Electronic and phononic properties of the chalcopyrite CuGaS2

The availability of ab initio electronic calculations and the concomitant techniques for deriving the corresponding lattice dynamics have been profusely used for calculating thermodynamic and vibrational properties of semiconductors, as well as their dependence on isotopic masses. The latter have been compared with experimental data for elemental and binary semiconductors with different isotopic compositions. Here we present theoretical and experimental data for several vibronic and thermodynamic properties of CuGa2, a canonical ternary semiconductor of the chalcopyrite family. Among these properties are the lattice parameters, the phonon dispersion relations and densities of states (projected on the Cu, Ga, and S constituents), the specific heat and the volume thermal expansion coefficient. The calculations were performed with the ABINIT and VASP codes within the LDA approximation for exchange and correlation and the results are compared with data obtained on samples with the natural isotope composition for Cu, Ga and S, as well as for isotope enriched samples.Comment: 9 pages, 8 Figures, submitted to Phys. Rev

Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

Statistical mechanics of RNA folding: importance of alphabet size

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two kinds of bases, there are many alternate folding configurations, yielding thermodynamically stable ground-states only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.Comment: 7 figures; uses revtex

Anomalous interactions in confined charge-stabilized colloid

Charge-stabilized colloidal spheres dispersed in weak 1:1 electrolytes are supposed to repel each other. Consequently, experimental evidence for anomalous long-ranged like-charged attractions induced by geometric confinement inspired a burst of activity. This has largely subsided because of nagging doubts regarding the experiments' reliability and interpretation. We describe a new class of thermodynamically self-consistent colloidal interaction measurements that confirm the appearance of pairwise attractions among colloidal spheres confined by one or two bounding walls. In addition to supporting previous claims for this as-yet unexplained effect, these measurements also cast new light on its mechanism.Comment: 8 pages, 5 figures, RevTeX4. Conference proceedings for CODEF-04, Colloidal Dispersions in External Fields, March 29 - April 1, 200

Like-charge attraction through hydrodynamic interaction

We demonstrate that the attractive interaction measured between like-charged colloidal spheres near a wall can be accounted for by a nonequilibrium hydrodynamic effect. We present both analytical results and Brownian dynamics simulations which quantitatively capture the one-wall experiments of Larsen and Grier (Nature 385, p. 230, 1997).Comment: 10 pages, 4 figure