Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Search for a multi-Higgs-boson cascade in W(+)W(-)b(b)over-bar events with the ATLAS detector in pp collisions at root s=8 TeV

A search is presented for new particles in an extension to the Standard Model that includes a heavy Higgs boson (H-0), an intermediate charged Higgs-boson pair (H-+/-), and a light Higgs boson (h(0)). The analysis searches for events involving the production of a single heavy neutral Higgs boson which decays to the charged Higgs boson and a W boson, where the charged Higgs boson subsequently decays into a W boson and the lightest neutral Higgs boson decaying to a bottom-antibottom-quark pair. Such a cascade results in a W-boson pair and a bottom-antibottom-quark pair in the final state. Events with exactly one lepton, missing transverse momentum, and at least four jets are selected from a data sample corresponding to an integrated luminosity of 20.3 fb(-1), collected by the ATLAS detector in proton-proton collisions at root s = 8 TeV at the LHC. The data are found to be consistent with Standard Model predictions, and 95% confidence-level upper limits are set on the product of cross section and branching ratio. These limits range from 0.065 to 43 pb as a function of H-0 and H-+/- masses, with m(h)o fixed at 125 GeV.

Intermediate linguistic task fine-tuning on Multi-lingual models

State-of-the-art NLP systems are generally based on the assumption that the underlying models are provided with vast datasets to train on. However, especially when working in multi-lingual contexts, datasets are often scarce, thus more research should be carried out in this field. This thesis investigates the benefits of introducing an additional training step when fine-tuning NLP models, named Intermediate Training, which could be exploited to augment the data used for the training phase. The Intermediate Training step is applied by training models on NLP tasks that are not strictly related to the target task, aiming to verify if the models are able to leverage the learned knowledge of such tasks. Furthermore, in order to better analyze the synergies between different categories of NLP tasks, experimentations have been extended also to Multi-Task Training, in which the model is trained on multiple tasks at the same time.

The flavor problem and discrete symmetries

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Gauging U(1) symmetries and the number of right-handed neutrinos

In this Letter we consider that assuming: (a) that the only left-handed neutral fermions are the active neutrinos, (b) that B - L is a gauge symmetry, and (c) that the L assignment is restricted to the integer numbers, the anomaly cancellation imply that at least three right-handed neutrinos must be added to the minimal representation content of the electroweak standard model. However, two types of models arise: (i) the usual one where each of the three identical right-handed neutrinos has total lepton number L = 1: (ii) and the other one in which two of them carry L = 4 while the third one carries L = -5. (C) 2009 Elsevier B.V. All rights reserved.

Geometric picture of generalized-CP and Higgs-family transformations in the two-Higgs-doublet model

In the two-Higgs-doublet model (THDM), generalized-CP transformations (phi(i) -> X-ij phi(*)(j) where X is unitary) and unitary Higgs-family transformations (phi(i) -> U-ij phi(j)) have recently been examined in a series of papers. In terms of gauge-invariant bilinear functions of the Higgs fields phi(i), the Higgs-family transformations and the generalized-CP transformations possess a simple geometric description. Namely, these transformations correspond in the space of scalar-field bilinears to proper and improper rotations, respectively. In this formalism, recent results relating generalized CP transformations with Higgs-family transformations have a clear geometric interpretation. We will review what is known regarding THDM symmetries, as well as derive new results concerning those symmetries, namely how they can be interpreted geometrically as applications of several CP transformations.

Flavor changing interaction models and strictly massless neutrinos

It is well known that experimental data, coming from solar and atmospheric neutrino detectors and also from experiments which look for neutrino oscillations. strongly suggest that neutrinos must have a mass different from zero. However at least the solar and/or the atmospheric neutrino data can be related to new flavor changing interactions beyond the standard model instead to the finite mass of neutrinos. This new physics may induce i) extra effects in neutrino-matter interactions, ii) CP violation in pion and lepton decays and, iii) muonium to antimuonium transition. We give two examples of models in which all those effects arise even with strictly massless neutrinos: the 331 model and multi-Higgs doublet extension of the standard model (mHDM) with flavor changing neutral currents in the charged lepton sector. It means that in this kind of models if neutrino masses were eventually needed, they will be independent of the parameters of the new interactions.

Anomalous gauge couplings from composite Higgs and warped extra dimensions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A review of multi-factor capacity expansion models for manufacturing plants:searching for a holistic decision aid

Investment in capacity expansion remains one of the most critical decisions for a manufacturing organisation with global production facilities. Multiple factors need to be considered making the decision process very complex. The purpose of this paper is to establish the state-of-the-art in multi-factor models for capacity expansion of manufacturing plants within a corporation. The research programme consisting of an extensive literature review and a structured assessment of the strengths and weaknesses of the current research is presented. The study found that there is a wealth of mathematical multi-factor models for evaluating capacity expansion decisions however no single contribution captures all the different facets of the problem.

Individual and societal bases of national identity - A comparative multi-level analysis

In a previous study (Jones and Smith, 1999) we established that much the same core pattern of national identity characterizes many developed countries. Using the national identity module from the 1995 International Social Survey Programme, we identified two dimensions of national identity: an ascriptive dimension resembling the concept of ethnic identity described in the historical and theoretical literature, and a voluntarist dimension closer to the notion of civic identity. Some writers view these dimensions in terms of a historical sequence but we find that both constructs coexist in the minds of individual respondents in the nations we examine (we exclude Bulgaria and the Philippines from the present but not the earlier analysis). The dataset used for the multilevel analyses reported here consists of 28 589 respondents in the remaining 21 countries included in the national identity database for the 1995 round of surveys. The macrosociological literature on national identity does not offer well-defined predictions about what precise patterns of national identification we might expect to find among the masses of the developed countries. There are, however, recurring themes from which one can construct plausible hypotheses about how countries might differ according to their level of development, broadly conceived. Thus, we hypothesize that forces such as post-industrialism and globalization tend to favour the more open voluntaristic form of national identity over the more restrictive ascribed form. We develop different multi-level models in order to evaluate specific hypotheses pertaining to such issues, by simultaneously relating individual and societal characteristics to the relative strength of individual commitment to these different types of national identity.

Modelado multi-dominio de máquinas eléctricas. Multi-domain modeling of electric machines

El objetivo general de este proyecto es desarrollar nuevos modelos multi-dominio de máquinas eléctricas para aplicaciones al control y al diagnóstico de fallas. Se propone comenzar con el modelo electromagnético del motor de inducción en base a circuitos magnéticos equivalentes (MEC) validándolo por medio de simulación y de resultados experimentales. Como segundo paso se pretende desarrollas modelos térmicos y mecánicos con el objetivo que puedan ser acoplados al modelo electromagnético y de esta estudiar la interacción de los dominios y se validará mediante resultados de simulación y experimentales el modelo completo. Finalmente se pretende utilizar el modelo multi-dominio como una herramienta para la prueba de nuevas estrategias de control y diagnóstico de fallas. The main objective of this project is the development of new multi-domain models of electric machines for control and fault diagnosis applications. The electromagnetic modeling of the induction motor (IM) will be done using the magnetic equivalent circuits approach. This model will be validated by simulation and by experimental results. As a second step of this project, new mechanical and thermal models for the IM will be developed, with the objective of coupling these models with the electromagnetic one. With this multi-domain model it will be possible to study the interaction between each others. After that, the complete model will be validated by simulation and experimental results. Finally, the model will be used as a tool for testing new control and fault diagnosis strategies.

A multi-objective model for a multi-period distribution management problem

The problems arising in commercial distribution are complex and involve several players and decision levels. One important decision is relatedwith the design of the routes to distribute the products, in an efficient and inexpensive way.This article deals with a complex vehicle routing problem that can beseen as a new extension of the basic vehicle routing problem. The proposed model is a multi-objective combinatorial optimization problemthat considers three objectives and multiple periods, which models in a closer way the real distribution problems. The first objective is costminimization, the second is balancing work levels and the third is amarketing objective. An application of the model on a small example, with5 clients and 3 days, is presented. The results of the model show the complexity of solving multi-objective combinatorial optimization problems and the contradiction between the several distribution management objective.

International Transmission of the Business Cycle in a Multi-Sector Model.

Multi-country models have not been very successful in replicating important features of the international transmission of business cycles. Standard models predict cross-country correlations of output and consumption which are respectively too low and too high. In this paper, we build a multi-country model of the business cycle with multiple sectors in order to analyze the role of sectoral shocks in the international transmission of the business cycle. We find that a model with multiple sectors generates a higher cross-country correlation of output than standard one-sector models, and a lower cross-country correlation of consumption. In addition, it predicts cross-country correlations of employment and investment that are closer to the data than the standard model. We also analyze the relative effects of multiple sectors, trade in intermediate goods, imperfect substitution between domestic and foreign goods, home preference, capital adjustment costs, and capital depreciation on the international transmission of the business cycle.