ICTP-SAIFR Meetings on Soft and Biological Matter

The ICTP South-American Institute for Fundamental Research hosted at the IFT-UNESP brings to you a series of meetings dedicated to discussing important recent findings in the field of Soft and Biological Matter. We will also host seminars by members of our community or visitors. Unless otherwise noted, our meetings will be held in-person on Fridays, starting at 2:30 pm, São Paulo Time.

Everyone is welcome to attend! 

For more information or to receive meetings announcements, please contact Danilo Liarte at danilo.liarte (at) ictp-saifr.org or Pablo de Castro at pablo.castro (at) ictp-saifr.org

Next meeting: Friday, 03/May/2024, 2:30 pm, Sala 1, IFT-UNESP

Rui Aquino (IFT-UNESP & ICTP-SAIFR)

Effects of the kinetic energy in heat for overdamped systems

The field of stochastic thermodynamics aims to describe exchange of energy in the mesoscale. In this regime, heat is a random variable with a probability distribution associated. Although intuition may lead us to consider that the dynamics and the energetics of Brownian systems are not completely attached, in this talk I will argue that to properly define the heat distribution in different dynamical regimes, one always needs to consider the effect of kinetic energy. This allows us to correctly compute a correspondence between the underdamped and overdamped cases, meaning that the velocity can not be fully ignored in the thermodynamics of these systems. This correction allows more fluctuations in generic Brownian systems and could be employed in the development of more efficient thermal machines.

Upcoming seminars

03/May/2024: Rui Aquino (IFT-UNESP & ICTP-SAIFR)

07/Jun/2024: André M. Timpanaro (UFABC)

14/Jun/2024: Jorge Escobar (IFT-UNESP)

21/Jun/2024: André de Pinho Vieira (IFUSP)

Previous seminars

19/Apr/2024: Guilherme S. Costa (IFT-UNESP & ICTP-SAIFR).

Extensions of the Kuramoto model for coupled oscillators

 Synchronization and its general features are of particular interest to scientists working on several areas, such as physics, engineering, social sciences and biology. From neurons to population dynamics and fireflies, nature showcases several examples of synchronized and collective behavior. The paradigmatic model to investigate synchronization  was proposed by Y. Kuramoto in 1975, with several extensions and generalizations being studied in the years that followed. This presentation aims at overviewing some interesting modifications of this model, in addition to discussing some fundamental aspects of synchronization phenomena. Finally, I will comment on some contributions from our research group and some prospects on this subject.

12/Apr/2024: Pablo de Castro (IFT-UNESP & ICTP-SAIFR).

Epidemic-like dynamics between agglomerates of active particles

Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate between them, as well as disease infection and recovery rates. While the emergence of agglomerates permits early interventions, it also explains longer real epidemics. We will discuss the spread of epidemics (or any sort of information exchange by contact) in spatially-structured systems. For that, we will employ a model of self-propelled particles which spontaneously form multiple clusters. In particular, we will examine the time evolution averaged over many epidemics and how it is affected by the existence of clusters [1]. Furthermore, we will discuss the scenario of phage therapy, i.e., when viruses are deliberately used to infect and kill colonies of bacteria.

 [1] P. de Castro, F. Urbina, A. Norambuena, and F. Guzmán-Lastra, Physical Review E 108, 044104 (2023).

05/Apr/2024: Danilo B. Liarte (IFT-UNESP & ICTP-SAIFR).

Effective-medium theories for disordered elastic systems

Effective-medium theory has become one of the most powerful theoretical tools to describe the universal critical behavior of disordered elastic systems near the onset of a rigidity transition. I will discuss the approximations involved in this formalism and apply it to suitably crafted network models that exhibit transitions to a disordered rigid phase. I will then extract well-tested critical exponents as well as explicit formulas for the universal scaling functions governing the behavior of a large class of disordered viscoelastic materials near the onset of rigidity.

22/Mar/2024: Ahmed El Hady (Max Planck Institute of Animal Behavior).  

Mechanistic theory of (social) foraging

Foraging is a ubiquitous behavior performed by all animals and human beings as they search for food needed to survive. Foraging theory has been key to understand a variety of model systems but it still lacks mechanistic insights that relate it to neurobiological and other physiological mechanisms. In this talk, I will present work that aims to develop a quantitative mechanistic framework of foraging with a specific focus on patch foraging either of an individual agent or in a social context. I will also present a learning model that accounts for how agents learn the structure of the environment.

13/Dez/2023: Fernando A. Oliveira (UnB).

Dynamics, fractal geometry and the exponents of the Kardar- Parisi-Zhang equation

The KPZ equation [1] is connected to a large number of processes, such as atomic deposition, evolution of bacterial colonies, the direct polymer model, the weakly asymmetric simple exclusion process, the totally asymmetric ex- clusion process, direct d-mer diffusion, fire propagation, turbulent liquid- crystal, spin dynamics, polymer deposition in semiconductors, and etching  [2]. We present a short review of the field, some modern problems and perspectives. We discuss as well how a new interpretation of the fluctuation-dissipation theorem [3] allows us to give a solution for the KPZ exponents [4], and fractal dimension [5].

 [1] M. Kardar, G. Parisi, and Y. C. Zhang, Phys. Rev. Lett. 56, 9, 889 (1986).

[2] B. A. Mello, A. S. Chaves, and F. A. Oliveira, Phys. Rev. E 63, 041113 (2001). — E. A. Rodrigues, B. A. Mello, and F. A. Oliveira, J. Phys. A 48, 035001 (2015). — W. S. Alves, E. A. Rodrigues, H. A. Fernandes, B. A. Mello, F. A. Oliveira and I. V. L. Costa 1, Phys. Rev. E 94, 042119 (2016). — W. R. Gomes, A. L. A. Penna and F. A. Oliveira, Phys. Rev. E 100 02101 (2019).

[3] M. S. Gomes-Filho, and F. A. Oliveira, EPL 133 10001 (2021) — P. R. H. dos Anjos, W. S. Alves, M. S. Gomes-Filho, D. L. Azevedo and F. A. Oliveira, Frontiers in Physics 9 , 741590 (2021) https://doi.org/10.3389/fphy.2021.741590.

[4] M. S. Gomes-Filho, A. L. A. Penna and F. A. Oliveira, Results in Physics 26, 104435 (2021).

[5] E. E. M. Luis, T. A. de Assis, F. A. Oliveira, Journal of Statistical Mechanics: Theory and Experiment 8, 083202 (2022).

29/Nov/2023: Carolina P. Vignoto (IFGW-UNICAMP).  

Transições de fase em monocamadas de Langmuir lipídicas: modelo teórico.

Moléculas anfifílicas, em particular, fosfolipídios, são constituintes essenciais das membranas celulares de todos seres vivos. Estas são formadas pela autoagregação de lipídios sob a forma de uma bicamada lipídica, na qual outras macromoléculas biológicas são agregadas a fim de manter sua função biológica. Embora soluções aquosas contendo bicamadas possam ser investigadas diretamente, as chamadas monocamadas de Langmuir representam um sistema modelo experimental de certa forma mais acessível e controlável, que se formam quando uma camada única de moléculas anfifílicas reside na interface ar-água. Do ponto de vista teórico, há várias propostas para a modelagem de transições de fase em fosfolipídios zwitteriônicos, quando a cabeça polar das moléculas não apresenta carga elétrica líquida. Dentre estas propostas, há o gás de rede de Doniach, que consiste num modelo de três estados [lipídio de caudas desordenadas, lipídio de caudas ordenadas e estado vacante (molécula de água)], que pode ser mapeado num modelo de spin-1. Tal modelo representa uma extensão do modelo Blume-Emery-Griffiths (BEG) proposto no contexto de misturas ternárias. Neste seminário apresentaremos uma sinopse dos resultados para o modelo de gás de rede de Doniach obtidos em duas aproximações: campo médio em redes bipartidas e de pares em redes tripartidas (cacto de Husimi). Em particular, através da comparação das duas abordagens, serão discutidas a profusão e diversidade dos diagramas de fases típicos encontrados em cada método. Além disso, será apresentada uma comparação entre os resultados do modelo teórico obtidos nos dois tratamentos com dados experimentais de isotermas de pressão lateral x área por molécula para o fosfolipídio DMPC (dimiristoilfosfatidilcolina).

08/Nov/2023: Carlos E. Fiore (USP).

Eficientes máquinas térmicas coletivas fora do equilíbrio.

Introduzimos uma classe de máquinas térmicas operando fora do equilíbrio, cuja operação coletiva melhora seu desempenho.  Para tal, propusemos um modelo  mínimo composto por unidades interagentes N colocadas em contato com dois reservatórios térmicos e sujeitas a uma fonte de trabalho constante. A interação entre unidades operando cooperativamente leva a um aumento da eficiência e potência bem como diferentes regimes de operação (máquina, refrigerador e outros). Resultados mostram que  interações do tipo Ising em um regime ordenado coletivo é crucial para operar como uma máquina térmica.  As principais características do sistema são investigadas por meio de uma análise linear próxima do equilíbrio e  desenvolvendo um modelo de estado discreto eficaz que captura os efeitos da fase síncrona.  A robustez de nossas descobertas vai além das interações de todos para todos e abre caminho para a construção de máquinas térmicas de não-equilíbrio promissoras baseadas em estruturas ordenadas.

01/Nov/2023: Guilherme S. Costa (IFT-UNESP & ICTP-SAIFR

Spreading dynamics in active matter models.

Spreading processes are a class of dynamical processes that mainly include the propagation of diseases, rumors and information on top of a given population of agents. For a long time, the study of these processes was mostly limited to static substrates or those lacking spatial structure. The popularization of research into active matter, that studies the dynamics of self-propelled agents, has opened up countless possibilities to investigate the behavior of some processes on top of them, as they simultaneously present the dynamics and spatial structure missing in usual substrates. In this presentation, I will review some important concepts and models on spreading dynamics followed by some findings and papers on epidemic spreading in self-propelled entities, ending with some research ideas in collaboration with Dr. Pablo de Castro.

27/Sep/2023: Pablo de Castro (IFT-UNESP & ICTP-SAIFR). 

Simple Models in Active Matter.

Active Matter is a fascinating field in Nonequilibrium Statistical Physics that investigates the dynamics of self-propelled entities such as fish, cells, and artificial particles. After a brief overview of the basic phenomenological features of active matter systems, I will review some simple theoretical approaches that are relevant to the field and which can be used as a starting point towards more complicated systems. In particular, I aim to discuss models for motility-induced phase separation, aligning self-propelled rods and cell tissues.

14/Aug/2023: Felipe Hawthorne (IFUSP). 

The role of translational noise in Motility Induced Phase Separation.

Active matter systems are composed of many self-propelled units, with examples ranging from birds and fish to bacteria, tissue cells and artificial colloids. Typically, the self-propulsion direction of each of these particles fluctuates stochastically and slowly in time. Thus, active particles are said to undergo persistent Brownian motion. For dense systems with low rotational noise (i.e., persistence), volume exclusion coupled with persistent motion generates the formation of clusters, a process called motility-induced phase separation (MIPS). Besides rotational noise dictating the evolution of the self-propulsion angular degree of freedom, translational noise can also exist, e.g., due to thermal noise from the surrounding fluid, acting on the self-propulsion velocity. We investigate the role of translational noise in MIPS and show how, by increasing the translational diffusivity, the system can first enter and then leave the coexistence region of parameters where MIPS occurs. Apart from our results in Active Matter, my research spans other areas within the field of non-equilibrium dynamics and stochastic thermodynamics. I hope to briefly discuss our investigations into the Majority Voter Model and a three-state quantum dot collisional model as a representation of heat engines.

24/Jul/2023: Hilda Cerdeira (IFT-UNESP & ICTP-SAIFR). 

Phase transitions in a system of swarmalators: the XY Model and other things.

Systems of oscillators called Swarmalators, whose phase and spatial dynamics are coupled, have been used to describe the dynamics of some living systems. Their collective behavior presents simultaneous aggregation in space and synchronization in phase which in turn leads in some cases to explosive synchronization in a finite population as a function of the coupling parameter between the phases of the internal dynamics. This phenomenon is described using the order parameter and the Hamiltonian formalism. Near the synchronization transition the internal phases of the particles are represented by the XY model, and their transition to synchronization, which will be discussed, can be of the first or second order. We shall also discuss a multilayer system of swarmalators, which presents some interesting phases on their way to synchronization.

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Last updated on Apr 16th, 2024.