Design Rules for Self-Assembly of 2D Nanocrystal/Metal-Organic Framework Superstructures.

We demonstrate the guiding principles behind simple two dimensional self-assembly of MOF nanoparticles (NPs) and oleic acid capped iron oxide (Fe3 O4 ) NCs into a uniform two-dimensional bi-layered superstructure. This self-assembly process can be controlled by the energy of ligand-ligand interactions between surface ligands on Fe3 O4 NCs and Zr6 O4 (OH)4 (fumarate)6 MOF NPs. Scanning transmission electron microscopy (TEM)/energy-dispersive X-ray spectroscopy and TEM tomography confirm the hierarchical co-assembly of Fe3 O4 NCs with MOF NPs as ligand energies are manipulated to promote facile diffusion of the smaller NCs. First-principles calculations and event-driven molecular dynamics simulations indicate that the observed patterns are dictated by combination of ligand-surface and ligand-ligand interactions. This study opens a new avenue for design and self-assembly of MOFs and NCs into high surface area assemblies, mimicking the structure of supported catalyst architectures, and provides a thorough fundamental understanding of the self-assembly process, which could be a guide for designing functional materials with desired structure

DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat

Jamming percolation and glassy dynamics

We present a detailed physical analysis of the dynamical glass-jamming transition which occurs for the so called Knight models recently introduced and analyzed in a joint work with D.S.Fisher \cite{letterTBF}. Furthermore, we review some of our previous works on Kinetically Constrained Models. The Knights models correspond to a new class of kinetically constrained models which provide the first example of finite dimensional models with an ideal glass-jamming transition. This is due to the underlying percolation transition of particles which are mutually blocked by the constraints. This jamming percolation has unconventional features: it is discontinuous (i.e. the percolating cluster is compact at the transition) and the typical size of the clusters diverges faster than any power law when $\rho\nearrow\rho_c$. These properties give rise for Knight models to an ergodicity breaking transition at $\rho_c$: at and above $\rho_{c}$ a finite fraction of the system is frozen. In turn, this finite jump in the density of frozen sites leads to a two step relaxation for dynamic correlations in the unjammed phase, analogous to that of glass forming liquids. Also, due to the faster than power law divergence of the dynamical correlation length, relaxation times diverge in a way similar to the Vogel-Fulcher law.Comment: Submitted to the special issue of Journal of Statistical Physics on Spin glasses and related topic

Cooperative Behavior of Kinetically Constrained Lattice Gas Models of Glassy Dynamics

Kinetically constrained lattice models of glasses introduced by Kob and Andersen (KA) are analyzed. It is proved that only two behaviors are possible on hypercubic lattices: either ergodicity at all densities or trivial non-ergodicity, depending on the constraint parameter and the dimensionality. But in the ergodic cases, the dynamics is shown to be intrinsically cooperative at high densities giving rise to glassy dynamics as observed in simulations. The cooperativity is characterized by two length scales whose behavior controls finite-size effects: these are essential for interpreting simulations. In contrast to hypercubic lattices, on Bethe lattices KA models undergo a dynamical (jamming) phase transition at a critical density: this is characterized by diverging time and length scales and a discontinuous jump in the long-time limit of the density autocorrelation function. By analyzing generalized Bethe lattices (with loops) that interpolate between hypercubic lattices and standard Bethe lattices, the crossover between the dynamical transition that exists on these lattices and its absence in the hypercubic lattice limit is explored. Contact with earlier results are made via analysis of the related Fredrickson-Andersen models, followed by brief discussions of universality, of other approaches to glass transitions, and of some issues relevant for experiments.Comment: 59 page

Mesoscopic models for DNA stretching under force: new results and comparison to experiments

Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. It has been proposed that the first transition, at forces of 60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). We derive analytical formula using a coupled discrete worm like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connexion with previous fitting parameter values for denaturation profiles. We find that: (i) ssDNA is fitted, using an analytical formula, over a nanoNewton range with only three free parameters, the contour length, the bending modulus and the monomer size; (ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; (iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; (v) this formula fits perfectly well poly(dG-dC) and $\lambda$-DNA force-extension curves with consistent parameter values; (vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges.Comment: 14 pages, 9 figure

Applications of Field-Theoretic Renormalization Group Methods to Reaction-Diffusion Problems

We review the application of field-theoretic renormalization group (RG) methods to the study of fluctuations in reaction-diffusion problems. We first investigate the physical origin of universality in these systems, before comparing RG methods to other available analytic techniques, including exact solutions and Smoluchowski-type approximations. Starting from the microscopic reaction-diffusion master equation, we then pedagogically detail the mapping to a field theory for the single-species reaction k A -> l A (l < k). We employ this particularly simple but non-trivial system to introduce the field-theoretic RG tools, including the diagrammatic perturbation expansion, renormalization, and Callan-Symanzik RG flow equation. We demonstrate how these techniques permit the calculation of universal quantities such as density decay exponents and amplitudes via perturbative eps = d_c - d expansions with respect to the upper critical dimension d_c. With these basics established, we then provide an overview of more sophisticated applications to multiple species reactions, disorder effects, L'evy flights, persistence problems, and the influence of spatial boundaries. We also analyze field-theoretic approaches to nonequilibrium phase transitions separating active from absorbing states. We focus particularly on the generic directed percolation universality class, as well as on the most prominent exception to this class: even-offspring branching and annihilating random walks. Finally, we summarize the state of the field and present our perspective on outstanding problems for the future.Comment: 10 figures include