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Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
This paper addresses analytical aspects of deterministic, continuous-time dynamical systems defined on networks. The goal is to model and analyze certain phenomena which must be framed beyond the context of networked dynamical systems,…
A fundamental premise of statistical physics is that the particles in a physical system are interchangeable, and hence the state of each specific component is representative of the system as a whole. This assumption breaks down for complex…
This paper studies the operation of multi-agent networks engaged in multi-task decision problems under the paradigm of simultaneous learning and adaptation. Two scenarios are considered: one in which a decision must be taken among multiple…
We study diffusion-driven pattern-formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing…
Mathematical modeling with Ordinary Differential Equations (ODEs) has proven to be extremely successful in a variety of fields, including biology. However, these models are completely deterministic given a certain set of initial conditions.…
Given a Bayesian network structure (directed acyclic graph), the celebrated d-separation algorithm efficiently determines whether the network structure implies a given conditional independence relation. We show that this changes drastically…
Discrete dynamical systems in which model components take on categorical values have been successfully applied to biological networks to study their global dynamic behavior. Boolean models in particular have been used extensively. However,…
Community detection in multi-layer networks is a fundamental task in complex network analysis across various areas like social, biological, and computer sciences. However, most existing algorithms assume that the number of communities is…
The dual phosphorylation network provides an essential component of intracellular signaling, affecting the expression of phenotypes and cell metabolism. For particular choices of kinetic parameters, this system exhibits multistationarity, a…
Molecular simulations as well as single molecule experiments have been widely analyzed in terms order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive,…
We consider the problem of performing parameter and state inference in a state-space model (SSM) parametrized by a static parameter $\theta$. A popular idea to address this problem consists of incorporating $\theta$ in the state of the…
We consider distributed systems with an arbitrary number of processes, modelled by timed automata that communicate through location guards: a process can take a guarded transition if at least one other process is in a given location. In…
The dynamics of a multiplex heterogeneous network of oscillators is studied. Two types of similar models based on the Hodgkin-Huxley formalism are used as the basic elements of the networks. The first type model demonstrates bursting…
Inferring parameters of models of biochemical kinetics from single-cell data remains challenging because of the uncertainty arising from the intractability of the likelihood function of stochastic reaction networks. Such uncertainty falls…
This paper studies the relations among system parameters, uniqueness, and stability of equilibria, for kinetic systems given in the form of polynomial ODEs. Such models are commonly used to describe the dynamics of nonnegative systems, with…
In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917 (2007)] investigate an artificial dynamic system on metabolic networks. They find a less complex time evolution of this dynamic system in real networks, compared to…
Whereas the positive equilibrium of a mass-action system with deficiency zero is always globally stable, for deficiency-one networks there are many different scenarios, mainly involving oscillatory behaviour. We present several examples,…
We develop a family of reformulations of an arbitrary consistent linear system into a stochastic problem. The reformulations are governed by two user-defined parameters: a positive definite matrix defining a norm, and an arbitrary discrete…