Statistics, distillation, and ordering emergence in a two-dimensional stochastic model of particles in counterflowing streams

In this paper, we proposed a stochastic model which describes two species of particles moving in counterflow. The model generalizes the theoretical framework describing the transport in random systems since particles can work as mobile obstacles, whereas particles of one species move in opposite direction to the particles of the other species, or they can work as fixed obstacles remaining in their places during the time evolution. We conducted a detailed study about the statistics concerning the crossing time of particles, as well as the effects of the lateral transitions on the time required to the system reaches a state of complete geographic separation of species. The spatial effects of jamming were also studied by looking into the deformation of the concentration of particles in the two-dimensional corridor. Finally, we observed in our study the formation of patterns of lanes which reach the steady state regardless the initial conditions used for the evolution. A similar result is also observed in real experiments involving charged colloids motion and simulations of pedestrian dynamics based on Langevin equations, when periodic boundary conditions are considered (particles counterflow in a ring symmetry). The results obtained through Monte Carlo numerical simulations and numerical integrations are in good agreement with each other. However, differently from previous studies, the dynamics considered in this work is not Newton-based, and therefore, even artificial situations of self-propelled objects should be studied in this first-principle modeling.Comment: 27 pages, 13 figure

Lipids, membranes, colloids and cells: A long view

This paper revisits long-standing ideas about biological membranes in the context of an equally long-standing, but hitherto largely unappreciated, perspective of the cell based on concepts derived from the physics and chemistry of colloids. Specifically, we discuss important biophysical aspects of lipid supramolecular structure to understand how the intracellular milieu may constrain lipid self-assembly. To this end we will develop four lines of thought: first, we will look at the historical development of the current view of cellular structure and physiology, considering also the plurality of approaches that influenced its formative period. Second, we will review recent basic research on the structural and dynamical properties of lipid aggregates as well as the role of phase transitions in biophysical chemistry and cell biology. Third, we will present a general overview of contemporary studies into cellular compartmentalization in the context of a very rich and mostly forgotten general theory of cell physiology called the Association-Induction Hypothesis, which was developed around the time that the current view of cells congealed into its present form. Fourth, we will examine some recent developments in cellular studies, mostly from our laboratory, that raise interesting issues about the dynamical aspects of cell structure and compartmentalization. We will conclude by suggesting what we consider are relevant questions about the nature of cellular processes as emergent phenomena.Fil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentina. Memphys - International And Interdisciplinary Research Network; Dinamarca. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Química. Cátedra de Química Biológica; ArgentinaFil: Stock, Roberto. Memphys - International And Interdisciplinary Research Network; Dinamarc

Mobile-to-clogging transition in a Fermi-like model of counterflowing particles

In this paper we propose a generalized model for the motion of a two-species self-driven objects ranging from a scenario of a completely random environment of particles of negligible excluded volume to a more deterministic regime of rigid objects in an environment. Each cell of the system has a maximum occupation level called σ max . Both species move in opposite directions. The probability of any given particle to move to a neighboring cell depends on the occupation of this cell according to a Fermi-Dirac-like distribution, considering a parameter α that controls the system randomness. We show that for a certain α = α c the system abruptly transits from a mobile scenario to a clogged state, which is characterized by condensates. We numerically describe the details of this transition by coupled partial differential equations (PDE) and Monte Carlo (MC) simulations that are in good agreement

Lattice Gas model to describe a nightclub dynamics

In this work, we propose a simple stochastic agent-based model to describe the revenue dynamics of a nightclub venue based on the relationship between profit and spatial occupation. The system consists of an underlying square lattice (nightclub's dance floor) where every attendee (agent) is allowed to move to its first neighboring cells. Each guess has a characteristic delayed time between drinks, denoted as $\tau$, after which it will show an urge to drink. At this moment, the attendee will tend to move towards the bar where a drink will be bought. After it has left the bar zone, $\tau$ time steps should pass so it shows once again the need to drink. Our model among other points show that it is no use filling the bar to obtain profit, and optimization should be analyzed. This can be done in a more secure way taking into consideration the ratio between income and ticket cost.Comment: 13 pages, 6 figure

Coupled response of membrane hydration with oscillating metabolism in live cells: An alternative way to modulate structural aspects of biological membranes?

We propose that active metabolic processes may regulate structural changes in biological membranes via the physical state of cell water. This proposition is based on recent results obtained from our group in yeast cells displaying glycolytic oscillations, where we demonstrated that there is a tight coupling between the oscillatory behavior of glycolytic metabolites (ATP, NADH) and the extent of the dipolar relaxation of intracellular water, which oscillates synchronously. The mechanism we suggest involves the active participation of a polarized intracellular water network whose degree of polarization is dynamically modulated by temporal ATP fluctuations caused by metabolism with intervention of a functional cytoskeleton, as conceived in the long overlooked association-induction hypothesis (AIH) of Gilbert Ling. Our results show that the polarized state of intracellular water can be propagated from the cytosol to regions containing membranes. Since changes in the extent of the polarization of water impinge on its chemical activity, we hypothesize that metabolism dynamically controls the local structure of cellular membranes via lyotropic effects. This hypothesis offers an alternative way to interpret membrane related phenomena (e.g., changes in local curvature pertinent to endo/exocytosis or dynamical changes in membranous organelle structure, among others) by integrating relevant but mostly overlooked physicochemical characteristics of the cellular milieu.Fil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Stock, Roberto P.. International and Interdisciplinary Research Network; DinamarcaFil: Olsen, Lars F.. University Of Southern Denmark; Dinamarc

Avaliação Institucional na ESEF: O desafio de uma construção coletiva

Artigo publicado na Revista Movimento – Edição Especial: ESEF 70 AnosEste artigo tem por objetivo apresentar algumas reflexões sobre a caminhada que o Núcleo de Avaliação da Escola de Educação Física da Universidade Federal do Rio Grande do Sul (NAU/ESEF/UFRGS) vem trilhando na área da avaliação institucional. Após uma breve contextualização histórica da avaliação do Ensino Superior nas Universidades brasileiras e, mais especificamente, na UFRGS, discorremos a respeito da metodologia empregada pelo NAU da ESEF no processo avaliativo desenvolvido dentro da Unidade. A partir desta experiência de construção coletiva, trazemos alguns questionamentos acerca do tema, na tentativa de contribuir para discussões que possam vir a ocorrer em diversos âmbitos.Produto do Projeto "ESCOLA DE EDUCAÇÃO FÍSICA DA UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL (1940-2010): mapeando cenários da formação profissional e da produção do conhecimento em políticas públicas de esporte e lazer", financiado pela Rede Cede

The cell as a gel: materials for a conceptual discussion

Recent results from our laboratory support the view that the intracellular milieu cannot be treated as a homogeneous dilute system and, more importantly, reveal for the first time a dynamical coupling between intracellular water and an active metabolic process involving fluctuations in ATP concentration. These results are difficult to understand in light of the premises that currently underpin the description of the function of cellular systems, e.g. van’t Hoff’s ideal solution theory, diffusion and mass action kinetics. Particularly, they emphasize the need to incorporate features of the cell interior that have been largely overlooked in the dominant model of the cell, such as crowding and limited availability of free water. This article discusses this problem by reconsidering an alternate view, called the association-induction hypothesis, which emphasizes the relevance of emergent properties of the cell cytosol during cellular function. This hypothesis provides a very reasonable theoretical framework to explain recently reported observations about the dynamical coupling of mechanochemical (i.e. viscoelastic) properties of the cell cytoplasm and cellular chemical transformations (metabolism).Los resultados experimentales obtenidos recientemente en nuestro laboratorio apoyan la idea que el medio intracelular no puede ser tratado como un sistema homogéneo (o solución diluida), revelando además por primera vez un acoplamiento dinámico entre el comportamiento colectivo del agua intracelular y un proceso metabólico activo que muestra fluctuaciones en la concentración de ATP. Estos nuevos resultados -que son difíciles de interpretar en base a los supuestos más generalmente utilizados para interpretar las bases fisicoquímicas de la fisiología de los sistemas celulares (p.ej. teoría de las soluciones ideales de van't Hoff, difusión, y cinética de acción de masas)- subrayan la necesidad urgente de incorporar características importantes del interior celular, tales como el hacinamiento molecular y la escasa disponibilidad de agua libre. Este artículo analiza críticamente este problema considerando una hipótesis alternativa, llamada hipótesis de asociación-inducción, la cual hace hincapié en la importancia de las propiedades emergentes del citosol durante la función celular. Esta hipótesis proporciona un marco teórico razonable para explicar nuestras observaciones, particularmente el acoplamiento dinámico entre las propiedades mecanoquímicas (o viscoelásticas) del citoplasma celular y las transformaciones químicas (metabolismo) en el interior celular.Sociedad Argentina de Fisiologí

Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence

Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.Fil: Lara Popoca, Jesús. Universidad Nacional Autónoma de México; MéxicoFil: Thoke, Henrik S.. International and Interdisciplinary Research Network; DinamarcaFil: Stock, Roberto P.. Universidad Nacional Autónoma de México; MéxicoFil: Rudino Pinera, Enrique. Universidad Nacional Autónoma de México; MéxicoFil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentin

Tight Coupling of Metabolic Oscillations and Intracellular Water Dynamics in <i>Saccharomyces cerevisiae</i>

We detected very strong coupling between the oscillating concentration of ATP and the dynamics of intracellular water during glycolysis in Saccharomyces cerevisiae. Our results indicate that: i) dipolar relaxation of intracellular water is heterogeneous within the cell and different from dilute conditions, ii) water dipolar relaxation oscillates with glycolysis and in phase with ATP concentration, iii) this phenomenon is scale-invariant from the subcellular to the ensemble of synchronized cells and, iv) the periodicity of both glycolytic oscillations and dipolar relaxation are equally affected by D2O in a dose-dependent manner. These results offer a new insight into the coupling of an emergent intensive physicochemical property of the cell, i.e. cell-wide water dipolar relaxation, and a central metabolite (ATP) produced by a robustly oscillating metabolic process