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Neural dynamics underlie behaviors from memory to sleep, yet identifying mechanisms for higher-order phenomena (e.g., social interaction) is experimentally challenging. Existing whole-brain models often fail to scale to single-neuron…

We explore the collective behaviours of 7 group sizes: 1, 2, 3, 5, 7, 10 and 20 AB zebrafish (Danio rerio) in a constraint environment composed of two identical squared rooms connected by a corridor. This simple set-up is similar to a…

Coupled biological oscillators can tick with the same period. How this collective period is established is a key question in understanding biological clocks. We explore this question in the segmentation clock, a population of coupled…

The infant microbiome undergoes rapid changes in composition over time and is associated with long-term risks of conditions such as immune strength, allergy, asthma, and other health outcomes. Modeling the associations between exposures or…

System dynamics and agent based simulation models can both be used to model and understand interactions of entities within a population. Our modeling work presented here is concerned with understanding the suitability of the different types…

Movement behavior of an indicator species, zebrafish (Danio rerio), was analyzed with one- and two-individual groups before and after treatment with a toxic chemical, formaldehyde, at a low concentration (1 ppm). After the boundary area had…

Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…

How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…

The coexistence of different viral strains (quasispecies) within the same host are nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have…

Ionizing radiation is known to delay the cell cycle progression. In particular after particle exposure significant delays have been observed and it has been shown that the extent of delay affects the expression of damage such as chromosome…

Notch signaling is a ubiquitous and versatile intercellular signaling system that drives collective behaviors and pattern formation in biological tissues. During embryonic development, Notch is involved in generation of collective…

We explore the role of cellular life cycles for viruses and host cells in an infection process. For this purpose, we derive a generalized version of the basic model of virus dynamics (Nowak, M.A., Bangham, C.R.M., 1996. Population dynamics…

In this work we applied several concepts on the modeling of complex systems in an attempt to save mankind in the case of a zombie apocalypse. We developed a dynamical system in order to model a zombie outbreak in which we, regular humans,…

The search to understand how the HIV virus spreads inside the human body and how the immune response works to control it has motivated studies related to Mathematical Immunology. Actually, researches include the idea of mathematical models…

In this paper we study a mathematical model for an infectious disease such as Cholera without life-time immunity. Due to the different mobility for susceptible, infected human and recovered human hosts, the diffusion coefficients are…

A model of bit-strings, that uses the technique of multi-spin coding, was previously used to study the time evolution of B-cell clone repertoire, in a paper by Lagreca, Almeida and Santos. In this work we extend that simplified model to…

Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. Here, we propose a simple…

Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…

Motivated by several recent experimental observations that vitamin-D could interact with antigen presenting cells (APCs) and T-lymphocyte cells (T-cells) to promote and to regulate different stages of immune response, we developed a coarse…

We develop a kinetic reaction model for cells having irradiated DNA molecules due to ionizing radiation exposure. Our theory simultaneously accounts for the time-dependent reactions of the DNA damage, the DNA mutation, the DNA repair, and…