Related papers: Why life is hot
Energy efficiency is closely related to the evolution of biological systems and is important to their information processing. In this paper, we calculated the excitation probability of a simple model of a bistable biological unit in…
Conceptual view of fitness and fitness measurement of strategic decisions on information systems, technological systems and innovation are becoming more important in recent years. This paper determines some dynamics of fitness landscape…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
Organisms must acquire and use environmental information to guide their behaviors. However, it is unclear whether and how information quantitatively limits behavioral performance. Here, we relate information to behavioral performance in…
We demonstrate diversification rather than optimisation for highly interacting organisms in a well mixed biological system by means of a simple model and reference to experiment, and find the cause to be the complex network of interactions…
The question of why we age is a fundamental one. It is about who we are, and it also might have critical practical aspects as we try to find ways to age slower. Or to not age at all. Different reasons point at distinct strategies for the…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
The rate at which nodes in a network increase their connectivity depends on their fitness to compete for links. For example, in social networks some individuals acquire more social links than others, or on the www some webpages attract…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
Highly-optimized complex transport networks serve crucial functions in many man-made and natural systems such as power grids and plant or animal vasculature. Often, the relevant optimization functional is non-convex and characterized by…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Living systems need to be highly responsive, and also to keep fluctuations low. These goals are incompatible in equilibrium systems due to the Fluctuation Dissipation Theorem (FDT). Here, we show that biological sensory systems, driven far…
Many microbial systems are known to actively reshape their proteomes in response to changes in growth conditions induced e.g. by nutritional stress or antibiotics. Part of the re-allocation accounts for the fact that, as the growth rate is…
We investigate the thermodynamic implications of two control mechanisms of open chemical reaction networks. The first controls the concentrations of the species that are exchanged with the surroundings, while the other controls the exchange…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
Modern ecology has re-emphasized the need for a quantitative understanding of the original 'survival of the fittest theme' based on analyzis of the intricate trade-offs between competing evolutionary strategies that characterize the…
The process of evolutionary emergence of purposeful adaptive behavior is investigated by means of computer simulations. The model proposed implies that there is an evolving population of simple agents, which have two natural needs: energy…
Complex systems can convert energy imparted by nonequilibrium forces to regulate how quickly they transition between long lived states. While such behavior is ubiquitous in natural and synthetic systems, currently there is no general…
Chemically active droplets provide simple models for cell-like systems that can grow and divide. Such active droplet systems are driven away from thermodynamic equilibrium and turn over chemically, which corresponds to a simple metabolism.…