Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

Work Fluctuations in Bosonic Josephson Junctions

We calculate the first two moments and full probability distribution of the work performed on a system of bosonic particles in a two-mode Bose-Hubbard Hamiltonian when the self-interaction term is varied instantaneously or with a finite-time ramp. In the instantaneous case, we show how the irreversible work scales differently depending on whether the system is driven to the Josephson or Fock regime of the bosonic Josephson junction. In the finite-time case, we use optimal control techniques to substantially decrease the irreversible work to negligible values. Our analysis can be implemented in present-day experiments with ultracold atoms and we show how to relate the work statistics to that of the population imbalance of the two modes.

Joint Information and Jamming Beamforming for Secrecy Rate Maximization in Cognitive Radio Networks

In this paper, we consider the secure beamforming design for an underlay cognitive radio multiple-input singleoutput broadcast channel in the presence of multiple passive eavesdroppers. Our goal is to design a jamming noise (JN) transmit strategy to maximize the secrecy rate of the secondary system. By utilizing the zero-forcing method to eliminate the interference caused by JN to the secondary user, we study the joint optimization of the information and JN beamforming for secrecy rate maximization of the secondary system while satisfying all the interference power constraints at the primary users, as well as the per-antenna power constraint at the secondary transmitter. For an optimal beamforming design, the original problem is a nonconvex program, which can be reformulated as a convex program by applying the rank relaxation method. To this end, we prove that the rank relaxation is tight and propose a barrier interior-point method to solve the resulting saddle point problem based on a duality result. To find the global optimal solution, we transform the considered problem into an unconstrained optimization problem. We then employ Broyden-Fletcher-Goldfarb-Shanno (BFGS) method to solve the resulting unconstrained problem which helps reduce the complexity significantly, compared to conventional methods. Simulation results show the fast convergence of the proposed algorithm and substantial performance improvements over existing approaches.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

Beam division multiple access for massive MIMO downlink transmission

We study a multiuser multicarrier downlink communication system in which the base station (BS) employs a large number of antennas. By assuming frequency-division duplex operation, we provide a beam domain channel model as the number of BS antennas grows asymptotically large. With this model, we first derive a closed-form upper bound on the achievable ergodic sum-rate before developing necessary conditions to asymptotically maximize the upper bound, with only statistical channel state information at the BS. Inspired by these conditions, we propose a beam division multiple access (BDMA) transmission scheme, where the BS communicates with users via different beams. For BDMA transmission, we design user scheduling to select users within non-overlapping beams, work out an optimal pilot design under a minimum mean square error criterion, and provide optimal pilot sequences by utilizing the Zadoff-Chu sequences. The proposed BDMA scheme reduces significantly the pilot overhead, as well as, the processing complexity at transceivers. Simulations demonstrate the high spectral efficiency of BDMA transmission and the advantages in the bit error rate performance of the proposed pilot sequences.

Effect of serviceability limits on optimal design of steel portal frames

The design of hot-rolled steel portal frames can be sensitive to serviceability deflection limits. In such cases, in order to reduce frame deflections, practitioners increase the size of the eaves haunch and / or the sizes of the steel sections used for the column and rafter members of the frame. This paper investigates the effect of such deflection limits using a real-coded niching genetic algorithm (RC-NGA) that optimizes frame weight, taking into account both ultimate as well as serviceability limit states. The results show that the proposed GA is efficient and reliable. Two different sets of serviceability deflection limits are then considered: deflection limits recommended by the Steel Construction Institute (SCI), which is based on control of differential deflections, and other deflection limits based on suggestions by industry. Parametric studies are carried out on frames with spans ranging between 15 m to 50 m and column heights between 5 m to 10 m. It is demonstrated that for a 50 m span frame, use of the SCI recommended deflection limits can lead to frame weights that are around twice as heavy as compared to designs without these limits.

Parameter sensitivity for optimal design of 65 nm node SOI transistors

Mixed-mode simulation, where device simulation is embedded directly within a circuit simulator, is used for the first time to provide scaling guidelines to achieve optimal digital circuit performance for double gate SOI MOSFETs. This significant advance overcomes the lack of availability of SPICE model parameters. The sensitivity of the gate delay and on-off current ratio to each of the key geometric and technological parameters of the transistor is quantified. The impact of the source-drain doping profile on circuit performance is comprehensively investigated.