Related papers: Autocatalytic Sets and Biological Specificity
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Very often, models in biology, chemistry, physics, and engineering are systems of polynomial or power-law ordinary differential equations, arising from a reaction network. Such dynamical systems can be generated by many different reaction…
Under mass-action kinetics, biochemical reaction networks give rise to polynomial autonomous dynamical systems whose parameters are often difficult to estimate. We deal in this paper with the problem of identifying the kinetic parameters of…
Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…
Selective rationalization has become a common mechanism to ensure that predictive models reveal how they use any available features. The selection may be soft or hard, and identifies a subset of input features relevant for prediction. The…
Traditional mathematical models of photosynthesis are based on mass action kinetics of light reactions. This approach requires the modeller to enumerate all the possible state combinations of the modelled chemical species. This leads to…
Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
Maintaining stability in an uncertain environment is essential for proper functioning of living systems. Robust perfect adaptation (RPA) is a property of a system that generates an output at a fixed level even after fluctuations in input…
With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable…
Response-Adaptive Randomization (RAR) is part of a wider class of data-dependent sampling algorithms, for which clinical trials are typically used as a motivating application. In that context, patient allocation to treatments is determined…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases of mild stress,…
Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Continual learning refers to the ability of a biological or artificial system to seamlessly learn from continuous streams of information while preventing catastrophic forgetting, i.e., a condition in which new incoming information strongly…
Modelling the Calvin cycle of photosynthesis leads to various systems of ordinary differential equations and reaction-diffusion equations. They differ by the choice of chemical substances included in the model, the choices of stoichiometric…
I analyse a model of an evolving network represented as a directed graph; each node corresponds to one molecular species and the links to catalytic interactions between species. Over short timescales the graph remains fixed while relative…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…