We present simulation results of a minimal life-like, artificial, molecular aggregate (i.e. protocell) that has been proposed by Steen Rasussen and coworkers and is currently pursued both experimentally and computationally in interdisciplinary international research projects. We develop a space-time continuous physically motivated simulation framework based on the method of dissipative particle dynamics (DPD) which we incrementally extend (most notably by chemical reactions) to cope with the needs of our model. The applicability of the method over the entire length scale of interest is reintroduced, by rejecting a concern that DPD introduces a freezing artifact for any model above the atomistic scale. This is achieved by deriving an alternative scaling procedure for interaction parameters in the model. We perform system-level simulations of the design which attempt to account for theoretical, and experimental knowledge, as well as results from other computational models. This allows us to address key issues of the replicating subsystems container, genome, and metabolism both individually and in mutual coupling. We analyze each step in the life-cycle of the molecular aggregate, and a finnal integrated simulation of the entire life-cycle is prepared. Our simulations confirm most assumptions of the theoretical designs, but also exhibit unanticipated system-level dynamics. These findings are used to revise the original design of the Los Alamos minimal protocell over the course of the analysis. The results support the hypothesis that self-replication and probably other life-like features can be achieved in systems of formerly unanticipated simplicity if these systems exploit physicochemical principles that are immanent to their physical scale.

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The traffic signal affects the life of virtually everyone every day. The effectiveness of signal systems can reduce the incidence of delays, stops, fuel consumption, emission of pollutants, and accidents. The problems related to rapid growth in traffic congestion call for more effective traffic signalization using robust feedback control methodology. Online traffic-responsive signalization is based on real-time traffic conditions and selects cycle, split, phase, and offset for the intersection according to detector data. A robust traffic feedback control begins with assembling traffic demands, traffic facility supply, and feedback control law for the existing traffic operating environment. This information serves the input to the traffic control process which in turn provides an output in terms of the desired performance under varying conditions. Traffic signalization belongs to a class of hybrid systems since the differential equations model the continuous behavior of the traffic flow dynamics and finite-state machines model the discrete state changes of the controller. A complicating aspect, due to the state-space constraint that queue lengths are necessarily nonnegative, is that the continuous-time system dynamics is actually the projection of a smooth system of ordinary differential equations. This also leads to discontinuities in the boundary dynamics of a sort common in queueing problems. The project is concerned with the design of a feedback controller to minimize accumulated queue lengths in the presence of unknown inflow disturbances at an isolated intersection and a traffic network with some signalized intersections. A dynamical system has finite L₂-gain if it is dissipative in some sense. Therefore, the H<SUB>infinity</SUB>-control problem turns to designing a controller such that the resulting closed loop system is dissipative, and correspondingly there exists a storage function. The major contributions of this thesis include 1) to propose state space models for both isolated multi-phase intersections and a class of queueing networks; 2) to formulate H<SUB>infinity</SUB> problems for the control systems with persistent disturbances; 3) to present the projection dynamics aspects of the problem to account for the constraints on the state variables; 4) formally to study this problem as a hybrid system; 5) to derive traffic-actuated feedback control laws for the multi-phase intersections. Though we have mathematically presented a robust feedback solution for the traffic signalization, there still remains some distance before the physical implementation. A robust adaptive control is an interesting research area for the future traffic signalization. / Ph. D.

PIP3 dynamics observed in membranes are responsible for the protruding edge formation in cancer and amoeboid cells. The mechanisms that maintain those PIP3 domains in three-dimensional space remain elusive, due to limitations in observation and analysis techniques. Recently, a strong relation between the cell geometry, the spatial confinement of the membrane, and the excitable signal transduction system has been revealed by Hörning and Shibata (2019) using a novel 3D spatiotemporal analysis methodology that enables the study of membrane signaling on the entire membrane (Hörning and Shibata, 2019). Here, using 3D spatial fluctuation and phase map analysis on actin polymerization inhibited Dictyostelium cells, we reveal a spatial asymmetry of PIP3 signaling on the membrane that is mediated by the contact perimeter of the plasma membrane—the spatial boundary around the cell-substrate adhered area on the plasma membrane. We show that the contact perimeter guides PIP3 waves and acts as a pinning site of PIP3 phase singularities, that is, the center point of spiral waves. The contact perimeter serves as a diffusion influencing boundary that is regulated by a cell size- and shape-dependent curvature. Our findings suggest an underlying mechanism that explains how local curvature can favor actin polymerization when PIP3 domains get pinned at the curved protrusive membrane edges in amoeboid cells.

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Dans cette thèse nous nous intéressons aux propriétés qualitatives et quantitatives des solutions de quelques équations d'ondes en milieux dispersifs ou dispersifs-dissipatifs. Dans une première partie, nous étudions le problème de Cauchy associé aux équations de Benjamin-Ono généralisées. A l'aide de transformées de jauge, combinées avec des outils d'analyse harmonique, nous prouvons des résultats concernant le caractère localement bien posé pour des données initiales de régularité minimale dans l'échelle des espaces de Sobolev. Dans une seconde partie, nous étudions le problème de Cauchy pour des versions dissipatives des équations de Benjamin-Ono et de Korteweg-de Vries. Nous mettons en évidence l'influence des effets dissipatifs sur ces équations en donnant des résultats optimaux sur leur caractère bien ou mal posé. Ceux-ci sont obtenus en travaillant dans des espaces de type Bourgain adaptés à la partie dispersive-dissipative. Pour finir nous étudions le comportement asymptotique des solutions des équations de KdV dissipatives, lorsque celles-ci existent pour tout temps, en calculant explicitement les premiers termes du développement asymptotique dans de nombreux espaces de Sobolev / This thesis deals with the qualitative and quantitative properties of solutions to some wave equations in dispersive or dispersive-dissipative media. In the first part, we study the Cauchy problem for the generalized Benjamin-Ono equations. By means of gauge transforms combined with some harmonic analysis tools, we prove some local well-posedness results for initial data with minimal regularity in Sobolev spaces. In the second part, we study the Cauchy problem for some dissipative versions of the Benjamin-Ono and Korteweg-de Vries equations. We show the influence of the dissipative effects and prove sharp well and ill-posedness results. This is obtained by working in suitable Bourgain's spaces, adapted to the dispersive-dissipative part of the equation. Finally, we study the asymptotic behavior of solutions to the dissipative KdV equations. We explicitly compute the first terms of the asymptotic expansion in Sobolev spaces

La présente thèse est consacrée à l’étude de la probabilité du chemin d’un mouvement aléatoire sur la base d’une extension de la mécanique Hamiltonienne/Lagrangienne à la dynamique stochastique. La probabilité d’un chemin est d’abord étudiée par simulation numérique dans le cas du mouvement stochastique Gaussien des systèmes non dissipatifs. Ce modèle dynamique idéal implique que, outre les forces aléatoires Gaussiennes, le système est seulement soumis à des forces conservatrices. Ce modèle peut être appliqué à un mouvement aléatoire réel de régime pseudo-périodique en présence d’une force de frottement lorsque l’énergie dissipée est négligeable par rapport à la variation de l’énergie potentielle. Nous constatons que la probabilité de chemin décroît exponentiellement lorsque le son action augmente, c’est à dire, P(A) ~ eˉγA, où γ est une constante caractérisant la sensibilité de la dépendance de l’action à la probabilité de chemin, l’action est calculée par la formule A = ∫T0 Ldt, intégrale temporelle du Lagrangien. L = K–V sur une période de temps fixe T, K est l’énergie cinétique et V est l’énergie potentielle. Ce résultat est une confirmation de l’existence d’un analogue classique du facteur de Feynman eiA/ħ pour le formalisme intégral de chemin de la mécanique quantique des systèmes Hamiltoniens. Le résultat ci-dessus est ensuite étendu au mouvement aléatoire réel avec dissipation. A cet effet, le principe de moindre action doit être généralisé au mouvement amorti de systèmes mécaniques ayant une fonction unique de Lagrange bien définie qui doit avoir la simple connexion habituelle au Hamiltonien. Cela a été fait avec l’aide du Lagrangien suivant L = K − V − Ed, où Ed est l’énergie dissipée. Par le calcul variationnel et la simulation numérique, nous avons prouvé que l’action A = ∫T0 Ldt est stationnaire pour les chemins optimaux déterminés par l’équation newtonienne. Plus précisément, la stationnarité est un minimum pour les mouvements de régime pseudo-périodique, un maximum pour les mouvements d’amortissement apériodique et une inflexion dans le cas intermédiaire. Sur cette base, nous avons étudié la probabilité du chemin du mouvement stochastique Gaussien des systèmes dissipatifs. On constate que la probabilité du chemin dépend toujours de façon exponentielle de l’action Lagrangien pour les mouvements de régime pseudo-périodique, mais dépend toujours de façon exponentielle de l’action cinétique A = ∫T0 Kdt pour régime apériodique. / The present thesis is devoted to the study of path probability of random motion on the basis of an extension of Hamiltonian/Lagrangian mechanics to stochastic dynamics. The path probability is first investigated by numerical simulation for Gaussian stochastic motion of non dissipative systems. This ideal dynamical model implies that, apart from the Gaussian random forces, the system is only subject to conservative forces. This model can be applied to underdamped real random motion in the presence of friction force when the dissipated energy is negligible with respect to the variation of the potential energy. We find that the path probability decreases exponentially with increasing action, i.e., P(A) ~ eˉγA, where γ is a constant characterizing the sensitivity of the action dependence of the path probability, the action is given by A = ∫T0 Ldt, a time integral of the Lagrangian L = K–V over a fixed time period T, K is the kinetic energy and V is the potential energy. This result is a confirmation of the existence of a classical analogue of the Feynman factor eiA/ħ for the path integral formalism of quantum mechanics of Hamiltonian systems. The above result is then extended to real random motion with dissipation. For this purpose, the least action principle has to be generalized to damped motion of mechanical systems with a unique well defined Lagrangian function which must have the usual simple connection to Hamiltonian. This has been done with the help of the following Lagrangian L = K – V – Ed, where Ed is the dissipated energy. By variational calculus and numerical simulation, we proved that the action A = ∫T0 Ldt is stationary for the optimal paths determined by Newtonian equation. More precisely, the stationarity is a minimum for underdamped motion, a maximum for overdamped motion and an inflexion for the intermediate case. On this basis, we studied the path probability of Gaussian stochastic motion of dissipative systems. It is found that the path probability still depends exponentially on Lagrangian action for the underdamped motion, but depends exponentially on kinetic action A = ∫T0 Kdt for the overdamped motion.

Orientador: Silvia Maria Giuliatti Winter / Resumo: Orbitando Saturno encontram-se Anthe, Methone e Aegaeon, três pequenos satélites coorbitais a arcos planetários e em ressonância de corrotação excêntrica com o satélite Mimas, do tipo 10:11 para o arco de Anthe, 14:15 para o arco de Methone e do tipo 7:6 para o arco do anel G (arco coorbital ao satélite Aegaeon). Neste trabalho é estudada a dinâmica de partículas micrométricas em ressonância de corrotação excêntrica, sob o efeito de forças perturbadoras (força de radiação solar e arrasto do plasma) e da influência gravitacional de pequenos satélites. A ressonância de corrotação excêntrica m + 1:m é responsável por criar m sítios nos quais as partículas permanecem azimutalmente confinadas. Quando incluídos satélites hipotéticos nos sítios, as partículas rapidamente colidem como estes, de modo que os sítios ficam vazios em algumas centenas de anos. Ainda foi constatado que existe uma correlação entre o tempo de vida das partículas com o tamanho físico do satélite, sendo verificado um aumento do tempo de vida dos sítios com o raio do satélite, para satélites com raios da ordem de metros, passando a decrescer para satélites com raios da ordem de quilômetros. Tal resultado se deve ao fato dos satélites pequenos tenderem a apenas perturbar a órbita das partículas, as quais realizam maiores excursões em relação ao centro do sítio, enquanto satélites maiores confinam as partículas azimutalmente, de modo que estas permanecem em ressonância de corrotação com Mimas e com o satélite. Efe... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Anthe, Methone and Aegaeon are three tiny saturnian moons. They are coorbital to planetary arcs and are trapped in corotation eccentric resonances with Mimas: 10:11 Anthe’s arc, 14:15 Methone’s arc and 7:6 G ring arc (Aegaeon’s arc). In this work we studied the dynamics of the particles trapped in the corotation eccentric resonances under the effects of dissipative forces (solar radiation force and plasma drag) and coorbitals moonlets. The m + 1:m corotation eccentric resonance creates m sites where the particles will be azimuthally confined for more than 100 thousand years. When satellites are located in the sites, the particles quickly collide with them and these sites are cleaned in a few hundred years. We verified an increase in the lifetime of the sites with the satellites’ radii, for moons with radius of the order of meters, and a decrease in the lifetime with an increase of the satellites’ radii, for kilometer-sized satellites. Satellites with radii of the order of meters only disturb the particles’ orbits, so the particles perform large excursions in relation to the site’s center. Satellites with kilometric radii azimuthally confine the particles, wich remain in resonance with Mimas and with the coorbital satellite. The solar radiation force and plasma drag effects on the semimajor axis remove particles from the azimuthal confinement and the effects on the eccentricity favor collisions with the satellites. The sites of the 7:6, 14:15 and 10:11 corotation resonance, if... (Complete abstract click electronic access below) / Mestre