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A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
In this project, we present a deep neural network (DNN)-based biophysics model that uses multi-scale and uniform topological and electrostatic features to predict protein properties, such as Coulomb energies or solvation energies. The…
We consider the dynamics of a reaction-diffusion system on a multigraph. The species share the same set of nodes but can access different links to explore the embedding spatial support. By acting on the topology of the networks we can…
The structural human connectome (i.e.\ the network of fiber connections in the brain) can be analyzed at ever finer spatial resolution thanks to advances in neuroimaging. Here we analyze several large data sets for the human brain network…
In the last decades, complex networks theory significantly influenced other disciplines on the modeling of both static and dynamic aspects of systems observed in nature. This work aims to investigate the effects of networks' topological…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
We consider a model of large regulatory gene expression networks where the thresholds activating the sigmoidal interactions between genes and the signs of these interactions are shuffled randomly. Such an approach allows for a qualitative…
The structural complexity of soft gels is at the origin of a versatile mechanical response that allows for large deformations, controlled elastic recovery and toughness in the same material. A limit to exploiting the potential of such…
Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for…
The splitting of the principal peak in the structure factor of liquid water is commonly interpreted as evidence of a competition between two distinct local environments. Here, we show that this peak splitting arises from medium-range…
Elastomers that can sustain large reversible strain are essential components for stretchable electronics. The stretchability and mechanical robustness of unfilled elastomers can be enhanced by introducing easier-to-break cross-links, e.g.…
The topological interaction arising in interlinked polymeric rings such as DNA catenanes is considered. More specifically, the free energy for a pair of linked random walk rings is derived where the distance $R$ between two segments each of…
A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate…
The endoplasmic reticulum (ER) is a dynamic network of interconnected sheets and tubules that orchestrates the distribution of lipids, ions, and proteins throughout the cell. The impact of its complex, dynamic morphology on its function as…
Many foraging microorganisms rely upon cellular transport networks to deliver nutrients, fluid and organelles between different parts of the organism. Networked organisms ranging from filamentous fungi to slime molds demonstrate a…
We study the permeability and selectivity (`permselectivity') of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations. The permeability…
Complex systems in the real world can be modeled as a network of connected components. The human brain, as a network of neurons among which the interactions cause perception, is a complex network. Synchronization is a dynamical phenomenon…
The transport of solvent molecules through soft, swollen networks is critical in both natural and engineered systems. While this poroelastic flow has traditionally been explored in networks where the mesh size is comparable to the solvent…
In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling…
Developmental approaches to neural architecture search grow functional networks from compact genomes through self-organisation, but the resulting networks operate with fixed post-growth weights. We characterise Hebbian and anti-Hebbian…