Atomistic and Coarse-Grained Simulations of Bulk Amorphous Amylose Above and Below the Glass Transition

Abstract

The present work reports a generic methodology for deriving coarse-grained force fields based on iterative Boltzmann inversion and a generic simulation strategy implementing a cooling protocol for obtaining fully relaxed structures of amorphous amylose below the glass transition temperature. A particular coarse-grained force field for amylose was constructed and was compared to Martini force field and its superiority to predict structural properties such as density, radius of gyration, end-to-end distance, glass transition temperature, and characteristic ratio for amorphous amylose over a wide range of temperatures and molecular weights. This work can be easily extended for studying other bio-based polymers like polysaccharides.

The Glass Transition Temperature of Heterogeneous Biopolymer Systems

“…Another advantage of the Tg models is that they can be used to indirectly determine the (virtual) transition of a glassy polymer by extrapolation to zero diluent concentration. Like many biopolymers, 26 the Tg of pristine Na-alginate cannot be determined since thermal decomposition is observed before the transition. From Figure 3 , all alginate-polyol datasets point toward a virtual Na-alginate Tg or Tg 1 , between 60 to 180 °C.…”

Extending the Martini 3 Coarse-Grained Force Field to Carbohydrates

“…As a consequence, large systems can be studied on a microsecond-long timescale and at reasonable computational cost. There exist several carbohydrate-dedicated CG models. − However, in most of the cases, a serious limitation is that the given model is restricted to the sole class of carbohydrates and there is no compatible set of models capable of describing other types of molecules and biomolecules that often coexist with carbohydrates in real systems. In 2009, the Martini-based CG model for unfunctionalized, glucopyranose-based carbohydrates has been proposed .…”