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Understanding the mutual interdependence between the behavior of dynamical processes on networks and the underlying topologies promises new insight for a large class of empirical networks. We present a generic approach to investigate this…
The analysis of biological networks is characterized by the definition of precise linear constraints used to cumulatively reduce the solution space of the computed states of a multi-omic (for instance metabolic, transcriptomic and…
We present a selective review of statistical modeling of dynamic networks. We focus on models with latent variables, specifically, the latent space models and the latent class models (or stochastic blockmodels), which investigate both the…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
In this article, we continue our mathematical study of organic solar cells (OSCs) and propose a two-scale (micro- and macro-scale) model of heterojunction OSCs with interface geometries characterized by an arbitrarily complex morphology.…
This work proposes to model the space environment as a stochastic dynamic network where each node is a group of objects of a given class, or species, and their relationship is represented by stochastic links. A set of stochastic dynamic…
Pathogen introduction in plant communities can cause serious impact and biodiversity losses that may take long time to manage and restore. Effective control of epidemic spreading in the wild is a problem of paramount importance, because of…
This paper deals with a new model for clonal network dynamics. We describe in detail this model and derive special equations governing immune system dynamics based on the general gradient type principles that can be inherent to a wide class…
Functional brain networks can change rapidly as a function of stimuli or cognitive shifts. Tracking dynamic functional connectivity is particularly challenging as it requires estimating the structure of the network at each moment as well as…
The spread of viruses in biological networks, computer networks, and human contact networks can have devastating effects; developing and analyzing mathematical models of these systems can be insightful and lead to societal benefits. Prior…
The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
A simple electrical network model, having logical gate capacities, is proposed here for computations in plant cells. It is compared and contrasted with the animal brain network structure and functions.
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
The neural mechanism of memory has a very close relation with the problem of representation in artificial intelligence. In this paper a computational model was proposed to simulate the network of neurons in brain and how they process…
Most networks of interest do not live in isolation. Instead they form components of larger systems in which multiple networks with distinct topologies coexist and where elements distributed amongst different networks may interact directly.…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological,…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…