Sergiy Markutsya

Self-recovery of stressed nanomembranes

Long-term stability and self-recovery properties were studied for the compliant nanomembranes with a thickness of 55nm free suspended over openings of several hundred microns across. These nanomembranes were assembled with spin-assisted layer-by-layer routines and were composed of polymer multilayers and gold nanoparticles. In a wide pressure range, the membranes behave like completely elastic freely suspended plates. Temporal stability was tested under extreme deformational conditions close to ultimate strain and very modest creep behavior was observed. A unique “self-recovery” ability of these nanomembranes was revealed in these tests. We observed a complete restoration of the initial nanomembrane shape and properties after significant inelastic deformation. These unique micromechanical properties are suggested to be the result of strong Coulombic interaction between the polyelectrolyte layers combined with a high level of biaxial orientation of polymer chains and in-plane prestretching stresses.

Ab Initio Study of Molecular Interactions in Cellulose Iα

Biomass recalcitrance, the resistance of cellulosic biomass to degradation, is due in part to the stability of the hydrogen bond network and stacking forces between the polysaccharide chains in cellulose microfibers. The fragment molecular orbital (FMO) method at the correlated Møller-Plesset second order perturbation level of theory was used on a model of the crystalline cellulose Iα core with a total of 144 glucose units. These computations show that the intersheet chain interactions are stronger than the intrasheet chain interactions for the crystalline structure, while they are more similar to each other for a relaxed structure. An FMO chain pair interaction energy decomposition analysis for both the crystal and relaxed structures reveals an intricate interplay between electrostatic, dispersion, charge transfer, and exchange repulsion effects. The role of the primary alcohol groups in stabilizing the interchain hydrogen bond network in the inner sheet of the crystal and relaxed structures of cellulose Iα, where edge effects are absent, was analyzed. The maximum attractive intrasheet interaction is observed for the GT-TG residue pair with one intrasheet hydrogen bond, suggesting that the relative orientation of the residues is as important as the hydrogen bond network in strengthening the interaction between the residues.

Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose

A fundamental understanding of the intermolecular forces that bind polysaccharide chains together in cellulose is crucial for designing efficient methods to overcome the recalcitrance of lignocellulosic biomass to hydrolysis. Because the characteristic time and length scales for the degradation of cellulose by enzymatic hydrolysis or chemical pretreatment span orders of magnitude, it is important to closely integrate the molecular models used at each scale so that, ultimately, one may switch seamlessly between quantum, atomistic, and coarse-grained descriptions of the system. As a step towards that goal, four multiscale coarse-grained models for polysaccharide chains in a cellulose-Iα microfiber are considered. Using the force matching method, effective coarse-grained forces are derived from all-atom trajectories. Performance of the coarse-grained models is evaluated by comparing the intrachain radial distribution functions with those obtained using the all-atom reference data. The all-atom simulation reveals a double peak in the radial distribution function for sites within each glucose residue that arises from the distinct conformations sampled by the primary alcohol group in the glucose residues. The three-site and four-site coarse-grained models have sufficient degrees of freedom to predict this double peak while the one-site and two-site models do not. This is the first time that coarse-grained models have been shown to reproduce such subtle, yet important, molecular features in a polysaccharide chain. The relative orientations between glucose residues along the polysaccharide chain are evaluated and it is found that the four-site coarse-grained model is best at reproducing the glucose-glucose conformations observed in the all-atom simulation. The success of the four-site coarse-grained model underscores the importance of decoupling the pyranose ring from the oxygen atom in the glycosidic bond when developing all-atom to coarse-grained mapping schemes for polysaccharides.

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

A coarse-grained model for β-d-glucose based on force matching

Cellulosic ethanol production is a two-stage process that involves the hydrolysis of cellulose to form simple sugars and the fermentation of these sugars to ethanol. Hydrolysis of cellulose is the rate-limiting step, and there is a great need to characterize the process with numerical simulations to better understand the complex mechanisms involved. The ultimate goal is to generate accurate coarse-grained molecular models that are capable of predicting the structure of lignocellulose before and after pretreatment so that subsequent ab initio calculations can be performed to probe the degradation pathways. As a first step toward that goal, the force-matching method is used to derive coarse-grained models for β-d-glucose molecules in aqueous solution. Using the same reference, an all-atom molecular dynamics simulation trajectory, two sets of three- and six-site coarse-grained models of β-d-glucose are developed using two definitions of the coarse-grained center site location: center of mass (CG-CM) and geometric center (CG-GC). The performance of these coarse-grained models is evaluated by comparing the coarse-grained predictions for bond-length distributions and radial distribution functions to those obtained from the all-atom reference simulation. The six-site coarse-grained models retain more structural details than the three-site coarse-grained models. Comparison between center site definitions shows that CG-CM models generally predict local ordering better, while CG-GC models predict long-range structure better.