Vindication of Yb2Ti2O7 as a model exchange quantum spin ice.

We use numerical linked-cluster expansions to compute the specific heat C(T) and entropy S(T) of a quantum spin ice Hamiltonian for Yb2Ti2O7 using anisotropic exchange interactions, recently determined from inelastic neutron scattering measurements, and find good agreement with experimental calorimetric data. This vindicates Yb2Ti2O7 as a model quantum spin ice. We find that in the perturbative weak quantum regime, such a system has a ferrimagnetic ordered ground state, with two peaks in C(T): a Schottky anomaly signaling the paramagnetic to spin ice crossover, followed at a lower temperature by a sharp peak accompanying a first-order phase transition to the ordered state. We suggest that the two C(T) features observed in Yb2Ti2O7 are associated with the same physics. Spin excitations in this regime consist of weakly confined spinon-antispinon pairs. We anticipate that the conventional ground state with exotic quantum dynamics will prove a prevalent characteristic of many real quantum spin ice materials.

Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways.

We employ all-atom structure-based models with a force field with multiple energetic basins for the C-terminal (residues 166-226) of the mammalian prion protein. One basin represents the known alpha-helical (αH) structure while the other represents the same residues in a left-handed beta-helical (LHBH) conformation. The LHBH structure has been proposed to help describe one class of in vitro grown fibrils, as well as possibly self-templating the conversion of normal cellular prion protein to the infectious form. Yet, it is unclear how the protein may make this global rearrangement. Our results demonstrate that the conformation changes are not strongly limited by large-scale geometry modification and that there may exist an overall preference for the LHBH conformation. Furthermore, our model presents novel intermediate trapping conformations with twisted LHBH structure.

Evaluating force field accuracy with long-time simulations of a ß-hairpin tryptophan zipper peptide.

We have combined graphics processing unit-accelerated all-atom molecular dynamics with parallel tempering to explore the folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this methodology to the synthetic ß-hairpin, trpzip2, and one of its sequence variants, W2W9. Each simulation consisted of over 8 µs of aggregated virtual time. Several measures of folding behavior showed good convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the intramolecular interactions of tryptophan side chains are responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 φ and ψ dihedral energies and an implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.