Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Modelling of biological systems using multidimensional population balances

Biological systems are intrinsically heterogeneous and, consequently, their mathematical descriptions should account for this heterogeneity as it often influences the dynamic behaviour of the individual cells. For example, in the cell cycle dependent production ofproteins, it is necessary to account for the distribution of the individual cells with respect to their position in the cell cycle as this has a strong influence on protein production. A second notable example is the formation of cancerous cells. In this case, the failure of regulatory mechanisms results in the transition of somatic cells to their cancerous state. Therefore, in developing the corresponding mathematical model, it is necessary to consider both the different states of the cells as well as their regulation. In this regard, the population balance equation is the ideal mathematical framework to capture cell population heterogeneity as it elegantly takes into account the distribution of cell populations with respect to their intracellular state together with the phenomena of cell birth, division, differentiation and recombination. Recent developments in solution algorithms together with the exponential increase in computational abilities now permit the efficient solution of one-dimensional population balance models which attribute the heterogeneity of cell populations to differences in the age or mass of individual cells. The inherent complexity of biological systems implies that the differentiation of cells based on a single characteristic alone may not be sufficient to capture the underlying biological phenomena. Therefore, current research is focussing on the development of multi-dimensional population balances that consider the differentiation of cells based on multiple characteristics, most notably, the state of cells with respect to key intracellular metabolites. However, conventional numerical techniques are inefficient for the solution of the formulated population balance models and this warrants the development of novel, tailor-made algorithms. This thesis presents one such solution algorithm and demonstrates its application to the study of several biological systems. The algorithm developed herein employs a finite-volume technique to convert the partial-differential equation comprising the population balance model into a set of ordinary differential equations. A two-tier technique based on the solution technique for inhomogeneous differential equations is then developed to solve the system of ordinary differential equations. This approach has two main advantages: (a) the decomposition technique considerably reduces the stiffness of the system of equations enabling more efficient solution, and (b) semianalytical solutions for the integrals employed in the modelling of cell division and differentiation can be obtained further reducing computation times. Further improvements in solution efficiency are obtained by the formulation of a two-level discretisation algorithm. In this approach, processes such as cell growth which are more sensitive to the discretisation are solved using a fine grid whereas less sensitive processes such as cell' division - which are usually more computationally expensive - are solved using a coarse grid at a higher level. Thus, further improvements are obtained in the efficiency of the technique. The solution algorithm is applied to various multi-dimensional population balance models of biological systems. The technique is first demonstrated on models of oscillatory dynamics in yeast glycolysis, cell-cycle related oscillations in eukaryotes, and circadian oscillations in crayfish. A model of cell division and proliferation control in eukaryotes is an example of a second class of problems where extracellular phenomena influence the behaviour of cells. As a third case for demonstration, a hybrid model of biopolymer accumulation in bacteria is formulated. In this case, cybernetic modelling principles are used to account for intracellular competitions while the population balance framework takes into consideration the heterogeneity of the cell population. Another important aspect in the formulation ofmulti-dimensional population balances is the development of the intracellular models themselves. While research in the biological sciences is permitting the formulation of detailed dynamic models of various bioprocesses, the accurate estimation of the kinetic parameters in these models can be difficult due to the unavailability of sufficient experimental data. This can result in considerable parametric uncertainty as is demonstrated on a simple cybernetic' model of biopolymer accumulation in bacteria. However, it is shown that, via the use of systems engineering tools, experiments can be designed that permit the accurate estimation of all model parameters even when measurements pertaining to all modelled quantities are unavailable.Imperial Users onl

Optimisation of Mobile Communication Networks - OMCO NET

The mini conference “Optimisation of Mobile Communication Networks” focuses on advanced methods for search and optimisation applied to wireless communication networks. It is sponsored by Research & Enterprise Fund Southampton Solent University. The conference strives to widen knowledge on advanced search methods capable of optimisation of wireless communications networks. The aim is to provide a forum for exchange of recent knowledge, new ideas and trends in this progressive and challenging area. The conference will popularise new successful approaches on resolving hard tasks such as minimisation of transmit power, cooperative and optimal routing

Meta-heuristic algorithms in car engine design: a literature survey

Meta-heuristic algorithms are often inspired by natural phenomena, including the evolution of species in Darwinian natural selection theory, ant behaviors in biology, flock behaviors of some birds, and annealing in metallurgy. Due to their great potential in solving difficult optimization problems, meta-heuristic algorithms have found their way into automobile engine design. There are different optimization problems arising in different areas of car engine management including calibration, control system, fault diagnosis, and modeling. In this paper we review the state-of-the-art applications of different meta-heuristic algorithms in engine management systems. The review covers a wide range of research, including the application of meta-heuristic algorithms in engine calibration, optimizing engine control systems, engine fault diagnosis, and optimizing different parts of engines and modeling. The meta-heuristic algorithms reviewed in this paper include evolutionary algorithms, evolution strategy, evolutionary programming, genetic programming, differential evolution, estimation of distribution algorithm, ant colony optimization, particle swarm optimization, memetic algorithms, and artificial immune system

Multi objective optimization in charge management of micro grid based multistory carpark

Distributed power supply with the use of renewable energy sources and intelligent energy flow management has undoubtedly become one of the pressing trends in modern power engineering, which also inspired researchers from other fields to contribute to the topic. There are several kinds of micro grid platforms, each facing its own challenges and thus making the problem purely multi objective. In this paper, an evolutionary driven algorithm is applied and evaluated on a real platform represented by a private multistory carpark equipped with photovoltaic solar panels and several battery packs. The algorithm works as a core of an adaptive charge management system based on predicted conditions represented by estimated electric load and production in the future hours. The outcome of the paper is a comparison of the optimized and unoptimized charge management on three different battery setups proving that optimization may often outperform a battery setup with larger capacity in several criteria.Web of Science117art. no. 179

Advanced Signal Processing Techniques Applied to Power Systems Control and Analysis

The work published in this book is related to the application of advanced signal processing in smart grids, including power quality, data management, stability and economic management in presence of renewable energy sources, energy storage systems, and electric vehicles. The distinct architecture of smart grids has prompted investigations into the use of advanced algorithms combined with signal processing methods to provide optimal results. The presented applications are focused on data management with cloud computing, power quality assessment, photovoltaic power plant control, and electrical vehicle charge stations, all supported by modern AI-based optimization methods

Cultural Algorithm based on Decomposition to solve Optimization Problems

Decomposition is used to solve optimization problems by introducing many simple scalar optimization subproblems and optimizing them simultaneously. Dynamic Multi-Objective Optimization Problems (DMOP) have several objective functions and constraints that vary over time. As a consequence of such dynamic changes, the optimal solutions may vary over time, affecting the performance of convergence. In this thesis, we propose a new Cultural Algorithm (CA) based on decomposition (CA/D). The objective of the CA/D algorithm is to decompose DMOP into a number of subproblems that can be optimized using the information shared by neighboring problems. The proposed CA/D approach is evaluated using a number of CEC 2015 optimization benchmark functions. When compared to CA, Multi-population CA (MPCA), and MPCA incorporating game strategies (MPCA-GS), the results obtained showed that CA/D outperformed them in 7 out of the 15 benchmark functions

Optimal control of particle size distribution in semi-batch emulsion polymerisation

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Enabling swarm aggregation of position data via adaptive stigmergy: a case study in urban traffic flows

Urban road congestion estimation is a challenge in traffic management. City traffic state can vary temporally and spatially between road links, depending on crossroads and lanes. In addition, congestion estimation requires some sort of tuning to “what is around” to trigger appropriate reactions. An adaptive aggregation mechanism of position data is therefore crucial for traffic control. We present a biologically-inspired technique to aggregate position samples coming from on-vehicle devices. In essence, each vehicle position sample is spatially and temporally augmented with digital pheromone information, locally deposited and evaporated. As a consequence, an aggregated pheromone concentration appears and stays spontaneously while many stationary vehicles and high density roads occur. Pheromone concentration is then sharpened to achieve a better distinction of critical phenomena to be triggered as detected traffic events. The overall mechanism can be actually enabled if structural parameters are correctly tuned for the given application context. Determining such correct parameters is not a simple task since different urban areas have different traffic flux and density. Thus, an appropriate tuning to adapt parameters to the specific urban area is desirable to make the estimation effective. In this paper, we show how this objective can be achieved by using differential evolution