Skip to content

You are here: Home

Why take a doctoral degree at the UPC

Video Home 3

Because of Excellence

The UPC is listed in the main international rankings as one of the top technological and research universities in southern Europe and is among the world's 40 best young universities.

Its main asset: people

Satisfaction with the work of the thesis supervisor is highlighted by 7 out of 10 UPC doctoral students. Support and availability get the best ratings.

Internationalisation

More than half of the students of the UPC’s Doctoral School are international and a third obtain the International Doctorate mention.

 

Graduate employment of a high quality

Almost all UPC doctoral degree holders are successful in finding employment, mostly in jobs related to their degree.

The best industrial doctorate

The UPC offers the most industrial doctoral programmes in Catalonia (a third) with a hundred companies involved.

The industrial setting

The UPC’s location in an especially creative and innovative industrial and technological ecosystem is an added value for UPC doctoral students.

Theses for defense agenda

Reading date: 26/11/2020
  • LABARRE, AURELIE: GENOME BASIS FOR FUNCTIONAL DIFFERENTIATION IN UNCULTURED LINEAGES OF MARINE BACTERIVORES
    Author: LABARRE, AURELIE
    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 MARINE SCIENCES
    Department: (DECA)
    Mode: Article-based thesis
    Deposit date: 06/10/2020
    Reading date: 26/11/2020
    Reading time: 11:00
    Reading place: Institut de Ciències del Mar. Defensa per videoconferència (COVID-19) https://meet.google.com/fwc-prmv-hbn
    Thesis director: MASSANA MOLERA, RAMON
    Committee:
         PRESIDENT: RUIZ TRILLO, IÑAKI
         SECRETARI: VAQUÉ VIDAL, DOLORS
         VOCAL NO PRESENCIAL: PIGANEAU, GWENAËL
    Thesis abstract: In the vast network of the ocean, microbes are abundant and unevenly distributed. As an important microbial component, the protists play a key role in global biogeochemical cycles and contribute to the recycling of nutrients necessary to sustain life on Earth. These unicellular eukaryotes exist and function as primary producers (drivers of photosynthesis), decomposers, parasites or as trophic linkers in aquatic food webs. Phagotrophic species, which acquire nutrition through feeding on other organisms, are commonly understudied due to the difficulty in culturing them. The recent characterization of their genomic and metabolic diversity starts to unveil their great ecological relevance in the oceans. In this dissertation, we focused on heterotrophic flagellates, the main bacterial grazers in marine systems, and especially on the MArine STramenopile (MAST) lineages that display numerous uncultured and, therefore, undefined species. The aim was to elucidate their ecological importance in marine food webs by understanding their presumed trophic strategy: phagocytosis, a process only well characterized in animals as an immune system response. We first attempted to provide new reference genomes of MAST species using single cell genomic sequencing and a co-assembly approach. Thus, we assembled 15 draft genomes from different MAST lineages, and predicted their gene repertoire with the objective to characterize specific genes related to their trophic strategy. Our comparative genomics analysis indicated that all MAST species were phagotrophs. We then targeted peptidases involved in prey digestion as well as proton pumps for vacuole acidification, but we did not find preferential genes specific for phagocytosis. In addition, this study revealed the relevant presence of rhodopsin proteins that may contribute in the acidification of the phagolysosome. In the second paper, we did a functional study of MASTs using metatranscriptomics in order to gain access to their gene expression within the natural environment. To do so, we started a grazing experiment with a natural sample from the Mediterranean Sea: in a controlled microcosm in the dark, we followed the cell growth of a natural community where we aimed to enrich for heterotrophic flagellates and therefore phagocytosis. We showed an increase in the relative abundance of heterotrophs, as compared with phototrophs, when phagocytosis occurred. Using the previously established reference genome collection of a few MASTs, we were able to target the MAST reads in the metatranscriptome and analyze the expression profile of genes involved in phagocytosis for a couple of MAST-4 species. Cathepsins and other digestive enzymes were highly expressed when bacterial consumption was observed. Finally, a similar experiment was conducted with a cultured organism, Cafeteria burkhardae, a cosmopolitan heterotrophic flagellate that proved to be a good model to study bacterivory within the Stramenopiles. Results demonstrated distinct expression profiles depending on the growth phase of this species. Upregulated genes at the Exponential phase were related to DNA duplication, transcription, translation, and phagocytosis, whereas upregulated genes in the Stationary phase were involved in signal transduction, cell adhesion and lipid metabolism. Phagocytosis genes, like peptidases and proton pumps, were highly expressed and could be used to target this ecologically relevant process in marine ecosystems. This thesis contributes to the understanding of the community of marine bacterial grazers, which include the smallest phagotrophs in the ocean, with a focus on their functional behavior within the natural and complex protistan assemblage.
Reading date: 27/11/2020
  • BORCHINI, LUCA: High-fidelity surrogate models for parametric shape design in microfluidics
    Author: BORCHINI, LUCA
    Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
    Programme: ERASMUS MUNDUS DOCTORAL DEGREE IN SIMULATION IN ENGINEERING AND ENTREPRENEURSHIP DEVELOPMENT
    Department: (DECA)
    Mode: Change of supervisor
    Deposit date: 27/10/2020
    Reading date: pending
    Reading time: pending
    Reading place: pending
    Thesis director: HUERTA CEREZUELA, ANTONIO | GIACOMINI, MATTEO | SEVILLA CÁRDENAS, RUBÉN
    Committee:
         PRESIDENT: MORGAN, KENNETH
         SECRETARI: ZLOTNIK MARTINEZ, SERGIO
         VOCAL: CUETO PRENDES, ELIAS
         VOCAL: GIORGIANI, GIORGIO
         VOCAL: OTHMER, CARSTEN
    Thesis abstract: Nowadays, the main computational bottleneck in computer-assisted industrial design proceduresis the necessity of testing multiple parameter settings for the same problem. Material properties,boundary conditions or geometry may have a relevant influence on the solution of thoseproblems. Consequently, the effects of changes in these quantities on the numerical solutionneed to be accurately estimated. That leads to significantly time-consuming multi-queryprocedures during decision-making processes. Microfluidics is one of the many fields affected by this issue, especially in the context of the design of robotic devices inspired by naturalmicroswimmers. Reduced-order modelling procedures are commonly employed to reduce thecomputational burden of such parametric studies with multiple parameters. Moreover, highfidelity simulation techniques play a crucial role in the accurate approximation of the flowfeatures appearing in complex geometries. This thesis proposes a coupled methodology basedon the high-order hybridisable discontinuous Galerkin (HDG) method and the proper generalized decomposition (PGD) technique. Geometrically parametrised Stokes equations are solved exploiting the innovative HDG-PGD framework. On the one hand, the parameters describing the geometry of the domain act as extra-coordinates and PGD is employed to construct a separated approximation of the solution. On the other hand, HDG mixed formulation allows separating exactly the terms introduced by the parametric mapping into products of functions depending either on the spatial or on the parametric unknowns. Convergence results validate the methodology and more realistic test cases, inspired by microswimmer devices involving variable geometries, show the potential of the proposed HDG-PGD framework in parametric shape design. The PGD-based surrogate models are also utilised to construct separated response surfaces for the drag force. A comparison between response surfaces obtained through the apriori and the a posteriori PGD is exposed. A critical analysis of the two techniques is presented reporting advantages and drawbacks of both in terms of computational costs and accuracy.
  • DIMIC, VLADIMIR: Runtime-assisted optimizations in the on-chip memory hierarchy
    Author: DIMIC, VLADIMIR
    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: 15/09/2020
    Reading date: 27/11/2020
    Reading time: 09:30
    Reading place: ETSETB C6-E101: Defensa per videoconferència COVID19- https://zoom.us/j/91011374678?pwd=SFlubjlsQ2szeDVTc09UUUJRNlpBZz09
    Thesis director: MORETÓ PLANAS, MIQUEL | CASAS GUIX, MARC
    Committee:
         PRESIDENT: NIKOLERIS, NIKOS
         SECRETARI: RADOJKOVIC, PETAR
         VOCAL: BEIVIDE PALACIO, JULIO RAMON
    Thesis abstract: Following Moore's Law, the number of transistors on chip has been increasing exponentially, which has led to the increasing complexity of modern processors. As a result, the efficient programming of such systems has become more difficult. Many programming models have been developed to answer this issue. Of particular interest are task-based programming models that employ simple annotations to define parallel work in an application. The information available at the level of the runtime systems associated with these programming models offers great potential for improving hardware design. Moreover, due to technological limitations, Moore's Law is predicted to eventually come to an end, so novel paradigms are necessary to maintain the current performance improvement trends.The main goal of this thesis is to exploit the knowledge about a parallel application available at the runtime system level to improve the design of the on-chip memory hierarchy. The coupling of the runtime system and the microprocessor enables a better hardware design without hurting the programmability.The first contribution is a set of insertion policies for shared last-level caches that exploit information about tasks and task data dependencies. The intuition behind this proposal revolves around the observation that parallel threads exhibit different memory access patterns. Even within the same thread, accesses to different variables often follow distinct patterns. The proposed policies insert cache lines into different logical positions depending on the dependency type and task type to which the corresponding memory request belongs.The second proposal optimizes the execution of reductions, defined as a programming pattern that combines input data to form the resulting reduction variable. This is achieved with a runtime-assisted technique for performing reductions in the processor's cache hierarchy. The proposal's goal is to be a universally applicable solution regardless of the reduction variable type, size and access pattern. On the software level, the programming model is extended to let a programmer specify the reduction variables for tasks, as well as the desired cache level where a certain reduction will be performed. The source-to-source compiler and the runtime system are extended to translate and forward this information to the underlying hardware. On the hardware level, private and shared caches are equipped with functional units and the accompanying logic to perform reductions at the cache level. This design avoids unnecessary data movements to the core and back as the data is operated at the place where it resides.The third contribution is a runtime-assisted prioritization scheme for memory requests inside the on-chip memory hierarchy. The proposal is based on the notion of a critical path in the context of parallel codes and a known fact that accelerating critical tasks reduces the execution time of the whole application. In the context of this work, task criticality is observed at a level of a task type as it enables simple annotation by the programmer. The acceleration of critical tasks is achieved by the prioritization of corresponding memory requests in the microprocessor.
  • WINKLER, PAMINA: Novel planar photonic antennas to address the dynamic nanoarchitecture of biological membranes
    Author: WINKLER, PAMINA
    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: 19/10/2020
    Reading date: 27/11/2020
    Reading time: 11:00
    Reading place: ICFO: Videoconferència per COVID-19 http://s.ic.fo/LxpQG
    Thesis director: GARCÍA PARAJO, MARÍA
    Committee:
         PRESIDENT: WIENTJES, INA EMILIA
         SECRETARI: VAN HULST, NIEK
         VOCAL: SEZGIN, ERDINC
    Thesis abstract: The cell membrane is the encompassing protective shield of every cell and it is composed of a multitude of proteins, lipids and other molecules. The organization of the cell membrane is inextricably intertwined with its function, and sensitive to perturbations from the underlying actin cytoskeleton and the extracellular environment at the nano- and the mesoscale. Elucidating the dynamic interplay between lipids and proteins diffusing on the cell membrane, forming transient domains and (re)organizing them according to signals from the juxtaposed inner and outer meshwork, is of paramount interest in fundamental cell biology. The overarching goal of this thesis is to gain deeper insight into how lipids and proteins dynamically organize in biological membranes at the nanoscale. Photonic nano-antennas are metallic nanostructures that localize and enhance the incident optical radiation into highly confined nanometric regions (< 20 nm), leading to greatly enhanced light-matter interactions. In this thesis, we exploit an innovative design of planar gold nano-antenna arrays of different gap sizes (10-45 nm) and embedded in nanometric-size boxes. To elucidate nanoscale diffusion dynamics in biological membranes with high spatiotemporal resolution and single-molecule detection sensitivity, we further combine our nanogap antenna arrays with fluorescence correlation spectroscopy (FCS) in a serial and multiplexed manner. In this dissertation, we first describe the fabrication process of these planar gold nanogap antennas and characterize their performance by means of electron microscopy and FCS of individual molecules in solution. We demonstrate giant fluorescence enhancement factors of up to 104-105 times provided by our planar nanogap antennas in ultra-confined detection volumes and with single molecule detection sensitivity in the micromolar range. Second, we apply these planar plasmonic nano-antennas in combination with FCS for assessing the dynamic organization of mimetic lipid membranes at the nanoscale. For a ternary composition of the model membranes that include unsaturated and saturated lipids together with cholesterol, we resolve transient nanoscopic heterogeneities as small as 10 nm in size, coexisting in both macroscopically phase-separated lipid phases.Third, we add a Hyaluronic Acid (HA) layer on top of the model lipid membranes to emulate the effect of the extracellular environment surrounding native biological membranes. We extend our nano-antenna-FCS approach with atomic force microscopy and spectroscopy. We reveal a distinct influence of HA on the nanoscale lipid organization of mimetic membranes composed of lipids constituting the more ordered lipid phase. Our results indicate a synergistic effect of cholesterol and HA re-organizing biological membranes at the nanoscale. Fourth, we apply our planar nano-antenna platform combined with FCS to elucidate the nanoscale dynamics of different lipids in living cells. With our nanogap antennas we were able to breach into the sub-30 nm spatial scale on living cell membranes for the first time. We provide compelling evidence of short-lived cholesterol-induced ~10 nm nanodomain partitioning in living plasma membranes. Fifth, we demonstrate the multiplexing capabilities of our planar gold nanogap antenna platform combined with FCS in a widefield illumination scheme combined with sCMOS camera detection. Our approach allows recording of fluorescence signal from more than 200 antennas simultaneously. Moreover, we demonstrate multiplexed FCS recording on 50 nano-antennas simultaneously, both in solution as well as in living cells, with a temporal resolution in the millisecond range. The dissertation finishes with a brief discussion of the main results achieved in this research and proposes new avenues for future research in the field.
Reading date: 30/11/2020
  • CUADRADO GUEVARA, MARLYN DAYANA: Multistage scenario trees generation for renewable energy systems optimization.
    Author: CUADRADO GUEVARA, MARLYN DAYANA
    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 STATISTICS AND OPERATIONS RESEARCH
    Department: Department of Statistics and Operations Research (EIO)
    Mode: Normal
    Deposit date: 22/10/2020
    Reading date: 30/11/2020
    Reading time: 12:00
    Reading place: FME: Videoconferència per COVID-19: https://meet.google.com/nsy-skve-ska
    Thesis director: HEREDIA CERVERA, FRANCISCO JAVIER
    Committee:
         PRESIDENT: RAMALHINHO DIAS LOURENÇO, HELENA
         SECRETARI: CASTRO PÉREZ, JORDI
         VOCAL: MORALES ESPAÑA, GERMAN ANDRES
    Thesis abstract: The presence of renewables in energy systems optimization have generated a high level of uncertainty in the data, which has led to a need for applying stochastic optimization to modelling problems with this characteristic. The method followed in this thesis is multistage Stochastic Programming (MSP). Central to MSP is the idea of representing uncertainty (which, in this case, is modelled with a stochastic process) using scenario trees. In this thesis, we developed a methodology that starts with available historical data; generates a set of scenarios for each random variable of the MSP model; define individual scenarios that are used to build the initial stochastic process (as a fan or an initial scenario tree); and builds the final scenario trees that are the approximation of the stochastic process. The methodology proposes consists of two phases. In the first phase, we developed a procedure similar to Muñoz et al. (2013), with the difference being that the VAR models are used to predict the next day for each random parameter of the MSP models. In the second phase, we build scenario trees from the Forward Tree Construction Algorithm(FTCA), developed by Heitsch and Römisch (2009a); and an adapted version of DynamicTree Generation with a Flexible Bushiness Algorithm (DTGFBA), developed by Pflugand Pichler (2014, 2015). This methodology was used to generate scenario trees for two MSP models. A first model, Multistage Stochastic Wind Battery Virtual Power Plantmodel (MSWBVPP model) and to a second model, which is the Multistage StochasticOptimal Operation of Distribution Networks model (MSOODN model). We developed extensive computational experiments for the MSWBVPP model and generated scenario trees with real data, which were based on MIBEL prices and wind power generation of the real wind farm called Espina, located in Spain. For the MSOODN model, we obtained scenario trees by also using real data from the power load provided by FEEC-UNICAMP and photovoltaic generation of a distribution grid located in Brazil. The results show that the scenario tree generation methodology proposed in this thesis can obtain suitable scenario trees for each MSP model. In addition, results were obtained for the model using the scenario trees as input data. In the case of the MSWBVPP model, we solved three different case studies corresponding to three different hypotheses on the virtual power plant¿s participation in electricity markets. In the case of the MSOODN model, two test cases were solved, with the results indicating that the EDN satisfied the limits imposed for each test case. Furthermore, the BESS case gave good results when taking into account the uncertainty in the model. Finally, the MSWBVPP model was used to study the relative performance of the FTCA and DTGFBA scenario trees, specifically by analyzing the value of the stochastic solution for the 366 daily optimal bidding problems. To this end, a variation of the classical VSS (the so-called ¿Forecasted Value of the Stochastic Solution¿, FVSS) was defined and used together with the classical VSS.

The Doctoral School today

  • 45PhD programs
  • 2328doctoral students 18/19
  • 290thesis supervisors 18/19
  • 328read theses 2019
  • 1072019 thesis with I.M. and/or I.D.
  • 183 I.D. projects (30% from G.C. total)

I.M: International Mention, I.D.: Industrial Doctorate, G.C.: Generalitat de Catalunya