A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems

Biochemical reactions underlying genetic regulation are often modelled as a continuous-time, discrete-state, Markov process, and the evolution of the associated probability density is described by the so-called chemical master equation (CME). However the CME is typically difficult to solve, since the state-space involved can be very large or even countably infinite. Recently a finite state projection method (FSP) that truncates the state-space was suggested and shown to be effective in an example of a model of the Pap-pili epigenetic switch. However in this example, both the model and the final time at which the solution was computed, were relatively small. Presented here is a Krylov FSP algorithm based on a combination of state-space truncation and inexact matrix-vector product routines. This allows larger-scale models to be studied and solutions for larger final times to be computed in a realistic execution time. Additionally the new method computes the solution at intermediate times at virtually no extra cost, since it is derived from Krylov-type methods for computing matrix exponentials. For the purpose of comparison the new algorithm is applied to the model of the Pap-pili epigenetic switch, where the original FSP was first demonstrated. Also the method is applied to a more sophisticated model of regulated transcription. Numerical results indicate that the new approach is significantly faster and extendable to larger biological models.

Dynamic state estimation for identifying earthquake support motions in instrumented structures

The problem of identification of multi-component and (or) spatially varying earthquake support motions based on measured responses in instrumented structures is considered. The governing equations of motion are cast in the state space form and a time domain solution to the input identification problem is developed based on the Kalman and particle filtering methods. The method allows for noise in measured responses, imperfections in mathematical model for the structure, and possible nonlinear behavior of the structure. The unknown support motions are treated as hypothetical additional system states and a prior model for these motions are taken to be given in terms of white noise processes. For linear systems, the solution is developed within the Kalman filtering framework while, for nonlinear systems, the Monte Carlo simulation based particle filtering tools are employed. In the latter case, the question of controlling sampling variance based on the idea of Rao-Blackwellization is also explored. Illustrative examples include identification of multi-component and spatially varying support motions in linear/nonlinear structures.

Characterisation of supramolecular structures by novel recoupling methods in solid-state NMR

In this work, solid-state NMR methods suitable for the investigation of supramolecular systems were developed and improved. In this context, special interest was focussed on non-covalent interactions responsible for the formation of supramolecular structures, such as pi-pi interacions and hydrogen-bonds. In the first part of this work, solid-state NMR methods were presented that provide information on molecular structure and motion via the investigation of anisotropic interactions, namely quadrupole and dipole-dipole couplings, under magic-angle spinning conditions. A two-dimensional 2H double quantum experiment was developed, which is performed under off magic-angle conditions and correlates 2H isotropic chemical shifts with quasistatic DQ-filtered line shapes. From the latter, the quadrupole coupling parameters of samples deuterated at multiple sites can be extracted in a site-selective fashion. Furthermore, 7Li quadrupole parameters of lithium intercalated into TiO2 were determined by NMR experiments performed under static and MAS conditions, and could provide information on the crystal geometry. For the determination of 7Li-7Li dipole-dipole couplings, multiple-quantum NMR experiments were performed. The 1H-13C REREDOR experiment was found to be capable of determining strong proton-carbon dipole-dipole couplings with an accuracy of 500~Hz, corresponding to a determination of proton-carbon chemical-bond lengths with picometer accuracy In the second part of this work, solid-state NMR experiments were combined with quantum-chemical calculations in order to aid and optimise the interpretation of experimental results. The investigations on Calix[4]hydroquinone nanotubes have shown that this combined approach can provide information on the presence of disordered and/or mobile species in supramolecular structures. As a second example, C3-symmetric discs arranging in helical columnar stacks were investigated. In these systems, 1H chemical shifts experience large pi-shifts due to packing effects, which were found to be long-ranged. Moreover, quantum-chemical calculations revealed that helicity in these systems is induced by the propeller-like conformation of the core of the molecules.

Computational Methods for Identification of Vibrating Structures

System identification deals with the problem of building mathematical models of dynamical systems based on observed data from the system" [1]. In the context of civil engineering, the system refers to a large scale structure such as a building, bridge, or an offshore structure, and identification mostly involves the determination of modal parameters (the natural frequencies, damping ratios, and mode shapes). This paper presents some modal identification results obtained using a state-of-the-art time domain system identification method (data-driven stochastic subspace algorithms [2]) applied to the output-only data measured in a steel arch bridge. First, a three dimensional finite element model was developed for the numerical analysis of the structure using ANSYS. Modal analysis was carried out and modal parameters were extracted in the frequency range of interest, 0-10 Hz. The results obtained from the finite element modal analysis were used to determine the location of the sensors. After that, ambient vibration tests were conducted during April 23-24, 2009. The response of the structure was measured using eight accelerometers. Two stations of three sensors were formed (triaxial stations). These sensors were held stationary for reference during the test. The two remaining sensors were placed at the different measurement points along the bridge deck, in which only vertical and transversal measurements were conducted (biaxial stations). Point estimate and interval estimate have been carried out in the state space model using these ambient vibration measurements. In the case of parametric models (like state space), the dynamic behaviour of a system is described using mathematical models. Then, mathematical relationships can be established between modal parameters and estimated point parameters (thus, it is common to use experimental modal analysis as a synonym for system identification). Stable modal parameters are found using a stabilization diagram. Furthermore, this paper proposes a method for assessing the precision of estimates of the parameters of state-space models (confidence interval). This approach employs the nonparametric bootstrap procedure [3] and is applied to subspace parameter estimation algorithm. Using bootstrap results, a plot similar to a stabilization diagram is developed. These graphics differentiate system modes from spurious noise modes for a given order system. Additionally, using the modal assurance criterion, the experimental modes obtained have been compared with those evaluated from a finite element analysis. A quite good agreement between numerical and experimental results is observed.

Space-state robust control of a Buck converter with amorphous core coil and variable load

Pulse-width modulation is widely used to control electronic converters. One of the most frequently used topologies for high DC voltage/low DC voltage conversion is the Buck converter. These converters are described by a second order system with an LC filter between the switching subsystem and the load. The use of a coil with an amorphous magnetic material core rather than an air core permits the design of smaller converters. If high switching frequencies are used to obtain high quality voltage output, then the value of the auto inductance L is reduced over time. Robust controllers are thus needed if the accuracy of the converter response must be preserved under auto inductance and payload variations. This paper presents a robust controller for a Buck converter based on a state space feedback control system combined with an additional virtual space variable which minimizes the effects of the inductance and load variations when a switching frequency that is not too high is applied. The system exhibits a null steady-state average error response for the entire range of parameter variations. Simulation results and a comparison with a standard PID controller are also presented.

Mathematical methods in power system stability studies

In this thesis various mathematical methods of studying the transient and dynamic stabiIity of practical power systems are presented. Certain long established methods are reviewed and refinements of some proposed. New methods are presented which remove some of the difficulties encountered in applying the powerful stability theories based on the concepts of Liapunov. Chapter 1 is concerned with numerical solution of the transient stability problem. Following a review and comparison of synchronous machine models the superiority of a particular model from the point of view of combined computing time and accuracy is demonstrated. A digital computer program incorporating all the synchronous machine models discussed, and an induction machine model, is described and results of a practical multi-machine transient stability study are presented. Chapter 2 reviews certain concepts and theorems due to Liapunov. In Chapter 3 transient stability regions of single, two and multi~machine systems are investigated through the use of energy type Liapunov functions. The treatment removes several mathematical difficulties encountered in earlier applications of the method. In Chapter 4 a simple criterion for the steady state stability of a multi-machine system is developed and compared with established criteria and a state space approach. In Chapters 5, 6 and 7 dynamic stability and small signal dynamic response are studied through a state space representation of the system. In Chapter 5 the state space equations are derived for single machine systems. An example is provided in which the dynamic stability limit curves are plotted for various synchronous machine representations. In Chapter 6 the state space approach is extended to multi~machine systems. To draw conclusions concerning dynamic stability or dynamic response the system eigenvalues must be properly interpreted, and a discussion concerning correct interpretation is included. Chapter 7 presents a discussion of the optimisation of power system small sjgnal performance through the use of Liapunov functions.

Smallest disentangling state spaces for general entangled bipartite quantum states

Entangled quantum states can be given a separable decomposition if we relax the restriction that the local operators be quantum states. Motivated by the construction of classical simulations and local hidden variable models, we construct `smallest' local sets of operators that achieve this. In other words, given an arbitrary bipartite quantum state we construct convex sets of local operators that allow for a separable decomposition, but that cannot be made smaller while continuing to do so. We then consider two further variants of the problem where the local state spaces are required to contain the local quantum states, and obtain solutions for a variety of cases including a region of pure states around the maximally entangled state. The methods involve calculating certain forms of cross norm. Two of the variants of the problem have a strong relationship to theorems on ensemble decompositions of positive operators, and our results thereby give those theorems an added interpretation. The results generalise those obtained in our previous work on this topic [New J. Phys. 17, 093047 (2015)].

Nonlinear control of the Reaction Wheel Pendulum

In this paper we introduce the Reaction Wheel Pendulum, a novel mechanical system consisting of a physical pendulum with a rotating bob. This system has several attractive features both from a pedagogical standpoint and from a research standpoint. From a pedagogical standpoint, the dynamics are the simplest among the various pendulum experiments available so that the system can be introduced to students earlier in their education. At the same time, the system is nonlinear and underactuated so that it can be used as a benchmark experiment to study recent advanced methodologies in nonlinear control, such as feedback linearization, passivity methods, backstepping and hybrid control. In this paper we discuss two control approaches for the problems of swingup and balance, namely, feedback linearization and passivity based control. We first show that the system is locally feedback linearizable by a local diffeomorphism in state space and nonlinear feedback. We compare the feedback linearization control with a linear pole-placement control for the problem of balancing the pendulum about the inverted position. For the swingup problem we discuss an energy approach based on collocated partial feedback linearization, and passivity of the resulting zero dynamics. A hybrid/switching control strategy is used to switch between the swingup and the balance control. Experimental results are presented.

Strengthening and formally verifying privacy in identity management systems

In a digital world, users’ Personally Identifiable Information (PII) is normally managed with a system called an Identity Management System (IMS). There are many types of IMSs. There are situations when two or more IMSs need to communicate with each other (such as when a service provider needs to obtain some identity information about a user from a trusted identity provider). There could be interoperability issues when communicating parties use different types of IMS. To facilitate interoperability between different IMSs, an Identity Meta System (IMetS) is normally used. An IMetS can, at least theoretically, join various types of IMSs to make them interoperable and give users the illusion that they are interacting with just one IMS. However, due to the complexity of an IMS, attempting to join various types of IMSs is a technically challenging task, let alone assessing how well an IMetS manages to integrate these IMSs. The first contribution of this thesis is the development of a generic IMS model called the Layered Identity Infrastructure Model (LIIM). Using this model, we develop a set of properties that an ideal IMetS should provide. This idealized form is then used as a benchmark to evaluate existing IMetSs. Different types of IMS provide varying levels of privacy protection support. Unfortunately, as observed by Jøsang et al (2007), there is insufficient privacy protection in many of the existing IMSs. In this thesis, we study and extend a type of privacy enhancing technology known as an Anonymous Credential System (ACS). In particular, we extend the ACS which is built on the cryptographic primitives proposed by Camenisch, Lysyanskaya, and Shoup. We call this system the Camenisch, Lysyanskaya, Shoup - Anonymous Credential System (CLS-ACS). The goal of CLS-ACS is to let users be as anonymous as possible. Unfortunately, CLS-ACS has problems, including (1) the concentration of power to a single entity - known as the Anonymity Revocation Manager (ARM) - who, if malicious, can trivially reveal a user’s PII (resulting in an illegal revocation of the user’s anonymity), and (2) poor performance due to the resource-intensive cryptographic operations required. The second and third contributions of this thesis are the proposal of two protocols that reduce the trust dependencies on the ARM during users’ anonymity revocation. Both protocols distribute trust from the ARM to a set of n referees (n > 1), resulting in a significant reduction of the probability of an anonymity revocation being performed illegally. The first protocol, called the User Centric Anonymity Revocation Protocol (UCARP), allows a user’s anonymity to be revoked in a user-centric manner (that is, the user is aware that his/her anonymity is about to be revoked). The second protocol, called the Anonymity Revocation Protocol with Re-encryption (ARPR), allows a user’s anonymity to be revoked by a service provider in an accountable manner (that is, there is a clear mechanism to determine which entity who can eventually learn - and possibly misuse - the identity of the user). The fourth contribution of this thesis is the proposal of a protocol called the Private Information Escrow bound to Multiple Conditions Protocol (PIEMCP). This protocol is designed to address the performance issue of CLS-ACS by applying the CLS-ACS in a federated single sign-on (FSSO) environment. Our analysis shows that PIEMCP can both reduce the amount of expensive modular exponentiation operations required and lower the risk of illegal revocation of users’ anonymity. Finally, the protocols proposed in this thesis are complex and need to be formally evaluated to ensure that their required security properties are satisfied. In this thesis, we use Coloured Petri nets (CPNs) and its corresponding state space analysis techniques. All of the protocols proposed in this thesis have been formally modeled and verified using these formal techniques. Therefore, the fifth contribution of this thesis is a demonstration of the applicability of CPN and its corresponding analysis techniques in modeling and verifying privacy enhancing protocols. To our knowledge, this is the first time that CPN has been comprehensively applied to model and verify privacy enhancing protocols. From our experience, we also propose several CPN modeling approaches, including complex cryptographic primitives (such as zero-knowledge proof protocol) modeling, attack parameterization, and others. The proposed approaches can be applied to other security protocols, not just privacy enhancing protocols.

Practical application of pseudospectral optimization to robot path planning

To obtain minimum time or minimum energy trajectories for robots it is necessary to employ planning methods which adequately consider the platform’s dynamic properties. A variety of sampling, graph-based or local receding-horizon optimisation methods have previously been proposed. These typically use simplified kino-dynamic models to avoid the significant computational burden of solving this problem in a high dimensional state-space. In this paper we investigate solutions from the class of pseudospectral optimisation methods which have grown in favour amongst the optimal control community in recent years. These methods have high computational efficiency and rapid convergence properties. We present a practical application of such an approach to the robot path planning problem to provide a trajectory considering the robot’s dynamic properties. We extend the existing literature by augmenting the path constraints with sensed obstacles rather than predefined analytical functions to enable real world application.

Stochastic modelling of T cell homeostasis for two competing clonotypes via the master equation

Stochastic models for competing clonotypes of T cells by multivariate, continuous-time, discrete state, Markov processes have been proposed in the literature by Stirk, Molina-París and van den Berg (2008). A stochastic modelling framework is important because of rare events associated with small populations of some critical cell types. Usually, computational methods for these problems employ a trajectory-based approach, based on Monte Carlo simulation. This is partly because the complementary, probability density function (PDF) approaches can be expensive but here we describe some efficient PDF approaches by directly solving the governing equations, known as the Master Equation. These computations are made very efficient through an approximation of the state space by the Finite State Projection and through the use of Krylov subspace methods when evolving the matrix exponential. These computational methods allow us to explore the evolution of the PDFs associated with these stochastic models, and bimodal distributions arise in some parameter regimes. Time-dependent propensities naturally arise in immunological processes due to, for example, age-dependent effects. Incorporating time-dependent propensities into the framework of the Master Equation significantly complicates the corresponding computational methods but here we describe an efficient approach via Magnus formulas. Although this contribution focuses on the example of competing clonotypes, the general principles are relevant to multivariate Markov processes and provide fundamental techniques for computational immunology.

Emergent task-specific object semantics through distributed experience networks

Autonomous development of sensorimotor coordination enables a robot to adapt and change its action choices to interact with the world throughout its lifetime. The Experience Network is a structure that rapidly learns coordination between visual and haptic inputs and motor action. This paper presents methods which handle the high dimensionality of the network state-space which occurs due to the simultaneous detection of multiple sensory features. The methods provide no significant increase in the complexity of the underlying representations and also allow emergent, task-specific, semantic information to inform action selection. Experimental results show rapid learning in a real robot, beginning with no sensorimotor mappings, to a mobile robot capable of wall avoidance and target acquisition.

State cycles, initialization and the Trivium stream cipher

Trivium is a keystream generator for a binary additive synchronous stream cipher. It was selected in the final portfolio for the Profile 2 category of the eSTREAM project. The keystream generator is constructed using bit- based shift registers. In this paper we present an alternate representation of Trivium using word-based shift registers, with a word size of three bits. This representation is useful for determining cycles of internal state values. Under this representation it is clear that the state space can be partitioned into subspaces and that over some of these subspaces the state update function is effectively linear. The role of the initialization process is critical in ensuring the states used for generating keystream are updated nonlinearly at some point, as the state update function alone does not provide this.

Hybrid frequency–time domain models for dynamic response analysis of marine structures

Time-domain models of marine structures based on frequency domain data are usually built upon the Cummins equation. This type of model is a vector integro-differential equation which involves convolution terms. These convolution terms are not convenient for analysis and design of motion control systems. In addition, these models are not efficient with respect to simulation time, and ease of implementation in standard simulation packages. For these reasons, different methods have been proposed in the literature as approximate alternative representations of the convolutions. Because the convolution is a linear operation, different approaches can be followed to obtain an approximately equivalent linear system in the form of either transfer function or state-space models. This process involves the use of system identification, and several options are available depending on how the identification problem is posed. This raises the question whether one method is better than the others. This paper therefore has three objectives. The first objective is to revisit some of the methods for replacing the convolutions, which have been reported in different areas of analysis of marine systems: hydrodynamics, wave energy conversion, and motion control systems. The second objective is to compare the different methods in terms of complexity and performance. For this purpose, a model for the response in the vertical plane of a modern containership is considered. The third objective is to describe the implementation of the resulting model in the standard simulation environment Matlab/Simulink.

Parameter estimation of structural commodity price models

Commodity price modeling is normally approached in terms of structural time-series models, in which the different components (states) have a financial interpretation. The parameters of these models can be estimated using maximum likelihood. This approach results in a non-linear parameter estimation problem and thus a key issue is how to obtain reliable initial estimates. In this paper, we focus on the initial parameter estimation problem for the Schwartz-Smith two-factor model commonly used in asset valuation. We propose the use of a two-step method. The first step considers a univariate model based only on the spot price and uses a transfer function model to obtain initial estimates of the fundamental parameters. The second step uses the estimates obtained in the first step to initialize a re-parameterized state-space-innovations based estimator, which includes information related to future prices. The second step refines the estimates obtained in the first step and also gives estimates of the remaining parameters in the model. This paper is part tutorial in nature and gives an introduction to aspects of commodity price modeling and the associated parameter estimation problem.