Related papers: Exploring the Protein G Helix Free Energy Surface …
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 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…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method…
Direct reduction of iron using hydrogen-rich gas is rapidly emerging as a key strategy for green steel production. This process involves complex, multiscale phenomena, encompassing solid-state phase transformations and gas transport through…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
When approaching the continuum limit in lattice QCD or other theories in a setup with topological sectors, conventional update algorithms experience a particularly severe form of critical slowing down that is caused by high action barriers…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Metadynamics is a popular enhanced sampling scheme wherein by periodic application of a repulsive bias, one can surmount high free energy barriers and explore complex landscapes. Recently metadynamics was shown to be mathematically well…
The solid-liquid interface free energy \gamma sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the…
We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…
Engineering the free-energy surfaces (FES) of proteins and peptides is central to controlling conformational ensembles and their responses to perturbations. However, predicting how chemical modifications such as point mutations reshape the…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
For a model glass-former we demonstrate via computer simulations how macroscopic dynamic quantities can be inferred from a PEL analysis. The essential step is to consider whole superstructures of many PEL minima, called metabasins, rather…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…