Perfect Sampling of the Master Equation for Gene Regulatory Networks

We present a Perfect Sampling algorithm that can be applied to the Master Equation of Gene Regulatory Networks (GRNs). The method recasts Gillespie's Stochastic Simulation Algorithm (SSA) in the light of Markov Chain Monte Carlo methods and combines it with the Dominated Coupling From The Past (DCFTP) algorithm to provide guaranteed sampling from the stationary distribution. We show how the DCFTP-SSA can be generically applied to genetic networks with feedback formed by the interconnection of linear enzymatic reactions and nonlinear Monod- and Hill-type elements. We establish rigorous bounds on the error and convergence of the DCFTP-SSA, as compared to the standard SSA, through a set of increasingly complex examples. Once the building blocks for GRNs have been introduced, the algorithm is applied to study properly averaged dynamic properties of two experimentally relevant genetic networks: the toggle switch, a two-dimensional bistable system, and the repressilator, a six-dimensional genetic oscillator.Comment: Minor rewriting; final version to be published in Biophysical Journa

Event-Driven Optimal Feedback Control for Multi-Antenna Beamforming

Transmit beamforming is a simple multi-antenna technique for increasing throughput and the transmission range of a wireless communication system. The required feedback of channel state information (CSI) can potentially result in excessive overhead especially for high mobility or many antennas. This work concerns efficient feedback for transmit beamforming and establishes a new approach of controlling feedback for maximizing net throughput, defined as throughput minus average feedback cost. The feedback controller using a stationary policy turns CSI feedback on/off according to the system state that comprises the channel state and transmit beamformer. Assuming channel isotropy and Markovity, the controller's state reduces to two scalars. This allows the optimal control policy to be efficiently computed using dynamic programming. Consider the perfect feedback channel free of error, where each feedback instant pays a fixed price. The corresponding optimal feedback control policy is proved to be of the threshold type. This result holds regardless of whether the controller's state space is discretized or continuous. Under the threshold-type policy, feedback is performed whenever a state variable indicating the accuracy of transmit CSI is below a threshold, which varies with channel power. The practical finite-rate feedback channel is also considered. The optimal policy for quantized feedback is proved to be also of the threshold type. The effect of CSI quantization is shown to be equivalent to an increment on the feedback price. Moreover, the increment is upper bounded by the expected logarithm of one minus the quantization error. Finally, simulation shows that feedback control increases net throughput of the conventional periodic feedback by up to 0.5 bit/s/Hz without requiring additional bandwidth or antennas.Comment: 29 pages; submitted for publicatio

Coalescence time and second largest eigenvalue modulus in the monotone reversible case

If T is the coalescence time of the Propp and Wilson [15], perfect simulation algorithm, the aim of this paper is to show that T depends on the second largest eigenvalue modulus of the transition matrix of the underlying Markov chain. This gives a relationship between the ordering based on the speed of convergence to stationarity in total variation distance and the ordering dened in terms of speed of coalescence in perfect simulation. Key words and phrases: Peskun ordering, Covariance ordering, Effciency ordering, MCMC, time-invariance estimating equations, asymptotic variance, continuous time Markov chains.