Simulated emergence of cyclic sexual-asexual reproduction

Motivated by the cyclic pattern of reproductive regimes observed in some species of green flies (``{\it aphids}''), we simulate the evolution of a population enduring harsh seasonal conditions for survival. The reproductive regime of each female is also seasonal in principle and genetically acquired, and can mutate for each newborn with some small probability. The results show a sharp transition at a critical value of the survival probability in the winter, between a reproductive regime in the fall that is predominantly sexual, for low values of this probability, or asexual, for high values.Comment: 9 pages, 4 figures, requires RevTe

Justification of Sexual Reproduction by Modified Penna Model of Ageing

We generalize the standard Penna bit-string model of biological ageing by assuming that each deleterious mutation diminishes the survival probability in every time interval by a small percentage. This effect is added to the usual lethal but age-dependent effect of the same mutation. We then find strong advantages or disadvantages of sexual reproduction (with males and females) compared to asexual cloning, depending on parameters.Comment: 4 pages, 2 figures, submitted to Physica

Positive mutations and mutation-dependent Verhulst factor in Penna ageing model

We twice modify the Penna model for biological ageing. First we introduce back (good) mutations and a memory for them into the model. It allows us to observe an improvement of the species fitness over long time scales as well as punctuated equilibrium. Second we adopt a food/space competition factor that depends on the number of accumulated mutations in the individuals genomes, and get rid of the fixed limiting number of allowed mutations. Besides reproducing the main results of the standard model, we also observe a mortality maximum for the oldest old.Comment: 9 pages, including 3 figures, to be submitted to Physica

Fragmentation Experiment and Model for Falling Mercury Drops

The experiment consists of counting and measuring the size of the many fragments observed after the fall of a mercury drop on the floor. The size distribution follows a power-law for large enough fragments. We address the question of a possible crossover to a second, different power-law for small enough fragments. Two series of experiments were performed. The first uses a traditional film photographic camera, and the picture is later treated on a computer in order to count the fragments and classify them according to their sizes. The second uses a modern digital camera. The first approach has the advantage of a better resolution for small fragment sizes. The second, although with a poorer size resolution, is more reliable concerning the counting of all fragments up to its resolution limit. Both together clearly indicate the real existence of the quoted crossover. The model treats the system microscopically during the tiny time interval when the initial drop collides with the floor. The drop is modelled by a connected cluster of Ising spins pointing up (mercury) surrounded by Ising spins pointing down (air). The Ising coupling which tends to keep the spins segregated represents the surface tension. Initially the cluster carries an extra energy equally shared among all its spins, corresponding to the coherent kinetic energy due to the fall. Each spin which touches the floor loses its extra energy transformed into a thermal, incoherent energy represented by a temperature used then to follow the dynamics through Monte Carlo simulations. Whenever a small piece becomes disconnected from the big cluster, it is considered a fragment, and counted. The results also indicate the existence of the quoted crossover in the fragment-size distribution.Comment: 6 pages, 3 figure

Electrochemical oxidation of abietanes

Trabalho Final de Mestrado Integrado, Ciências Farmacêuticas, 2021, Universidade de Lisboa, Faculdade de Farmácia.Os pinheiros são coníferos, dos quais se pode adquirir a madeira e extrair o “tall oil” bruto, a resina e a goma da madeira. Através da destilação da resina podemos adquirir a colofónia e terebintina. A colofónia consiste numa mistura complexa de terpenos neutros e diterpenos ácidos, onde se incluem os abietanos, que são diterpenoides tricíclicos aos quais o ácido abiético (AA) e dehidroabiético (DHA) pertencem. A eletroquímica combina a transferência de eletrões no elétrodo com uma reação química, sendo que podem ser controladas utilizando corrente ou potencial constante. Acabam por ser reações “mais verdes”, seguras, eficientes e económicas. A eletrólise pode ser direta, onde se oxida/reduz diretamente a molécula, ou indireta, onde um se utiliza mediadores, reagentes capazes de oxidar/reduzir seletivamente a molécula. A eletroquímica em fluxo é uma técnica que permite o scale up industrial da eletroquímica, tendo vantagens sobre esta como o oferecer uma maior proximidade entre elétrodos e uma maior área de superfície do elétrodo, o que diminui o tempo de reação e permite a dispensa do uso de eletrólitos de suporte. Neste contexto, o principal objetivo desta investigação assentou em acrescentar valor biossintético à colofónia e aos seus abietanos, utilizando reações orgânicas clássicas, eletroquímica e química em fluxo para sintetizar novos derivados e estudar os potenciais de oxidação destes compostos. Relativamente ao trabalho experimental, começou se por preparar os derivados metil éster do AA e do DHA, pois seriam compostos mais estáveis. Estudamos os potenciais de oxidação destes compostos. Desenvolvemos e otimizamos protocolos para a oxidação eletroquímica, onde conseguimos alcançar a oxidação benzílica direta tanto do DHA como do MDHA com bons rendimentos, a oxidação indireta do MDHA (utilizando Cl4NHPI como mediador) e também conseguimos alcançar a oxidação de AA e MAA com rendimentos moderados. Por fim estudou-se o uso de eletroquímica em fluxo para realizar estas oxidações, usando-se o DHA como material de partida.Pine trees are coniferous, from which we can extract wood, raw tall oil, wood gum, and gum. Through the distillation of gum, we can acquire turpentine and colophony. Colophony is a complex mixture of neutral terpenes and acidic diterpenes, including abietanes, which are tricyclic diterpenoids to which abietic acid (AA) and dehydroabietic acid (DHA) both belong. Electrochemical reactions combine the electron transfer at an electrode with a chemical reaction and can be controlled using constant current or constant potential. Overall, they are very environmentally friendly, safer, efficient, and economical. The electrolysis process can be direct, where we are able to directly oxidize/reduce the molecule, or indirect, where we use a mediator – a selective oxidizing/reducing reagent. Flow electrochemistry is a technique that allows the industrial scale up of electrochemistry, having advantages over it such as offering greater proximity between electrodes and a higher surface area of the electrode, which decreases the reaction time and allows the dispensation of the use of supporting electrolytes. In this regard, the main objective of this research was to add biosynthetic value to colophony and its abietanes, using classic organic reactions and electrochemistry to synthesize new derivates and then study the oxidation potentials of these compounds. Regarding the experimental work, we started by preparing the methyl ester derivatives of AA and DHA, as they would be more stable compounds. We studied the oxidation potentials of these compounds. We developed and optimized protocols for electrochemical oxidation, where we achieved the direct benzylic oxidation of both DHA and MDHA with good yields, the indirect oxidation of MDHA (using Cl4NHPI as a mediator) and we also achieved the oxidation of AA and MAA with moderate yields. Finally, we studied the use of flow electrochemistry to achieve these oxidations using DHA as starting material.Com o patrocínio do Plano de Desenvolvimento Rural 2014-2020 (PDR2020-101-032319 (Parceiro)) and Fundação para a Ciência e a Tecnologia (FCT) (UIDB/04138/2020 and UIDP/04138/2020) for financial support. The project leading to this application has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 951996)

Visualization of security in industrial control systems respecting IEC-62443

The importance of visualizing security in industrial control systems respecting the IEC62443 security standards has increased. This is due to the increase in cyber attacks, its complexity over time, and the security standards created to protect users from compromising them. Through an adequate visualization of security information, it is possible to manage and analyze information to make decisions for good management of systems' security. In this sense, this study's main objective was to describe a possible solution to assist in security management, having been developed in partnership with Siemens Technology, based in Germany. Thus, appropriate tools were used and evaluated to model the data and create visual elements to represent the industrial control system's components. Their security attributes were chosen to be in a dashboard. Kibana was used for three case studies, the last one being the most important for Siemens. The data were obtained through the security software test tool. These were organized and treated to be in a configuration that allowed them to be imported into Kibana and create a dashboard containing the information needed to make decisions and discover gaps in the system. Subsequently, the proposed solution was evaluated through a questionnaire applied to the specialists responsible for industrial control systems security to obtain suggestions that would improve its usefulness and security management assistance. From the results obtained, it was possible to observe the security representation using a visualization tool, demonstrate compliance with IEC-62443 security protocols, thus enabling a simplified security analysis of an industrial control system.A importância de visualizar segurança em sistemas de controlo industrial respeitando as normas de segurança IEC-62443 tem vindo a aumentar. Isto deve-se, ao aumento dos ciberataques, da sua complexidade e das normas criadas para proteger os sistemas. Através de uma adequada visualização de informação sobre a segurança torna-se possível gerir e analisar a informação para tomar decisões e fazer uma boa gestão de segurança. O presente estudo teve como principal objetivo descrever uma solução possível para auxiliar na gestão de segurança tendo sido desenvolvida em parceria com Siemens Technology, sediada na Alemanha. Assim, recorreu-se à avaliação das ferramentas utilizadas para modelar dados e criar elementos visuais para representar os componentes num sistema de controlo industrial e os atributos de segurança escolhidos para estarem num "dashboard". O "Kibana" foi utilizado para três casos, sendo o último o mais importante para a Siemens. Os dados foram obtidos através da ferramenta de teste do software de segurança. Estes foram organizados e tratados de forma a criar um "dashboard" contendo a informação necessária para tomar decisões e descobrir lacunas no sistema. Posteriormente, a solução proposta foi avaliada através de um questionário aplicado aos especialistas de segurança de sistemas de controlo industrial, com o propósito de se obterem sugestões que permitissem melhorar a sua utilidade e assistência na gestão da segurança. Com os resultados obtidos foi possível observar a representação de segurança utilizando uma ferramenta de visualização, respeitando os protocolos de segurança IEC-62443, possibilitando, uma análise simplificada da segurança num sistema de controlo industrial