Bond Order via Light-Induced Synthetic Many-body Interactions of Ultracold Atoms in Optical Lattices

We show how bond order emerges due to light mediated synthetic interactions in ultracold atoms in optical lattices in an optical cavity. This is a consequence of the competition between both short- and long-range interactions designed by choosing the optical geometry. Light induces effective many-body interactions that modify the landscape of quantum phases supported by the typical Bose-Hubbard model. Using exact diagonalization of small system sizes in one dimension, we present the many-body quantum phases the system can support via the interplay between the density and bond (or matter-wave coherence) interactions. We find numerical evidence to support that dimer phases due to bond order are analogous to valence bond states. Different possibilities of light-induced atomic interactions are considered that go beyond the typical atomic system with dipolar and other intrinsic interactions. This will broaden the Hamiltonian toolbox available for quantum simulation of condensed matter physics via atomic systems.Comment: Accepted in New Journal of Physic

Stability of a stochastically perturbed model of intracellular single-stranded RNA virus replication

Replication of single-stranded RNA virus can be complicated, compared to that of double-stranded virus, as it require production of intermediate antigenomic strands that then serve as template for the genomic-sense strands. Moreover, for ssRNA viruses, there is a variability of the molecular mechanism by which genomic strands can be replicated. A combination of such mechanisms can also occur: a fraction of the produced progeny may result from a stamping-machine type of replication that uses the parental genome as template, whereas others may result from the replication of progeny genomes. F. Mart\'{\i}nez et al. and J. Sardany\'{e}s at al. suggested a deterministic ssRNA virus intracellular replication model that allows for the variability in the replication mechanisms. To explore how stochasticity can affect this model principal properties, in this paper we consider the stability of a stochastically perturbed model of ssRNA virus replication within a cell. Using the direct Lyapunov method, we found sufficient conditions for the stability in probability of equilibrium states for this model. This result confirms that this heterogeneous model of single-stranded RNA virus replication is stable with respect to stochastic perturbations of the environment

On a general implementation of hh- and pp-adaptive curl-conforming finite elements

Edge (or N\'ed\'elec) finite elements are theoretically sound and widely used by the computational electromagnetics community. However, its implementation, specially for high order methods, is not trivial, since it involves many technicalities that are not properly described in the literature. To fill this gap, we provide a comprehensive description of a general implementation of edge elements of first kind within the scientific software project FEMPAR. We cover into detail how to implement arbitrary order (i.e., $p$-adaptive) elements on hexahedral and tetrahedral meshes. First, we set the three classical ingredients of the finite element definition by Ciarlet, both in the reference and the physical space: cell topologies, polynomial spaces and moments. With these ingredients, shape functions are automatically implemented by defining a judiciously chosen polynomial pre-basis that spans the local finite element space combined with a change of basis to automatically obtain a canonical basis with respect to the moments at hand. Next, we discuss global finite element spaces putting emphasis on the construction of global shape functions through oriented meshes, appropriate geometrical mappings, and equivalence classes of moments, in order to preserve the inter-element continuity of tangential components of the magnetic field. Finally, we extend the proposed methodology to generate global curl-conforming spaces on non-conforming hierarchically refined (i.e., $h$-adaptive) meshes with arbitrary order finite elements. Numerical results include experimental convergence rates to test the proposed implementation