Related papers: Single-Molecule Morphology of Topologically Digest…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
We prove that for a broad class of permutation-equivariant learning rules (including SGD, Adam, and others), the training process induces a bi-Lipschitz mapping between neurons and strongly constrains the topology of the neuron distribution…
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…
The geometric renormalization technique for complex networks has successfully revealed the multiscale self-similarity of real network topologies and can be applied to generate replicas at different length scales. In this letter, we extend…
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…
Understanding how multi-scale network structure influences circadian rhythms in the suprachiasmatic nucleus (SCN) is essential for uncovering the principles of rhythmic robustness and synchronization. Previous studies using synthetic SCN…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
In this Master's thesis, the graph properties of a multi-level drug-protein network are studied, as well as how the network's shape has informed discoveries over the years, identifying primarily crawling discoveries and a smaller number of…
Advances in imaging techniques enable high resolution 3D visualisation of vascular networks over time and reveal abnormal structural features such as twists and loops, and their quantification is an active area of research. Here we showcase…
Topological and metric entropies of the DNA sequences from different organisms were calculated. Obtained results were compared each other and with ones of corresponding artificial sequences. For all envisaged DNA sequences there is a…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…
In self-organizing networks, topology and dynamics coevolve in a continuous feedback, without exogenous driving. The World Trade Network (WTN) is one of the few empirically well documented examples of self-organizing networks: its topology…
Understanding conformational change is crucial for programming and controlling the function of many mechanical systems such as allosteric enzymes and tunable metamaterials. Of particular interest is the relationship between the network…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…