2020/02/02 by Sumantra Sarkar, Sarkar, Sumantra
Biochemistry, Genetics and Molecular Biology · Medicine · #Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #Diffusion and Search Dynamics #FOS: Biological sciences #FOS: Physical sciences #Gene Regulatory Network Analysis #Mathematical and Theoretical Epidemiology and Ecology Models #Soft Condensed Matter (cond-mat.soft) #Statistical Mechanics (cond-mat.stat-mech) #Subcellular Processes (q-bio.SC)
paper · pdf · doi:10.48550/arxiv.2002.00485
openalex publication_date 2020/02/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Diffusion-limited association reactions are ubiquitous in nature. They are\nparticularly important for biological reactions, where the reaction rates are\noften determined by the diffusive transport of the molecules on two-dimensional\nsurfaces, such as the cell membrane. The peculiarities of diffusion on\ntwo-dimensional surfaces may lead to nontrivial reaction kinetics, such as\nconcentration dependent rate of association between two molecules. However,\ntraditionally, the kinetics of biomolecular association reactions has been\nmodeled using the law of mass action, which assumes that the rate of reaction\nis a concentration independent constant. In this paper, using multiscale\nmolecular simulation, we investigate the concentration dependence of\ndiffusion-limited association reactions on 2D surfaces. In particular, we\nquantify the influence of short-ranged pair interactions on the concentration\ndependence of the reaction rates and codify it in an empirical law. Using this\nlaw in a chemical kinetic model, we find that the the steady state behaviors of\nsimple chemical systems are drastically modified by the presence of\nconcentration dependent rates. In particular, we find that it leads to\nsuppression of intrinsic noise in dimerization reaction and destabilizes robust\noscillation in Lotka-Volterra predator-prey systems. In fact, we see a\ntransition from robust to fine-tuned behavior in the latter. In addition, we\nshow that concentration dependent reaction rates arise naturally in stochastic\npredator-prey systems due to intrinsic noise. We comment on the consequences of\nthese results and discuss their implications in the modeling of complex\nchemical and biological systems. In particular, we comment on the range of\nvalidity of the law of mass action, which is a staple in all theoretical\nmodeling of these systems.\n