A core calculus for the analysis and implementation of biologically inspired languages

The application of Concurrency Theory to Systems Biology is in its earliest stage of progress. The metaphor of cells as computing systems by Regev and Shapiro opened the employment of concurrent languages for the modelling of biological systems. Their peculiar characteristics led to the design of many bio-inspired formalisms which achieve higher faithfulness and specificity. In this thesis we present pi@, an extremely simple and conservative extension of the pi-calculus representing a keystone in this respect, thanks to its expressiveness capabilities. The pi@ calculus is obtained by the addition of polyadic synchronisation and priority to the pi-calculus, in order to achieve compartment semantics and atomicity of complex operations respectively. In its direct application to biological modelling, the stochastic variant of the calculus, Spi@, is shown able to model consistently several phenomena such as formation of molecular complexes, hierarchical subdivision of the system into compartments, inter-compartment reactions, dynamic reorganisation of compartment structure consistent with volume variation. The pivotal role of pi@ is evidenced by its capability of encoding in a compositional way several bio-inspired formalisms, so that it represents the optimal core of a framework for the analysis and implementation of bio-inspired languages. In this respect, the encodings of BioAmbients, Brane Calculi and a variant of P Systems in pi@ are formalised. The conciseness of their translation in pi@ allows their indirect comparison by means of their encodings. Furthermore it provides a ready-to-run implementation of minimal effort whose correctness is granted by the correctness of the respective encoding functions. Further important results of general validity are stated on the expressive power of priority. Several impossibility results are described, which clearly state the superior expressiveness of prioritised languages and the problems arising in the attempt of providing their parallel implementation. To this aim, a new setting in distributed computing (the last man standing problem) is singled out and exploited to prove the impossibility of providing a purely parallel implementation of priority by means of point-to-point or broadcast communication.

Hybrid Methods for Resource Allocation and Scheduling Problems in Deterministic and Stochastic Environments

This work presents exact, hybrid algorithms for mixed resource Allocation and Scheduling problems; in general terms, those consist into assigning over time finite capacity resources to a set of precedence connected activities. The proposed methods have broad applicability, but are mainly motivated by applications in the field of Embedded System Design. In particular, high-performance embedded computing recently witnessed the shift from single CPU platforms with application-specific accelerators to programmable Multi Processor Systems-on-Chip (MPSoCs). Those allow higher flexibility, real time performance and low energy consumption, but the programmer must be able to effectively exploit the platform parallelism. This raises interest in the development of algorithmic techniques to be embedded in CAD tools; in particular, given a specific application and platform, the objective if to perform optimal allocation of hardware resources and to compute an execution schedule. On this regard, since embedded systems tend to run the same set of applications for their entire lifetime, off-line, exact optimization approaches are particularly appealing. Quite surprisingly, the use of exact algorithms has not been well investigated so far; this is in part motivated by the complexity of integrated allocation and scheduling, setting tough challenges for ``pure'' combinatorial methods. The use of hybrid CP/OR approaches presents the opportunity to exploit mutual advantages of different methods, while compensating for their weaknesses. In this work, we consider in first instance an Allocation and Scheduling problem over the Cell BE processor by Sony, IBM and Toshiba; we propose three different solution methods, leveraging decomposition, cut generation and heuristic guided search. Next, we face Allocation and Scheduling of so-called Conditional Task Graphs, explicitly accounting for branches with outcome not known at design time; we extend the CP scheduling framework to effectively deal with the introduced stochastic elements. Finally, we address Allocation and Scheduling with uncertain, bounded execution times, via conflict based tree search; we introduce a simple and flexible time model to take into account duration variability and provide an efficient conflict detection method. The proposed approaches achieve good results on practical size problem, thus demonstrating the use of exact approaches for system design is feasible. Furthermore, the developed techniques bring significant contributions to combinatorial optimization methods.

Dynamic power management: from portable devices to high performance computing

Electronic applications are nowadays converging under the umbrella of the cloud computing vision. The future ecosystem of information and communication technology is going to integrate clouds of portable clients and embedded devices exchanging information, through the internet layer, with processing clusters of servers, data-centers and high performance computing systems. Even thus the whole society is waiting to embrace this revolution, there is a backside of the story. Portable devices require battery to work far from the power plugs and their storage capacity does not scale as the increasing power requirement does. At the other end processing clusters, such as data-centers and server farms, are build upon the integration of thousands multiprocessors. For each of them during the last decade the technology scaling has produced a dramatic increase in power density with significant spatial and temporal variability. This leads to power and temperature hot-spots, which may cause non-uniform ageing and accelerated chip failure. Nonetheless all the heat removed from the silicon translates in high cooling costs. Moreover trend in ICT carbon footprint shows that run-time power consumption of the all spectrum of devices accounts for a significant slice of entire world carbon emissions. This thesis work embrace the full ICT ecosystem and dynamic power consumption concerns by describing a set of new and promising system levels resource management techniques to reduce the power consumption and related issues for two corner cases: Mobile Devices and High Performance Computing.

Stochastic models and dynamic measures for the characterization of bistable circuits

During the last few years, a great deal of interest has risen concerning the applications of stochastic methods to several biochemical and biological phenomena. Phenomena like gene expression, cellular memory, bet-hedging strategy in bacterial growth and many others, cannot be described by continuous stochastic models due to their intrinsic discreteness and randomness. In this thesis I have used the Chemical Master Equation (CME) technique to modelize some feedback cycles and analyzing their properties, including experimental data. In the first part of this work, the effect of stochastic stability is discussed on a toy model of the genetic switch that triggers the cellular division, which malfunctioning is known to be one of the hallmarks of cancer. The second system I have worked on is the so-called futile cycle, a closed cycle of two enzymatic reactions that adds and removes a chemical compound, called phosphate group, to a specific substrate. I have thus investigated how adding noise to the enzyme (that is usually in the order of few hundred molecules) modifies the probability of observing a specific number of phosphorylated substrate molecules, and confirmed theoretical predictions with numerical simulations. In the third part the results of the study of a chain of multiple phosphorylation-dephosphorylation cycles will be presented. We will discuss an approximation method for the exact solution in the bidimensional case and the relationship that this method has with the thermodynamic properties of the system, which is an open system far from equilibrium.In the last section the agreement between the theoretical prediction of the total protein quantity in a mouse cells population and the observed quantity will be shown, measured via fluorescence microscopy.

Comparative Analysis of Alternative Hybrid Systems for Automotive Applications

The main objective of this work was to investigate the impact of different hybridization concepts and levels of hybridization on fuel economy of a standard road vehicle where both conventional and non-conventional hybrid architectures are treated exactly in the same way from the point of view of overall energy flow optimization. Hybrid component models were developed and presented in detail as well as the simulations results mainly for NEDC cycle. The analysis was performed on four different parallel hybrid powertrain concepts: Hybrid Electric Vehicle (HEV), High Speed Flywheel Hybrid Vehicle (HSF-HV), Hydraulic Hybrid Vehicle (HHV) and Pneumatic Hybrid Vehicle (PHV). In order to perform equitable analysis of different hybrid systems, comparison was performed also on the basis of the same usable system energy storage capacity (i.e. 625kJ for HEV, HSF and the HHV) but in the case of pneumatic hybrid systems maximal storage capacity was limited by the size of the systems in order to comply with the packaging requirements of the vehicle. The simulations were performed within the IAV Gmbh - VeLoDyn software simulator based on Matlab / Simulink software package. Advanced cycle independent control strategy (ECMS) was implemented into the hybrid supervisory control unit in order to solve power management problem for all hybrid powertrain solutions. In order to maintain State of Charge within desired boundaries during different cycles and to facilitate easy implementation and recalibration of the control strategy for very different hybrid systems, Charge Sustaining Algorithm was added into the ECMS framework. Also, a Variable Shift Pattern VSP-ECMS algorithm was proposed as an extension of ECMS capabilities so as to include gear selection into the determination of minimal (energy) cost function of the hybrid system. Further, cycle-based energetic analysis was performed in all the simulated cases, and the results have been reported in the corresponding chapters.

Essays On CEO Compensation: New Evidence On The Managerial-Power Vs. Optimal Contracting Debate

This dissertation analyzes the effect of market analysts’ expectations of share prices (price targets) on executive compensation. It examines how well the estimated effects of price targets on compensation fit with two competing views on determining executive compensation: the arm’s length bargaining model, which assumes that a board seeks to maximize shareholders’ interests, and the managerial power model, which assumes that a board seeks to maximize managers’ compensation (Bebchuk et al. 2005). The first chapter documents the pattern of CEO pay from fiscal year 1996 to 2010. The second chapter analyzes the Institutional Broker Estimate System Detail History Price Target data file, which that reports analysts’ price targets for firms. I show that the number of price target announcements is positively associated with company share price’s volatility, that price targets are predictive of changes in the value of stocks, and that when analysts announce positive (negative) expectations of future stock price, share prices change in the same direction in the short run. The third chapter analyzes the effect of price targets on executive compensation. I find that analysts' price targets alter the composition of executive pay between cash-based compensation and stock-based compensation. When analysts forecast a rise (fall) in the share price for a firm, the compensation package tilts toward stock-based (cash-based) compensation. The substitution effect is stronger in companies that have weaker corporate governance. The fourth chapter explores the effect of the introduction of the Sarbanes-Oxley Act (SOX) in 2002 and its reinforcement in 2006 on the options granting process. I show that the introduction of SOX and its reinforcement eliminated the practice of backdating options but increased “spring-loading” of option grants around price targets announcements. Overall, the dissertation shows that price targets provide insights into the determinants of executive pay in favor of the managerial power model.

Ribosome Biogenesis and cell cycle regulation: Effect of RNA Polymerase III inhibition

In cycling cells positive stimuli like nutrient, growth factors and mitogens increase ribosome biogenesis rate and protein synthesis to ensure both growth and proliferation. In contrast, under stress situation, proliferating cells negatively modulate ribosome production to reduce protein synthesis and block cell cycle progression. The main strategy used by cycling cell to coordinate cell proliferation and ribosome biogenesis is to share regulatory elements, which participate directly in ribosome production and in cell cycle regulation. In fact, there is evidence that stimulation or inhibition of cell proliferation exerts direct effect on activity of the RNA polymerases controlling the ribosome biogenesis, while several alterations in normal ribosome biogenesis cause changes of the expression and the activity of the tumor suppressor p53, the main effector of cell cycle progression inhibition. The available data on the cross-talk between ribosome biogenesis and cell proliferation have been until now obtained in experimental model in which changes in ribosome biogenesis were obtained either by reducing the activity of the RNA polymerase I or by down-regulating the expression of the ribosomal proteins. The molecular pathways involved in the relationship between the effect of the inhibition of RNA polymerase III (Pol III) activity and cell cycle progression have been not yet investigated. In eukaryotes, RNA Polymerase III is responsible for transcription of factors involved both in ribosome assembly (5S rRNA) and rRNA processing (RNAse P and MRP).Thus, the aim of this study is characterize the effects of the down-regulation of RNA Polymerase III activity, or the specific depletion of 5S rRNA. The results that will be obtained might lead to a deeper understanding of the molecular pathway that controls the coordination between ribosome biogenesis and cell cycle, and might give useful information about the possibility to target RNA Polymerase III for cancer treatment.

Power Transient Analysis of Experimental Devices for Jules Horowitz Material Testing Reactor (JHR)

The objective of this thesis is the power transient analysis concerning experimental devices placed within the reflector of Jules Horowitz Reactor (JHR). Since JHR material testing facility is designed to achieve 100 MW core thermal power, a large reflector hosts fissile material samples that are irradiated up to total relevant power of 3 MW. MADISON devices are expected to attain 130 kW, conversely ADELINE nominal power is of some 60 kW. In addition, MOLFI test samples are envisaged to reach 360 kW for what concerns LEU configuration and up to 650 kW according to HEU frame. Safety issues concern shutdown transients and need particular verifications about thermal power decreasing of these fissile samples with respect to core kinetics, as far as single device reactivity determination is concerned. Calculation model is conceived and applied in order to properly account for different nuclear heating processes and relative time-dependent features of device transients. An innovative methodology is carried out since flux shape modification during control rod insertions is investigated regarding the impact on device power through core-reflector coupling coefficients. In fact, previous methods considering only nominal core-reflector parameters are then improved. Moreover, delayed emissions effect is evaluated about spatial impact on devices of a diffuse in-core delayed neutron source. Delayed gammas transport related to fission products concentration is taken into account through evolution calculations of different fuel compositions in equilibrium cycle. Provided accurate device reactivity control, power transients are then computed for every sample according to envisaged shutdown procedures. Results obtained in this study are aimed at design feedback and reactor management optimization by JHR project team. Moreover, Safety Report is intended to utilize present analysis for improved device characterization.