Related papers: Two-state folding over a weak free-energy barrier
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
Using Monte Carlo simulation, we analyse the behaviour of two-dimensional hard rods in four different types of geometric confinement: (i) a slit pore where the particles are confined between two parallel walls with homeotropic anchoring;…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
We show that gels formed by arrested spinodal decomposition of protein solutions exhibit elastic properties in two distinct frequency domains, both elastic moduli exhibiting a remarkably strong dependence on volume fraction. Considering the…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…
Reaction-diffusion systems with reversible reactions generically display power-law relaxation towards chemical equilibrium. In this work we investigate through numerical simulations aging processes that characterize the non-equilibrium…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…
The force laws governing the extension behavior of homopolypeptides are obtained from a phenomenological free energy capable of describing the helix-coil transition. Just above the melting temperature of the free chains, T*, the plot of…
We present a thermodynamic model which explains the presence of a negative slope in the melt curve, as observed in systems as diverse as the alkali metals and molecular hydrogen at high pressure. We assume that components of the system can…
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…