Related papers: Numerical comparison of two approaches for the stu…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.
We study helix-coil transitions in an all-atom model of polyalanine. Molecules of up to length 30 residues are investigated by multicanonical simulations. Results from two implicit solvent models are compared with each other and with that…
In view of the important role helix-sheet transitions play in protein aggregation, we introduce a simple model to study secondary structural transitions of helix-coil-sheet systems using a Potts model starting with an effective Hamiltonian.…
The similarity in the thermodynamic properties of two completely different theoretical models for the helix-coil transition is examined critically. The first model is an all-atomic representation for a poly-alanine chain, while the second…
We investigate the first-order phase transitions of the $q$-state Potts models with $q = 5, 6, 7$, and $8$ on the two-dimensional square lattice, using Monte Carlo simulations. At the very weakly first-order transition of the $q=5$ system,…
We report results from multicanonical simulations of poly-alanine. Homopolymers of up to 30 amino acids were considered and various thermodynamic quantities as a function of temperature calculated. We study the nature of the observed…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
An asymmetric generalization of the zero-temperature q-state Potts model on a one dimensional lattice, with and without boundaries, has been studied. The dynamics of the particle number, and specially the large time behavior of the system…
Monte Carlo simulations are performed to study the two-dimensional Potts models with q=3 and 4 states on directed Small-World network. The disordered system is simulated applying the Heat bath Monte Carlo update algorithm. A first-order and…
In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory…
In studies of the QCD deconfining phase transition or crossover by means of heavy ion experiments, one ought to be concerned about non-equilibrium effects due to heating and cooling of the system. Motivated by this, we look at hysteresis…
Large-scale Monte Carlo simulations of the bond-diluted three-dimensional 4-state Potts model are performed. The phase diagram and the physical properties at the phase transitions are studied using finite-size scaling techniques. Evidences…
Despite the fact that a complete theoretical description of critical phenomena in connection with phase transitions has been well-established through the renormalization group theory, the microscopic nature of the phase transitions remains…
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…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…
The critical behaviour in short time dynamics for the q=6 and 7 state Potts models in two-dimensions is investigated. It is shown that dynamic finite-size scaling exists for first-order phase transitions.
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
We face the problem of phase transitions in diluted systems both from theoretical and numerical sides. We study the effects of quenched site-dilution in classical models (Heisenberg, Ising and Potts) in 2, 3, and 4 dimensions both by using…