Bortolo Matteo Mognetti

Re-entrant melting as a design principle for DNA-coated colloids

Colloids functionalized with DNA hold great promise as building blocks for complex self-assembling structures. However, the practical use of DNA-coated colloids (DNACCs) has been limited by the narrowness of the temperature window where the target structures are both thermodynamically stable and kinetically accessible. Here we propose a strategy to design DNACCs, whereby the colloidal suspensions crystallize on cooling and then melt on further cooling. In a phase diagram with such a re-entrant melting, kinetic trapping of the system in non-target structures should be strongly suppressed. We present model calculations and simulations that show that real DNA sequences exist that should bestow this unusual phase behaviour on suitably functionalized colloidal suspensions. We present our results for binary systems, but the concepts that we develop apply to multicomponent systems and should therefore open the way towards the design of truly complex self-assembling colloidal structures.

A general theory of DNA-mediated and other valence-limited colloidal interactions

We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the configurational and combinatorial entropic factors that play a key role in valence-limited interactions. By rigorously enforcing self-consistency, it achieves near-quantitative accuracy with respect to detailed Monte Carlo calculations. With suitable approximations and in particular geometries, our theory reduces to previous successful treatments, which are now united in a common and extensible framework. We expect our tools to be useful to other researchers investigating ligand-mediated interactions. A complete and well-documented Python implementation is freely available at http://github.com/patvarilly/DNACC.

Superselective Targeting Using Multivalent Polymers

Despite their importance for material and life sciences, multivalent interactions between polymers and surfaces remain poorly understood. Combining recent achievements of synthetic chemistry and surface characterization, we have developed a well-defined and highly specific model system based on host/guest interactions. We use this model to study the binding of hyaluronic acid functionalized with host molecules to tunable surfaces displaying different densities of guest molecules. Remarkably, we find that the surface density of bound polymer increases faster than linearly with the surface density of binding sites. Based on predictions from a simple analytical model, we propose that this superselective behavior arises from a combination of enthalpic and entropic effects upon binding of nanoobjects to surfaces, accentuated by the ability of polymer chains to interpenetrate.

Modeling receding contact lines on superhydrophobic surfaces.

We use mesoscale simulations to study the depinning of a receding contact line on a superhydrophobic surface patterned by a regular array of posts. For the simulations to be feasible, we introduce a novel geometry where a column of liquid dewets a capillary bounded by a superhydrophobic plane that faces a smooth hydrophilic wall of variable contact angle. We present results for the dependence of the depinning angle on the shape and spacing of the posts and discuss the form of the meniscus at depinning. We find, in agreement with ref 17 , that the local post concentration is a primary factor in controlling the depinning angle and show that the numerical results agree well with recent experiments. We also present two examples of metastable pinned configurations where the posts are partially wet.

Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment.

The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, and short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on thermodynamic perturbation theory is discussed. Molecules are described by coarse grained models, where either the whole molecule (carbon dioxide, benzene, and methane) or a group of a few successive CH(2) groups (in the case of alkanes) are lumped into an effective point particle. Interactions among these point particles are fitted by Lennard-Jones (LJ) potentials such that the vapor-liquid critical point of the fluid is reproduced in agreement with experiment; in the case of quadrupolar molecules a quadrupole-quadrupole interaction is included. These models are shown to provide a satisfactory description of the liquid-vapor phase diagram of these pure fluids. Investigations of mixtures, using the Lorentz-Berthelot (LB) combining rule, also produce satisfactory results if compared with experiment, while in some previous attempts (in which polar solvents were modeled without explicitly taking into account quadrupolar interaction), strong violations of the LB rules were required. For this reason, the present investigation is a step towards predictive modeling of polar mixtures at low computational cost. In many cases Monte Carlo simulations of such models (employing the grand-canonical ensemble together with reweighting techniques, successive umbrella sampling, and finite size scaling) yield accurate results in very good agreement with experimental data. Simulation results are quantitatively compared to an analytical approximation for the equation of state of the same model, which is computationally much more efficient, and some systematic discrepancies are discussed. These very simple coarse-grained models of small molecules developed here should be useful, e.g., for simulations of polymer solutions with such molecules as solvent.

Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes

Short DNA linkers are increasingly being exploited for driving-specific self-assembly of Brownian objects. DNA-functionalized colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach has been applied to compliant units, including emulsion droplets and lipid vesicles. The liquid structure of these substrates introduces new degrees of freedom: the tethers can diffuse and rearrange, radically changing the physics of the interactions. Unlike droplets, vesicles are extremely deformable and DNA-mediated adhesion causes significant shape adjustments. We investigate experimentally the thermal response of pairs and networks of DNA-tethered liposomes and observe two intriguing and possibly useful collective properties: negative thermal expansion and tuneable porosity of the liposome networks. A model providing a thorough understanding of this unexpected phenomenon is developed, explaining the emergent properties out of the interplay between the temperature-dependent deformability of the vesicles and the DNA-mediated adhesive forces.

Efficient prediction of thermodynamic properties of quadrupolar fluids from simulation of a coarse-grained model: the case of carbon dioxide.

Monte Carlo simulations are presented for a coarse-grained model of real quadrupolar fluids. Molecules are represented by particles interacting with Lennard-Jones forces plus the thermally averaged quadrupole-quadrupole interaction. The properties discussed include the vapor-liquid coexistence curve, the vapor pressure along coexistence, and the surface tension. The full isotherms are also accessible over a wide range of temperatures and densities. It is shown that the critical parameters (critical temperature, density, and pressure) depend almost linearly on a quadrupolar parameter q=Q(*4)T*, where Q* is the reduced quadrupole moment of the molecule and T* the reduced temperature. The model can be applied to a variety of small quadrupolar molecules. We focus on carbon dioxide as a test case, but consider nitrogen and benzene, too. Experimental critical temperature, density, and quadrupolar moment are sufficient to fix the parameters of the model. The resulting agreement with experiments is excellent and marks a significant improvement over approaches which neglect quadrupolar effects. The same coarse-grained model was also applied in the framework of perturbation theory in the mean spherical approximation. As expected, the latter deviates from the Monte Carlo results in the critical region, but is reasonably accurate at lower temperatures.

Virial coefficients and osmotic pressure in polymer solutions in good-solvent conditions.

We determine the second, third, and fourth virial coefficients appearing in the density expansion of the osmotic pressure Pi of a monodisperse polymer solution in good-solvent conditions. Using the expected large-concentration behavior, we extrapolate the low-density expansion outside the dilute regime, obtaining the osmotic pressure for any concentration in the semidilute region. Comparison with field-theoretical predictions and experimental data shows that the obtained expression is quite accurate. The error is approximately 1%-2% below the overlap concentration and rises at most to 5%-10% in the limit of very large polymer concentrations.

Capillary filling in microchannels patterned by posts.

We investigate the capillary filling of three-dimensional microchannels with surfaces patterned by posts of square cross section. We show that pinning on the edges of the posts suppresses and can halt capillary filling. We stress the importance of the channel walls in controlling whether filling can occur. In particular for channels higher than the distance between adjacent posts, filling occurs for contact angles less than a threshold angle of approximately 55 degrees , independent of the height of the channel.

Effect of Inert Tails on the Thermodynamics of DNA Hybridization

The selective hybridization of DNA is of key importance for many practical applications such as gene detection and DNA-mediated self-assembly. These applications require a quantitative prediction of the hybridization free energy. Existing methods ignore the effects of non-complementary ssDNA tails beyond the first unpaired base. We use experiments and simulations to show that the binding strength of complementary ssDNA oligomers is altered by these sequences of non-complementary nucleotides. Even a small number of non-binding bases are enough to raise the hybridization free energy by approximately 1 kcal/mol at physiological salt concentrations. We propose a simple analytical expression that accounts quantitatively for this variation as a function of tail length and salt concentration.