Baker's First-person Perspectives: They Are Not What They Seem

Lynne Baker's concept of a first-person perspective is not as clear and straightforward as it might seem at first glance. There is a discrepancy between her argumentation that we have first-person perspectives and some characteristics she takes first-person perspectives to have, namely, that the instances of this capacity necessarily persist through time and are indivisible and unduplicable. Moreover, these characteristics cause serious problems concerning personal identity

Triviality of the 2D stochastic Allen-Cahn equation

We consider the stochastic Allen-Cahn equation driven by mollified space-time white noise. We show that, as the mollifier is removed, the solutions converge weakly to 0, independently of the initial condition. If the intensity of the noise simultaneously converges to 0 at a sufficiently fast rate, then the solutions converge to those of the deterministic equation. At the critical rate, the limiting solution is still deterministic, but it exhibits an additional damping term

Diplodia seriata, cause of black fruit rot in organically grown apples in Holland, Belgium and Northern Germany

A fruit rot resembling Gloeosporium infections but appearing on fruits prior to harvest was noticed in organic apple orchards in Holland, Belgium and Northern Germany in 2007. Infections were most commonly observed on ‘Elstar’, but other cultivars were also affected. Fruit colonisation progressed in two steps, whereby a latent stage of sunken black lesions in immature fruits gave rise to a rapidly spreading firm brown rot upon fruit ripening. Isolation experiments from both stages consistently yielded a single species of fungus identified as Diplodia seriata, formerly known under the teleomorph name Botryosphaeria obtusa. Lesions of D. seriata were also seen on leaves as necrotic light brown spots surrounded by a purple halo, and occasionally on small twigs as cankers. Fruit mummies on apple twigs were heavily colonised by D. seriata and are thus likely to carry inoculum for fruit infections during late summer or in the following growing season

Timing and Virtual Observability in Ultimatum Bargaining and "Weak Link" Coordination Games

Previous studies have shown that simply knowing one player moves first can affect behavior in games, even when the first-mover's moves are known to be unobservable. This observation violates the game-theoretic principle that timing of unobserved moves is irrelevant, but is consistent with virtual observability, a theory of how timing can matter without the ability to observe actions. However, this previous research only shows that timing matters in games where knowledge that one player moved first can help select that player's preferred equilibrium, presenting an alternative explanation to virtual observability. We extend this work by varying timing of unobservable moves in ultimatum bargaining games and “weak link” coordination games. In the latter, the equilibrium selection explanation does not predict any change in behavior due to timing differences. We find that timing without observability affects behavior in both games, but not substantially

Stochastic Effects in Quorum Sensing

[cat] En aquesta tesi, estudiem els efectes de la estocàsticitat en la aparició del comportament col·lectiu en poblacions de bacteris que comuniquen per quorum sensing (QS). Ens centrem en el interruptor genètic com a paradigma dels processos de decisió cel·lulars tant en sistemes de bacteris naturals com sintètics. El nostre mètode es basa en la modelització matemàtica i en les simulacions estocàstiques, tant a nivell d'una cèl·lula individual com a nivell d'una població de cèl·lules. A nivell d'una cèl·lula individual, mostrem que el soroll afavoreix l'estabilitat del fenotip de l'estat ``baix'' de l'interruptor genètic autoactivador i que la regió de biestabilitat s'estén quan creix la intensitat de les fluctuacions, un efecte que hem anomenat estabilització estocàstica. A nivell d'una població de cèl·lules, mostrem que el procés de difusió del mecanisme de QS modifica les fluctuacions i la dinàmica de la molècula autoinductora dins de la cèl·lula i interactua amb el soroll en la expressió genètica. En el sistema canònic de QS LuxR/LuxI, mostrem que el soroll en la expressió genètica de LuxR és el principal factor que controla la variabilitat transitòria de l'activació del QS. El soroll intrínsec disminueix la precisió de la coordinació de la població i modifica la dinàmica de la transició de QS. A més, presentem un model d'una població d'interruptors genètics de toggle switch que comuniquen per l'intercanvi de dos senyals difusius de QS. Mostrem que l'increment de la velocitat de difusió, que augmenta la força de l'acoblament entre les cèl·lules, porta a una transició de fase: va des d'una fase desordenada on les cèl·lules salten de manera aleatòria entre els dos estats de l'interruptor, fins a una fase ordenada amb totes les cèl·lules bloquejades en el mateix estat estable. La mateixa transició s'ha trobat en una població de cèl·lules que creixen exponencialment en un volum tancat, amb totes les cèl·lules entrant en l'estat ordenat quan arriben a una mida crítica del sistema. Els nostres resultats suggereixen un nou mecanisme per la decisió cel·lular col·lectiva basat en el fenomen de la transició de fase.[eng] Stochastic fluctuations, or noise, are ubiquitous in biological systems and play an important role in many cellular processes. Experimental evidences have shown that noise affects the reliability of cell coordination in populations of communicating cells. In this thesis, we study the effects of stochasticity in the emergence of collective behavior in populations of bacteria communicating by QS. We focus on the genetic switch as a paradigm of cellular decision making in both natural and synthetic bacterial systems. Our approach is based on mathematical modeling and stochastic simulations, both at the level of the single cell and at the level of the cell population. We focus on four main topics. In the first topic, we analyze the interplay between intracellular noise and the diffusion process of the QS signaling mechanism. We build a model describing the expression of the signaling molecule and its diffusion in a population of cells, focusing on the situation of very low constitutive expression rate. We show that varying the diffusion rate produces a repertoire of dynamics for the signaling molecule. Our results reveal the contribution of intrinsic noise and transcriptional noise (mRNA copy number fluctuations) in the fluctuations of the signaling molecule. We observe that the total noise exhibits a maximum as a function of the diffusion rate, in contrast to previous studies. Thus, the QS communication mechanism modifies the fluctuations of the signaling molecule inside the cell and interacts with the gene expression noise. In the second topic, we study the effects of gene expression noise on the precision of the population coordination in the QS activation of the LuxR/LuxI system. We analyze the response and dynamics of a population of cells to different levels of autoinducer. Our results show that gene expression noise in LuxR is the main factor that controls the transient variability of the QS activation. This study sheds light on the relation between the single cell stochastic dynamics and the collective behavior in a population of communicating cells. In the third topic, we analyze the effects of intrinsic noise in an autoactivating switch in an isolated single cell. We show that noise promotes the stability of the low-state phenotype of the switch and that the bistable region is extended when increasing the intensity of the fluctuations, an effect that we call stochastic stabilization. Our results show that intrinsic noise modifies the epigenetic landscape as well as the switching rate, which results in complex behavior of the stochastic switching dynamics when varying the intensity of noise. Thus, at the level of a single cell, intrinsic noise contributes to the cell-to-cell variability of the genetic switch and can modify its stable states and its dynamics. In the fourth topic, we build a model of a population of toggle switches communicating by the exchange of two diffusible QS signals. We show that increasing the diffusion rate, which increases the coupling strength between the cells, leads to a phase transition from an unordered phase where the cells randomly flip between the two states of the switch, to an ordered phase with all the cells locked into the same stable state. The same transition is found in a population of cells growing exponentially in a closed volume. Moreover, the response of the cells to a varying external signal exhibits a hysteresis loop. We show that the cell-cell coupling enhances the sensitivity of the population response to the external signal and suggest that this new mechanism could be used to increase the robustness and sensitivity of biosensors. Our results suggest a new mechanism for collective cell decision making based on the phenomenon of phase transition

The study of creep in machine elements using finite element methods

Bibliography: pages 92-98.In this thesis a simplified analysis procedure is developed, in which creep laws are decoupled from damage laws, for the purposb of constructing methods of use in the early stages of high temperature design. The procedure is based on the creep and damage laws proposed by Kachanov and Rabotnov. The creep laws are normalised. with respect to a convenient normalising stress. As a consequence of this normalisation, the dependence of the creep law on the stress constant, the time and temperature functions, and the actual load level is removed. In addition, if the reference stress of the component is chosen as the normalising stress, the creep law becomes insensitive to the stress exponent. The non-dimensional creep laws are then implemented in a standard finite element scheme, from which the results of a stationary state creep analysis are then in non-dimensional form. In order to estimate rupture times, the maximum stationary stresses in a component are used together with the damage laws. Conservative failure criteria are derived from the creep and damage laws to extend the method to residual life assessment and damage monitoring. The procedure is illustrated and tested against simple examples and case studies

Stochastic structural analysis of engineering components using the finite element method

Bibliography: p. 113-123.This thesis investigates probabilistic and stochastic methods for structural analysis which can be integrated into existing, commercially available finite element programs. It develops general probabilistic finite element routines which can be implemented within deterministic finite element programs without requiring major code development. These routines are implemented in the general purpose finite element program ABAQUS through its user element subroutine facility and two probabilistic finite elements are developed: a three-dimensional beam element limited to linear material behaviour and a two-dimensional plane element involving elastic-plastic material behaviour. The plane element incorporates plane strain, plane stress and axisymmetric formulations. The numerical accuracy and robustness of the routines are verified and application of the probabilistic finite element method is illustrated in two case studies, one involving a four-story, two-bay frame structure, the other a reactor pressure vessel nozzle. The probabilistic finite element routines developed in this thesis integrate point estimate methods and mean value first order methods within the same program. Both methods require a systematic sequence involving the perturbation of the random parameters to be evaluated, although the perturbation sequence of the methods differ. It is shown that computer-time saving techniques such as Taylor series and iterative perturbation schemes, developed for mean value based methods, can also be used to solve point estimate method problems. These efficient techniques are limited to linear problems; nonlinear problems must use full perturbation schemes. Finally, it is shown that all these probabilistic methods and perturbation schemes can be integrated within one program and can follow many of the existing deterministic program structures and subroutines. An overall strategy for converting deterministic finite element programs to probabilistic finite element programs is outlined