Wang-Landau sampling of lattice multiblock copolymers.

Synthetic multiblock copolymers are an interesting class of polymeric chains and have emerged as promising materials to mimic the function of complex biomolecules. In this work, we use Wang-Landau sampling to study sequences of multiblock (AnBn)m copolymers on the simple cubic lattice, where n represents the block length and m represents the number of blocks. We first compare to the thermodynamic and structural properties of four sequences previously studied in the continuum [W. Wang et al., J. Chem. Phys. 141, 244907 (2014)] to observe the differences that arise during the collapse process. We then focus on the structural transitions that occur at temperatures below the coil-to-globule transition in the lattice. Moreover, by studying additional sequences, we detail the relationship between the block length, number of blocks, and, thus, overall polymer length with respect to said structural transitions. Finally, we observe how the formation and shape of a ground state core of the more strongly interacting monomer type affect the procession of structural changes that occurs as temperature increases.

Effects of lattice constraints in coarse-grained protein models.

We compare and contrast folding behavior in several coarse-grained protein models, both on- and off-lattice, in an attempt to uncover the effect of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods-Wang-Landau sampling, multicanonical sampling, replica-exchange Wang-Landau sampling, and replica-exchange multicanonical sampling, we investigate the thermodynamic and structural behavior of the protein Crambin within the context of the hydrophobic-polar, hydrophobic-"neutral"-polar (H0P), and semi-flexible H0P model frameworks. We uncover the folding process in all cases; all models undergo, at least, the two major structural transitions observed in nature-the coil-globule collapse and the folding transition. As the complexity of the model increases, these two major transitions begin to split into multi-step processes, wherein the lattice coarse-graining has a significant impact on the details of these processes. The results show that the level of structural coarse-graining is coupled to the level of interaction coarse-graining.

The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study.

Using Monte Carlo simulations, we investigate simple, physically motivated extensions to the hydrophobic-polar lattice protein model for the small (46 amino acid) protein Crambin. We use two-dimensional replica-exchange Wang-Landau sampling to study the effects of a bond angle stiffness parameter on the folding and uncover a new step in the collapse process for particular values of this stiffness parameter. A physical interpretation of the folding is developed by analysis of changes in structural quantities, and the free energy landscape is explored. For these special values of stiffness, we find non-degenerate ground states, a property that is consistent with behavior of real proteins, and we use these unique ground states to elucidate the formation of native contacts during the folding process. Through this analysis, we conclude that chain-stiffness is particularly influential in the low energy, low temperature regime of the folding process once the lattice protein has partially collapsed.