Related papers: Autocatalytic Sets and Biological Specificity
Autocatalysis underlies the ability of chemical and biochemical systems to replicate. Recently, Blokhuis et al. gave a stoechiometric definition of autocatalysis for reaction networks, stating the existence of a combination of reactions…
The Jacobian matrix of a dynamic system and its principal minors play a prominent role in the study of qualitative dynamics and bifurcation analysis. When interpreting the Jacobian as an adjacency matrix of an interaction graph, its…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Motivated by the theory of reaction kinetics based on nonequilibrium thermodynamics and the linear stability of driven reaction-diffusion, we apply the Fokker-Planck equation to describe the population dynamics of an ensemble of reactive…
Presented in this paper is a derivation of a 2D catalytic reaction-based model to solve combinatorial optimization problems (COPs). The simulated catalytic reactions, a computational metaphor, occurs in an artificial chemical reactor that…
We investigate the effects of hyperbolic hydrodynamical mixing on the reaction kinetics of autocatalytic systems. Exact results are derived for the two dimensional open baker map as an underlying mixing dynamics for a two-component…
Diagrammatic models of feeding choices reveal fundamental robotic behaviors. Successful choices are reinforced by positive feedback, while unsuccessful ones by negative feedback. This paper will address robotic feeding by casually relating…
Experience in the physical sciences suggests that the only realistic means of understanding complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Perfect adaptation is a phenomenon whereby the output variables of a system can maintain certain values despite external disturbances. Robust perfect adaptation (RPA) refers to an adaptation property that does not require fine-tuning of…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
We derive a self-consistent hydrodynamic theory of coupled binary-fluid-surfactant systems from the underlying microscopic physics using Rayleigh's variational principle. At the microscopic level, surfactant molecules are modelled as…
This article characterizes certain small multistationary chemical reaction networks. We consider the set of fully open networks, those for which all chemical species participate in inflow and outflow, containing one non-flow (reversible or…
The chapter presents some new approaches to describing the collective behavior of complex systems of mathematical biology based on the evolution equations of observables such as open systems. This representation of kinetic evolution has…
Self-replicability is the unique attribute observed in all the living organisms and the question how the life was physically initiated could be equivalent to the question how self-replicating informative polymers were formed in the abiotic…
We study the equilibrium properties of a model for a binary mixture of catalytically-reactive monomers adsorbed on a two-dimensional substrate decorated by randomly placed catalytic bonds. The interacting $A$ and $B$ monomer species undergo…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…