Related papers: The thermodynamics of computational copying in bio…
With the tremendous increase in the amount of biological literature, developing automated methods for extracting big data from papers, building models and explaining big mechanisms becomes a necessity. We describe here our approach to…
Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
In recent years experiments have demonstrated that living cells can measure low chemical concentrations with high precision, and much progress has been made in understanding what sets the fundamental limit to the precision of chemical…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
We consider the thermodynamic properties of systems in contact with an information source and focus on the consequences of energetic cost associated with the exchange of information. To this end we introduce the model of a thermal tape and…
Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on…
The Q-cycle mechanism entering the electron and proton transport chain in oxygenic photosynthesis is an example of how biological processes can be efficiently investigated with elementary microscopic models. Here we address the problem of…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
Cells generally convert external nutrient resources to support metabolismand growth. Understanding the thermodynamic efficiency of this conversion is essential to determine the general characteristics of cellular growth. Using a simple…
We present a parallel implementation of cellular automata to simulate chemical reactions on surfaces. The scaling of the computer time with the number of processors for this parallel implementation is quite close to the ideal T/P, where T…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…
We establish a rigorous connection between fundamental resource theories at the quantum scale. Correlations and entanglement constitute indispensable resources for numerous quantum information tasks. However, their establishment comes at…
Molecular simulations are essential tools in computational chemistry, enabling the prediction and understanding of molecular interactions and thermodynamic properties of biomolecules. However, traditional force fields face significant…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
The molecular energies of chemical systems have been successfully calculated on quantum computers, however, more attention has been paid to the dynamic process of chemical reactions in practical application, especially in catalyst design,…