Related papers: Zygotic combinatorial process in plants
We investigate a novel variant of the exclusion process in which particles perform asymmetric nearest-neighbor jumps across a bond \((k, k+1)\) only if the preceding site \((k-1)\) is unoccupied. This next-nearest-neighbor constraint…
Several recent studies show that companion cells in flowering plant gametophytes relax epigenetic control of transposable elements (TEs) to promote production of small RNA that presumably assist nearby reproductive cells in management of…
Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…
The origin of organelles (mitochondrion, chloroplast and nucleus) remains enigmatic. The endosymbiotic hypothesis that chloroplasts, mitochondria and nuclei descend from the endosymbiotic cyanobacterium, bacterium and archaebacterium…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
Mixed-order phase transitions display a discontinuity in the order parameter like first-order transitions yet feature critical behavior like second-order transitions. Such transitions have been predicted for a broad range of equilibrium and…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Agglomeration, adsorption, and extraction in dispersed multiphase systems are ubiquitously encountered in biological systems, energy industry, and medical science. In this work, a novel lattice model is extended to the three-component…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
The homological information about a filtered simplicial complex over the poset of positive real numbers is often presented by a barcode which depicts the evolution of the associated Betti numbers. However, there is a wonderfully complex…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…
The exact factorized ground state of a heterogeneous (ferrimagnetic) spin model which is composed of two spins ($\rho, \sigma$) has been presented in detail. The Hamiltonian is not necessarily translational invariant and the exchange…
Hybridization effects play a crucial role in determining the electronic properties of hybrid inorganic/organic interfaces. To gain insight into these important interactions, we perform a first-principles study based on hybrid…
We study the different phases and the phase transitions in a system of $Y$-shaped particles, examples of which include Immunoglobulin-G and trinaphthylene molecules, on a triangular lattice interacting exclusively through excluded volume…
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through…
The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The link between a modified Higgs self-coupling and the strong first-order phase transition necessary for baryogenesis is well explored for polynomial extensions of the Higgs potential. We broaden this argument beyond leading polynomial…
We investigate the phase transition properties of the polymer-Potts model, a chain composed of monomers with magnetic degrees of freedom, with the motivation to study the conformation and mark switching dynamics of chromatin. By the…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…