Effects of the interaction range on structural phases of flexible polymers

Abstract

We systematically investigate how the range of interaction between non-bonded monomers influences the formation of structural phases of elastic, flexible polymers. Massively parallel replica-exchange simulations of a generic, coarse-grained model, performed partly on graphics processing units and in multiple-gaussian modified ensembles, pave the way for the construction of the structural phase diagram, parametrized by interaction range and temperature. Conformational transitions between gas-like, liquid, and diverse solid (pseudo) phases are identified by microcanonical statistical inflection-point analysis. We find evidence for finite-size effects that cause the crossover of "collapse" and "freezing" transitions for very short interaction ranges.

Identifying transitions in finite systems by means of partition function zeros and microcanonical inflection-point analysis: A comparison for elastic flexible polymers

“…The trend is that the solidsolid transition will shift to higher microcanonical temperatures than the liquid-solid transition when increasing L towards L = 309. This microcanonical crossover behavior has already been known in other systems and is a pure finite-size effect [26]. The corresponding root map shown in Fig.…”

“…This approach has been successfully applied to a variety of structural transitions in macromolecular systems such as folding [1,[20][21][22], aggregation [23], and adsorption processes of polymers and proteins [24,25]. One particular problem that has gained increased interest recently is the influence of the interaction range on the stability of structural phases [21,26]. This has been addressed by means of systematic microcanonical analyses in discrete and continuous polymer models.…”

Significance of bending restraints for the stability of helical polymer conformations

“…More recently and only possible because of now available computational resources, computer simulations of effective-potential models have become an invaluable resource for studying thermodynamic properties of flexible [13][14][15] and semiflexible polymers [16][17][18], polymer and peptide aggregation [19,20] and adsorption onto a substrate [21][22][23][24], as well as systematic parameter variation in the effective potentials contained in coarse-grained models [25,26]. Simulations of polymer systems yielded also insight into the folding dynamics [27][28][29][30][31][32][33], conformation geometry [34][35][36], and stability [37][38][39][40] of macromolecules.…”

Confinement effects upon the separation of structural transitions in linear systems with restricted bond fluctuation ranges

“…In particular, the growing necessity to understand protein folding boosted also investigations of cooperative conformational phase behavior of small linear polymers, which can be described by rather simple models. Coarse-grained polymer and protein models have been proven to be useful for the investigation of collapse, freezing, or folding of individual macromolecules such as proteins [3][4][5][6][7][8][9][10][11][12] and polymers [1,[13][14][15][16][17][18][19][20][21][22][23]. Generic features of polymer adsorption on substrates [24][25][26][27][28][29][30][31][32][33][34][35][36] and the aggregation of macromolecules [38][39][40][41] can also be described adequately by means of simplified models.…”