Related papers: Recent developments in research on catalytic react…
Over the past decade, extensive research into single-atom catalysts (SACs) has revealed that the catalytic behavior of metal adatoms is highly dependent on how they interact with their support. A strong dependence on the local coordination…
Current artificial intelligence systems show near-human-level capabilities when deployed in isolation. Systems of a few collaborating intelligent agents are being engineered to perform tasks collectively. This raises the question of whether…
It has been proposed that cultural evolution was made possible by a cognitive transition brought about by onset of the capacity for self-triggered recall and rehearsal. Here we develop a novel idea that models of collectively autocatalytic…
We undertake a systematic study of the dynamics of Boolean networks to determine the origin of chaos observed in recent experiments. Networks with nodes consisting of ideal logic gates are known to display either steady states, periodic…
Stochastic models for biochemical reaction networks are widely used to explore their complex dynamics but face significant challenges, including difficulties in determining rate constants and high computational costs. To address these…
This paper analyses of a stochastic model of a chemical reaction network with three types of chemical species ${\cal R}$, ${\cal M}$ and ${\cal U}$ that interact to transform a flow of external resources, the chemical species ${\cal Q}$, to…
Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…
Whether it be physical, biological or social processes, complex systems exhibit dynamics that are exceedingly difficult to understand or predict from underlying principles. Here we report a striking correspondence between the collective…
Stochastic chemical processes are described by the chemical master equation satisfying the law of mass-action. We first ask whether the dual master equation, which has the same steady state as the chemical master equation, but with inverted…
Living systems maintain stable internal states despite environmental fluctuations. Absolute concentration robustness (ACR) is a striking homeostatic phenomenon in which the steady-state concentration of a species remains invariant despite…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
Open chemical reaction systems involve matter-exchange with the surroundings. As a result, species can accumulate inside a system during the course of the reaction. We study the role of network topology in governing the concentration…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes impossible to maintain a significant…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
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…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…