Related papers: Phyllotaxis, a model
Systems with two species of active molecular motors moving on (cytoskeletal) filaments into opposite directions are studied theoretically using driven lattice gas models. The motors can unbind from and rebind to the filaments. Two motors…
Living cells sense their environment through the binding of extra-cellular molecular ligands to cell surface receptors. Puzzlingly, vast numbers of signaling pathways exhibit a high degree of cross talk between different signals whereby…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
We have introduced a novel multiplex recurrence network (MRN) approach by combining recurrence networks with the multiplex network approach in order to investigate multivariate time series. The potential use of this approach is demonstrated…
A ubiquitous motif in nature is the self-similar hierarchical buckling of a thin lamina near its margins. This is seen in leaves, flowers, fungi, corals, and marine invertebrates. We investigate this morphology from the perspective of…
(Bi)multi-partite interaction patterns are commonly observed in real world systems which have inhibitory and excitatory couplings. We hypothesize these structural interaction pattern to be stable and naturally arising in the course of…
We construct a simple model of a proto-cell that simulates a stochastic dynamics of abstract chemicals on a two-dimensional lattice. We assume that chemicals catalyze their reproduction through interaction with each other, and that between…
Self-organized monolayers of highly flexible \Frechet dendrons were deposited on graphite surfaces by solution casting. Scanning tunneling microscopy (STM) reveals an unprecedented variety of patterns with up to seven stable hierarchical…
A model of a phase-separating two-component Langmuir monolayer in the presence of a photo-induced reaction interconvering two components is formulated. An interplay between phase separation, orientational ordering and treaction is found to…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
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…
Network representation learning has exploded recently. However, existing studies usually reconstruct networks as sequences or matrices, which may cause information bias or sparsity problem during model training. Inspired by a cognitive…
Many cells exhibit large-scale active circulation of their entire fluid contents, a process termed cytoplasmic streaming. This phenomenon is particularly prevalent in plant cells, often presenting strikingly regimented flow patterns. The…
The three-dimensional shapes of thin lamina such as leaves, flowers, feathers, wings etc, are driven by the differential strain induced by the relative growth. The growth takes place through variations in the Riemannian metric, given on the…
Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the…
The purpose of this paper is to present a model of a phenomenon of plant stem morphogenesis observed by Cesar Gomez-Campo in 1970. We consider a simplified model of auxin dynamics in plant stems, showing that, after creation of the original…
Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic…
Several mechanisms have been proposed to explain the spontaneous generation of self-organized patterns, hypothesised to play a role in the formation of many of the magnificent patterns observed in Nature. In several cases of interest, the…
We present a one-dimensional model for diffusion in a fluctuating lattice; that is a lattice which can be in two or more states. Transitions between the lattice states are induced by a combination of two processes: one periodic…