Density of States for Hp Lattice Proteins
نویسندگان
چکیده
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 for heteropolymers that is widely used for studying statistical properties of proteins. For short chains, we have derived exact results from conformational enumeration, while for longer ones we developed a multicanonical Monte Carlo variant of the nPERM-based chain growth method in order to directly simulate the density of states. For simplification, only two types of monomers with respective hydrophobic (H) and polar (P) residues are regarded and only the next-neighbour interaction between hydrophobic monomers, being nonadjacent along the chain, is taken into account. This is known as the HP model for the folding of lattice proteins.
منابع مشابه
Optimized Wang-Landau sampling of lattice polymers: ground state search and folding thermodynamics of HP model proteins.
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 demanding and the quest for efficient algorithms is as old as the models themselves. Expanding on our previous work [T. Wüst and D. P. Landau, Phys. Rev. Lett....
متن کاملThermodynamics of lattice heteropolymers.
We calculate thermodynamic quantities of hydrophobic-polar (HP) lattice proteins by means of a multicanonical chain-growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method and flat histogram sampling of the entire energy space. Since our method directly simulates the density of states, we obtain results for thermodynamic quantities of the system for all temperat...
متن کاملVersatile approach to access the low temperature thermodynamics of lattice polymers and proteins.
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 the interacting self-avoiding walk (ISAW) model for homopolymers. We obtain accurate estimates of thermodynamic quantities for HP sequences with >100 monomers...
متن کاملTime-Dependent Real-Space Renormalization Group Method
In this paper, using the tight-binding model, we extend the real-space renormalization group method to time-dependent Hamiltonians. We drive the time-dependent recursion relations for the renormalized tight-binding Hamiltonian by decimating selective sites of lattice iteratively. The formalism is then used for the calculation of the local density of electronic states for a one dimensional quant...
متن کاملComparative Study of Hydrophobic-Polar and Miyazawa-Jernigan Energy Functions in Protein Folding on a Cubic Lattice Using Pruned-Enriched Rosenbluth Monte Carlo Algorithm
In this analysis of the contact energies guiding the protein folding, the performance of the PERM algorithm on a simple, cubic lattice is examined when Miyazawa-Jernigan (MJ) and Hydrophobic-Polar (HP) energy matrices are applied. Geometric similarity of minimum energy conformations of twenty proteins, generated when HP and MJ are used, is determined by the Root Mean Square Difference (RMSD) an...
متن کامل