Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma

Table summarizing the RNA-seq results. Differential gene expression results in BAP1-knockdown compared to control OCM-1A cells are shown from the RNA-seq data. Each row gives the unique Ensembl identifier, gene name, and description for each gene, as well as the log of the fold change (logFC), average expression, adjusted p-value, and linear fold change. (XLSX 1392 kb

Cu/Ag EAM Potential Optimized for Heteroepitaxial Diffusion from ab initio Data

A binary embedded-atom method (EAM) potential is optimized for Cu on Ag(111) by fitting to ab initio data. The fitting database consists of DFT calculations of Cu monomers and dimers on Ag(111), specifically their relative energies, adatom heights, and dimer separations. We start from the Mishin Cu-Ag EAM potential and first modify the Cu-Ag pair potential to match the FCC/HCP site energy difference then include Cu-Cu pair potential optimization for the entire database. The optimized EAM potential reproduce DFT monomer and dimer relative energies and geometries correctly. In trimer calculations, the potential produces the DFT relative energy between FCC and HCP trimers, though a different ground state is predicted. We use the optimized potential to calculate diffusion barriers for Cu monomers, dimers, and trimers. The predicted monomer barrier is the same as DFT, while experimental barriers for monomers and dimers are both lower than predicted here. We attribute the difference with experiment to the overestimation of surface adsorption energies by DFT and a simple correction is presented. Our results show that the optimized Cu-Ag EAM can be applied in the study of larger Cu islands on Ag(111).Comment: 15 pages, 7 figure

Graphene kirigami as a platform for stretchable and tunable quantum dot arrays

The quantum transport properties of a graphene kirigami similar to those studied in recent experiments are calculated in the regime of elastic, reversible deformations. Our results show that, at low electronic densities, the conductance profile of such structures replicates that of a system of coupled quantum dots, characterized by a sequence of minibands and stop-gaps. The conductance and I-V curves have different characteristics in the distinct stages of elastic deformation that characterize the elongation of these structures. Notably, the effective coupling between localized states is strongly reduced in the small elongation stage, whereas in the large elongation regime the development of strong, localized pseudomagnetic field barriers can reinforce the coupling and reestablish resonant tunneling across the kirigami. This provides an interesting example of interplay between geometry and pseudomagnetic field-induced confinement. The alternating miniband and stop-gaps in the transmission lead to I-V characteristics with negative differential conductance in well defined energy/doping ranges. These effects should be stable in a realistic scenario that includes edge roughness and Coulomb interactions, as these are expected to further promote localization of states at low energies in narrow segments of graphene nanostructures.Comment: 10 pages, 10 figure

Transformation Optics Approach to Plasmon-Exciton Strong Coupling in Nanocavities

We investigate the conditions yielding plasmon-exciton strong coupling at the single emitter level in the gap between two metal nanoparticles. A quasi-analytical transformation optics approach is developed that makes possible a thorough exploration of this hybrid system incorporating the full richness of its plasmonic spectrum. This allows us to reveal that by placing the emitter away from the cavity center, its coupling to multipolar dark modes of both even and odd parity increases remarkably. This way, reversible dynamics in the population of the quantum emitter takes place in feasible implementations of this archetypal nanocavity.Comment: 5 pages, 4 figure

Quantum key distribution with "dual detectors"

To improve the performance of a quantum key distribution (QKD) system, high speed, low dark count single photon detectors (or low noise homodyne detectors) are required. However, in practice, a fast detector is usually noisy. Here, we propose a "dual detectors" method to improve the performance of a practical QKD system with realistic detectors: the legitimate receiver randomly uses either a fast (but noisy) detector or a quiet (but slow) detector to measure the incoming quantum signals. The measurement results from the quiet detector can be used to bound eavesdropper's information, while the measurement results from the fast detector are used to generate secure key. We apply this idea to various QKD protocols. Simulation results demonstrate significant improvements in both BB84 protocol with ideal single photon source and Gaussian-modulated coherent states (GMCS) protocol; while for decoy-state BB84 protocol with weak coherent source, the improvement is moderate. We also discuss various practical issues in implementing the "dual detectors" scheme.Comment: 22 pages, 9 figure

Landau level spectroscopy of surface states in the topological insulator Bi0.91_{0.91}Sb0.09_{0.09} via magneto-optics

We have performed broad-band zero-field and magneto-infrared spectroscopy of the three dimensional topological insulator Bi$_{0.91}$Sb$_{0.09}$. The zero-field results allow us to measure the value of the direct band gap between the conducting $L_a$ and valence $L_s$ bands. Under applied field in the Faraday geometry (\emph{k} $||$ \emph{H} $||$ C1), we measured the presence of a multitude of Landau level (LL) transitions, all with frequency dependence $\omega \propto \sqrt{H}$. We discuss the ramification of this observation for the surface and bulk properties of topological insulators.Comment: 7 pages, 8 figures, March Meeting 2011 Abstract: J35.0000

Side-channel-free quantum key distribution

Quantum key distribution (QKD) offers the promise of absolutely secure communications. However, proofs of absolute security often assume perfect implementation from theory to experiment. Thus, existing systems may be prone to insidious side-channel attacks that rely on flaws in experimental implementation. Here we replace all real channels with virtual channels in a QKD protocol, making the relevant detectors and settings inside private spaces inaccessible while simultaneously acting as a Hilbert space filter to eliminate side-channel attacks. By using a quantum memory we find that we are able to bound the secret-key rate below by the entanglement-distillation rate computed over the distributed states.Comment: Considering general quantum systems, we extended QKD to the presence of an untrusted relay, whose measurement creates secret correlations in remote stations (achievable rate lower-bounded by the coherent information). This key ingredient, i.e., the use of a measurement-based untrusted relay, has been called 'measurement-device independence' in another arXiv submission (arXiv:1109.1473

Monte Carlo simulation of melting transition on DNA nanocompartment

DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force microscopy. Interesting and novel phenomena emerged during the switching of the device. We have found that DNAs in this system exhibit a much steep melting transition compared to ones in bulk solution or conventional DNA array. To achieve an understanding to this discrepancy, we introduced DNA-DNA interaction potential to the conventional Ising-like Zimm-Bragg theory and Peyrard-Bishop model of DNA melting. To avoid unrealistic numerical calculation caused by modification of the Peyrard-Bishop nonlinear Hamiltonian with the DNA-DNA interaction, we established coarse-gained Monte Carlo recursion relations by elucidation of five components of energy change during melting transition. The result suggests that DNA-DNA interaction potential accounts for the observed steep transition.Comment: 12 pages, 5 figure