Flat histogram simulation of lattice polymer systems

Exact sequence analysis for three-dimensional hydrophobic-polar lattice proteins

We have exactly enumerated all sequences and conformations of hydrophobic-polar (HP) proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the HP model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a nondegenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets.

Thermodynamics 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 temperatures. In particular, this algorithm enables us to accurately simulate the usually difficult accessible low-temperature region. Therefore, it becomes possible to perform detailed analyses of the low-temperature transition between ground states and compact globules.