Related papers: Microcanonical versus Canonical Analysis of Protei…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
Microcanonical thermodynamics (MT) is analysed for phase transitions of first and second order in finite systems. The transiton temperature, the latent heat and the surface tension of first order transitions can easily be determined by MT…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
In this micro-canonical simulation the temperature and also the specific heat are determined as averages of expressions easy to implement. The XY-chain is studied for a test. The second order transition on a cubic lattice and the first…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
In detailed microcanonical analyses of densities of states obtained by extensive multicanonical Monte Carlo computer simulations, we investigate the caloric properties of conformational transitions adsorbing polymers experience near…
Using Monte Carlo histogram methods, the microcanonical caloric curve is computed for the Ising model in two and three dimensions with fixed magnetization. Whereas the signatures of a first order phase transition are clearly visible for…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
The microcanonical ensemble is in important physical situations different from the canonical one even in the thermodynamic limit. In contrast to the canonical ensemble it does not suppress spatially inhomogeneous configurations like phase…
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…
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…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions…
We compare phase transition(-like) phenomena in small model systems for both microcanonical and canonical ensembles. The model systems correspond to a few classical (non-quantum) point particles confined in a one-dimensional box and…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…