Related papers: Cooperative Function with Thermal Fluctuations in …
We study the influence of thermal fluctuations on the fracture of elastic networks, via simulations of the uniaxial extension of central-force spring networks with varying rigidity, i.e. connectivity. Studying their failure response, both…
Disordered elastic networks are a model material system in which it is possible to achieve tunable and trainable functions. This work investigates the modification of local mechanical properties in disordered networks inspired by allosteric…
In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
Coupled learning is a contrastive scheme for tuning the properties of individual elements within a network in order to achieve desired functionality of the system. It takes advantage of physics both to learn using local rules and to…
The thermodynamics and dynamics of supercooled liquids correlate with their elasticity. In particular for covalent networks, the jump of specific heat is small and the liquid is {\it strong} near the threshold valence where the network…
Allosteric proteins transmit a mechanical signal induced by binding a ligand. However, understanding the nature of the information transmitted and the architectures optimizing such transmission remains a challenge. Here we show using an…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
Under an external field a double-stranded peptide chain can separate in a fragile or ductile transition. It is usually believed that these two regimes are driven either by chemical and thermal fields, or through non-local mechanical…
Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a coarse-grained C$_\alpha$ chain representation. We…
Jammed packings of repulsive elastic spheres have emerged as a rich model system within which elastic properties of disordered glassy materials may be elucidated. Most of the work on these packings have focused on the case of vanishing…
The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
The rigidity of elastic networks depends sensitively on their internal connectivity and the nature of the interactions between constituents. Particles interacting via central forces undergo a zero-temperature rigidity-percolation transition…
Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate…
The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and…
For several decades, experimental and computational studies have been used to investigate the potential functional role of knots in protein structures. A property that has attracted considerable attention is thermal stability, i.e., the…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…