Related papers: Recursiveness, Switching, and Fluctuations in a Re…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes impossible to maintain a significant…
The succession of suggested mechanisms of solid-state phase transitions - Second-order, Lambda, Martensitic, Displacive, Topological, Order-Disorder, Soft-mode, Incommensurate, Scaling and Quantum - are analyzed and explained why they…
We consider classical hard-core particles moving on two parallel chains in the same direction. An interaction between the channels is included via the hopping rates. For a ring, the stationary state has a product form. For the case of…
In a diffusion-based molecular communication system, molecules are employed to convey information. When propagation and reception processes are considered in a framework of first passage processes, we need to focus on absorbing receivers.…
The properties of the first-order phase transition in a set of plasma models with common feature - absence of individual correlations between charges of op-posite sign, have been studied. Predicted discontinuities in equilibrium non-uniform…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
Stochastic processes generated by non-stationary distributions are difficult to represent with conventional models such as Gaussian processes. This work presents Recurrent Autoregressive Flows as a method toward general stochastic process…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters…
An important component in studying mathematical models in many biochemical systems, such as those found in developmental biology, is phase transition. The purpose of this work is to analyze the phase transition property of a…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as chemical markers for understanding adaptive…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
We study the lattice reaction diffusion model 3A -> 4A, A -> 0 (``triplet creation") using numerical simulations and n-site approximations. The simulation results provide evidence of a discontinuous phase transition at high diffusion rates.…
In this work, we study the percolation transition and large deviation properties of generalized canonical network ensembles. This new type of random networks might have a very rich complex structure, including high heterogeneous degree…
We study the phase transition in a class of fiber bundle models in which the fiber strengths are distributed randomly within a finite interval and global load sharing is assumed. The dynamics is expressed as recursion relations for the…
Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of…
The smooth piecewise-linear models cover a wide range of applications nowadays. Basically, there are two classes of them: models are transitional or hyperbolic according to their behaviour at the phase-transition zones. This study explored…