivalent to the addition of a large hydrophobic surface patch with a large attractive potential energy well, which produces a significant increase in the temperature at which liquid-liquid phase separation occurs, even for very low fractions of fluorescently labelled proteins. These results are therefore directly relevant to all applications based on the use of fluorescent labelling by chemical modification, which have become increasingly important in the understanding of biological processes and biophysical interactions.

Cluster formation and phase separation in heteronuclear Janus dumbbells.

We have recently investigated the phase behavior of model colloidal dumbbells constituted by two identical tangent hard spheres, with the first being surrounded by an attractive square-well interaction (Janus dumbbells, Munaó et al 2014 Soft Matter 10 5269). Here we extend our previous analysis by introducing in the model the size asymmetry of the hard-core diameters and study the enriched phase scenario thereby obtained. By employing standard Monte Carlo simulations we show that in such 'heteronuclear Janus dumbbells' a larger hard-sphere site promotes the formation of clusters, whereas in the opposite condition a gas-liquid phase separation takes place, with a narrow interval of intermediate asymmetries wherein the two phase behaviors may compete. In addition, some peculiar geometrical arrangements, such as lamellæ, are observed only around the perfectly symmetric case. A qualitative agreement is found with recent experimental results, where it is shown that the roughness of molecular surfaces in heterogeneous dimers leads to the formation of colloidal micelles.

Structure and phase behavior of colloidal dumbbells with tunable attractive interactions.

We investigate thermodynamic and structural properties of colloidal dumbbells in the framework provided by the Reference Interaction Site Model (RISM) theory of molecular fluids and Monte Carlo simulations. We consider two different models: in the first one we set identical square-well attractions on the two tangent spheres constituting the molecule (SW-SW model); in the second scheme, one of the square-well interactions is switched off (HS-SW model). Appreciable differences emerge between the physical properties of the two models. Specifically, the k → 0 behavior of SW-SW structure factors S(k) points to the presence of a gas-liquid coexistence, as confirmed by subsequent fluid phase equilibria calculations. Conversely, the HS-SW S(k) develops a low-k peak, signaling the presence of aggregates; such a process destabilizes the gas-liquid phase separation, promoting at low temperatures the formation of a cluster phase, whose structure depends on the system density. We further investigate such differences by studying the phase behavior of a series of intermediate models, obtained from the original SW-SW by progressively reducing the depth of one square-well interaction. RISM structural predictions positively reproduce the simulation data, including the rise of S(k → 0) in the SW-SW model and the low-k peak in the HS-SW structure factor. As for the phase behavior, RISM agrees with Monte Carlo simulations in predicting a gas-liquid coexistence for the SW-SW model (though the critical parameters appear overestimated by the theory) and its progressive disappearance when moving toward the HS-SW model.

Cluster phases of decorated micellar solutions with macrocyclic ligands.

An aqueous self-assembled micellar system (sodium dodecyl sulfate, SDS, decorated with various adhesive sites, cryptand Kryptofix 222 and crown ether 18-Crown-6 molecules) has been investigated by dynamic light scattering (DLS) and small angle x-ray scattering (SAXS) to have insights into the micellar structure, the micellar interactions, and the aggregation properties of the system. DLS demonstrates the existence of populations of aggregates in the submicrometer/micrometer range, while the Guinier analysis of the SAXS curves helps in detailing objects smaller than 30 nm. The aggregates of micelles are here named cluster phases of micelles (CPMs). Considering that SDS micelles in water do not aggregate at low concentration, it is shown that macrocyclic ligands induce the SDS micelle aggregation as a function of the concentration (i.e., investigated ligand/SDS molar ratios are 5.0, 1.5, 1.0, and 0.5) and hydrophobicity of the adhesive sites. The sizes and the percentages of the micelles and the CPMs have been monitored to test the stability and reversibility of the system. DLS results clearly show that the aggregation processes of the decorated micelles are reproducible at time intervals of the order of 1 month, while the stability may not be entirely maintained after a year. As an issue of particular relevance, the higher the ligand/surfactant molar ratio, the larger are the CPMs induced. The K222 ligand results in being more effective in promoting the micellar aggregation than 18C6 as a consequence of the different hydrophobicity.

Re-entrant phase behaviour of network fluids: a patchy particle model with temperature-dependent valence.

We study a model consisting of particles with dissimilar bonding sites ("patches"), which exhibits self-assembly into chains connected by Y-junctions, and investigate its phase behaviour by both simulations and theory. We show that, as the energy cost ε(j) of forming Y-junctions increases, the extent of the liquid-vapour coexistence region at lower temperatures and densities is reduced. The phase diagram thus acquires a characteristic "pinched" shape in which the liquid branch density decreases as the temperature is lowered. To our knowledge, this is the first model in which the predicted topological phase transition between a fluid composed of short chains and a fluid rich in Y-junctions is actually observed. Above a certain threshold for ε(j), condensation ceases to exist because the entropy gain of forming Y-junctions can no longer offset their energy cost. We also show that the properties of these phase diagrams can be understood in terms of a temperature-dependent effective valence of the patchy particles.

Quantitative investigation of the two-state picture for water in the normal liquid and the supercooled regime.

Several evidences have helped to establish the two-state nature of liquid water. Thus, within the normal liquid and supercooled regimes water has been shown to consist of a mixture of well-structured, low-density molecules and unstructured, high-density ones. However, quantitative analyses have faced the burden of unambiguously determining both the presence and the fraction of each kind of water "species". A recent approach by combining a local structure index with potential-energy minimisations allows us to overcome this difficulty. Thus, in this work we extend such study and employ it to quantitatively determine the fraction of structured molecules as a function of temperature for different densities. This enables us to validate predictions of two-state models.

Simulation and theory of a model for tetrahedral colloidal particles.

We study the thermodynamic and structural properties of a five-site tetrahedral molecular model by means of different Monte Carlo simulation techniques, and the reference interaction site model (RISM) theory of molecular fluids. Simulations and theory signal the onset, at sufficiently low temperatures, of two different tetrahedral molecular arrangements, with a more open topology progressively giving place to a fully bonded one, as the temperature decreases. The RISM theory reproduces the splitting of the static structure factor at low temperatures, a feature intimately related to the onset of the tetrahedral ordering. Less accurate predictions are obtained for the liquid-vapor coexistence and the short-range correlations.

Reentrant phase diagram of network fluids.

We introduce a microscopic model for particles with dissimilar patches which displays an unconventional "pinched" phase diagram, similar to the one predicted by Tlusty and Safran in the context of dipolar fluids [Science 290, 1328 (2000)]. The model-based on two types of patch interactions, which account, respectively, for chaining and branching of the self-assembled networks-is studied both numerically via Monte Carlo simulations and theoretically via first-order perturbation theory. The dense phase is rich in junctions, while the less-dense phase is rich in chain ends. The model provides a reference system for a deep understanding of the competition between condensation and self-assembly into equilibrium-polymer chains.

Interaction between like-charged polyelectrolyte-colloid complexes in electrolyte solutions: a Monte Carlo simulation study in the Debye-Hückel approximation.

We study the effective interaction between differently charged polyelectrolyte-colloid complexes in electrolyte solutions via Monte Carlo simulations. These complexes are formed when short and flexible polyelectrolyte chains adsorb onto oppositely charged colloidal spheres, dispersed in an electrolyte solution. In our simulations the bending energy between adjacent monomers is small compared to the electrostatic energy, and the chains, once adsorbed, do not exchange with the solution, although they rearrange on the particles surface to accommodate further adsorbing chains or due to the electrostatic interaction with neighbor complexes. Rather unexpectedly, when two interacting particles approach each other, the rearrangement of the surface charge distribution invariably produces antiparallel dipolar doublets that invert their orientation at the isoelectric point. These findings clearly rule out a contribution of dipole-dipole interactions to the observed attractive interaction between the complexes, pointing out that such suspensions cannot be considered dipolar fluids. On varying the ionic strength of the electrolyte, we find that a screening length kappa(-1), short compared with the size of the colloidal particles, is required in order to observe the attraction between like-charged complexes due to the nonuniform distribution of the electric charge on their surface ("patch attraction"). On the other hand, by changing the polyelectrolyte/particle charge ratio xi(s), the interaction between like-charged polyelectrolyte-decorated particles, at short separations, evolves from purely repulsive to strongly attractive. Hence, the effective interaction between the complexes is characterized by a potential barrier, whose height depends on the net charge and on the nonuniformity of their surface charge distribution.

Equilibrium self-assembly of colloids with distinct interaction sites: thermodynamics, percolation, and cluster distribution functions.

We calculate the equilibrium thermodynamic properties, percolation threshold, and cluster distribution functions for a model of associating colloids, which consists of hard spherical particles having on their surfaces three short-ranged attractive sites (sticky spots) of two different types, A and B. The thermodynamic properties are calculated using Wertheim's perturbation theory of associating fluids. This also allows us to find the onset of self-assembly, which can be quantified by the maxima of the specific heat at constant volume. The percolation threshold is derived, under the no-loop assumption, for the correlated bond model: In all cases it is two percolated phases that become identical at a critical point, when one exists. Finally, the cluster size distributions are calculated by mapping the model onto an effective model, characterized by a--state-dependent--functionality f and unique bonding probability p. The mapping is based on the asymptotic limit of the cluster distributions functions of the generic model and the effective parameters are defined through the requirement that the equilibrium cluster distributions of the true and effective models have the same number-averaged and weight-averaged sizes at all densities and temperatures. We also study the model numerically in the case where BB interactions are missing. In this limit, AB bonds either provide branching between A-chains (Y-junctions) if epsilon(AB)/epsilon(AA) is small, or drive the formation of a hyperbranched polymer if epsilon(AB)/epsilon(AA) is large. We find that the theoretical predictions describe quite accurately the numerical data, especially in the region where Y-junctions are present. There is fairly good agreement between theoretical and numerical results both for the thermodynamic (number of bonds and phase coexistence) and the connectivity properties of the model (cluster size distributions and percolation locus).