Gilberto L. Thomas

Gilberto L. Thomas
Universidade Federal do Rio Grande do Sul | UFRGS · Departamento de Física

PhD

About

48
Publications
4,569
Reads
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1,097
Citations
Additional affiliations
January 2011 - February 2012
Indiana University Bloomington
Position
  • Researcher

Publications

Publications (48)
Article
Full-text available
To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 in vitro infection of a human lung epithelial cell li...
Article
Cell migration plays essential roles in development, wound healing, diseases, and in the maintenance of a complex body. Experiments in collective cell migration generally measure quantities such as cell displacement and velocity. The observed short-time diffusion regime for mean square displacement in single-cell migration experiments on flat surfa...
Article
Active-Matter models commonly consider particles with overdamped dynamics subject to a force (speed) with constant modulus and random direction. Some models also include random noise in particle displacement (a Wiener process), resulting in diffusive motion at short time scales. On the other hand, Ornstein–Uhlenbeck processes apply Langevin dynamic...
Preprint
Full-text available
Cell migration plays essential roles in development, wound healing, diseases, and in the maintenance of a complex body. Experiments in collective cell migration generally measure quantities such as cell displacement and velocity. The observed short-time diffusion regime for mean square displacement in single-cell migration experiments on flat surfa...
Preprint
Full-text available
To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 in vitro infection of a human lung epithelial cell li...
Article
Mesenchymal cell crawling is a critical process in normal development, tissue function and in many diseases. Quantitatively predictive numerical simulations of cell crawling thus have multiple scientific, medical and technological applications. However, we still lack a low-computational-cost approach to simulate mesenchymal 3D cell crawling. Here w...
Article
Cell crawling has usually been characterized by a diffusion constant D and instantaneous velocity 〈|v→|2〉. However, experimentally 〈|v→|2〉 diverges. A three regime (diffusive-ballistic-diffusive) modified Fürth equation parameterized by D, the dimensionless excess diffusion coefficient S and the persistence time P is compatible with experiment. S a...
Preprint
Full-text available
Active Matter models commonly consider particles with overdamped dynamics subject to a force (speed) with constant modulus and random direction. Some models include also random noise in particle displacement (Wiener process) resulting in a diffusive motion at short time scales. On the other hand, Ornstein-Uhlenbeck processes consider Langevin dynam...
Preprint
Full-text available
Cell crawling is critical to biological development, homeostasis and disease. In many cases, cell trajectories are quasi-random-walk. In vitro assays on flat surfaces often described such quasi-random-walk cell trajectories as approximations to a solution of a Langevin process. However, experiments show quasi-diffusive behavior at small timescales,...
Article
Full-text available
Tumor cells and structure both evolve due to heritable variation of cell behaviors and selection over periods of weeks to years (somatic evolution). Micro-environmental factors exert selection pressures on tumor-cell behaviors, which influence both the rate and direction of evolution of specific behaviors, especially the development of tumor-cell a...
Article
In wet liquid foams, slow diffusion of gas through bubble walls changes bubble pressure, volume and wall curvature. Large bubbles grow at the expenses of smaller ones. The smaller the bubble, the faster it shrinks. As the number of bubbles in a given volume decreases in time, the average bubble size increases: i.e. the foam coarsens. During coarsen...
Article
Full-text available
In wet liquid foams, slow diffusion of gas through bubble walls changes bubble pressure, volume and wall curvature. Large bubbles grow at the expenses of smaller ones. The smaller the bubble, the faster it shrinks. As the number of bubbles in a given volume decreases in time, the average bubble size increases: i.e. the foam coarsens. During coarsen...
Article
Fusion of cell tissues is an ubiquitous phenomenon and has important technological applications including tissue biofabrication. In this work we present experimental results of aggregates fusion using adipose derived stem cells (ADSC) and a three dimensional computer simulation of the process using the cellular Potts model with aggregates reaching...
Article
Full-text available
The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at th...
Conference Paper
Full-text available
Developing models that simulate the behavior of different types of interacting biological cells can be a very time consuming and error prone task. CompuCell3D is an open source application that addresses this challenge. It provides interactive and customizable visualizations that help a user detect when a model is producing the desired behavior and...
Article
Full-text available
We study the topology and geometry of two dimensional coarsening foams with arbitrary liquid fraction. To interpolate between the dry limit described by von Neumann's law, and the wet limit described by Marqusee equation, the relevant bubble characteristics are the Plateau border radius and a new variable, the e?ective number of sides. We propose a...
Data
Sorting of cells expressing two cadherin levels - [1, 23]. (WMV)
Data
Sorting of cells expressing three cadherin levels - [1, 12, 23]. (WMV)
Data
Sorting of cells expressing five cadherin levels (as above) and motility = 5. (WMV)
Data
Same five cadherin levels but motility = 40. (WMV)
Data
Same five cadherin levels but motility = 60. (WMV)
Data
XML configuration file and python scripts for the simulations presented in the text. (BZ2)
Data
Sorting of cells expressing five cadherin levels - [1, 6.5, 12, 17.5, 23]. (WMV)
Data
Sorting of cells expressing nine cadherin levels - [1, 3.75, 6.5, 10.25, 12, 14.75, 17.5, 20.25, 23]. (WMV)
Data
Same five cadherin levels but motility = 80. (WMV)
Data
Same five cadherin levels but motility = 10. (WMV)
Article
Full-text available
The actions of cell adhesion molecules, in particular, cadherins during embryonic development and morphogenesis more generally, regulate many aspects of cellular interactions, regulation and signaling. Often, a gradient of cadherin expression levels drives collective and relative cell motions generating macroscopic cell sorting. Computer simulation...
Article
Full-text available
A self-propelled particle model is introduced to study cell sorting occurring in some living organisms. This allows us to evaluate the influence of intrinsic cell motility separately from differential adhesion with fluctuations, a mechanism previously shown to be sufficient to explain a variety of cell rearrangement processes. We find that the tend...
Article
We perform extensive Potts model simulations of 3D dry foam coarsening and we report reaching a scaling state. Starting with 2.25 million bubbles, we have enough time for the transient to end and reach the scaling state; enough time in the scaling state to characterize its properties; and finally, enough bubbles at the end to avoid spurious finite...
Article
Full-text available
We perform extensive Potts model simulations of three-dimensional dry foam coarsening. Starting with 2.25 million bubbles, we have enough statistics to fulfill the three constraints required for the study of statistical scale invariance: first, enough time for the transient to end and reach the scaling state; then, enough time in the scaling state...
Article
We simulate the shape relaxation of foam clusters and compare them with the time exponential expected for Newtonian fluid. Using two-dimensional Potts Model simulations, we artificially create holes in a foam cluster and shuffle it by applying shear strain cycles. We reproduce the experimentally observed time exponential relaxation of cavity shapes...
Article
The influence of surface tension and size on rounding of cell aggregates is studied using chick embryonic cells and numerical simulations based on the cellular Potts model. Our results show exponential relaxation in both cases as verified in previous studies using 2D Hydra cell aggregates. The relaxation time decreases with higher surface tension a...
Article
A classical model for developmental patterning invokes a chemical ‘prepattern’ which cells read out as developmental instructions. The ‘prepattern’ arises from the Turing Instability of two reacting and diffusing chemicals, an ‘activator’ and an ‘inhibitor.’ We propose a novel developmental mechanism, based on cell–cell adhesion and cell–extracellu...
Article
We present a stochastic cellular automaton model for the behavior of limb bud precartilage mesenchymal cells undergoing chondrogenic patterning. This "agent-oriented" model represents cells by points on a lattice that obey rules motivated by experimental findings. The "cells" follow these rules as autonomous agents, interacting with other cells and...
Conference Paper
Full-text available
Early development of multicellular organisms (morphogenesis) is a complex phenomenon. We present COMPUCELL, a multi-model software framework for simulations of morphogenesis. As an example, we simulate the formation of the skeletal pattern in the avian limb bud, which requires simula- tions based on interactions of the genetic regulatory network wi...
Article
Full-text available
Early development of multicellular organisms (morphogenesis) is a complex phenomenon. We present COMPUCELL, a multi-model software framework for simulations of morphogenesis. As an example, we simulate the formation of the skeletal pattern in the avian limb bud, which requires simulations based on interactions of the genetic regulatory network with...
Article
We present experimental results and a simulation in two dimensions of the expansion and bursting of aggregates of Hydra cells formed from an initially disordered mixture. In the experiments, after cell sorting, the aggregate rounds and swells until violent bursts occur, forcibly expelling internal fluid and loose cells. We use Monte Carlo technique...
Article
The aim of this work is to calculate the complete order 1/Nc corrections to the baryon masses in the bound state approach to the three flavor Skyrme model. We consider the strange-strange interactions which take the form of a meson-meson interaction in the expansion of the chiral Lagrangian to quartic order in the kaon fields. This type of interact...
Article
We discuss, in the framework of the bound state approach to SU(3) Skyrme model, the baryonic number-two strange sector. We study situations where the baryons involved are bound to form dibaryons and where free baryons are simply scattered. In the first case, the dibaryon spectrum is calculated with a generalized axially symmetric ansatz. A predicti...
Article
Full-text available
In this paper we consider a generalization to the asexual version of the Penna model for biological aging, where we take a continuous time limit. The genotype associated to each individual is an interval of real numbers over which Dirac $\delta$--functions are defined, representing genetically programmed diseases to be switched on at defined ages o...
Article
We present a simulation in two dimensions of an important process of biological development: the burst of an aggregate of cells due to the expansion of an internal cavity by influx of external medium. The burst is quantitatively characterized by discontinuous change of the pressure of the aggregate. The influence of dimensionality on the process an...
Article
We develop the formalism to study the hyperon-nucleon interaction potential within the bound state approach to the SU(3) Skyrme model. The general framework is illustrated by applying it to the diagonal $\Lambda N$ potential. The central, spin-spin and tensor components of this interaction are obtained and compared with those derived using alternat...
Article
Full-text available
We develop the formalism to study the hyperon - nucleon interaction potential within the bound-state approach to the SU(3) Skyrme model. The general framework is illustrated by applying it to the diagonal ΛN potential. The central, spin-spin and tensor components of this interaction are obtained and compared with those derived using alternative sch...
Article
Dibaryon configurations are studied in the framework of the bound-state soliton model. A generalized axially symmetric ansatz is used to determine the soliton background. We show that once the constraints imposed by the symmetries of the lowest-energy torus configuration are satisfied, all spurious states are removed from the dibaryon spectrum. In...

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Projects

Projects (2)
Project
Our goal is to infrastructure to support the collaborative development of meaningful SARS-CoV-2 infection and the progression of COVID-19. The aim is to define a modular structure that allows parallel submodel development and build models of key processes and components, especially primary and secondary sites of infection and immune response.
Project
Mechanistic modeling is an integral part of contemporary bioscience, used for hypothesis generation and testing, experiment design and interpretation and the design of therapeutic interventions. The CompuCell3D modeling environment allow researchers with modest programming experience to rapidly build and execute complex Virtual Tissue simulations of development, homeostasis, toxicity and disease in tissues, organs and organisms, covering sub-cellular, multi-cell and continuum tissue scales. Virtual-Tissue simulations developed using CompuCell3D run on Windows, Mac and Linux. CompuCell3D is open source, allowing users to extend, improve, validate, modify and share the core software. By the end of the Summer Schools and Hackathons, participants will have implemented a basic simulation of their particular biological problem of interest. Post-course support and collaboration will be available to continue simulation development.