Related papers: Frustration in Biomolecules
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule…
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…
Geometric frustration results from a discrepancy between the locally favored arrangement of the constituents of a system and the geometry of the embedding space. Geometric frustration can be either non-cumulative, which implies an extensive…
In 1977, G\'erard Toulouse has proposed a new concept termed as "frustration" in spin systems. Using this definition, several frustrated models have been created and studied, among them we can mention the Villain's model, the fully…
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the…
It's been said that "mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better". Here we aim for something even better. We try to combine mathematical physics and biology into a picoscope of…
Packings of macroscopic granular chains capture some of the essential aspects of molecular polymer systems and have been suggested as a paradigm to understand the physics on a molecular scale. However, here we demonstrate that the…
We investigate the full phase diagram of a column of grains near jamming, as a function of varying levels of frustration. Frustration is modelled by the effect of two opposing fields on a grain, due respectively to grains above and below…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
This article reviews and extends recent results concerning entanglement and frustration in multipartite systems which have some symmetry with respect to the ordering of the particles. Starting point of the discussion are Bell inequalities:…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Frustration of classical many-body systems can be used to distinguish ferromagnetic interactions from anti-ferromagnetic ones via the Toulouse conditions. A quantum version of the Toulouse conditions provides a similar classification based…
The remarkable range of biological forms in and around us, such as the undulating shape of a leaf or flower in the garden, the coils in our gut, or the folds in our brain, raise a number of questions at the interface of biology, physics and…