We have performed atomistic molecular dynamics simulations of an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. The micelle consisted of 60 surfactant molecules, and the polymer chain lengths varied from 20 to 40 monomers. The force field parameters for PEO were adjusted by using 1,2-dimethoxymethane (DME) as a model compound and matching its hydration enthalpy and conformational behavior to experiment. Excellent agreement with previous experimental and simulation work was obtained through these modifications. The simulated scaling behavior of the PEO radius of gyration was also in close agreement with experimental results. The SDS-PEO simulations show that the polymer resides on the micelle surface and at the hydrocarbon-water interface, leading to a selective reduction in the hydrophobic contribution to the solvent-accessible surface area of the micelle. The association is mainly driven by hydrophobic interactions between the polymer and surfactant tails, while the interaction between the polymer and sulfate headgroups on the micelle surface is weak. The 40-monomer chain is mostly wrapped around the micelle, and nearly 90% of the monomers are adsorbed at low PEO concentration. Simulations were also performed with multiple 20-monomer chains, and gradual addition of polymer indicates that about 120 monomers are required to saturate the micelle surface. The stoichiometry of the resulting complex is in close agreement with experimental results, and the commonly accepted "beaded necklace" structure of the SDS-PEO complex is recovered by our simulations.

Background: Cellobiohydrolase enzymes processively degrade crystalline cellulose into free sugar molecules. Results: A spatially resolved kinetic model has been developed to understand the effects of interfacial confinement on cellobiohydrolase activity. Conclusion: Cellobiohydrolase activity is limited by slow rates of complexation with cellulose and traffic jamming among enzymes on the substrate. Significance: Identifying kinetic effects imposed by interfacial confinement is crucial for understanding and engineering cellulose bioconversion.

We introduce a multiscale framework to simulate inhomogeneous fluids by coarse-graining an all-atom molecular dynamics (MD) trajectory onto sequential snapshots of hydrodynamic fields. We show that the field representation of an atomistic trajectory is quantitatively described by a dynamic field-theoretic model that couples hydrodynamic fluctuations with a Ginzburg-Landau free energy. For liquid-vapor interfaces of argon and water, the parameters of the field model can be adjusted to reproduce the bulk compressibility and surface tension calculated from the positions and forces of atoms in an MD simulation. These optimized parameters also enable the field model to reproduce the static and dynamic capillary wave spectra calculated from atomistic coordinates at the liquid-vapor interface. In addition, we show that a density-dependent gradient coefficient in the Ginzburg-Landau free energy enables bulk and interfacial fluctuations to be controlled separately. For water, this additional degree of freedom is necessary to capture both the bulk compressibility and surface tension emergent from the atomistic trajectory. The proposed multiscale framework illustrates that bottom-up coarse-graining and top-down phenomenology can be integrated with quantitative consistency to simulate the interfacial fluctuations in nanoscale transport processes.

We performed atomistic molecular dynamics simulations of anionic and cationic micelles in the presence of poly(ethylene oxide) (PEO) to understand why nonionic water-soluble polymers such as PEO interact strongly with anionic micelles but only weakly with cationic micelles. Our micelles include sodium n-dodecyl sulfate (SDS), n-dodecyl trimethylammonium chloride (DTAC), n-dodecyl ammonium chloride (DAC), and micelles in which we artificially reverse the sign of partial charges in SDS and DTAC. We observe that the polymer interacts hydrophobically with anionic SDS but only weakly with cationic DTAC and DAC, in agreement with experiment. However, the polymer also interacts with the artificial anionic DTAC but fails to interact hydrophobically with the artificial cationic SDS, illustrating that large headgroup size does not explain the weak polymer interaction with cationic micelles. In addition, we observe through simulation that this preference for interaction with anionic micelles still exists in a dipolar "dumbbell" solvent, indicating that water structure and hydrogen bonding alone cannot explain this preferential interaction. Our simulations suggest that direct electrostatic interactions between the micelle and polymer explain the preference for interaction with anionic micelles, even though the polymer overall carries no net charge. This is possible given the asymmetric distribution of negative charges on smaller atoms and positive charges on larger units in the polymer chain.

The mechanism of synergistic cooperation between cellulases in decomposing cellulose is revealed by resolving the molecular structures of enzymes and substrates via kinetic modeling. The emergence of endo−exo and exo− exo synergy through enzyme−enzyme and enzyme−substrate couplings was investigated with the main exoglucanases (TrCel7A and TrCel6A) and endoglucanase (TrCel7B) of the Trichoderma reesei fungus. The degree of synergy was found to depend on the interplay between two competing effects: (1) enhancement of the complexation rates of exoglucanases with the chain ends created by endoglucanases and (2) surface inhibition of processive exoglucanases by uneven layers of glucan chains on cellulose. We show that the sole effect of TrCel7B in creating more free ends for TrCel7A is insufficient to cause synergistic activity. The combined actions of TrCel7A and TrCel7B produce a rougher substrate surface that subsequently promotes blocking of processing TrCel7A enzymes. This anti-synergy can be counteracted by enhancing the rates of complexation of TrCel7A with the TrCel7B-created chain ends, allowing their synergistic cooperation. Similarly, kinetic simulations show that exo−exo synergy does not occur if TrCel6A and TrCel7A have only opposite specificities in targeting the two ends of glucan chains. Incorporating endo activity into TrCel6A with complexation rate enhancement, however, can lead to synergy with TrCel7A. Therefore, we find that endo−exo and exo−exo synergies may share the same mechanistic origin. The results of work also highlight that resolving molecular configurations in kinetic modeling allows systematic analysis for elucidating the mechanism of interfacial biocatalysis.