Doctoral School

Reading date: 24/05/2024

• AGUIRRE RUZ, ALEJANDRO: Numerical approximation of thin structures using stabilized mixed formulations for Infinitesimal and Finite Strain theories, including Fluid-Structure Interaction problem applications.
  
  Author: AGUIRRE RUZ, ALEJANDRO
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN STRUCTURAL ANALYSIS
  Department: (DECA)
  Mode: Normal
  Deposit date: 22/04/2024
  Reading date: 24/05/2024
  Reading time: 12:00
  Reading place: Aula C1002, Edifici C1, Campus Nord ETSECCPB (Escola Tècnica Superior d'Engineria de Camins, Canals i Ports de Barcelona)
  Thesis director: CODINA ROVIRA, RAMON | BAIGES AZNAR, JOAN
  Committee:
       PRESIDENT: ROMERO OLLEROS, IGNACIO
       SECRETARI: ROSSI BERNECOLI, RICCARDO
       VOCAL NO PRESENCIAL: COLOMÉS GENÉ, JOSEP ORIOL
  Thesis abstract: The theories of thin structures can be classified into two main branches depending upon whether shear deformation in the transverse direction is taken into consideration or not. In this context, theories accounting for shear deformations prove suitable for modeling structures with both thin and thick profiles. In the Finite Element context, they are referred to as C0 theories due to the minimum continuity order of shape functions required to pose a discretized approximation. However, there are space incompatibilities in the standard discrete approximation that exhibits spurious solutions, particularly evident in thin structures. These instabilities, known as numerical locking, result in an artificial stiffening of the structure, whose effect becomes more pronounced for thinner structures. Various forms of numerical locking can be triggered, influenced not only by the slenderness of the structure but also by its shape and the nature of the applied loads. In this context, flat structures are prone to shear locking when exposed to transverse loads. Conversely, curved structures may confront different mechanisms leading to various forms of numerical locking, namely membrane, thickness, and trapezoidal locking. The initial part of the study aims to develop a specialized framework to address instabilities in the context of flat structures in the context of Reissner-Mindlin theory. Subsequently, the second part of the study aims to expand the framework to effectively address instabilities arising in of curved structures in the context of Solid-Shell elements. The locking problem is approached by means of a mixed formulation that considers displacements and stress as unknowns in a curvilinear coordinate framework. This approach allows to isolate the components of the stress tensor in order to study the mechanisms in which every type of numerical locking are triggered. The third part of the thesis is dedicated to integrating the previous advancements into Finite Strain analysis by the inclusion of standard hyperelastic constitutive behavior. With this approach, the problem becomes even more difficult to solve because of the non-linearity and the large deformations the shell is subject to. Lastly, the fourth and final part is dedicated to addressing the Fluid-Structure Interaction problem using an embedded mesh approach, which has consistently been a topic of great research interest in the literature, because of its complexity and wide variety of applications. This problem introduces a variety of challenges that have to be properly addressed: the discontinuous pressure field arising for the structure separating the fluid domain, the computation and imposition of transmission conditions between domains, the coupling strategy, and the algorithmic work needed to join all of these ingredients together. This thesis mainly focuses on overcoming challenges associated with thin structures when employing the conventional Galerkin Finite Element approach. It seeks solutions through stabilized methods, specifically within the Variational Multiscale framework. As result, the formulations developed through the investigations have proven to be robust, allowing to model locking-free thin structures efficiently, and to accurately describe the physics of thin shells immersed in fluid flows and being subject to large deformations.
  

• ORNELAS HERRERA, SELENE IVETTE: PREFERENCIAS DE LOS CONSUMIDORES Y AGRICULTORES HACIA UN SISTEMA AGROALIMENTARIO MÁS SOSTENIBLE
  
  Author: ORNELAS HERRERA, SELENE IVETTE
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN SUSTAINABILITY
  Department: University Research Institute for Sustainability Science and Technology (IS.UPC)
  Mode: Normal
  Deposit date: 17/04/2024
  Reading date: 24/05/2024
  Reading time: 11:00
  Reading place: Sala Polivalente de la Escola d'Enginyeria Agroalimentària i de Biosistemes de Barcelona (Castelldefels)
  Thesis director: KALLAS CALOT, ZEIN
  Committee:
       PRESIDENT: SÁNCHEZ GARCÍA, M. MERCEDES
       SECRETARI: RAHMANI MEDDOUR, DJAMEL
       VOCAL: IGLESIAS MARTÍNEZ, EVA
  Thesis abstract: The adaptation of the agri-food system towards more sustainable models is a pressing need to guarantee food security for current and future generations, in the face of population growth, scarce natural resources and climate change. To meet the challenges of producing more sustainably, new food production systems have been developed, they incorporate the principles of circular economy. Circular production systems reduce the consumption of new external inputs and the generation of waste, reducing adverse environmental effects and allowing the recovery of nutrients. This thesis addresses two of the main links in the shortest value chain of the agri-food system, "the producer and the consumer", and their response towards the incorporation of sustainability approaches, such as circularity. The objective is to analyze whether the circular agriculture practices identified as more sustainable are accepted by agricultural producers and the factors that influence their adoption, as well as the preference of consumers and their willingness to pay for these circular production innovations, in order to try to convert the results obtained into evidence that can serve as a basis for generating adequate and coherent public policies, to support and facilitate the adoption of circular innovations. . In relation to the above, in the first instance a semi-structured questionnaire was applied to agricultural producers from: Spain, Austria, Czech Republic and Italy, in which the hierarchical analysis method (AHP) to measure preferences and the scale of the New Ecological Paradigm NEP were included to measure environmental attitudes. Results showed an adoption readiness of 48.24% and that the acceptance of the proposed circular innovations is closely related to the environmental objectives, level of education, previous adoption experience and environmental attitudes of farmers. We also found that institutional support plays an important role in adoption decisions. With regard to consumers, in a first approach, through a survey of 5,246 consumers in Germany, the Netherlands, Italy, the Czech Republic and Spain, their willingness to pay for beef fillet produced in a circular livestock system was analyzed, using the Discrete Choice Experiments (DCE) method. This study included the analysis of the behaviors that influence their preferences, based on the Theory of Planned Behavior (TPB). The results allowed us to observe that there is a potential market for circular beef fillet. Although preferences are heterogeneous, consumers are generally willing to pay a higher premium for circular beef steak than conventional steak and lower than for organic beef. Of the components of planned behavior theory, social norms and behavioral control perception increased preferences for circular production beef steak, while environmental attitudes increased preferences for organic beef steak, and reduced preference for conventional beef steak. Subsequently, the preferences of 5,591 consumers in Spain, Poland, Italy, Hungary, Croatia and Belgium were analyzed, as well as their willingness to pay for pork, milk and bread labelled as circular and presented as more sustainable, in terms of reducing greenhouse gas emissions and optimizing nutrients. This analysis included sustainable consumption behavior, focused on purchasing, use, and recycling habits. The results showed that about 27% of participating consumers preferred foods from circular systems. As in the previous study, the results highlighted the importance of consumers' environmental attitudes in determining their preferences for environmentally sustainable products. All of the above results on consumers allow us to suggest to governments, policy makers and other sectors involved in sustainable food production, the standardization of food labels obtained through circular agriculture systems and the design of educational programs to increase knowledge about the problems generated by unsustainable consumption habits.
  

Reading date: 27/05/2024

• LIN, LI CHUN: Deciphering the role of mechanical stress during ageing and in neurodegenerative diseases
  
  Author: LIN, LI CHUN
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN PHOTONICS
  Department: Institute of Photonic Sciences (ICFO)
  Mode: Normal
  Deposit date: 29/04/2024
  Reading date: pending
  Reading time: pending
  Reading place: pending
  Thesis director: KRIEG, MICHAEL
  Committee:
       PRESIDENT: MARTÍN BLANCO, ENRIQUE
       SECRETARI: SANDOVAL ÁLVAREZ, ÁNGEL
       VOCAL: PEREZ BROWNE, MARCOS FRANCISCO
  Thesis abstract: The locomotion of Caenorhabditis elegans (C. elegans) offers a unique platform for studying complex postures and motor behaviors. In this study, I investigated locomotor patterns across different ages and genetic backgrounds of C. elegans, utilizing customized tracking systems and advanced analysis techniques. A comprehensive examination of locomotion behaviors was conducted using the eigenworm approach. Eigenworms are the principal components of the animals¿ posture space. I identified specific eigenworms associated with forward movement, turning, and exaggerated bends. Notably, spectrin-mutant animals showed a strong correlation between their bending movements and a specific eigenworm for turning in wild-type animals. These findings suggest that eigenworms offer a universal framework to compare different types of worm movement and assess the effects of mutations. This paves the way for a more informative analysis of worm behavior, especially when combined with studies of neuronal networks.Additionally, I explored the role of proprioception in coordinating motor activities within C. elegans, employing genetic and modeling approaches. The focus of my research was to elucidate the mechanisms underlying proprioceptive feedback, including mechanical stress and neuronal signaling, with a focus on age-related deficits. My findings elucidate that the spectral network associated with a singular proprioceptive DVA interneuron, which modulates tension and compression states, serves as a critical determinant of body posture. Intriguingly, a striking resemblance was observed between animals of early ageing and the mutant animals for ß-spectrin, where both animals crawled with exaggerated body bends. Moreover, I show that proprioceptive neurons are found to encode body posture and exhibit age-dependent structural and functional alterations, including protein aggregation and decreased mechanical tension. Notably, spectrin, a cytoskeletal component, emerges as a key player in maintaining proprioceptive integrity during ageing.Furthermore, I investigated the molecular pathways underlying age-associated proprioceptive defects, more specifically, the role CLP-1 protease in the cleavage of UNC-70/ß-spectrin in ageing animals. Conditional knockout of clp-1 in DVA interneuron revealed altered locomotor behaviors, along with the pan-neuronal knockout of clp-1. Given the role of spectrin in proprioception through DVA interneuron suggests that clp-1 regulates spectrin in age-related neurodegeneration. Lastly, I explored the effect of ectopic expression of human ¿ßcrystalline on ageing. We hypothesized that ¿ß-crystallin (HSPB5), a small heat shock protein (sHsp), will stabilize ß-spectrin and shield it from clp-1 proteolytic degradation during ageing. I ectopically expressed the constitutively active 3E mutant of ¿ß-crystallin pan-neuronally or specifically in DVA. Through locomotion analysis of animals from young adult to adult day 6, I observed a modest rescue in the locomotion behavioral pattern in both DVA specific and pan-neuronally expressed ¿ß-crystallin animals. We speculate that constitutively active ¿ß-crystallin may bind to proteolytically vulnerable domains/residues of the UNC-70 protein, providing protection against proteases such as clp-1. Collectively, these findings contribute to our understanding of proprioceptive mechanisms in ageing and offer insights into potential therapeutic targets for age-related neurodegenerative diseases.
  

Reading date: 28/05/2024

• JOSEPH, DIYA: Improving memory access efficiency for real-time rendering in tile-based GPU architectures
  
  Author: JOSEPH, DIYA
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN COMPUTER ARCHITECTURE
  Department: (DAC)
  Mode: Normal
  Deposit date: 30/04/2024
  Reading date: pending
  Reading time: pending
  Reading place: pending
  Thesis director: GONZÁLEZ COLÁS, ANTONIO MARIA | ARAGÓN ALCARAZ, JUAN LUIS
  Committee:
       PRESIDENT: XEKALAKIS, POLYCHRONIS
       SECRETARI: JIMENEZ GONZALEZ, DANIEL
       VOCAL: DE LUCAS CASAMAYOR, ENRIQUE
  Thesis abstract: Following the growing demands of applications mobile GPUs have greatly evolved in the past decade with expectations for continued advancement. These developments must address the rising performance demands and prioritize energy efficiency to accommodate the energy and temperature constraints of battery-powered, handheld devices. Main memory accesses are one of the main sources of energy consumption and occasionally a source of performance bottleneck in GPUs. The adoption of Tile-Based Rendering (TBR) architecture for many mobile GPUs in the late 1990s, marks a leap towards energy efficiency for mobile GPUs by enhancing locality and minimizing bandwidth-intensive memory accesses.The objective of this thesis is to enhance memory access efficiency in TBR GPU architectures for graphics applications. The strategy involves fine-tuning the structures in the memory hierarchy or altering the memory access patterns directed towards the memory hierarchy. By capitalizing on the unique characteristics of graphics applications, the goal is to boost both performance and energy efficiency with minimal hardware adjustments, thereby avoiding any adverse impact on general-purpose workloads running on GPUs.TBR architectures introduce an overhead through the creation of a specialized data structure for tiling which is stored in memory and cached in L1 and shared L2 caches. The OPT replacement policy, has been formally proven as optimal for minimizing misses but it is near-impossible to implement in hardware. The first proposal in this thesis brings the OPT to life, for this data structure. Along with other improvements in the L2, this proposal called TCOR results in a 13.8% decrease in the memory hierarchy energy consumption and an increased throughput in the Tiling Engine. DTexL, the second proposal in this thesis, increases the aggregated capacity of certain L1 caches by reducing replication of memory blocks. Contemporary GPUs have multiple GPU cores and a scheduler that distributes work (warps) among them, focusing on load balancing. These load balancing techniques are detrimental to texture memory locality in the L1 caches. We propose a new workload scheduler that favours texture locality and to overcome the resulting load imbalance, we propose a minor modification to the GPU architecture. DTexL results in a 46.8% decrease in L2 Accesses, a 19.3% increase in performance and a 6.3% decrease in total GPU energy. All this with a negligible overhead.Literature is plentiful in works exploiting cache locality for GPUs. A majority of them explore replacement or bypassing policies. In our third proposal, we surpass this exploration by fabricating a formal proof for a no-overhead quasi-optimal caching technique in the shared L2 for textures. We exploit the frame-to-frame reuse of textures by traversing frames in a boustrophedonic manner w.r.t. the conventional frame-to-frame tile order. We first approximate the texture access trace to a circular trace and then forge a formal proof for our proposal being optimal for such traces. We call our proposal Boustrophedonic Frames.Hiding memory latency is becoming a problem in contemporary GPUs. To address this challenge, we introduce WaSP as the final work in this thesis, a lightweight warp scheduler tailored for GPUs in graphics applications. WaSP strategically mimics prefetching by initiating a select subset of warps, termed priority warps, early in execution to reduce memory latency for subsequent warps. WaSP reduces average memory latency while maintaining locality for the majority of warps. While maximizing memory parallelism utilization, WaSP prevents saturating the caches with misses to avoid filling up the MSHRs. This approach reduces cache stalls that halt further accesses to the cache. Overall, WaSP yields a 3.9% performance speedup with a negligible overhead.
  

• KNAPP, CHRISTIAN: Quantitative Fluorescence Imaging of Spatiotemporal Dynamics of DNA Damage and DNA Replication in Health and Disease
  
  Author: KNAPP, CHRISTIAN
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN PHOTONICS
  Department: Institute of Photonic Sciences (ICFO)
  Mode: Normal
  Deposit date: 30/04/2024
  Reading date: pending
  Reading time: pending
  Reading place: pending
  Thesis director: GARCÍA PARAJO, MARÍA | CAMPELO AUBARELL, FELIX
  Committee:
       PRESIDENT: MANZO, CARLO
       SECRETARI: KRIEG, MICHAEL
       VOCAL: SIMÖES DA SILVA CARDOSO, MARIA CRISTINA
  Thesis abstract: Genomic instability, caused by DNA damage, is the main determinant for cancer and aging. To safeguard genomic integrity, cells evolved complex mechanisms to ensure error-free DNA replication and DNA damage repair. However, cells are not always able to repair DNA damage, and have to halt proliferation in a state of senescence, or perform the programmed cell death, apoptosis, to prevent giving rise to tumors and to protect the organism. Yet, this loss of proliferative potential ultimately leads to aging of the organism.The significance of DNA damage repair is underlined by mutations in genes encoding DNA repair proteins, which lead to premature aging diseases associated with a wide spectrum of early-onset age-related diseases. Notably, Hutchinson-Gildford progeria syndrome (HGPS), the most severe premature aging disease, is not caused by mutations in a DNA repair protein, but in the nuclear intermediate filament protein lamin A. Nonetheless, DNA damage is considered a main driver of this disease.The affected protein lamin A is a main component of the nuclear lamina, which is an intermediate filament meshwork and one of the layers of the nuclear envelope which surrounds the nucleus. To date, the pathological mechanism how the mutant form of lamin A leads to DNA damage in HGPS is poorly understood.Here, we propose our hypothesis that this mutations disturbs the interactions between the nuclear lamina and peripheral DNA in a manner that mechanically interferes with the local progression of DNA replication sites. Consequently, our hypothesis predicts that DNA damage predominantly arises during DNA replication of peripheral DNA in close proximity to the nuclear lamina. This creates a spatial correlation between the occurrence of DNA damage and the nuclear periphery, as well as a temporal correlation with DNA replication of peripheral DNA which occurs during late S-phase of the cell cycle.Hence, in Chapter 3, we present our approach to characterize the spatiotemporal dynamics of DNA damage throughout the cell cycle. This approach employs simple reporter cell models of DNA damage and DNA replication, along with long-term multi-color fluorescence live cell imaging microcopy, and a quantitative analysis pipeline. This analysis pipeline monitors and follows cells over multiple days and quantifies DNA damage foci formed by fluorescent DNA damage repair proteins, and employs machine learning-based algorithms to classify distribution patterns of the DNA replication protein PCNA to perform post hoc in silico synchronization of cell cycles. In Chapter 4, we describe how we employed this approach to quantify DNA damage foci and to characterize their distributions throughout the cell cycle in cell models of HGPS. We conducted these experiments under different conditions and with different cell lines, however we could not detect differences between HGPS cell models and healthy controls. Finally, we discuss our findings as well as technical and biological aspects of our approach in the context of literature.In Chapter 5, we present an approach which we developed to study the influence of the mutant form of lamin A on the mobility of DNA replication sites, and thus to test the mechanical aspects of our hypothesis. This approach is based on single molecule tracking of the DNA replication protein PCNA. While we could not detect differences between HGPS cell models and healthy controls with this approach, we revealed two slow mobility states of PCNA within DNA replication sites. These two mobility states are consistent the the PCNA meshwork model proposed by Boehm et al. in 2016 and may represent DNA replication condensates.Finally, in Chapter 6, we summarize the main results of this thesis and discuss future and potential applications of our approaches to advance our understanding of the cell cycle-dependent dynamics of genome maintenance, and the structural organization of DNA replication sites.