Simons-FAPESP talks
Monday, April 8 10:00 Andre Sadofyev(online)
Video: https://youtu.be/0bfVq8s7GBw
Title: Jet quenching from large to small systems
Abstract: Over the last decades, the theoretical picture of how hadronic jets interact with nuclear matter has been extended to account for the medium’s finite longitudinal length and expansion. However, only recently a first-principle approach has been developed that allows to couple the jet evolution to the medium flow and anisotropic structure. In this talk, I will review these developments, and discuss the features of jet quenching in evolving matter. I will consider the modifications of the single particle momentum broadening distribution and single-gluon production rate, and briefly discuss the potential phenomenological implications.
Thursday April 11 8:30 Matthew Ricci (online)
Video: https://www.youtube.com/watch?v=W2rlAQQiNXE
Title: Building low-dimensional representations of reaction-diffusion dynamics
Abstract: This seminar presents ongoing research on the qualitative dynamics of reaction-diffusion processes, cornerstone complex systems in physics and biology. These equations, fundamental to modeling phenomena ranging from chemical reactions to ecological and cellular processes, encapsulate the intricate balance between transport mechanisms and local interactions. A central aim in the study of such systems is to decipher the macroscopic or qualitative behaviors that emerge from these complex interactions, seeking to understand how patterns, waves, and structures develop on larger scales. However, despite the valuable analytical insights offered by perturbation or renormalization techniques, these approaches can struggle in highly nonlinear or multi-scale regimes and do not easily generalize to new parameters. Addressing these challenges, this work leverages recent advancements in data-driven dynamical systems theory to uncover the low-dimensional dynamics governing macroscopic features of interest. By employing machine learning techniques to derive low-dimensional representations, this approach clarifies the emergence of qualitative structures which are often obscured in the high-dimensional data of the original systems. This method not only facilitates a deeper understanding of the system’s dynamics but also opens new avenues for control and parameter identification. Preliminary results demonstrate the efficacy of this methodology in shedding light on the behavior of the Gray Scott model and Min protein dynamics, both examples of reaction-diffusion systems with significant theoretical and biological implications. The seminar will detail the theoretical underpinnings, methodological developments, and early outcomes of this research, highlighting its potential to advance our understanding of reaction-diffusion systems as they arise in biology.
Thursday April 11, 13:30 Alessandro Trani (online)
Video: https://www.youtube.com/watch?v=XVYx39pskmc
Title. Gravitational wave mergers of black holes in active galactic nuclei: challenges and opportunities
Abstract: Despite eight years since the initial detection of gravitational waves, the astrophysical origin of these phenomena remains elusive. Recent years have witnessed a growing interest in a novel gravitational wave formation pathway: the active galactic nuclei (AGN) channel. I will begin by providing an overview of the current status of gravitational wave detections, the main astrophysical mechanisms driving the pairing and coalescence of black holes, and the observational signatures crucial for distinguishing between various formation scenarios.
I will then describe the key features of the AGN channel, discuss our ongoing efforts in modeling compact objects within accretion disks in AGNs, and highlight the primary challenges associated with modeling black hole-gas disk interactions. Partially based on: arXiv:2403.00060, arXiv:2312.13281
Tuesday April 16, 11:00 Nahuel Freitas (auditorium)
Video: https://youtu.be/oUp_kMtgEpk
Title (colloquium): Non-Equilibrium Stochastic Thermodynamics
Abstract: Stochastic thermodynamics consists of a family of formalisms able to describe non-equilibrium processes in a general way and from a thermodynamic standpoint. It allows to obtain powerful results of universal nature, and has been employed in recent years to a wide variety of problems in different areas. I will introduce the basic concepts of the field and review recent developments. In particular, I will discuss a recent extension of the Second Law of thermodynamics to non-equilibrium steady states (Freitas and Esposito, Nat. Commun. 13, 5084 (2022)). I will also discuss the application of stochastic thermodynamics to non-linear electronic circuits (Freitas et. al. Phys. Rev. X 11, 031064 (2021)), and population dynamics models.
Wednesday April 17, 10:00 Antonio Oliveira Jr. (auditorium)
Video: https://youtu.be/JKh_n9KhGJE
Title (colloquium): Physical modeling of the genome: structural insights and biological consequences
Abstract: The genome is organized within a nucleus where chromosomes fold into an ensemble of conformations. This spatial arrangement within the nucleus is critical for regulating gene expression and other DNA-templated processes. Chromosome conformation capture techniques such as Hi-C provide information about the genome architecture by creating 2D contact maps. Recently, measuring efforts were expanded to several organisms, cell lines, tissues, and cell cycle phases, in which obtaining high-quality maps is still challenging. These contact maps serve as an essential input for top-down theoretical models. Aided by the under-development chromatin folding and structure theory, we create a framework using polymer theory enriched with the Maximum Entropy Approach to learn and understand the chromosome spatial organization. To enhance the training of the energy functions, we included a combined machine learning minimization method that allows us to speed up the modeling, even for large systems. We use our developed platform, Open-MiChroM, to perform fast simulations and training. The models generated are precise compared to the experimental Hi-Cs, and the 3D structures ensemble is consistent with the crystal liquid theory for chromosomes. Additionally, we are able to predict important features of chromosome organization, such as the phase separation between chromatin types and the formation of chromosome territories. This novel modeling allows the exploration of a broad spectrum of 3D genome organizations on different organisms, cell lines, and cell phases.
Thursday April 18, 11:00 Antonio Oliveira Jr. (auditorium)
Video: https://youtu.be/qxxTQLQRH18
Title (blackboard): Beyond the DNA Double Helix: Physics’ Role in Understanding Genomic Organization Complexity
Friday April 19, 15:00 Nahuel Freitas (auditorium)
Video Part 1: https://youtu.be/mJm9OTKPl18
Video Part 2: https://youtu.be/_HutOa6qrfQ
Title (blackboard): Emergent Second Law in macroscopic stochstic thermodynamics
Abstract: I will discuss the derivation of the Emergent Second Law recently identified in Freitas and Esposito, Nat. Commun. 13, 5084 (2022). For stochastic systems with a well defined macroscopic limit, this result provides a link between the deterministic dynamics that emerges in such a limit, and the fluctuations that are observed at steady state. I will also discuss ongoing work about the generalization of this result to evolving non-equilibrium states.
Monday April 29, 10:30 Jaron Kent-Dobias
Video: https://youtu.be/6HYKP5A3ogU
Title (colloquium): Geometry and descent in random landscapes
Abstract: From quenched physical systems to simple optimization algorithms, descent in an energy or cost landscape is thought to underpin many interesting phenomena. Likewise, the geometry of this landscape is thought to explain diverse outcomes of this descent: in those with few minima, the lowest are easily found; while in those with very many, getting stuck among a proliferation of high minima is overwhelmingly likely. In mean-field spin glasses and inference problems, we can hope to use geometry to explain when transitions between these behaviors occur and which kind of minima will typically be found. I will describe the past success of this approach in the simplest spin glass models and its recent failure in slightly less simple ones. I will share several new results on the statistics and arrangement of metastable states and saddle points which together indicate that traditional mean-field geometric tools may not be able to answer everything. Finally, I share some thoughts on what extensions might be needed to precisely predict where descent goes.
Tuesday April 30, 15:00 Emiliano Ipiña Perez
Video: https://youtu.be/fBh60zDKbiw
Title (colloquium): Self-regulated cell motility by substrates: the cases of cellular footprints and bacterial adhesion
Abstract: Eukaryotic cells and bacteria can use the substrate to self-regulate their movement. Eukaryotic cells, such as MDCK epithelial cells, leave footprints on the substrate, which are then used to regulate their motility and exploratory behavior. On the other hand, Escherichia coli bacteria stop and adhere to the surface to break confinement when swimming close to the surface and explore their surroundings more efficiently. In this talk, I will explore these mechanisms through mathematical models highlighting how both cells and bacteria, at two different biological scales, use the environment to self-regulate the way they explore their surroundings.
Wednesday May 1, 10:30 Jaron Kent-Dobias
Video: https://youtu.be/TgQgqLg_LlM
Title (blackboard): Statistics of metastable states in the spherical models and beyond
Abstract: Characterizing metastable states and saddle points in complex systems can shed light on a variety of equilibrium and out-of-equilibrium behaviors. In this talk, I will discuss the most versatile theoretical technique for this, the Kac–Rice method, and its application to family of mean-field models, the spherical spin glasses. I will draw connections from this technique to random matrix theory and Faddeev–Popov gauge fixing. For the spherical models, writing down an effective action is straightforward but finding physical saddle points can be challenging. I will show how, for the lowest-energy states, a BRST supersymmetry can be used to simplify the action and map it to a more tractable equilibrium problem. Finally, I will discuss challenges to using these techniques in inference problems with non-Gaussian energy functions, and current work being done to address them.
Thursday May 2, 10:30 Emiliano Ipiña Perez
Video: https://youtu.be/GDGFPE3A_Sg
Title (blackboard): Cells in Motion: the interplay between motility, migration, and the environment
Abstract: The movement of microorganisms, including some eukaryotic cells and bacteria, is essential for numerous biological functions. The motility mechanisms of bacteria and eukaryotic cells are very different. Still, they share something in common: cell motility and its transport properties result from a complex interplay between the internal machinery of cells and the environment. As cells move, they actively modify their surroundings, which inevitably affects their movement. Yet, these two aspects have often been studied independently, resulting in a limited and incomplete understanding of how microorganisms migrate. I am interested in understanding how this interplay occurs in nature. Specifically, I am interested in how cells sense and respond to signals at the individual and collective level, what mechanisms they use to guide themselves, their motility properties and search strategies for locating targets, or how the environment modifies their motility behavior. Here, I will outline how I plan to address these questions by studying two fascinating problems: (i) the role of cellular footprints as a guidance mechanism and (ii) the effect of physical obstacles in bacterial infections.
Tuesday May 7, 15:00 Felipe Andrade-Oliveira
Video: https://youtu.be/6Z0zMpUeAhk
Title (colloquium): Measuring the Universe with Galaxy Surveys: Present and Future
Abstract: In recent years, large galaxy surveys have played a key role in cosmology, drawing together the effort of hundreds of researchers towards a common goal: accurate and precise measurements of the components of the Universe. In this colloquium, I present some details on how these experiments are built and the rich science behind them. I show the recent cosmological results achieved by the Dark Energy Survey, the Dark Energy Spectroscopic Instrument, and the combination of these experiments with other probes. Finally, I will discuss the new challenges and expected advances by the next generation of surveys.
Thursday May 9, 14:30 Felipe Andrade-Oliveira
Video: https://youtu.be/tOXPOu4a-jg
Title (blackboard): Extracting Cosmological Information from Galaxy Surveys
Abstract: In this lecture, I explore the techniques employed in major observational projects such as the Dark Energy Survey (DES) and the upcoming Legacy Survey of Space and Time (LSST). The focus will be on understanding the basics of the construction of correlation functions and power spectra for photometric surveys, which are critical tools for analysing the distribution of galaxies and measuring cosmic parameters such as dark energy and dark matter.