Related papers: Network Thermodynamical Modelling of Bioelectrical…

Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…

One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…

Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and…

Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…

Thermodynamics (in concert with its sister discipline, statistical physics) can be regarded as a data reduction scheme based on partitioning a total system into a subsystem and a bath that weakly interact with each other. The ubiquity and…

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…

A model of an electron-beam-plasma system is introduced to model the electrical breakdown physics of low-pressure nitrogen irradiated by an intense pulsed electron beam. The rapidly rising beam current induces an electric field which drives…

Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…

The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…

We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…

Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…

The imminent impact of immersive technologies in society urges for active research in real-time and interactive physics simulation for virtual worlds to be realistic. In this context, realistic means to be compliant to the laws of physics.…

Intramolecular ion-pair interactions yield shape and functionality to many molecules. With proper orientation, these interactions overcome steric factors and are responsible for the compact structures of several peptides. In this study, we…

Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…

Modern communication networks are inherently complex in nature. First of all, they have a large number of heterogeneous components. Secondly, their connectivity is extremely dynamic. Nodes can come and go, links can be removed and added…

We study the structure of Fermionic networks, i.e., a model of networks based on the behavior of fermionic gases, and we analyze dynamical processes over them. In this model, particle dynamics have been mapped to the domain of networks,…

Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…

Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…

Interacting systems can be studied as the networks where nodes are system units and edges denote correlated interactions. Although percolation on network is a unified way to model the emergence and propagation of correlated behaviours, it…

In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which…