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Network analysis became a powerful tool in recent years. Heat shock is a well-characterized model of cellular dynamics. S. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and…
Threshold rules of spreading in binary-state networks lead to cascades. We study persistent cascade-recovery dynamics on quasi-robust networks, i.e., networks which are robust against small trigger but may collapse for larger one. It is…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Typically, contagion strength is modeled by a transmission rate $\lambda$, whereby all nodes in a network are treated uniformly in a mean-field approximation. However, local agents react differently to the same contagion based on their…
Recent empirical studies have confirmed the key roles of complex contagion mechanisms such as memory, social reinforcement, and decay effects in information diffusion and behaviour spreading. Inspired by this fact, we here propose a new…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
We describe how noise propagates through a network by calculating the variance of the outputs. Using stochastic calculus and dynamical systems theory, we study the network topologies that accentuate or alleviate the effect of random…
Robustness to perturbation is a key topic in the study of complex systems occurring across a wide variety of applications from epidemiology to biochemistry. Here we analyze the eigenspectrum of the Jacobian matrices associated to a general…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
The dynamics of cascading activation, such as rapid changes in public opinion and the outbreak of disease epidemics, have a crucial dependence on the connectivity patterns among the agents. We study cascading dynamics in modular,…
We study the response of an ensemble of synchronized phase oscillators to an external harmonic perturbation applied to one of the oscillators. Our main goal is to relate the propagation of the perturbation signal to the structure of the…
Understanding how local perturbations induce the transient dynamics of a network of coupled units is essential to control and operate such systems. Often a perturbation initiated in one unit spreads to other units whose dynamical state they…
Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This property has well-established implications in statistical physics but remains underexplored…
Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction…
The biological processes that execute complex multiple functions, such as cell cycle, must ensure the order of sequential events and keep the dynamic robustness against various fluctuations. Here, we examine the dynamic mechanism and the…
Many important cellular functions are implemented by protein complexes that act as sophisticated molecular machines of varying size and temporal stability. Here we demonstrate quantitatively that protein complexes in the yeast,…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
[abridged] Background: The distribution of chemical species in an open system at metastable equilibrium can be expressed as a function of environmental variables which can include temperature, oxidation-reduction potential and others.…
Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…