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We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can…
Nakao and Mikhailov proposed using continuous models (mean-field models) to study reaction-diffusion systems on networks and the corresponding Turing patterns. This work aims to show that p-adic analysis is the natural tool to carry out…
By discretising space into compartments and letting system dynamics be governed by the reaction-diffusion master equation, it is possible to derive and simulate a stochastic model of reaction and diffusion on an arbitrary domain. However,…
Deriving emergent patterns from models of biological processes is a core concern of mathematical biology. In the context of partial differential equations (PDEs), these emergent patterns sometimes appear as local minimisers of a…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
An asymptotic scaling theory is presented using the conceptual basis of trapping-free subspace (i.e., orthogonal subspace) to establish the generic mechanism of optimal efficiency of excitation energy transfer (EET) in light-harvesting…
We study the temperature dependence of energy diffusion in two chaotic gapped quantum spin chains, a tilted-field Ising model and an XZ model, using an open system approach. We introduce an energy imbalance by coupling the chain to thermal…
We consider the classical Turing instability in a reaction-diffusion system as the secend part of our study on pattern formation. We prove that nonlinear dynamics of a general perturbation of the Turing instability is determined by the…
In this paper, we investigate the emergence of a predator-prey system with Ivlev-type functional response and reaction-diffusion. We study how diffusion affects the stability of predator-prey coexistence equilibrium and derive the…
In this paper, we introduce a novel approach to study reaction-diffusion systems -- dynamic transition theory approach developed in Ma and Wang 2015. This approach generalizes Turing's classical result (linear stability analysis) on pattern…
Understanding the asymptotic behavior of reaction-diffusion (RD) systems is crucial for modeling processes ranging from species coexistence in ecology to biochemical interactions within cells. In this work, we analyze RD systems in which…
This paper explores a novel connection between a thermodynamic and a dynamical systems perspective on emergent dynamical order. We provide evidence for a conjecture that Hamiltonian systems with mixed chaos spontaneously find regular…
The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive…
Subcritical Turing bifurcations of reaction-diffusion systems in large domains lead to spontaneous onset of well-developed localised patterns via the homoclinic snaking mechanism. This phenomenon is shown to occur naturally when balancing…
Turing patterns are fundamental in biophysics, emerging from short-range activation and long-range inhibition processes. However, their paradigm is based on diffusive transport processes, which yields Turing patters that are less sharp than…
Many mathematical models describing vegetation patterns are based on biomass--water interactions, due to the impact of this limited resource in arid and semi-arid environments. However, in recent years, a novel biological factor called…
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…
This is the fourth paper, the last one, on solution to the problem of absence of detailed balance in nonequilibrium processes. It is an approach based on another known universal dynamics: The evolutionary dynamics first conceived by Darwin…
Turing's theory of pattern formation is a universal model for self-organization, applicable to many systems in physics, chemistry and biology. Essential properties of a Turing system, such as the conditions for the existence of patterns and…
We estimate density of defects frozen into a biological Turing pattern which was turned on at a finite rate. A self-locking of gene expression in individual cells, which makes the Turing transition discontinuous, stabilizes the pattern…