Step-up simultaneous tests for identifying active effects in orthogonal saturated designs

A sequence of null hypotheses regarding the number of negligible effects (zero effects) in orthogonal saturated designs is formulated. Two step-up simultaneous testing procedures are proposed to identify active effects (nonzero effects) under the commonly used assumption of effect sparsity. It is shown that each procedure controls the experimentwise error rate at a given $\alpha$ level in the strong sense.Comment: Published at http://dx.doi.org/10.1214/009053606000001136 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Modeling genetic circuit behavior in transiently transfected mammalian cells

Binning cells by plasmid copy number is a common practice for analyzing transient transfection data. In many kinetic models of transfected cells, protein production rates are assumed to be proportional to plasmid copy number. The validity of this assumption in transiently transfected mammalian cells is not clear; models based on this assumption appear unable to reproduce experimental flow cytometry data robustly. We hypothesize that protein saturation at high plasmid copy number is a reason previous models break down and validate our hypothesis by comparing experimental data and a stochastic chemical kinetics model. The model demonstrates that there are multiple distinct physical mechanisms that can cause saturation. On the basis of these observations, we develop a novel minimal bin-dependent ODE model that assumes different parameters for protein production in cells with low versus high numbers of plasmids. Compared to a traditional Hill-function-based model, the bin-dependent model requires only one additional parameter, but fits flow cytometry input-output data for individual modules up to twice as accurately. By composing together models of individually fit modules, we use the bin-dependent model to predict the behavior of six cascades and three feed-forward circuits. The bin-dependent models are shown to provide more accurate predictions on average than corresponding (composed) Hill-function-based models and predictions of comparable accuracy to EQuIP, while still providing a minimal ODE-based model that should be easy to integrate as a subcomponent within larger differential equation circuit models. Our analysis also demonstrates that accounting for batch effects is important in developing accurate composed models.Accepted manuscrip

Greenberger-Horne-Zeilinger generation protocol for N superconducting transmon qubits capacitively coupled to a quantum bus

We propose a circuit quantum electrodynamics (QED) realization of a protocol to generate a Greenberger-Horne-Zeilinger (GHZ) state for $N$ superconducting transmon qubits homogeneously coupled to a superconducting transmission line resonator in the dispersive limit. We derive an effective Hamiltonian with pairwise qubit exchange interactions of the XY type, $\tilde{g}(XX+YY)$, that can be globally controlled. Starting from a separable initial state, these interactions allow to generate a multi-qubit GHZ state within a time $t_{\text{GHZ}}\sim \tilde{g}^{-1}$. We discuss how to probe the non-local nature and the genuine $N$-partite entanglement of the generated state. Finally, we investigate the stability of the proposed scheme to inhomogeneities in the physical parameters.Comment: 9 pages, 4 figures, accepted for publication in PR