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We analyze pattern formation on a network of cells where each cell inhibits its neighbors through cell-to-cell contact signaling. The network is modeled as an interconnection of identical dynamical subsystems each of which represents the…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
We present a novel form of Liquid Automata, using this to simulate autopoiesis, whereby living machines self-organise in the physical realm. This simulation is based on an earlier Cellular Automaton described by Francisco Varela. The basis…
Spontaneous pattern formation in living systems is driven by reaction-diffusion chemistry and active mechanics. The feedback between chemical and mechanical forces is often essential to robust pattern formation, yet it remains poorly…
The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar…
The model system manifesting phenomena peculiar to complex analytic maps is offered. The system is a non-autonomous ring cavity with nonlinear elements and filters,
We investigate bifurcations in feedforward coupled cell networks. Feedforward structure (the absence of feedback) can be defined by a partial order on the cells. We use this property to study generic one-parameter steady state bifurcations…
A self-organization is an universal phenomenon in nature and, in particular, is highly important in materials systems and biology. We proposed a new theory that allowed us to model the most challenging cases of atomic self-assembling whose…
The objective of the paper is to identify laws and mechanisms that allow the creation of more order from disorder using natural means i.e., without the help of conscious beings. While this is not possible for the collection of all dynamical…
Biomolecular phase separation is typically attributed to the polymer physics of long, disordered chains. However, the underlying chemical grammar, i.e. the specific interactions between protein and RNA building blocks, remains poorly…
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
Process of stripe formation is analyzed numerically in a binary mixture. The system consists of particles of two sizes, without any direct mutual interactions. Overlapping of large particles, surrounded by a dense system of smaller…
Decisions in the cell that lead to its ultimate fate are important for cellular functions such as proliferation, growth, differentiation, development and death. Understanding this decision process is imperative for advancements in the…
The dual phosphorylation network provides an essential component of intracellular signaling, affecting the expression of phenotypes and cell metabolism. For particular choices of kinetic parameters, this system exhibits multistationarity, a…
Biological systems are notorious for complex behavior within short timescales (e.g. metabolic activity) and longer time scales (e.g. evolutionary selection), along with their complex spatial organization. Because of their complexity and…
The improbability of a spontaneously generated self-assembling molecule has suggested that life began with a set of simpler, collectively replicating elements, such as an enclosed autocatalytic set of polymers (or protocell). Since…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
Buoyant plumes, evolving free of boundary constraints, may develop well-defined mushroom shaped heads. In normal plumes, overturning flow in the head entrains less buoyant fluid from the surroundings as the head rises, robbing the plume of…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…