Parallel implementation of stochastic simulation for large scale cellular processes

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Simulation of guiding-centre soliton transmission system stability in the presence of polarisation mode dispersion

Results of full numerical simulations of a guiding-centre soliton system with randomly birefringent SMF fibre are shown and analysed. It emerges that the soliton system becomes unstable even for small amounts of PMD.

Q parameter estimation using numerical simulations for linear and nonlinear transmission systems

We compare the Q parameter obtained from scalar, semi-analytical and full vector models for realistic transmission systems. One set of systems is operated in the linear regime, while another is using solitons at high peak power. We report in detail on the different results obtained for the same system using different models. Polarisation mode dispersion is also taken into account and a novel method to average Q parameters over several independent simulation runs is described. © 2006 Elsevier B.V. All rights reserved.

Numerical implementation of the coarse step method with a varying differential group delay

The effect of having a fixed differential group delay term in the coarse step method results in a periodic pattern in the inserting a varying DGD term at each integration step, according to a Gaussian distribution. Simulation results are given to illustrate the phenomenon and provide some evidence about its statistical nature.

Numerical modelling of devices and advanced transmission schemes embracing Raman effect

This thesis presents a theoretical investigation on applications of Raman effect in optical fibre communication as well as the design and optimisation of various Raman based devices and transmission schemes. The techniques used are mainly based on numerical modelling. The results presented in this thesis are divided into three main parts. First, novel designs of Raman fibre lasers (RFLs) based on Phosphosilicate core fibre are analysed and optimised for efficiency by using a discrete power balance model. The designs include a two stage RFL based on Phosphosilicate core fibre for telecommunication applications, a composite RFL for the 1.6 μm spectral window, and a multiple output wavelength RFL aimed to be used as a compact pump source for fiat gain Raman amplifiers. The use of Phosphosilicate core fibre is proven to effectively reduce the design complexity and hence leads to a better efficiency, stability and potentially lower cost. Second, the generalised Raman amplified gain model approach based on the power balance analysis and direct numerical simulation is developed. The approach can be used to effectively simulate optical transmission systems with distributed Raman amplification. Last, the potential employment of a hybrid amplification scheme, which is a combination between a distributed Raman amplifier and Erbium doped amplifier, is investigated by using the generalised Raman amplified gain model. The analysis focuses on the use of the scheme to upgrade a standard fibre network to 40 Gb/s system.

Computer simulation of form-roll design

Changes in modern structural design have created a demand for products which are light but possess high strength. The objective is a reduction in fuel consumption and weight of materials to satisfy both economic and environmental criteria. Cold roll forming has the potential to fulfil this requirement. The bending process is controlled by the shape of the profile machined on the periphery of the rolls. A CNC lathe can machine complicated profiles to a high standard of precision, but the expertise of a numerical control programmer is required. A computer program was developed during this project, using the expert system concept, to calculate tool paths and consequently to expedite the procurement of the machine control tapes whilst removing the need for a skilled programmer. Codifying the expertise of a human and the encapsulation of knowledge within a computer memory, destroys the dependency on highly trained people whose services can be costly, inconsistent and unreliable. A successful cold roll forming operation, where the product is geometrically correct and free from visual defects, is not easy to attain. The geometry of the sheet after travelling through the rolling mill depends on the residual strains generated by the elastic-plastic deformation. Accurate evaluation of the residual strains can provide the basis for predicting the geometry of the section. A study of geometric and material non-linearity, yield criteria, material hardening and stress-strain relationships was undertaken in this research project. The finite element method was chosen to provide a mathematical model of the bending process and, to ensure an efficient manipulation of the large stiffness matrices, the frontal solution was applied. A series of experimental investigations provided data to compare with corresponding values obtained from the theoretical modelling. A computer simulation, capable of predicting that a design will be satisfactory prior to the manufacture of the rolls, would allow effort to be concentrated into devising an optimum design where costs are minimised.

Towards a practical implementation of coherent WDM:analytical, numerical, and experimental studies

Future optical networks will require the implementation of very high capacity (and therefore spectral efficient) technologies. Multi-carrier systems, such as Orthogonal Frequency Division Multiplexing (OFDM) and Coherent WDM (CoWDM), are promising candidates. In this paper, we present analytical, numerical, and experimental investigations of the impact of the relative phases between optical subcarriers of CoWDM systems, as well as the effect that the number of independently modulated subcarriers can have on the performance. We numerically demonstrate a five-subcarrier and three-subcarrier 10-GBd CoWDM system with direct detected amplitude shift keying (ASK) and differentially/coherently detected (D) phase shift keying (PSK). The simulation results are compared with experimental measurements of a 32-Gbit/s DPSK CoWDM system in two configurations. The first configuration was a practical 3-modulator array where all three subcarriers were independently modulated, the second configuration being a traditional 2-modulator odd/even configuration, where only odd and even subcarriers were independently modulated. Simulation and experimental results both indicate that the independent modulation implementation has a greater dependency on the relative phases between subcarriers, with a stronger penalty for the center subcarrier than the odd/even modulation scheme.

Acousto-optic effect in microstructured polymer fiber bragg gratings : simulation and experimental overview

A fine control of the microstructured polymer fiber Bragg grating spectrum properties, such as maximum reflected power and 3-dB bandwidth, through acousto-optic modulation is presented. For simulation purposes, the device is modelled as a single structure, comprising a silica horn and a fiber Bragg grating. For similar sized structures a good correlation between the numerical results and the experimental data is obtained, allowing the strain field to be completely characterized along the whole structure. It is also shown that the microstructured polymer fiber Bragg grating requires less effort from the piezoelectric actuator to produce modification in the grating spectrum when compared with a silica fiber Bragg grating. This technique has potential to be applied on tunable optical filters and tunable cavities for photonic applications.

Numerical implementation of the coarse step method with a varying differential group delay

The effect of having a fixed differential-group delay term in the coarse-step method results in a periodic pattern in the autocorrelation function. We solve this problem by inserting a varying DGD term at each integration step, according to a Gaussian distribution. Simulation results are given to illustrate the phenomenon and provide some evidence, about its statistical nature.

Acousto-optic effect in microstructured polymer fiber bragg gratings:simulation and experimental overview

A fine control of the microstructured polymer fiber Bragg grating spectrum properties, such as maximum reflected power and 3-dB bandwidth, through acousto-optic modulation is presented. For simulation purposes, the device is modelled as a single structure, comprising a silica horn and a fiber Bragg grating. For similar sized structures a good correlation between the numerical results and the experimental data is obtained, allowing the strain field to be completely characterized along the whole structure. It is also shown that the microstructured polymer fiber Bragg grating requires less effort from the piezoelectric actuator to produce modification in the grating spectrum when compared with a silica fiber Bragg grating. This technique has potential to be applied on tunable optical filters and tunable cavities for photonic applications.

Numerical solution of parabolic Cauchy problems in planar corner domains

An iterative method for the parabolic Cauchy problem in planar domains having a finite number of corners is implemented based on boundary integral equations. At each iteration, mixed well-posed problems are solved for the same parabolic operator. The presence of corner points renders singularities of the solutions to these mixed problems, and this is handled with the use of weight functions together with, in the numerical implementation, mesh grading near the corners. The mixed problems are reformulated in terms of boundary integrals obtained via discretization of the time-derivative to obtain an elliptic system of partial differential equations. To numerically solve these integral equations a Nyström method with super-algebraic convergence order is employed. Numerical results are presented showing the feasibility of the proposed approach. © 2014 IMACS.

Exploration by Means of Computer Simulation of Nonlinear Hierarchical Structure of Neuronal Memory on the Model of Olfactory Bulb

Results of numerical experiments are introduced. Experiments were carried out by means of computer simulation on olfactory bulb for the purpose of checking of thinking mechanisms conceptual model, introduced in [2]. Key role of quasisymbol neurons in processes of pattern identification, existence of mental view, functions of cyclic connections between symbol and quasisymbol neurons as short-term memory, important role of synaptic plasticity in learning processes are confirmed numerically. Correctness of fundamental ideas put in base of conceptual model is confirmed on olfactory bulb at quantitative level.

Evaluation of Pareto/D/1/k Queue by Simulation

The finding that Pareto distributions are adequate to model Internet packet interarrival times has motivated the proposal of methods to evaluate steady-state performance measures of Pareto/D/1/k queues. Some limited analytical derivation for queue models has been proposed in the literature, but their solutions are often of a great mathematical challenge. To overcome such limitations, simulation tools that can deal with general queueing system must be developed. Despite certain limitations, simulation algorithms provide a mechanism to obtain insight and good numerical approximation to parameters of queues. In this work, we give an overview of some of these methods and compare them with our simulation approach, which are suited to solve queues with Generalized-Pareto interarrival time distributions. The paper discusses the properties and use of the Pareto distribution. We propose a real time trace simulation model for estimating the steady-state probability showing the tail-raising effect, loss probability, delay of the Pareto/D/1/k queue and make a comparison with M/D/1/k. The background on Internet traffic will help to do the evaluation correctly. This model can be used to study the long- tailed queueing systems. We close the paper with some general comments and offer thoughts about future work.