The non-equilibrium dynamics of a gas of cold atoms in which Rydberg states are off-resonantly excited is studied in the presence of noise. The interplay between interaction and off-resonant excitation leads to an initial dynamics where aggregates of
excited Rydberg atoms slowly nucleate and grow, eventually reaching long-lived meta-stable arrangements which then relax further on much longer timescales. This growth dynamics is governed by an effective Master equation which permits a transparent and largely analytical understanding of the underlying physics. By means of extensive numerical simulations we study the many-body dynamics and the correlations of the resulting non-equilibrium states in various dimensions. Our results provide insight into the dynamical richness of strongly interacting Rydberg gases in noisy environments, and highlight the usefulness of these kind of systems for the exploration of soft-matter-type collective behaviour.
We show that the dynamics of a laser driven Rydberg gas in the limit of strong dephasing is described by a master equation with manifest kinetic constraints. The equilibrium state of the system is uncorrelated but the constraints in the dynamics lead
to spatially correlated collective relaxation reminiscent of glasses. We study and quantify the evolution towards equilibrium in one and two dimensions, and analyze how the degree of glassiness and the relaxation time are controlled by the interaction strength between Rydberg atoms. We also find that spontaneous decay of Rydberg excitations leads to an interruption of glassy relaxation that takes the system to a highly correlated non-equilibrium stationary state. The results presented here, which are in principle also applicable other systems such as polar molecules and atoms with large magnetic dipole moments, show that the collective behavior of cold atomic and molecular ensembles can be similar to that found in soft condensed-matter systems.
We explore the dynamical large-deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of non-equilibrium dynamical phase-transitions in ensembles of trajectories between active and
inactive dynamical phases, whose nature depends on properties of the interaction potential. When the full heterogeneity of interactions due to the amino-acid sequence is preserved, as in a fully interacting model or in a heterogeneous version of the G={o} model where only native interactions are considered, the transition is between the equilibrium native state and a highly native but kinetically trapped state. In contrast, for the homogeneous G={o} model, where there is a single native energy and the sequence plays no role, the dynamical transition is a direct consequence of the static bi-stability between unfolded and native states. In the heterogeneous case the native-active and native-inactive states, despite their static similarity, have widely varying dynamical properties, and the transition between them occurs even in lattice proteins whose sequences are designed to make them optimal folders.
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a crucial as
sumption that has never been critically evaluated in a broad context: Detailed mechanisms of protein folding are not biased by non-native contacts, typically imagined as a consequence of sequence design and/or topology. Here we present, using computer simulations of a well-studied lattice heteropolymer model, the first systematic test of this oft-assumed correspondence over the statistically significant range of hundreds of thousands of amino acid sequences, and a concomitantly diverse set of folding pathways. Enabled by a novel means of fingerprinting folding trajectories, our study reveals a profound insensitivity of the order in which native contacts accumulate to the omission of non-native interactions. Contrary to conventional thinking, this robustness does not arise from topological restrictions and does not depend on folding rate. We find instead that the crucial factor in discriminating among topological pathways is the heterogeneity of native contact energies. Our results challenge conventional thinking on the relationship between sequence design and free energy landscapes for protein folding, and help justify the widespread use of Go-like models to scrutinize detailed folding mechanisms of real proteins.
