Matrix operations for the simulation and immediate reverse-engineering of time series data

We present a new method for constructing and decomposing square matrices. This method, based on the computed parameterisation of their implied determinants and minors, operates on the product of factors of a new form of matrix decomposition. This method may be employed to build new matrices with fixed determinant(s). We demonstrate that this new approach is fundamentally well-connected to the Cholesky decomposition if applied on symmetric matrices. We also demonstrate that it is related to the LU decomposition method via a diagonal matrix multiplier. Also through this new method a direct relation between Cholesky decomposition and LU factorisation is shown. This method, presented for the first time, is useful for (re)constructing matrices with a predefined determinant and simulating inverse problems. The inference method introduced here also is based on new matrix manipulation techniques that we have developed for the identification of systems from reproducible time series data

Instantaneous modelling and reverse engineering of data-consistent prime models in seconds!

A theoretical framework that supports automated construction of dynamic prime models purely from experimental time series data has been invented and developed, which can automatically generate (construct) data-driven models of any time series data in seconds. This has resulted in the formulation and formalisation of new reverse engineering and dynamic methods for automated systems modelling of complex systems, including complex biological, financial, control, and artificial neural network systems. The systems/model theory behind the invention has been formalised as a new, effective and robust system identification strategy complementary to process-based modelling. The proposed dynamic modelling and network inference solutions often involve tackling extremely difficult parameter estimation challenges, inferring unknown underlying network structures, and unsupervised formulation and construction of smart and intelligent ODE models of complex systems. In underdetermined conditions, i.e., cases of dealing with how best to instantaneously and rapidly construct data-consistent prime models of unknown (or well-studied) complex system from small-sized time series data, inference of unknown underlying network of interaction is more challenging. This article reports a robust step-by-step mathematical and computational analysis of the entire prime model construction process that determines a model from data in less than a minute

Reverse engineering of drug induced DNA damage response signalling pathway reveals dual outcomes of ATM kinase inhibition

The DNA Damage Response (DDR) pathway represents a signalling mechanism that is activated in eukaryotic cells following DNA damage and comprises of proteins involved in DNA damage detection, DNA repair, cell cycle arrest and apoptosis. This pathway consists of an intricate network of signalling interactions driving the cellular ability to recognise DNA damage and recruit specialised proteins to take decisions between DNA repair or apoptosis. ATM and ATR are central components of the DDR pathway. The activities of these kinases are vital in DNA damage induced phosphorylational induction of DDR substrates. Here, firstly we have experimentally determined DDR signalling network surrounding the ATM/ATR pathway induced following double stranded DNA damage by monitoring and quantifying time dependent inductions of their phosphorylated forms and their key substrates. We next involved an automated inference of unsupervised predictive models of time series data to generate in silico (molecular) interaction maps. We characterized the complex signalling network through system analysis and gradual utilisation of small time series measurements of key substrates through a novel network inference algorithm. Furthermore, we demonstrate an application of an assumption-free reverse engineering of the intricate signalling network of the activated ATM/ATR pathway. We next studied the consequences of such drug induced inductions as well as of time dependent ATM kinase inhibition on cell survival through further biological experiments. Intermediate and temporal modelling outcomes revealed the distinct signaling profile associated with ATM kinase activity and inhibition and explained the underlying signalling mechanism for dual ATM functionality in cytotoxic and cytoprotective pathways

Time-dependent opportunities in energy business : a comparative study of locally available renewable and conventional fuels

This work investigates and compares energy-related, private business strategies, potentially interesting for investors willing to exploit either local biomass sources or strategic conventional fuels. Two distinct fuels and related power-production technologies are compared as a case study, in terms of economic efficiency: the biomass of cotton stalks and the natural gas. The carbon capture and storage option are also investigated for power plants based on both fuel types. The model used in this study investigates important economic aspects using a "real options" method instead of traditional Discounted Cash Flow techniques, as it might handle in a more effective way the problems arising from the stochastic nature of significant cash flow contributors' evolution like electricity, fuel and CO(2) allowance prices. The capital costs have also a functional relationship with time, thus providing an additional reason for implementing, "real options" as well as the learning-curves technique. The methodology as well as the results presented in this work, may lead to interesting conclusions and affect potential private investment strategies and future decision making. This study indicates that both technologies lead to positive investment yields, with the natural gas being more profitable for the case study examined, while the carbon capture and storage does not seem to be cost efficient with the current CO(2) allowance prices. Furthermore, low interest rates might encourage potential investors to wait before actualising their business plans while higher interest rates favor immediate investment decisions. (C) 2009 Elsevier Ltd. All rights reserved

Parameter estimation for Boolean models of biological networks

Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean network models based on experimental data and biological input. The key feature is a discrete analog of parameter estimation for continuous models. With only experimental data as input, the software can be used as a tool for reverse-engineering of Boolean network models from experimental time course data.Comment: Web interface of the software is available at http://polymath.vbi.vt.edu/polynome

Aircraft systems architecting: a functional-logical domain perspective

Presented is a novel framework for early systems architecture design. The framework defines data structures and algorithms that enable the systems architect to operate interactively and simultaneously in both the functional and logical domains. A prototype software tool, called AirCADia Architect, was implemented, which allowed the framework to be evaluated by practicing aircraft systems architects. The evaluation confirmed that, on the whole, the approach enables the architects to effectively express their creative ideas when synthesizing new architectures while still retaining control over the process

Time and frequency domain analysis of sampled data controllers via mixed operation equations

Specification of the mathematical equations required to define the dynamic response of a linear continuous plant, subject to sampled data control, is complicated by the fact that the digital components of the control system cannot be modeled via linear ordinary differential equations. This complication can be overcome by introducing two new mathematical operations; namely, the operation of zero order hold and digial delay. It is shown that by direct utilization of these operations, a set of linear mixed operation equations can be written and used to define the dynamic response characteristics of the controlled system. It also is shown how these linear mixed operation equations lead, in an automatable manner, directly to a set of finite difference equations which are in a format compatible with follow on time and frequency domain analysis methods