Related papers: Protein folding as a jamming transition
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
The microcanonical analysis is shown to be a powerful tool to characterize the protein folding transition and to neatly distinguish between good and bad folders. An off-lattice model with parameter chosen to represent polymers of these two…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
In marginally jammed solids confined by walls, we calculate the particle and ensemble averaged value of an order parameter, $\left<\Psi(r)\right>$, as a function of the distance to the wall, $r$. Being a microscopic indicator of structural…
Determining the folding core of a protein yields information about its folding process and dynamics. The experimental procedures for identifying the amino acids which make up the folding core include hydrogen-deuterium exchange and…
We track the motion of a horizontally vibrated amorphous assembly of bidisperse hard disks, for densities ranging across the jamming transition. We derive on very general grounds a bound on the dynamical susceptibility in terms of the…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
The expression for the higher temperature dependence of the mean squared displacement in proteins is obtained. The quantum multi-well model explains the dynamic transitions of the proteins and minimizes the amount of parameters to a single…
The jamming transition is ubiquitous. It is present in granular matter, colloids, glasses, and many other systems. Yet, it defines a critical point whose properties still need to be fully understood. A major breakthrough came about when the…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
By exploring the properties of the energy landscape of a bidisperse system of soft harmonic disks in two dimensions we determine the thermal jamming transition. To be specific, we study whether the ground state of the system where the…
Numerous soft materials jam into an amorphous solid at high packing fraction. This non-equilibrium phase transition is best understood in the context of a model system in which particles repel elastically when they overlap. Recently,…
We have studied how 2- and 3- dimensional systems made up of particles interacting with finite range, repulsive potentials jam (i.e., develop a yield stress in a disordered state) at zero temperature and applied stress. For each…
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p,…
We experimentally investigate jamming in a quasi-two-dimensional granular system of automatically swelling particles and show that a maximum in the height of the first peak of the pair correlation function is a structural signature of the…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determine characteristic temperatures that relate to the…