Doctoral School

Reading date: 16/04/2026

• PUCH GINER, IGNASI: Optimization of Monte Carlo and Molecular Dynamics Techniques for Receptor–Ligand Binding Studies
  
  Author: PUCH GINER, IGNASI
  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 COMPUTATIONAL AND APPLIED PHYSICS
  Department: Department of Physics (FIS)
  Mode: Normal
  Deposit date: 16/02/2026
  Reading date: 16/04/2026
  Reading time: 10:00
  Reading place: Sala TeleensenyamentEdifici B3 - Ricardo Valle Sala 103 Planta 1Campus Nord
  Thesis director: GUALLAR TASIES, VÍCTOR
  Thesis abstract: Drug discovery is a complex and resource-intensive process that requires the identification of molecular candidates with optimal binding properties to their corresponding targets. Computational techniques play a central role in streamlining this process by predicting biomolecular interactions, optimizing molecular properties, and accelerating early-stage drug development.This thesis focuses on advancing computational strategies for biomolecular modeling, integrating molecular mechanics techniques—such as Monte Carlo and molecular dynamics simulations—with state-of-the-art machine learning tools. The objective is to improve scoring functions, enhance simulation accuracy, and develop a framework that enables the application of these methods to real-world pharmacological challenges.A key contribution of this work is the systematic characterization of the PELE (Protein Energy Landscape Exploration) simulation framework, including the rationalization of binding energy estimators and the assessment of their predictive performance and computational efficiency. These benchmarks address existing knowledge gaps in scoring functions and facilitate more accurate predictions of protein–ligand interactions, thereby supporting the prioritization of promising molecules for experimental evaluation.Beyond methodological advances, this thesis applies the developed computational approaches to pharmacologically relevant case studies. The structural characterization of the amino acid transporter Asc1/CD98hc was carried out using an integrated computational pipeline, providing new insights into its binding and transport mechanisms. Furthermore, the study of the Meis1–Hoxb13 transcription factors explores novel drug–DNA interactions with potential implications for targeted therapies. Another application focuses on Charcot–Marie–Tooth disease, where computational simulations contributed to understanding GDAP1–LAMP1 tethering dysfunction and possible therapeutic interventions. These examples highlight the versatility of the proposed computational strategies across diverse biological contexts.The results of this research propose a practical framework for improving ligand-binding predictions. The explored methodologies strengthen molecular modeling by combining physics-based techniques with varying speed–accuracy trade-offs and data-driven approaches, bridging the gap between traditional simulation methods and AI-driven predictions. The findings have implications for both academic research and industrial drug discovery, offering scalable and generalizable solutions for structure-based and ligand-based design.
  

Reading date: 17/04/2026

• PERA I FERRERUELA, JORDI: Itinerant ferromagnetism and polarons in SU(N) Fermi gases
  
  Author: PERA I FERRERUELA, JORDI
  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 COMPUTATIONAL AND APPLIED PHYSICS
  Department: Department of Physics (FIS)
  Mode: Normal
  Deposit date: 13/03/2026
  Reading date: 17/04/2026
  Reading time: 11:00
  Reading place: Aula Graus, Edifici C4, Planta baixa, Campus Nord - UPC
  Thesis director: CASULLERAS AMBROS, JOAQUIN | BORONAT MEDICO, JORDI
  Thesis abstract: This thesis presents an in-depth study of the magnetic properties of repulsive Fermi gases in the continuum. Once a purely academic subject, Fermi gases can now be realized experimentally in ultracold atom laboratories, making a theoretical understanding of their behavior both timely and necessary. Our analysis focuses primarily on whether such systems favor a transition to a ferromagnetic state or remain paramagnetic. As technique, we use a perturbative approach that systematically includes the effects of higher-order terms, temperature, and mass imbalance. In the final part of the thesis, we also study the Fermi polaron problem. First, we examine a simple case: a Fermi gas with equal masses at zero temperature up to second order in perturbation theory. As this chapter can be considered an introduction to the magnetic phenomenology of Fermi gases, we compare the outcome of our second order analysis with the well-known scenario of the Stoner model, which is the first-order model. In both cases, a ferromagnetic transition always occurs. Moving from the Stoner model to the second-order one, there are two differences to point out: the continuous phase transition observed at S=1/2 becomes discontinuous, and the ferromagnetic phase arises at lower densities. The next step is to improve the description of the potential interaction. We do so by going up to third order in perturbation theory. However, this improvement comes with a cost; as we now have more information about the potential, the complexity of the problem is higher. We split the analysis into two parts. We first consider a hard-sphere potential without p-wave intra-particle interaction. We observe the same tendencies that we encounter when we move from first order to second order, but, more importantly, we recover the continuous phase transition for S=1/2. Having now at hand the third-order energies, we explore a wide range of different potentials. Surprisingly, for each spin S we observe a richness of scenarios: continuous transitions, discontinuous ones, combinations of the other two, stairs-like cases, and even, no transition at all. Next, we introduce another variable to our problem: the temperature. Thermal effects do not eliminate the ferromagnetic phase for any potential, but they clearly go against it: either they force the system to remain paramagnetic or make the transition to occur at higher densities, which probably hinders the ferromagnetic phase. Nevertheless, larger spins better resist these thermal effects. Additionally, temperature reduces the diversity of magnetic behavior, leading to more universal patterns: continuous transitions for S=1/2 and discontinuous ones for larger spins. Up to this point, we assumed that all the particles have the same mass. The next step is to consider different relations of masses. Adding another variable increases even more the complexity of the problem and, hence, we only inspect it at second order and at zero temperature. As we have commented above, at second order there is always a ferromagnetic transition. Now, this is also the case, but with some nuances. The massive particles are always the promoted ones, even at low densities. For S=1/2, this is the end of the story. But for larger spins, as we can have many mass relations, we can obtain lots of configurations, which may give us more tunability. Finally, we move beyond magnetic properties to study the Fermi polaron problem: an impurity immersed in a Fermi sea. We focus on how impurities affect our system. We examine the main properties of the Fermi polaron at third order and the effects of mass. Specifically, the massive polaron works just fine, but the light polaron is unstable. Altogether, this work offers a detailed and thorough exploration of Fermi gases, providing both qualitative insight and quantitative predictions relevant to experimental efforts.
  

• PINEDO VILCAHUAMÁN, PAUL JOSÉ: Simulation of blast-induced liquefaction with an unconventional elastoplasticity model
  
  Author: PINEDO VILCAHUAMÁN, PAUL JOSÉ
  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 GEOTECHNICAL ENGINEERING
  Department: Department of Civil and Environmental Engineering (DECA)
  Mode: Normal
  Deposit date: 19/03/2026
  Reading date: pending
  Reading time: pending
  Reading place: pending
  Thesis director: ARROYO ALVAREZ DE TOLEDO, MARCOS | GENS SOLE, ANTONIO
  Thesis abstract: Soil liquefaction is a phenomenon that typically occurs following earthquakes, although it may also be triggered by non-seismic loading. During liquefaction, a substantial and rapid reduction in the strength and stiffness of soils occurs due to pore pressure generation. Soil liquefaction is systematically investigated in the laboratory using element and model tests; however, certain aspects that prove critical in field liquefaction (e.g., soil fabric, dynamic loading, drainage conditions and ageing effects) are challenging to reproduce in the laboratory. This has prompted researchers to investigate liquefaction directly in the field by means of blast tests, i.e. experiments in which liquefaction is induced by controlled explosive detonations.Numerical simulation is nowadays frequently employed to simulate the onset and development of soil liquefaction. In this context, the primary objective of the present study is the numerical simulation of a controlled blast-induced liquefaction test conducted at a silty sand site in Bondeno, Ferrara, Italy. To this end, a constitutive model named CASM-SM has been implemented to reproduce soil behaviour during cyclic loading, having been recast within a subloading plasticity framework. The modelling of soil behaviour under blast loading is challenging due to several factors, including the characteristics of soil deformation close to the explosive, soil stiffness degradation, high frequencies in acceleration records (exceeding 100 Hz), and a significant increase of excess pore water pressure over a short timeframe (on the order of milliseconds). The Bondeno blast test simulation served as an excellent platform for validating the performance of the CASM-SM model. Particular attention was paid to the reproduction of the acceleration records, as well as velocities, Arias intensity, Fourier spectra, and spectral acceleration. Moreover, excess pore water pressures were compared against pore pressure transducer data. The results obtained from the numerical simulation provide relevant insights into blast-induced liquefaction within the silty sand layer.
  

Reading date: 20/04/2026

• BORGES CAVALCANTI, DANILO: Finite Element Method with Embedded Strong Discontinuities for Coupled Hydro-Mechanical Problems
  
  Author: BORGES CAVALCANTI, DANILO
  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: Department of Civil and Environmental Engineering (DECA)
  Mode: Change of supervisor + Article-based thesis
  Deposit date: 09/03/2026
  Reading date: 20/04/2026
  Reading time: 14:00
  Reading place: Sala Zienkiewich (CIMNE) Building C1, UPC - Campus North Gran Capitan S/N 08034 Barcelona
  Thesis director: DE POUPLANA SARDÀ, IGNASI | CAMPOS RAMOS MARTHA, LUIZ FERNANDO | DE MESQUITA ROEHL, DEANE
  Thesis abstract: Coupled hydro–mechanical (HM) processes in fractured porous media govern the performance and safety of several subsurface engineering applications, where pressure-driven changes in stress and permeability can control injectivity, leakage pathways, and fault reactivation potential. This thesis develops a robust and versatile finite element formulation for transient HM problems in the presence of pre-existing strong discontinuities that remains practical for integration into standard finite element workflows. The proposed approach is formulated within the Embedded Finite Element Method (E-FEM) and grounded on the Strong Discontinuity Approach (SDA), enabling an implicit representation of fractures and faults while circumventing mesh conformity constraints. A unified description is introduced to model discontinuities acting either as preferential flow paths or as hydraulic barriers, capturing the longitudinal flow along the discontinuity and the transversal exchange with the porous matrix in steady-state and transient settings. The formulation is systematically verified against discrete fracture models with interface elements and applied to benchmark problems representative of fractured-reservoir conditions, including a coupled fault reactivation scenario. In addition, the thesis investigates the occurrence of spurious oscillations in cohesive traction fields along embedded discontinuities and demonstrates that the choice of an SDA-based embedded formulation can markedly improve traction smoothness. These improvements strengthen the use of E-FEM for HM assessments involving pre-existing fractures and faults.
  

• FORERO QUINTERO, JOSE FERNANDO: Flexibility Management System with Distributed Energy Resources
  
  Author: FORERO QUINTERO, JOSE FERNANDO
  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 ELECTRICAL ENGINEERING
  Department: Department of Electrical Engineering (DEE)
  Mode: Article-based thesis
  Deposit date: 19/02/2026
  Reading date: 20/04/2026
  Reading time: 12:00
  Reading place: Aula 28.8 Sala de Conferències. ETSEIB-UPC
  Thesis director: VILLAFÁFILA ROBLES, ROBERTO | MONTESINOS MIRACLE, DANIEL
  Thesis abstract: The challenge of climate change is ever demanding more technological and political efforts to respond adequately to its adverse effects, which could put life on the planet at risk. Diverse plans have been proposed to incorporate more renewable generation and digitalize the power system in a decarbonizing energy transition framework. However, such plans are either not being accomplished or are insufficient according to the Paris Agreement. At the same time, emerging technologies such as artificial intelligence, high-performance sensing and automation, and real-time information and communication systems, among others, are transforming electrical networks into smart grids, aggregating more complexity.This thesis, based on a papers compendium, first surveys the existing energy management systems with distributed energy resources, delving into their configuration, energy and flexibility sources, information and communication systems, profitability analysis and indicators, and flexibility services. After reviewing the state of the art, this thesis focuses on boosting management systems towards the real-time horizon, proposing a flexibility management system. This system is a hierarchical three-level management system based on an adaptive autoregression algorithm, cost-benefits analysis, and redispatching and unit recommitment submodules to control and manage the power, and short-term flexibility requests.To validate the proposed system, not only several simulations and sensitivity analyses are carried out, but real-world energy assets are addressed in PVZEN microgrid lab in Torino, Italy. The results demonstrate that proposed system can reduce the cost overruns of real-time power deviations of the distributed resources, leverage the excess of renewable energy, and generate profits providing flexibility services to the grid. Chapters 2, 3, and 4 show the papers related to this thesis, starting with reviewing the art status, passing through the simulations and analysis, and finishing with the essays on real-world energy assets. Main conclusions and future work are depicted at the end of the document.