Coarse-Grained Water Model Development for Accurate Dynamics and Structure Prediction.

Several coarse-graining (CG) methods have been combined to develop a CG model of water capable of the accurate prediction of structure and dynamics properties. The multiscale coarse-graining (MS-CG) method based on force matching and the PDF-based coarse-graining method were used for accurate dynamics prediction. The iterative Boltzmann inversion (IBI) method was added for accurate structure representation. The approach is applied to bulk water, and the results show close reproduction of the CG structure when compared with the reference atomistic data. The combination of MS-CG and IBI methods facilitates the development of CG force fields at different temperatures based on a single MS-CG coarse-graining procedure. The dynamic properties of the CG water model closely match those obtained from the reference atomistic system. The general application of this approach to any existing coarse-graining methods is discussed.

Coarse-Grained Dynamically Accurate Simulations of Ionic Liquids: [pyr14][TFSI] and [EMIM][BF4].

In this work, coarse-grained (CG) models for two different sets of ionic liquids were developed from atomistic molecular dynamics (MD) reference systems, expanding their system size and time duration capabilities. The bonded force field of the CG systems was built using harmonic oscillator potential (HOP) fitting, while the nonbonded force field was generated with the multiscale coarse-graining (MS-CG) approach based on force matching. The dynamics of each system were corrected using the probability distribution function-based coarse-grained molecular dynamics (PDF-based CGMD) method. The structure and dynamics of each system were proven to match reference system data at two temperature scales. CG models and force fields for these liquids were developed to exemplify a general purpose methodology for producing MD results of ionic liquids and other fluids with accurate structural as well as dynamic properties. As an application, developed ionic liquids CG models were then applied to study vacuum-interface interaction. Density profile results of vacuum-interface exposure show significant deviation from bulk behavior. At the interface, multilayer ordering of ionic liquids is predicted to be similar to those observed from an experimental work. This ordering is intensified by decreasing temperature and use of the PDF-based CGMD method as opposed to conventional CG methods.

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.

Characterization of sheared colloidal aggregation using Langevin dynamics simulation.

Aggregation of colloidal particles under shear is studied in model systems using a Langevin dynamics model with an improved interparticle interaction potential. In the absence of shear, aggregates that form are characterized by compact structure at small scales and ramified structure at larger scales. This confirms the structural crossover mechanism previously suggested by Sorensen and coworkers, that colloidal aggregation occurs due to monomer addition at small scales and due to cluster-cluster aggregation at large scales. The fractal dimension of nonsheared aggregates is scale-dependent. Smaller aggregates have a higher fractal dimension than larger ones, but the radius of gyration where this crossover occurs is independent of potential well depth for sufficiently deep wells. When these aggregates are subjected to shear they become anisotropic and form extended cigar-like structures. The size of sheared anisotropic aggregates in the direction perpendicular to the shear flow is limited by shear-induced breakage because the shear force dominates interparticle attraction for sufficiently large aggregates. Anisotropic aggregates are not completely characterized by a single radius of gyration, but rather by an inertia ellipsoid. Consequently the fractal dimension is no longer an adequate metric to properly characterize them, and to identify changes in their structure from their nonsheared isotropic counterparts. We introduce a new compactness-anisotropy analysis that characterizes the structure of anisotropic aggregates and allows us to distinguish between aggregates from sheared and nonsheared systems. Finally, using the ratio of interparticle force to the shear force f_{pot,sh} we are able to characterize different outcomes of sheared aggregation as a function of dimensionless well depth and Péclet number.

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.

Freely suspended nanocomposite membranes as highly sensitive sensors.

Highly sensitive sensor arrays are in high demand for prospective applications in remote sensing and imaging. Measuring microscopic deflections of compliant micromembranes and cantilevers is developing into one of the most versatile approaches for thermal, acoustic and chemical sensing. Here, we report on an innovative fabrication of compliant nanocomposite membranes with nanoscale thickness showing extraordinary sensitivity and dynamic range, which makes them candidates for a new generation of membrane-based sensor arrays. These nanomembranes with a thickness of 25-70 nm, which can be freely suspended over large (hundred micrometres) openings are fabricated with molecular precision by time-efficient, spin-assisted layer-by-layer assembly. They are designed as multilayered molecular composites made of a combination of polymeric monolayers and a metal nanoparticle intralayer. We demonstrate that these nanocomposite membranes possess unparalleled sensitivity and a unique autorecovering ability. The membrane nanostructure that is responsible for these outstanding properties combines multilayered polymer/nanoparticle organization, high polymer-chain orientation, and a pre-stretched state.

Collective and individual plasmon resonances in nanoparticle films obtained by spin-assisted layer-by-layer assembly.

Nanoscale uniform films containing gold nanoparticle and polyelectrolyte multilayer structures were fabricated by the using spin-assembly or spin-assisted layer-by-layer (SA-LbL) deposition technique. These SA-LbL films with a general formula [Au/(PAH-PSS)nPAH]m possessed a well-organized microstructure with uniform surface morphology and high surface quality at a large scale (tens of micrometers across). Plasmon resonance peaks from isolated nanoparticles and interparticle interactions were revealed in the UV-visible extinction spectra of the SA-LbL films. All films showed the strong extinction peak in the region of 510-550 nm, which is due to the plasmon resonance of the individual gold nanoparticles redshifted because of a local dielectric environment. For films with sufficient density of gold nanoparticles within the layers, the second strong peak was consistently observed between 620 and 660 nm, which is the collective plasmon resonance from intralayer interparticle coupling. Finally, we suggested that, for certain film designs, interlayer interparticle resonance might be revealed as an independent contribution at 800 nm in UV-visible spectra. The observation of independent and concurrent individual, intralayer, and interlayer plasmon resonances can be critical for sensing applications, which involve monitoring of optomechanical properties of ultrathin optically active compliant membranes.