Related papers: Thermodynamics of Lattice Heteropolymers
We present a temperature-independent Monte Carlo method for the determination of the density of states of lattice proteins that combines the fast ground-state search strategy of the nPERM chain growth and multicanonical reweighting for…
Two improved versions of the pruned-enriched-Rosenbluth method (PERM) are proposed and tested on simple models of lattice heteropolymers. Both are found to outperform not only the previous version of PERM, but also all other stochastic…
We present Monte Carlo simulations of lattice models of polymers. These simulations are intended to demonstrate the strengths of a powerful new flat histogram algorithm which is obtained by adding microcanonical reweighting techniques to…
The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model…
We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as…
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…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P.~Grassberger, Phys.~Rev.~{\bf E 56} (1997) 3682) leads to very efficient algorithms for the folding of simple model proteins. We test it on several models…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for…
Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P. Grassberger, Phys. Rev. E, in press (1997)) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models…
In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed…
We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the pruned-enriched-Rosenbluth method (PERM), hitherto employed to…
We present three different neural network algorithms to calculate thermodynamic properties as well as dynamic correlation functions at finite temperatures for quantum lattice models. The first method is based on purification, which allows…
Lattice models are crucial for studying thermodynamic properties in many physical, biological and chemical systems. We investigate Lattice Restricted Primitive Model (LRPM) of electrolytes with different discretization parameters in order…
Accurate descriptions of reference systems are a central task in liquid-state theories for the study of more complex systems. Using scaled particle theory (SPT), we derive a fully analytical description of the thermodynamic properties of a…
We consider the antiferromagnetic Heisenberg model and the repulsive Hubbard model for a class of frustrated lattices with a completely dispersionless (flat) lowest one-particle (either one-magnon or one-electron) band. We construct exact…
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…
Efficient sampling from ensembles of Hamiltonian cycles is critical for predicting the thermodynamic properties of compact polymers, with applications including modeling protein and RNA folding and designing soft materials. Although…
We employ the numerical linked-cluster expansion to study finite-temperature properties of the uniform cubic lattice Hubbard model in the thermodynamic limit for a wide range of interaction strengths and densities. We carry out the…
Monte Carlo simulations using Wang-Landau sampling are performed to study three-dimensional chains of homopolymers on a lattice. We confirm the accuracy of the method by calculating the thermodynamic properties of this system. Our results…