One-Port Coaxial Line Sample Holder Characterisation Method of Dielectric Spectra.

A technique for solving the one-port closed coaxial transmission line sample holder scattering equation for complex permittivity inversion for lossy materials is presented. A non-linear least-squares procedure is used for the determination of parameters for the specification of the spectral functional form of the complex permittivity. The method allows for accurate retrieval of many low- and high-permittivity dielectric materials in the frequency range of 1 GHz to 3 GHz inserted into the coaxial cell.

Holimap: an accurate and efficient method for solving stochastic gene network dynamics.

Gene-gene interactions are crucial to the control of sub-cellular processes but our understanding of their stochastic dynamics is hindered by the lack of simulation methods that can accurately and efficiently predict how the distributions of gene product numbers vary across parameter space. To overcome these difficulties, here we present Holimap (high-order linear-mapping approximation), an approach that approximates the protein or mRNA number distributions of a complex gene regulatory network by the distributions of a much simpler reaction system. We demonstrate Holimap's computational advantages over conventional methods by applying it to predict the stochastic time-dependent dynamics of various gene networks, including transcriptional networks ranging from simple autoregulatory loops to complex randomly connected networks, post-transcriptional networks, and post-translational networks.

A stochastic vs deterministic perspective on the timing of cellular events.

Cells are the fundamental units of life, and like all life forms, they change over time. Changes in cell state are driven by molecular processes; of these many are initiated when molecule numbers reach and exceed specific thresholds, a characteristic that can be described as "digital cellular logic". Here we show how molecular and cellular noise profoundly influence the time to cross a critical threshold-the first-passage time-and map out scenarios in which stochastic dynamics result in shorter or longer average first-passage times compared to noise-less dynamics.

Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction.

We introduce a biologically detailed, stochastic model of gene expression describing the multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA export, cytoplasmic mRNA degradation and translation of mRNA into protein. The processes in sub-cellular compartments are described by an arbitrary number of processing stages, thus accounting for a significantly finer molecular description of gene expression than conventional models such as the telegraph, two-stage and three-stage models of gene expression. We use two distinct tools, queueing theory and model reduction using the slow-scale linear-noise approximation, to derive exact or approximate analytic expressions for the moments or distributions of nuclear mRNA, cytoplasmic mRNA and protein fluctuations, as well as lower bounds for their Fano factors in steady-state conditions.