Related papers: How flexibility can enhance catalysis
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
We show that entanglement-assisted transformations of bipartite entangled states can be more efficient than catalysis [D. Jonathan and M. B. Plenio, Phys. Rev. Lett. 83, 3566 (1999)}, i.e., given two incomparable bipartite states not only…
Flexible mechanical metamaterials possess repeating structural motifs that imbue them with novel, exciting properties including programmability, anomalous elastic moduli and nonlinear and robust response. We address such structures via…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
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…
This letter proposes an enhanced sufficient battery model (ESBM) as well as a binary search algorithm for a sharp inner-approximation of the aggregate flexibility of thermostatically controlled load (TCL) arrays. Compared with the previous…
We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
The mechanical process of progressively debonding an adhesive membrane from a substrate is described as a quasistatic variational evolution of sets and herein investigated. Existence of energetic solutions, based on global minimisers of a…
The binding of a ligand molecule to a protein is often accompanied by conformational changes of the protein. A central question is whether the ligand induces the conformational change (induced-fit), or rather selects and stabilizes a…
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
The selective etching of carbon nanotubes has been widely explored as a post-synthetic route for enriching semiconducting species. As nanoelectronic applications increasingly demand pure semiconducting nanotubes for use in field-effect…
Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found…
This paper presents and experimentally demonstrates a novel framework for variable assistance on lower body exoskeletons, based upon safety-critical control methods. Existing work has shown that providing some freedom of movement around a…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we…
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…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
A variational approach is employed to find stationary solutions to a free boundary problem modeling an idealized electrostatically actuated MEMS device made of an elastic plate coated with a thin dielectric film and suspended above a rigid…
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…
Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…