Atomic Entanglement vs Photonic Visibility for Quantum Criticality of Hybrid System

To characterize the novel quantum phase transition for a hybrid system consisting of an array of coupled cavities and two-level atoms doped in each cavity, we study the atomic entanglement and photonic visibility in comparison with the quantum fluctuation of total excitations. Analytical and numerical simulation results show the happen of quantum critical phenomenon similar to the Mott insulator to superfluid transition. Here, the contour lines respectively representing the atomic entanglement, photonic visibility and excitation variance in the phase diagram are consistent in the vicinity of the non-analytic locus of atomic concurrences.Comment: 4 pages, 2 figure

Peierls distorted chain as a quantum data bus for quantum state transfer

We systematically study the transfer of quantum state of electron spin as the flying qubit along a half-filled Peierls distorted tight-binding chain described by the Su-Schrieffer-Heeger (SSH) model, which behaves as a quantum data bus. This enables a novel physical mechanism for quantum communication with always-on interaction: the effective hopping of the spin carrier between sites $A$ and $B$ connected to two sites in this SSH chain can be induced by the quasi-excitations of the SSH model. As we prove, it is the Peierls energy gap of the SSH quasi-excitations that plays a crucial role to protect the robustness of the quantum state transfer process. Moreover, our observation also indicates that such a scheme can also be employed to explore the intrinsic property of the quantum system.Comment: 10 pages, 6 figure

Quantum Quench from a Thermal Initial State

We consider a quantum quench in a system of free bosons, starting from a thermal initial state. As in the case where the system is initially in the ground state, any finite subsystem eventually reaches a stationary thermal state with a momentum-dependent effective temperature. We find that this can, in some cases, even be lower than the initial temperature. We also study lattice effects and discuss more general types of quenches.Comment: 6 pages, 2 figures; short published version, added references, minor change

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing (DNase-seq) experiment with accuracy comparable to that of chromatin immunoprecipitation followed by sequencing (ChIP-seq). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into prepancreatic and intestinal endoderm. We identified 120 and experimentally validated eight 'pioneer' TF families that dynamically open chromatin. Four pioneer TF families only opened chromatin in one direction from their motifs. Furthermore, we identified 'settler' TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and nondirectional pioneer activity shapes the chromatin landscape for population by settler TFs.National Institutes of Health (U.S.) (Common Fund 5UL1DE019581)National Institutes of Health (U.S.) (Common Fund RL1DE019021)National Institutes of Health (U.S.) (Common Fund 5TL1EB008540)National Institutes of Health (U.S.) (Grant 1U01HG007037)National Institutes of Health (U.S.) (Grant 5P01NS055923