Related papers: Spontaneous Reaction Silencing in Metabolic Optimi…
We study the transient dynamics of an $A+B \rightarrow 0$ process on a pair of randomly coupled networks, where reactants are initially separated. We find that, for sufficiently small fractions $q$ of cross-couplings, the concentration of…
We study the current response to periodic driving of a crucial biochemical reaction network, namely, substrate inhibition. We focus on the conversion rate of substrate into product under time-varying metabolic conditions, modeled by a…
System-level properties of metabolic networks may be the direct product of natural selection or arise as a by-product of selection on other properties. Here we study the effect of direct selective pressure for growth or viability in…
We find that the spontaneous and collective emissions have a strong influence on the excitation of two-level absorbers (atoms, molecules) interacting in resonance with the plasmonic mode near the metal nanoparticle. The spontaneous and…
In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
Learning and memory are acquired through long-lasting changes in synapses. In the simplest models, such synaptic potentiation typically leads to runaway excitation, but in reality there must exist processes that robustly preserve overall…
Within a mathematical model, the metabolic process of glycolysis is studied. The general scheme of glycolysis is considered as a natural result of the biochemical evolution. By using the theory of dissipative structures, the conditions of…
Behavioral changes in animals and humans, as a consequence of an error or a verbal instruction, can be extremely rapid. Improvement in behavioral performances are usually associated in machine learning and reinforcement learning to synaptic…
We analyze networked heterogeneous nonlinear systems, with diffusive coupling and interconnected over a generic static directed graph. Due to the network's hetereogeneity, complete synchronization is impossible, in general, but an emergent…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Selective control in a population is the ability to control a member of the population while leaving the other members relatively unaffected. The concept of selective control is developed using cell death or apoptosis in heterogeneous cell…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Self-organization creates new order and shifts sub-boundaries while reorganizing energy and entropy within a control volume. This article examines pathway selection and tests whether maximizing the entropy generation rate can forecast…
The concept of limiting step gives the limit simplification: the whole network behaves as a single step. However, in its simplest form this idea is applicable only to the simplest linear cycles in steady states. For such the simplest cycles…
A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability.…
We apply the phase-reduction analysis to examine synchronization properties of periodic fluid flows. The dynamics of unsteady flows are described in terms of the phase dynamics reducing the high-dimensional fluid flow to its single scalar…
A heterogeneous and dilute suspension of catalytically active colloids is studied as a non-equilibrium analogue of ionic systems, which has the remarkable feature of action-reaction symmetry breaking. Symmetrically coated colloids are found…