Aspects of Markov Chains and Particle Systems

Thesis (Ph.D.)--University of Washington, 2016-06

Cytochrome c(551) from Starkeya novella - Characterization, spectroscopic properties, and phylogeny of a diheme protein of the SoxAX family

Cytochromes from the SoxAX family have a major role in thiosulfate oxidation via the thiosulfate-oxidizing multi-enzyme system (TOMES). Previously characterized SoxAX proteins from Rhodovulum sulficlophilum and Paracoccus pantotrophus contain three heme c groups, two of which are located on the SoxA subunit. In contrast, the SoxAX protein purified from Starkeya novella was found to contain only two heme groups. Mass spectrometry showed that a disulfide bond replaced the second heme group found in the diheme SoxA subunits. Apparent molecular masses of 27,229 +/- 10.3 Da and 20,258.6 +/- 1 Da were determined for SoxA and SoxX with an overall mass of 49.7 kDa, indicating a heterodimeric structure. Optical redox potentiometry found that the two heme cofactors are reduced at similar potentials (versus NHE) that are as follows: + 133 mV (pH 6.0); + 104 mV (pH 7.0); +49 (pH 7.9) and +10 mV (pH 8.7). EPR spectroscopy revealed that both ferric heme groups are in the low spin state, and the spectra were consistent with one heme having a His/Cys axial ligation and the other having a His/Met axial ligation. The His/Cys ligated heme is present in different conformational states and gives rise to three distinct signals. Amino acid sequencing was used to unambiguously assign the protein to the encoding genes, soxAX, which are part of a complete sox gene cluster found in S. novella. Phylogenetic analysis of soxA- and soxX-related gene sequences indicates a parallel development of SoxA and SoxY, with the diheme and monoheme SoxA sequences located on clearly separated branches of a phylogenetic tree.

Teleonomic entropy: measuring the phase-space of end-directed systems

We introduce a novel way of measuring the entropy of a set of values undergoing changes. Such a measure becomes useful when analyzing the temporal development of an algorithm designed to numerically update a collection of values such as artificial neural network weights undergoing adjustments during learning. We measure the entropy as a function of the phase-space of the values, i.e. their magnitude and velocity of change, using a method based on the abstract measure of entropy introduced by the philosopher Rudolf Carnap. By constructing a time-dynamic two-dimensional Voronoi diagram using Voronoi cell generators with coordinates of value- and value-velocity (change of magnitude), the entropy becomes a function of the cell areas. We term this measure teleonomic entropy since it can be used to describe changes in any end-directed (teleonomic) system. The usefulness of the method is illustrated when comparing the different approaches of two search algorithms, a learning artificial neural network and a population of discovering agents. (C) 2004 Elsevier Inc. All rights reserved.

The effect of finite bandwidth squeezed light on entanglement creation in the Dicke model

We analyse the relation between local two-atom and total multi-atom entanglements in the Dicke system composed of a large number of atoms. We use concurrence as a measure of entanglement between two atoms in the multi-atom system, and the spin squeezing parameter as a measure of entanglement in the whole n-atom system. In addition, the influence of the squeezing phase and bandwidth on entanglement in the steady-state Dicke system is discussed. It is shown that the introduction of a squeezed field leads to a significant enhancement of entanglement between two atoms, and the entanglement increases with increasing degree of squeezing and bandwidth of the incident squeezed field. In the presence of a coherent field the entanglement exhibits a strong dependence on the relative phase between the squeezed and coherent fields, that can jump quite rapidly from unentangled to strongly entangled values when the phase changes from zero to pi. We find that the jump of the degree of entanglement is due to a flip of the spin squeezing from one quadrature component of the atomic spin to the other component when the phase changes from zero to pi. We also analyse the dependence of the entanglement on the number of atoms and find that, despite the reduction in the degree of entanglement between two atoms, a large entanglement is present in the whole n-atom system and the degree of entanglement increases as the number of atoms increases.

Intelligent decision support for family financial planning

In today’s financial markets characterized by constantly changing tax laws and increasingly complex transactions, the demand for family financial planning (FFP) services is rising dramatically. However, the current trend to develop advisory systems that focus mainly on the financial or investment side fails to consider the whole picture of FFP. Separating financial or investment advice from legal and accounting advice may result in conflicting advice or important omissions that could lead to users suffering financial loss. In this paper, we propose a conceptual model for FFP decision-making process, followed by a novel architecture to support an aggregated FFP decision process by utilizing intelligentagents and Web-services technology. A prototype system for supporting FFP decision is presented to demonstrate the advances of the proposed Web-service multi-agentsbased system architecture and business value.

Belief revision for adaptive negotiation agents

Existing negotiation agents are primitive in terms of what they can learn and how responsive they are towards the changing negotiation contexts. These weaknesses can be alleviated if an expressive representation language is used to represent negotiation contexts and a sound inference mechanism is applied to reason about the preferential changes arising in these negotiation contexts. This paper illustrates a novel adaptive negotiation agent model, which is underpinned by the well-known AGM belief revision logic. Our preliminary experiments show that the performance of the belief-based adaptive negotiation agents is promising.

Monitoring Infants By Automatic Video Processing

This work has, as its objective, the development of non-invasive and low-cost systems for monitoring and automatic diagnosing specific neonatal diseases by means of the analysis of suitable video signals. We focus on monitoring infants potentially at risk of diseases characterized by the presence or absence of rhythmic movements of one or more body parts. Seizures and respiratory diseases are specifically considered, but the approach is general. Seizures are defined as sudden neurological and behavioural alterations. They are age-dependent phenomena and the most common sign of central nervous system dysfunction. Neonatal seizures have onset within the 28th day of life in newborns at term and within the 44th week of conceptional age in preterm infants. Their main causes are hypoxic-ischaemic encephalopathy, intracranial haemorrhage, and sepsis. Studies indicate an incidence rate of neonatal seizures of 0.2% live births, 1.1% for preterm neonates, and 1.3% for infants weighing less than 2500 g at birth. Neonatal seizures can be classified into four main categories: clonic, tonic, myoclonic, and subtle. Seizures in newborns have to be promptly and accurately recognized in order to establish timely treatments that could avoid an increase of the underlying brain damage. Respiratory diseases related to the occurrence of apnoea episodes may be caused by cerebrovascular events. Among the wide range of causes of apnoea, besides seizures, a relevant one is Congenital Central Hypoventilation Syndrome (CCHS) \cite{Healy}. With a reported prevalence of 1 in 200,000 live births, CCHS, formerly known as Ondine's curse, is a rare life-threatening disorder characterized by a failure of the automatic control of breathing, caused by mutations in a gene classified as PHOX2B. CCHS manifests itself, in the neonatal period, with episodes of cyanosis or apnoea, especially during quiet sleep. The reported mortality rates range from 8% to 38% of newborn with genetically confirmed CCHS. Nowadays, CCHS is considered a disorder of autonomic regulation, with related risk of sudden infant death syndrome (SIDS). Currently, the standard method of diagnosis, for both diseases, is based on polysomnography, a set of sensors such as ElectroEncephaloGram (EEG) sensors, ElectroMyoGraphy (EMG) sensors, ElectroCardioGraphy (ECG) sensors, elastic belt sensors, pulse-oximeter and nasal flow-meters. This monitoring system is very expensive, time-consuming, moderately invasive and requires particularly skilled medical personnel, not always available in a Neonatal Intensive Care Unit (NICU). Therefore, automatic, real-time and non-invasive monitoring equipments able to reliably recognize these diseases would be of significant value in the NICU. A very appealing monitoring tool to automatically detect neonatal seizures or breathing disorders may be based on acquiring, through a network of sensors, e.g., a set of video cameras, the movements of the newborn's body (e.g., limbs, chest) and properly processing the relevant signals. An automatic multi-sensor system could be used to permanently monitor every patient in the NICU or specific patients at home. Furthermore, a wire-free technique may be more user-friendly and highly desirable when used with infants, in particular with newborns. This work has focused on a reliable method to estimate the periodicity in pathological movements based on the use of the Maximum Likelihood (ML) criterion. In particular, average differential luminance signals from multiple Red, Green and Blue (RGB) cameras or depth-sensor devices are extracted and the presence or absence of a significant periodicity is analysed in order to detect possible pathological conditions. The efficacy of this monitoring system has been measured on the basis of video recordings provided by the Department of Neurosciences of the University of Parma. Concerning clonic seizures, a kinematic analysis was performed to establish a relationship between neonatal seizures and human inborn pattern of quadrupedal locomotion. Moreover, we have decided to realize simulators able to replicate the symptomatic movements characteristic of the diseases under consideration. The reasons is, essentially, the opportunity to have, at any time, a 'subject' on which to test the continuously evolving detection algorithms. Finally, we have developed a smartphone App, called 'Smartphone based contactless epilepsy detector' (SmartCED), able to detect neonatal clonic seizures and warn the user about the occurrence in real-time.

A concept-based framework for retrieving evidence to support emergency physician decision making at the point of care

The goal of evidence-based medicine is to uniformly apply evidence gained from scientific research to aspects of clinical practice. In order to achieve this goal, new applications that integrate increasingly disparate health care information resources are required. Access to and provision of evidence must be seamlessly integrated with existing clinical workflow and evidence should be made available where it is most often required - at the point of care. In this paper we address these requirements and outline a concept-based framework that captures the context of a current patient-physician encounter by combining disease and patient-specific information into a logical query mechanism for retrieving relevant evidence from the Cochrane Library. Returned documents are organized by automatically extracting concepts from the evidence-based query to create meaningful clusters of documents which are presented in a manner appropriate for point of care support. The framework is currently being implemented as a prototype software agent that operates within the larger context of a multi-agent application for supporting workflow management of emergency pediatric asthma exacerbations. © 2008 Springer-Verlag Berlin Heidelberg.

Effect of mobility on violence in a bi-communal population

We develop a multi-agent based model to simulate a population which comprises of two ethnic groups and a peacekeeping force. We investigate the effects of different strategies for civilian movement to the resulting violence in this bi-communal population. Specifically, we compare and contrast random and race-based migration strategies. Race-based migration leads the formation of clusters. Previous work in this area has shown that same-race clustering instigates violent behavior in otherwise passive segments of the population. Our findings confirm this. Furthermore, we show that in settings where only one of the two races adopts race-based migration it is a winning strategy especially in violently predisposed populations. On the other hand, in relatively peaceful settings clustering is a restricting factor which causes the race that adopts it to drift into annihilation. Finally, we show that when race-based migration is adopted as a strategy by both ethnic groups it results in peaceful co-existence even in the most violently predisposed populations.

Mathematical modelling and control of agitated extraction columns

Liquid-liquid extraction has long been known as a unit operation that plays an important role in industry. This process is well known for its complexity and sensitivity to operation conditions. This thesis presents an attempt to explore the dynamics and control of this process using a systematic approach and state of the art control system design techniques. The process was studied first experimentally under carefully selected. operation conditions, which resembles the ranges employed practically under stable and efficient conditions. Data were collected at steady state conditions using adequate sampling techniques for the dispersed and continuous phases as well as during the transients of the column with the aid of a computer-based online data logging system and online concentration analysis. A stagewise single stage backflow model was improved to mimic the dynamic operation of the column. The developed model accounts for the variation in hydrodynamics, mass transfer, and physical properties throughout the length of the column. End effects were treated by addition of stages at the column entrances. Two parameters were incorporated in the model namely; mass transfer weight factor to correct for the assumption of no mass transfer in the. settling zones at each stage and the backmixing coefficients to handle the axial dispersion phenomena encountered in the course of column operation. The parameters were estimated by minimizing the differences between the experimental and the model predicted concentration profiles at steady state conditions using non-linear optimisation technique. The estimated values were then correlated as functions of operating parameters and were incorporated in·the model equations. The model equations comprise a stiff differential~algebraic system. This system was solved using the GEAR ODE solver. The calculated concentration profiles were compared to those experimentally measured. A very good agreement of the two profiles was achieved within a percent relative error of ±2.S%. The developed rigorous dynamic model of the extraction column was used to derive linear time-invariant reduced-order models that relate the input variables (agitator speed, solvent feed flowrate and concentration, feed concentration and flowrate) to the output variables (raffinate concentration and extract concentration) using the asymptotic method of system identification. The reduced-order models were shown to be accurate in capturing the dynamic behaviour of the process with a maximum modelling prediction error of I %. The simplicity and accuracy of the derived reduced-order models allow for control system design and analysis of such complicated processes. The extraction column is a typical multivariable process with agitator speed and solvent feed flowrate considered as manipulative variables; raffinate concentration and extract concentration as controlled variables and the feeds concentration and feed flowrate as disturbance variables. The control system design of the extraction process was tackled as multi-loop decentralised SISO (Single Input Single Output) as well as centralised MIMO (Multi-Input Multi-Output) system using both conventional and model-based control techniques such as IMC (Internal Model Control) and MPC (Model Predictive Control). Control performance of each control scheme was. studied in terms of stability, speed of response, sensitivity to modelling errors (robustness), setpoint tracking capabilities and load rejection. For decentralised control, multiple loops were assigned to pair.each manipulated variable with each controlled variable according to the interaction analysis and other pairing criteria such as relative gain array (RGA), singular value analysis (SVD). Loops namely Rotor speed-Raffinate concentration and Solvent flowrate Extract concentration showed weak interaction. Multivariable MPC has shown more effective performance compared to other conventional techniques since it accounts for loops interaction, time delays, and input-output variables constraints.

Functional localisation of human sensory-motor cortex using magnetoencephalography

The 19 channel Neuromagnetometer system in the Clinical Neurophysiology Unit at Aston University is a multi-channel system, unique in the United Kingdom. A bite bar head localisation and MRI co-registration strategy which enabled accurate and reproducible localisation of MEG data into cortical space was developed. This afforded the opportunity to study magnetic fields of the human cortex generated by stimulation of peripheral nerve, by stimulation of visceral sensory receptors and by those evoked through voluntary finger movement. Initially, a study of sensory-motor evoked data was performed in a healthy control population. The techniques developed were then applied to patients who were to undergo neurosurgical intervention for the treatment of epilepsy and I or space occupying lesions. This enabled both validation of the effective accuracy of source localisation using MEG as well as to determine the clinical value of MEG in presurgical assessment of functional localisation in human cortex. The studies in this thesis have demonstrated that MEG can repeatedly and reliably locate sources contained within a single gyrus and thus potentially differentiate between disparate gyral activation. This ability is critical in the clinical application of any functional imaging technique; which is yet to be fully validated by any other 'non-invasive' functional imaging methodology. The technique was also applied to the study of visceral sensory representation in the cortex which yielded important data about the multiple cortical representation of visceral sensory function.

The effect of social influence and curfews on civil violence

We investigate the policies of (1) restricting social influence and (2) imposing curfews upon interacting citizens in a community. We compare and contrast their effects on the social order and the emerging levels of civil violence. Influence models have been used in the past in the context of decision making in a variety of application domains. The policy of curfews has been utilised with the aim of curbing social violence but little research has been done on its effectiveness. We develop a multi-agent-based model that is used to simulate a community of citizens and the police force that guards it. We find that restricting social influence does indeed pacify rebellious societies, but has the opposite effect on peaceful ones. On the other hand, our simple model indicates that restricting mobility through curfews has a pacifying effect across all types of society.

Evolution of competing strategies in a threshold model for task allocation

A nature inspired decentralised multi-agent algorithm is proposed to solve a problem of distributed task allocation in which cities produce and store batches of different mail types. Agents must collect and process the mail batches, without global knowledge of their environment or communication between agents. The problem is constrained so that agents are penalised for switching mail types. When an agent process a mail batch of different type to the previous one, it must undergo a change-over, with repeated change-overs rendering the agent inactive. The efficiency (average amount of mail retrieved), and the flexibility (ability of the agents to react to changes in the environment) are investigated both in static and dynamic environments and with respect to sudden changes. New rules for mail selection and specialisation are proposed and are shown to exhibit improved efficiency and flexibility compared to existing ones. We employ a evolutionary algorithm which allows the various rules to evolve and compete. Apart from obtaining optimised parameters for the various rules for any environment, we also observe extinction and speciation.

The influence of memory in a threshold model for distributed task assignment

A nature inspired decentralised multi-agent algorithm is proposed to solve a problem of distributed task selection in which cities produce and store batches of different mail types. Agents must collect and process the mail batches, without a priori knowledge of the available mail at the cities or inter-agent communication. In order to process a different mail type than the previous one, agents must undergo a change-over during which it remains inactive. We propose a threshold based algorithm in order to maximise the overall efficiency (the average amount of mail collected). We show that memory, i.e. the possibility for agents to develop preferences for certain cities, not only leads to emergent cooperation between agents, but also to a significant increase in efficiency (above the theoretical upper limit for any memoryless algorithm), and we systematically investigate the influence of the various model parameters. Finally, we demonstrate the flexibility of the algorithm to changes in circumstances, and its excellent scalability.