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Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
Previous work has shown that species interacting in an ecosystem and actors transacting in an economic context may have notable similarities in behavior. However, the specific mechanism that may underlie similarities in nature and human…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Biological networks are customarily described as structurally robust. This means that they often function extremely well under large forms of perturbations affecting both the concentrations and the kinetic parameters. In order to explain…
Robustness and evolvability are essential properties to the evolution of biological networks. To determine if a biological network is robust and/or evolvable, it is required to compare its functions before and after mutations. However, this…
External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical…
Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive equilibria, we identify structural network conditions that…
We provide a sufficient and necessary condition in terms of the stoichiometric coefficients for a bi-reaction network to admit multistability. Also, this result completely characterizes the bi-reaction networks according to if they admit…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
This work concerns the development of deep networks that are certifiably robust to adversarial attacks. Joint robust classification-detection was recently introduced as a certified defense mechanism, where adversarial examples are either…
Understanding the causes and effects of network structural features is a key task in deciphering complex systems. In this context, the property of network nestedness has aroused a fair amount of interest as regards ecological networks.…
A convolutional neural network strongly robust to adversarial perturbations at reasonable computational and performance cost has not yet been demonstrated. The primate visual ventral stream seems to be robust to small perturbations in…
The mathematical analysis of a three-tiered food-web describing anaerobic chlorophenol mineralisation has suggested the emergence of interesting dynamical behaviour through its specific ecological interactions, which include competition,…
Absolute concentration robustness (ACR) means the concentration of certain species stays the same in all the steady states. In this work, we study how conservation laws might effect non-vacuous ACR in reaction networks. The goal is to show…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
Robustness is key to engineering, automation, and science as a whole. However, the property of robustness is often underpinned by costly requirements such as over-provisioning, known uncertainty and predictive models, and known adversaries.…