Secondary Structure Analysis of Native Cellulose by Molecular Dynamics Simulations with Coarse Grained Model

Advancing plant cell wall modelling: Atomistic insights into cellulose, disordered cellulose, and hemicelluloses - A review

The complexity of plant cell walls on different hierarchical levels still impedes the detailed understanding of biosynthetic pathways, interferes with processing in industry and finally limits applicability of cellulose materials. While there exist many challenges to readily accessing these hierarchies at (sub-) angström resolution, the development of advanced computational methods has the potential to unravel important questions in this field. Here, we summarize the contributions of molecular dynamics simulations in advancing the understanding of the physico-chemical properties of natural fibres. We aim to present a comprehensive view of the advancements and insights gained from molecular dynamics simulations in the field of carbohydrate polymers research. The review holds immense value as a vital reference for researchers seeking to undertake atomistic simulations of plant cell wall constituents. Its significance extends beyond the realm of molecular modeling and chemistry, as it offers a pathway to develop a more profound comprehension of plant cell wall chemistry, interactions, and behavior. By delving into these fundamental aspects, the review provides invaluable insights into future perspectives for exploration. Researchers within the molecular modeling and carbohydrates community can greatly benefit from this resource, enabling them to make significant strides in unraveling the intricacies of plant cell wall dynamics.

A Review of Cellulose Coarse-Grained Models and Their Applications

Cellulose is the most common biopolymer and widely used in our daily life. Due to its unique properties and biodegradability, it has been attracting increased attention in the recent years and various new applications of cellulose and its derivatives are constantly being found. The development of new materials with improved properties, however, is not always an easy task, and theoretical models and computer simulations can often help in this process. In this review, we give an overview of different coarse-grained models of cellulose and their applications to various systems. Various coarse-grained models with different mapping schemes are presented, which can efficiently simulate systems from the single cellulose fibril/crystal to the assembly of many fibrils/crystals. We also discuss relevant applications of these models with a focus on the mechanical properties, self-assembly, chiral nematic phases, conversion between cellulose allomorphs, composite materials and interactions with other molecules.

Mechanical Properties of Cellulose Nanocrystal (CNC) Bundles: Coarse-Grained Molecular Dynamic Simulation

Cellulose nanocrystals (CNCs) is a promising biodegradable nanomaterial with outstanding physical, chemical, and mechanical properties for many applications. Although aligned CNCs can self-assemble into bundles, their mechanical performance is reduced by interfacial strength between CNCs and a twisted structure. In this paper, we employ developed coarse-grained (CG) molecular dynamic (MD) simulations to investigate the influence of twist and interface energy on the tensile performance of CNC bundles. CNC bundles of different sizes (number of particles) are tested to also include the effect of size on mechanical performance. The effect of interfacial energy and twist on the mechanical performance shows that elastic modulus, strength, and toughness are more sensitive to twisted angle than interfacial energy. In addition, the effect of size on the bundle and twist on their mechanical performance revealed that both size and twist have a significant effect on the results and can reduce the strength and elastic modulus by 75% as a results of covalent bond dissociation. In addition, a comparison of the broken regions for different values of twist shows that by increasing the twist angle the crack propagates in multiple locations with a twisted shape.

Unraveling cellulose microfibrils: a twisted tale

Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface.

A coarse-grain force-field for xylan and its interaction with cellulose

We have built a coarse-grain (CG) model describing xylan and its interaction with crystalline cellulose surfaces. Each xylosyl or glucosyl unit was represented by a single grain. Our calculations rely on force-field parameters adapted from the atomistic description of short xylan fragments and their adsorption on cellulose. This CG model was first validated for xylan chains both isolated and in the bulk where a good match was found with its atomistic counterpart as well as with experimental measurements. A similar agreement was also found when short xylan fragments were adsorbed on the (110) surface of crystalline cellulose. The CG model, which was extended to the (100) and (1-10) surfaces, revealed that the adsorbed xylan, which was essentially extended in the atomistic situation, could also adopt coiled structures, especially when laying on the hydrophobic cellulose surfaces.