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Speaker: Artemy Kolchinsky (Universitat Pompeu Fabra, Spain)
Date: 29/02/2024
Time: 10:00

Research in the field of "stochastic thermodynamics" has uncovered a set of fundamental relationships between energy, information, and temporal irreversibility in nonequilibrium stochastic processes. Recently, these relationships have been used to derive thermodynamic bounds on the performance of molecular machines, including very general tradeoffs such as “thermodynamic uncertainty relations” and “thermodynamic speed limits”. I will review the basics of the field, as well as some promising recent developments and applications to molecular-scale biological systems. I will also discuss the challenges faced when applying these approaches at the cellular scale.

 
 

Speaker: Bernat Corominas Murtra (University of Graz, Austria)
Date: 29/02/2024
Time: 10:00

Several molecular markers have been described to predict stem cell potential with great success, e.g., in tissues like the blood, where a clear hierarchy of functional cell types can be identified. In other tissues, neutral competitive dynamics has been reported to remove a large fraction of biochemically identifiable stem cells, thereby creating a severe mismatch between cell-specific biochemical identity and the actual role of them as functional stem cells within the collective. In the case of the intestinal epithelium, this mismatch goes even further: In spite the number of biochemically identifiable (LGR5+) stem cells is the same in the crypts of both large and small intestines, lineage tracing techniques show that the number of them that actually play the role of stem cell displays remarkable differences. In that context, a natural question arises: How to determine the functional number and location of stem cells? To address this problem, I will revise a recent mathematical approach that proposes a new stem cell regulation mechanism, leading the final stem cell population to emerge only from the collective stochastic dynamics of cell movements and geometric considerations. Within this framework, one can accurately predict the robust emergence of a region made of functional stem cells and the actual number of them, as well as the lineage-survival probabilities, among other observables. The presented approach does not neglect the key role of biomarkers: Instead, it points towards the existence of complementary regulatory mechanisms --based on collective phenomena, stochastic dynamics and organ geometry--, playing an active role in determining the emergence and location of different cell functionalities.

 
 

Speaker: Susanna Manrubia (CNB-CSIC, Spain)
Date: 15/02/2024
Time: 10:00

The exploration of vast genotype spaces poses a major challenge to evolving populations. As the number of genotype sequences representing viable phenotypes grows exponentially with genome length, understanding how populations navigate and adapt within such spaces becomes paramount. In this contribution, we delve into the dynamics of populations within genotype spaces using data from the environmental adaptation of populations of a small phage infecting E. coli (Qbeta phage) and SARS-CoV-2 genomes. Despite the vastness of the spaces they have in principle access to, even the largest realizable viral populations cover only a tiny fraction of possible sequences, constrained by a local, blind exploration of the nearest attainable. We explore how these populations achieve phenotypic improvements and evolutionary innovations, presenting data-driven insights from extensive datasets. Our analysis reveals crucial features of empirical populations that challenge established theoretical expectations, shedding light on the dynamic interplay between genotype and phenotype in the evolutionary process.

 
 

Speaker: Josep Sardanyés (Centre de Recerca Matemàtica, Barcelona)
Date: 04/04/2024
Time: 10:00

Complex systems unfold nonlinear interactions and can suffer regime shifts which are of paramount importance since they can involve the emergence and persistence of a disease or the extinction of a species within an ecosystem. Such regime shifts can be achieved by different mechanisms and their understanding is crucial to potentially anticipate them and have information about the time scales of such shifts. Dynamical systems theory and computational research allows the study of such mechanisms in a general way or for specific complex systems such as ecosystems or viral infections. In this seminar, I will discuss different mechanisms causing regime shifts, paying special attention to critical transitions given by tipping points. I will discuss important dynamical properties arising close to critical transitions such as transients and the so-called warning signals. These signals provide a powerful way to detect that a given system is approaching a critical transition without the necessity to have a detailed knowledge of the underlying system dynamics. To foster discussion and possible new collaborations, I will provide examples of these topics identified in experimental and natural systems.

 
 

Speaker: Jaume Casademunt (Universitat de Barcelona)
Date: 18/01/2024
Time: 10:00

The collective migration of cohesive groups of cells is a hallmark of the tissue remodeling events that underlie embryonic morphogenesis, wound repair, and cancer invasion. Collective cell migration is characterized by the emergence of supra-cellular properties that control large-scale tissue organization. This suggests that a coarse-grained approach based on a hydrodynamic description of tissues as continuous active materials may shed some light on our understanding of the underlying physics of various tissue processes. Within this spirit, we reflect on the extent to which biological complexity can be encoded in a series of material parameters to build predictive, purely mechanical models of tissues based on very general physical principles. We present an overview of such a hydrodynamic approach to cell tissues as active polar fluids and discuss some examples where relatively simple models have been instrumental in elucidating relevant physical mechanisms behind collective cell behavior in epithelia, including active wetting, collective durotaxis, and spontaneous motility of cell clusters.

 
 

Speaker: Amélie Baud (CRG, Barcelona)
Date: 11/01/2024
Time: 10:00

Our goal is to better understand why individuals from a population differ from each other in terms of their phenotypes and susceptibility to disease. We focus on genetic effects, considering not only the individual’s own genes but also the genes of their social partners and the genes of their microbiome. I will present the conceptual framework and quantitative genetics models we use to study this extended genotype to phenotype map.

 

If you would like to attend the seminar, please register here

 
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