Coupled Oscillations and Circadian Rhythms in Molecular Replication Networks.
Living organisms often display rhythmic and oscillatory behavior. We investigate here a challenge in contemporary Systems Chemistry, that is, to construct "bottom-up" molecular networks that display such complex behavior. We first describe oscillations during self-replication by applying kinetic parameters relevant to peptide replication in an open environment. Small networks of coupled oscillators are then constructed in silico, producing various functions such as logic gates, integrators, counters, triggers, and detectors. These networks are finally utilized to simulate the connectivity and network topology of the Kai proteins circadian clocks from the S. elongatus cyanobacteria, thus producing rhythms whose constant frequency is independent of the input intake rate and robust toward concentration fluctuations. We suggest that this study helps further reveal the underlying principles of biological clocks and may provide clues into their emergence in early molecular evolution.
†Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel.
Nathaniel
N
Wagner
†Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel.
Samaa
S
Alasibi
‡Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States.
Enrique
E
Peacock-Lopez
†Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel.
Gonen
G
Ashkenasy
D002940:Circadian Rhythm; D008962:Models, Theoretical
Chemical kinetics simulations; Chemical oscillations; Circadian clock; Replication networks; Systems Chemistry