An interesting discovery in biology is that most genes in an organism are dispensable. That means these genes have minor effects on survival of the organism in standard laboratory conditions. One explanation of this discovery is that some genes play important roles in specific conditions and are essential genes under those conditions. E. coli is a model organism, which is widely used. It can adapt to many stress conditions, including temperature, pH, osmotic, antibiotic, etc. Underlying mechanisms and associated genes of each stress condition responses are usually different. In our analysis, we combined protein abundance data and mutant conditional fitness data into E. coli constraint-based metabolic models to study conditionally essential metabolic genes under temperature and pH stress conditions. Flux Balance Analysis was employed as the modeling method to analysis these data. We discovered lists of metabolic genes, which are E. coli dispensable genes, but conditionally essential under some stress conditions. Among these conditionally essential genes, atpA in low pH stress and nhaA in high pH stress found experimental evidences from previous studies. Our study provides new conditionally essential gene candidates for biologists to explore stress condition mechanisms.

In recent years, the Soil-Plant-Atmosphere (SPA) continuum has faced unprecedented challenges due to anthropogenic modifications and climate change. Understanding the complex dynamics of this system in response to such changes is crucial for addressing contemporary environmental concerns. Albert Einstein's famous quote, "The measure of intelligence is the ability to change", resonates deeply throughout this doctoral thesis. This thesis aims to address the complex issue of SPA interactions by developing a comprehensive set of models capable of representing the intricate dynamics of this system. At the core of this research lies the integration of sophisticated descriptions of hydrological and plant biochemical processes into a novel ecohydrological model, GEOSPACE-1D (Soil Plant Atmosphere Continuum Estimator model in GEOframe). Through a combination of theoretical exploration, engineering methodologies, and empirical experiments, this thesis aims to advance our understanding of SPA interactions. The development of adaptable models, represents a significant contribution to the field. The thesis emphasizes the practical implications of employing models to analyze experimental data, thereby enhancing our comprehension of various phenomena. In conclusion, this thesis provides valuable insights into SPA interactions and lays the groundwork for future research and applications. By embracing the challenge of understanding and modeling the SPA continuum, this work contributes to the ongoing efforts to address environmental challenges and promote sustainable practices.

Submitted by Debora de Oliveira Medeiros null (deboraomedeiros@gmail.com) on 2017-06-13T19:08:30Z No. of bitstreams: 1 dissertacao_arquivar.pdf: 4524135 bytes, checksum: 33a027db23ff40bebc026b9090443d53 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-06-19T12:58:15Z (GMT) No. of bitstreams: 1 medeiros_do_me_prud.pdf: 4524135 bytes, checksum: 33a027db23ff40bebc026b9090443d53 (MD5) / Made available in DSpace on 2017-06-19T12:58:15Z (GMT). No. of bitstreams: 1 medeiros_do_me_prud.pdf: 4524135 bytes, checksum: 33a027db23ff40bebc026b9090443d53 (MD5) Previous issue date: 2017-04-24 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Neste trabalho é apresentado um estudo das equações de Navier Stokes incompressível com superfície livre e métodos de projeção com uma formulação recente denominada laplaciano superficial. Esta formulação tem como finalidade uma melhor descrição da força de tensão superficial e grandezas, como curvatura e vetores tangencial e normal, descritas sobre a interface. Assim, uma condição de tensão normal alternativa é definida, e esta quando discretizada implicitamente e combinada com o método de projeção, descrevem a formulação laplaciano superficial, cuja sua solução é utilizada como condições de contorno para resolver o sistema de equações que descrevem o escoamento. A nova formulação destina-se a resolver um sistema tridiagonal de equações gerado sobre a interface, e usar a solução deste sistema de equações como uma condição de contorno na superfície livre para o sistema linear da correção da pressão no interior do domínio, que é resultante da aplicação do método de projeção. A nova equação que define a condição de tensão normal conta com grandezas definidas na malha euleriana, no contexto Marker-And-Cell (MAC), que devem ser projetadas sobre a malha lagrangeana e também considera a curvatura e os vetores tangente e normal na sua descrição, sendo importante um estudo detalhado de geometria diferencial. Finalmente, variações da formulação laplaciano superficial com tensão superficial para diferenças finitas são aplicadas para resolver os testes numéricos da oscilação da gota e da gota apoiada que possuem solução de referência, além da simulação de um problema com movimento de interface (fountain flow). Nestes testes, concluímos que a variação mais precisa e estável é aquela que aplica uma discretização da equação da tensão normal utilizando médias de valores alocados na malha MAC. / This work presents a study of the Navier-Stokes equations incompressible with free surface and a projection methods with a recent formulation defined as surface laplacian. The purpose of this formulation is to improve the description of the force of stress tension and quantities, as curvature and tangent and normal vectors, present at the interface. Thus, an alternative normal stress condition is defined, and when this is discretized implicitly and combined with the employ of projection method, describe the surface laplacian formulation, whose solution is used as boundary condition to solve the system of equations describing the flow. The new formulation is intended to solve the tridiagonal system of equations generated at the interface, and to use this solution as a boundary condition at free surface for the linear system of the pressure correction inside of domain, which results of the application of the projection method. The new equation used to define the normal stress condition considers quantities defined in the Eulerian mesh, in the Marker-And-Cell context (MAC), that should be projected on the Lagrangian mesh. In addition, in the new equation, it is also considered the influence of the curvature and normal and tangential vectors in your description, so that a detailed study of differential geometry for this computation is important. Finally, variations of the surface laplacian formulation for finite differences are applied for solving numerical tests of the drop oscillation and sessile drop which have reference solutions, beyond of the simulation of a problem with free surface moving (fountain flow). In these tests, we concluded that the most accurate and stable variation is the one that applies a discretization of the normal stress equation using the mean of values in the MAC mesh. / FAPESP: 2015/01243-0