A Note on Distance-Based Entropy of Dendrimers

This paper introduces a variant of entropy measures based on vertex eccentricity and applies it to all graphs representing the isomers of octane. Taking into account the vertex degree as well (degree-ecc-entropy), we find a good correlation with the acentric factor of octane isomers. In particular, we compute the degree-ecc-entropy for three classes of dendrimer graphs

A model of inversion of DNA charge by a positive polymer: fractionization of the polymer charge

Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is considered. We assume that, in the neutral state of the DNA-PE complex, each of the DNA charges is locally compensated by a PE charge. When an additional PE molecule is adsorbed by DNA, its charge gets fractionized into monomer charges of defects (tails and arches) on the background of the perfectly neutralized DNA. These charges spread all over the DNA eliminating the self-energy of PE. This fractionization mechanism leads to a substantial inversion of the DNA charge, a phenomenon which is widely used for gene delivery.Comment: 4 pages, 2 figures. Improved figures and various corrections to tex

A density-functional theory investigation of cluster formation in an effective-potential model of dendrimers

We consider a system of particles interacting via a purely repulsive, soft-core potential recently introduced to model effective pair interactions between dendrimers, which is expected to lead to the formation of crystals with multiple occupancy of the lattice sites. The phase diagram is investigated by density-functional theory (DFT) without making any a priori assumption on the functional form of the density profile or on the type of crystal lattice. As the average density $\rho$ is increased, the system displays first a transition from a fluid to a bcc phase, and subsequently to hcp and fcc phases. In the inhomogeneous region, the behavior is that found in previous investigations of this class of cluster-forming potentials. Specifically, the particles arrange into clusters strongly localized at the lattice sites, and the lattice constant depends very weakly on $\rho$, leading to an occupancy number of the sites which is a nearly linear function of $\rho$. These results are compared to those predicted by the more widespread approach, in which the DFT minimization is carried out by representing the density profile by a given functional form depending on few variational parameters. We find that for the model potential studied here, the latter approach recovers most of the predictions of the unconstrained minimization.Comment: 22 pages, 7 figures. To appear in a Festschrift Issue of Transactions of The Royal Norwegian Society of Sciences and Letters (DKNVS) dedicated to Johan Hoye on his 70th birthda

Self Assembly of Soft Matter Quasicrystals and Their Approximants

The surprising recent discoveries of quasicrystals and their approximants in soft matter systems poses the intriguing possibility that these structures can be realized in a broad range of nano- and micro-scale assemblies. It has been theorized that soft matter quasicrystals and approximants are largely entropically stabilized, but the thermodynamic mechanism underlying their formation remains elusive. Here, we use computer simulation and free energy calculations to demonstrate a simple design heuristic for assembling quasicrystals and approximants in soft matter systems. Our study builds on previous simulation studies of the self-assembly of dodecagonal quasicrystals and approximants in minimal systems of spherical particles with complex, highly-specific interaction potentials. We demonstrate an alternative entropy-based approach for assembling dodecagonal quasicrystals and approximants based solely on particle functionalization and shape, thereby recasting the interaction-potential-based assembly strategy in terms of simpler-to-achieve bonded and excluded-volume interactions. Here, spherical building blocks are functionalized with mobile surface entities to encourage the formation of structures with low surface contact area, including non-close-packed and polytetrahedral structures. The building blocks also possess shape polydispersity, where a subset of the building blocks deviate from the ideal spherical shape, discouraging the formation of close-packed crystals. We show that three different model systems with both of these features -- mobile surface entities and shape polydispersity -- consistently assemble quasicrystals and/or approximants. We argue that this design strategy can be widely exploited to assemble quasicrystals and approximants on the nano- and micro- scales. In addition, our results further elucidate the formation of soft matter quasicrystals in experiment.Comment: 12 pages 6 figure

Cluster and reentrant anomalies of nearly Gaussian core particles

We study through integral equation theory and numerical simulations the structure and dynamics of fluids composed of ultrasoft, nearly Gaussian particles. Namely, we explore the fluid phase diagram of a model in which particles interact via the generalized exponential potential u(r)=\epsilon exp[-(r/\sigma)^n], with a softness exponent n slightly larger than 2. In addition to the well-known anomaly associated to reentrant melting, the structure and dynamics of the fluid display two additional anomalies, which are visible in the isothermal variation of the structure factor and diffusivity. These features are correlated to the appearance of dimers in the fluid phase and to the subsequent modification of the cluster structure upon compression. We corroborate these results through an analysis of the local minima of the potential energy surface, in which clusters appear as much tighter conglomerates of particles. We find that reentrant melting and clustering coexist for softness exponents ranging from 2^+ up to values relevant for the description of amphiphilic dendrimers, i.e., n=3.Comment: 10 pages, 8 figure