Analysis of signalling pathways using continuous time Markov chains

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Nonlinearity Management in Higher Dimensions

In the present short communication, we revisit nonlinearity management of the time-periodic nonlinear Schrodinger equation and the related averaging procedure. We prove that the averaged nonlinear Schrodinger equation does not support the blow-up of solutions in higher dimensions, independently of the strength in the nonlinearity coefficient variance. This conclusion agrees with earlier works in the case of strong nonlinearity management but contradicts those in the case of weak nonlinearity management. The apparent discrepancy is explained by the divergence of the averaging procedure in the limit of weak nonlinearity management.Comment: 9 pages, 1 figure

Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.Comment: 15 pages, 5 figures, submitted to ISBRA 201

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

Background: Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix ( bHLH) family of transcription factors as an example. Results: Network representations that arrange nodes ( proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion: We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available

Frequencies and Damping rates of a 2D Deformed Trapped Bose gas above the Critical Temperature

We derive the equation of motion for the velocity fluctuations of a 2D deformed trapped Bose gas above the critical temperature in the hydrodynamical regime. From this equation, we calculate the eigenfrequencies for a few low-lying excitation modes. Using the method of averages, we derive a dispersion relation in a deformed trap that interpolates between the collisionless and hydrodynamic regimes. We make use of this dispersion relation to calculate the frequencies and the damping rates for monopole and quadrupole mode in both the regimes. We also discuss the time evolution of the wave packet width of a Bose gas in a time dependent as well as time independent trap.Comment: 13 pages, latex fil

Superposition rules for higher-order systems and their applications

Superposition rules form a class of functions that describe general solutions of systems of first-order ordinary differential equations in terms of generic families of particular solutions and certain constants. In this work we extend this notion and other related ones to systems of higher-order differential equations and analyse their properties. Several results concerning the existence of various types of superposition rules for higher-order systems are proved and illustrated with examples extracted from the physics and mathematics literature. In particular, two new superposition rules for second- and third-order Kummer--Schwarz equations are derived.Comment: (v2) 33 pages, some typos corrected, added some references and minor commentarie

A New Vaccum Type Mercury Still

The still consists of a compact single unit of Pyrex glass embodying a boiler, a water cooled condenser, and a receiver. Mercury can be poured from the receiver as required without disturbing the contents of the boiler

Fundamentals of X-Ray

X-rays were first detected in the year of 1895 by the German physicist, William Conrad Roentgen. The discovery occurred during a systematic search for radiation capable of penetrating materials opaque to ordinary light

Some Effects Associated with Negative Corona Onset

Using concentric cylinder electrodes, observations were made on negative corona in hydrogen, argon, and nitrogen at pressures between 1 and 10 cm. of mercury. Positive ions produced by X-rays passing through argon in the corona chamber produced no measurable secondary effects at potentials below onset. Currents maintained by photo emission from the cathode became unstable at a potential near but definitely below onset

Photocells for Laboratory Use

Cells having various types of composite coatings have been prepared. Particular attention has been given to better insulation and greater stability than is found in commercial cells