Topics in complex systems

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Fundamental laws of physics, although successful in explaining many phenomena observed in nature and society, cannot account for the behaviour of complex, non-Hamiltonian systems. Much effort has been devoted to better understanding the topological properties of these systems. Neither ordered nor disordered, these systems of high variability are found in many areas of science. Studies on sandpiles, earthquakes and lattice gases have all yielded evidence of complexity in the form of power law distributions. This scalefree characteristic is believed to be the hall-mark of complexity known as self-organised criticality. Systems in the self-organised critical state regulate themselves and are resistant to error and attacks. The aim of this thesis is to further current knowledge of complex systems by proposing and analysing three models of real systems. Statistical mechanics and numerical simulations are used to analyse these models. The first model mimics herd behaviour in social groups and encompasses growth and addition. It has been found that when the growth rate is fast enough, the group size distribution conforms to a power law. When the growth rate is slow, the system runs out of free agents in finite time. The second model aims to capture the basic empirical measurements from hospital waiting lists. This model illustrates how the power law distributions found in empirical studies might arise, but also indicates that these distributions are unlikely to be caused by the preferential behaviour of patients or physicians. The third model is a salary comparison model; the salary distributions of most of its variants are power laws. Both mean field and 1-d versions of the model are analysed, and differences between the two versions are identified by looking at the mean absolute difference between the salaries in each version

A prediction module to optimize scheduling in a grid computing environment

Heterogeneous computing environment such as grid computing allows sharing and aggregation of a wide variety of geographically distributed computational resources (such as supercomputers, clusters, data sources, people and storage systems) and present them as a single, unified resource for solving large-scale and data-intensive computing applications. A common problem arising in grid computing is to select the most efficient resource to run a particular program. Also users are required to reserve in advance the resources needed to run their program on the grid. At present the execution time of any program submission depends on guesswork by the user. This leads to inefficient use of resources, incurring extra operation costs such as idling queues or machines. Thus a prediction module was designed and developed to aid the user. This module estimates the execution time of a program by using aspects of static analysis, analytical benchmarking and compiler based approach. It consists of 4 main stages; each with its own functionality. An incoming program is categorized accordingly, parsed and then broken down into smaller units known as tokens. The complexity and relationship amongst these tokens are then analyzed and finally the execution time is estimated for the entire program that was submitted

Characterization of partitioning behaviors of immunoglobulin G in polymer-salt aqueous two-phase systems

The partitioning behavior of immunoglobulin G (IgG) in the aqueous two-phase system (ATPS) composed of poly(ethylene glycol) (PEG) and phosphate was studied. The parameters of ATPS exhibiting the pronounced effects on the partitioning behavior of IgG include phase composition, PEG molecular weight, and the addition of sodium chloride (NaCl). The accumulation of IgG at the interface of the ATPS increased drastically as the tie-line length (TLL) was increased. This trend was correlated with a linear relationship relating the natural logarithm of interfacial partition coefficient (ln G) to the difference of PEG concentration between the top phase and the bottom phase (Δ[PEG]), and a good fit was obtained. An attempt was made to correlate the natural logarithm of partition coefficient (ln K) to the presence of NaCl with the proposed linear relationship, ln K = α″ ln [Cl-] + β″. The proposed relationship, which serves as a better description of the underlying mechanics of the protein partitioning behavior in the polymer-salt ATPS, provides a good fit (r2 > 0.95) for the data of IgG partitioning. An optimum recovery of 99.97% was achieved in an ATPS (pH 7.5) composed of 14.0% (w/w) PEG 1450, 12.5% (w/w) phosphate and 5.0% (w/w) NaCl

Extractive Bioconversion of Gamma-Cyclodextrin and Recycling of Cyclodextrin Glycosyltransferase in Liquid Biphasic System Using Thermo-Separating Polymer

An extractive bioconversion conducted on soluble starch with cyclodextrin glycosyltransferase (CGTase) enzyme in ethylene oxide-propylene oxide (EOPO)/potassium phosphates liquid biphasic system (LBS) to extract gamma-cyclodextrin (γ-CD) was examined. A range of EOPO (with potassium phosphates) molecular weights was screen to investigate the effect of the latter on the partioning efficency of CGTase and γ-CD. The results show that the optimal top phase γ-CD yield (74.4%) was reached in 35.0% (w/w) EOPO 970 and 10.0% (w/w) potassium phosphate with 2.0% (w/w) sodium chloride. A theoretical explanation for the effect of NaCl on γ-CD was also presented. After a 2 h bioconversion process, a total of 0.87 mg/mL concentration of γ-CD was produced in the EOPO/ phosphates LBS top phase. After the extraction of top phase from LBS, four continuous repetitive batches were successfully conducted with relative CGTase activity of 1.00, 0.86, 0.45, and 0.40 respectively

Production of y-cyclodextrin by Bacillus cereus cyclodextrin glycosyltransferase using extractive bioconversion in polymer-salt aqueous two-phase system

Aqueous two-phase system (ATPS) extractive bioconversion provides a technique which integrates bioconversion and purification into a single step process. Extractive bioconversion of gamma-cyclodextrin (γ-CD) from soluble starch with cyclodextrin glycosyltransferase (CGTase, EC 2.4.1.19) enzyme derived from Bacillus cereus was evaluated using polyethylene glycol (PEG)/potassium phosphate based on ATPS. The optimum condition was attained in the ATPS constituted of 30.0% (w/w) PEG 3000 g/mol and 7.0% (w/w) potassium phosphate. A γ-CD concentration of 1.60 mg/mL with a 19% concentration ratio was recovered after 1 h bioconversion process. The γ-CD was mainly partitioned to the top phase (YT = 81.88%), with CGTase partitioning in the salt-rich bottom phase (KCGTase = 0.51). Repetitive batch processes of extractive bioconversion were successfully recycled three times, indicating that this is an environmental friendly and a cost saving technique for γ-CD production and purification

Interfacial partitioning behaviour of bovine serum albumin in polymer-salt aqueous two-phase system

A relationship is proposed for the interfacial partitioning of protein in poly(ethylene glycol) (PEG)-phosphate aqueous two-phase system (ATPS). The relationship relates the natural logarithm of interfacial partition coefficient, ln G to the PEG concentration difference between the top and bottom phases, Δ[PEG], with the equation ln G = AΔ[PEG] + B. Results showed that this relationship provides good fits to the partition of bovine serum albumin (BSA) in ATPS which is comprised of phosphate and PEG of four different molecular weight 1450 g/mol, 2000 g/mol, 3350 g/mol and 4000 g/mol, with the tie-line length (TLL) in the range of 44–60% (w/w) at pH 7.0. The decrease of A values with the increase of PEG molecular weight indicates that the correlation between ln G and Δ[PEG] decreases with the increase in PEG molecular weight and the presence of protein–polymer hydrophobic interaction. When temperature was increased, a non-linear relationship of ln G inversely proportional to temperature was observed. The amount of proteins adsorbed at the interface increased proportionally with the amount of BSA loaded whereas the partition coefficient, K remained relatively constant. The relationship proposed could be applied to elucidate interfacial partitioning behaviour of other biomolecules in polymer-salt ATPS

Plasmodium knowlesi malaria an emerging public health problem in Hulu Selangor, Selangor, Malaysia (2009–2013) : epidemiologic and entomologic analysis.

Background: While transmission of the human Plasmodium species has declined, a significant increase in Plasmodium knowlesi/Plasmodium malariae cases was reported in Hulu Selangor, Selangor, Malaysia. Thus, a study was undertaken to determine the epidemiology and the vectors involved in the transmission of knowlesi malaria. Methods: Cases of knowlesi/malariae malaria in the Hulu Selangor district were retrospectively reviewed and analyzed from 2009 to 2013. Mosquitoes were collected from areas where cases occurred in order to determine the vectors. Leucosphyrus group of mosquitoes were genetically characterized targeting the nuclear internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit I (CO1). In addition, temporal and spatial analyses were carried out for human cases and vectors. Results: Of the 100 microscopy diagnosed P. knowlesi/P. malariae cases over the 5 year period in the Hulu Selangor district, there was predominance of P. knowlesi/P. malariae cases among the young adults (ages 20–39 years; 67 cases; 67%). The majority of the infected people were involved in occupations related to agriculture and forestry (51; 51%). No death was recorded in all these cases. Five hundred and thirty five mosquitoes belonging to 14 species were obtained during the study. Anopheles maculatus was the predominant species (49.5%) followed by Anopheles letifer (13.1%) and Anopheles introlatus (11.6%). Molecular and phylogenetic analysis confirmed the species of the Leucosphyrus group to be An. introlatus. In the present study, only An. introlatus was positive for oocysts. Kernel Density analysis showed that P. knowlesi hotspot areas overlapped with areas where the infected An. introlatus was discovered. This further strengthens the hypothesis that An. introlatusis is the vector for P. knowlesi in the Hulu Selangor district. Unless more information is obtained on the vectors as well as macaque involved in the transmission, it will be difficult to plan effective control strategies. The utilization of modern analytical tools such as GIS (Geographic Information System) is crucial in estimating hotspot areas for targeted control strategies. Conclusions: Anopheles introlatus has been incriminated as vector of P. knowlesi in Hulu Selangor. The cases of P. knowlesi are on the increase and further research using molecular techniques is needed

Uncovering Genes with Divergent mRNA-Protein Dynamics in Streptomyces coelicolor

Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in many studies, examples of divergent trends are frequently observed. Here, we present a comparative transcriptome and proteome analysis of growth and stationary phase adaptation in Streptomyces coelicolor, taking the time-dynamics of process into consideration. These processes are of immense interest in microbiology as they pertain to the physiological transformations eliciting biosynthesis of many naturally occurring therapeutic agents. A shotgun proteomics approach based on mass spectrometric analysis of isobaric stable isotope labeled peptides (iTRAQ™) enabled identification and rapid quantification of approximately 14% of the theoretical proteome of S. coelicolor. Independent principal component analyses of this and DNA microarray-derived transcriptome data revealed that the prominent patterns in both protein and mRNA domains are surprisingly well correlated. Despite this overall correlation, by employing a systematic concordance analysis, we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends. Integrating this data with biological information, we discovered that certain groups of functionally related genes exhibit mRNA-protein discordance in a similar fashion. Our observations suggest that differences between mRNA and protein synthesis/degradation mechanisms are prominent in microbes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level

Execution time prediction of imperative paradigm tasks for grid scheduling optimization

An efficient functioning of a complicated and dynamic grid environment requires a resource manager to monitor and identify the idling resources and to schedule users’ submitted jobs (or programs) accordingly. A common problem arising in grid computing is to select the most efficient resource to run a particular program. At present the execution time of any program submission depends mostly on guesswork by the user. The inaccuracy of guesswork leads to inefficient resource usage, incurring extra operational costs such as idling queues or machines. Thus, in this paper we propose a job execution time prediction module to aid the user. The proposed system will function as a standalone unit where its services can be offered to users as part of a grid portal. This system focuses on imperative paradigm tasks as they are commonly used in a grid environment. We propose a novel methodology and architecture to predict the execution time of jobs using aspects of static analysis, analytical benchmarking and compiler based approach. Essentially a program is analyzed in segments for execution time and these times are combined together to give the total execution time of the program. The experimental results show that the technique is successful in achieving a prediction accuracy of greater than 80%. Future work may involve handling other paradigms such as object-oriented programming and investigating the possibility of integrating the prediction module into a real grid environment