Related papers: Rediscovering the power of pairwise interactions
Higher-order interactions play a key role for the stability and function of a complex system. However, how to identify them is still an open problem. Here, we propose a method to fully reconstruct the structural connectivity of a system of…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
Simultaneously recorded neurons exhibit correlations whose underlying causes are not known. Here, we use a population of threshold neurons receiving correlated inputs to model neural population recordings. We show analytically that small…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Correlations are employed in modern physics to explain microscopic and macroscopic phenomena, like the fractional quantum Hall effect and the Mott insulator state in high temperature superconductors and ultracold atoms. Simultaneously…
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Network Models with couplings between link pairs are the simplest models for a class of networks with Higher Order interactions. In this paper we give an analytic, general solution to this family of Random Graph Models extending previous…
Maximum Entropy models can be inferred from large data-sets to uncover how collective dynamics emerge from local interactions. Here, such models are employed to investigate neurons recorded by multielectrode arrays in the human and monkey…
Many natural, technological, and social systems incorporate multiway interactions, yet are characterized and measured on the basis of weighted pairwise interactions. In this article, I propose a family of models in which pairwise…
We show that a proportionality between the entanglement Hamiltonian and the Hamiltonian of a subsystem exists near the limit of maximal entanglement under certain conditions. Away from that limit, solvable models show that the coupling…
Recent experiments appear to have revealed the possibility of quantum entanglement between spatially separated human subjects. In addition, a similar condition might exist between basins containing human neurons adhering to printed circuit…
Electron spin-dependent chemical reactions in proteins, often discussed under the 'radical-pair mechanism', remain the leading microscopic proposal for magnetic field sensing in biology. Yet the essential physics is often obscured by the…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
Patterns arise spontaneously in a range of systems spanning the sciences, and their study typically focuses on mechanisms to understand their evolution in space-time. Increasingly, there has been a transition towards controlling these…
Monte Carlo calculations of the irreducible particle-particle interaction on a two-leg Hubbard ladder doped near half-filling are reported. As the temperature is lowered, this interaction develops structure in momentum space similar to the…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…