Large-scale molecular dynamics simulations of bubble collapse in water: Effects of system size, water model, and nitrogen.

Molecular dynamics simulations in the microcanonical ensemble are performed to study the collapse of a bubble in liquid water using the single-site mW and the four-site TIP4P/2005 water models. To study system size effects, simulations for pure water systems are performed using periodically replicated simulation boxes with linear dimensions, L, ranging from 32 to 512 nm with the largest systems containing 8.7 × 106 and 4.5 × 109 molecules for the TIP4P/2005 and mW water models, respectively. The computationally more efficient mW water model allows us to reach converging behavior when the bubble dynamics results are plotted in reduced units, and the limiting behavior can be obtained through linear extrapolation in L-1. Qualitative differences are observed between simulations with the mW and TIP4P/2005 water models, but they can be explained by the models' differences in predicted viscosity and surface tension. Although bubble collapse occurs on time scales of only hundreds of picoseconds, the system sizes used here are sufficiently large to obtain bubble dynamics consistent with the Rayleigh-Plesset equation when using the models' thermophysical properties as input. For the conditions explored here, extreme heating of the interfacial water molecules near the time of collapse is observed for the larger mW water systems (but the model underpredicts the viscosity), whereas heating is less pronounced for the TIP4P/2005 water systems because its larger viscosity contribution slows the collapse dynamics. The presence of nitrogen within the bubble only starts to affect bubble dynamics near the very end of the initial collapse, leading to an incomplete collapse and strong rebound for the mW water model. Although nitrogen is non-condensable at 300 K, it becomes highly compressed and reaches a liquid-like density near the collapse point. We find that the dissolution of nitrogen is much slower than the movement of the collapsing water front, and the re-expansion of the dense nitrogen droplet gives rise to bubble rebound. The incompatibility of the collapse and dissolution time scales should be considered for continuum-scale modeling of bubble dynamics. We also confirm that the diffusion coefficient for dissolved nitrogen is insensitive to pressure as the liquid transitions from a compressed to a stretched state.

A Nanocavitation Approach to Understanding Water Capture, Water Release, and Framework Physical Stability in Hierarchically Porous MOFs.

Chemically stable metal-organic frameworks (MOFs) featuring interconnected hierarchical pores have proven to be promising for a remarkable variety of applications. Nevertheless, the framework's susceptibility to capillary-force-induced pore collapse, especially during water evacuation, has often limited practical applications. Methodologies capable of predicting the relative magnitudes of these forces as functions of the pore size, chemical composition of the pore walls, and fluid loading would be valuable for resolution of the pore collapse problem. Here, we report that a molecular simulation approach centered on evacuation-induced nanocavitation within fluids occupying MOF pores can yield the desired physical-force information. The computations can spatially pinpoint evacuation elements responsible for collapse and the chemical basis for mitigation of the collapse of modified pores. Experimental isotherms and difference-electron density measurements of the MOF NU-1000 and four chemical variants validate the computational approach and corroborate predictions regarding relative stability, anomalous sequence of pore-filling, and chemical basis for mitigation of destructive forces.

Discrete Orientations of Interfacial Waters Direct Crystallization of Mica-Binding Proteins.

Understanding the basis of templated molecular assembly on a solid surface requires a fundamental comprehension of both short- and long-range aqueous response to the surface under a variety of solution conditions. Herein we provide a detailed picture of how the molecular-scale response to different mica surfaces yields distinct solvent orientations that produce quasi-static directional potentials onto which macromolecules can adsorb. We connect this directionality to observed (a)symmetric epitaxial alignment of designed proteins onto these surfaces, corroborate our findings with 3D atomic force microscopy experiments, and identify slight differences in surface structure as the origin of this effect. Our work provides a detailed picture of the intrinsic electrolyte response in the vicinity of mineral interfaces, with clear predictions for experiment, and highlights the role of solvent on the predictive assembly of hierarchical materials on mineral surfaces.

Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction.

Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.

Ion-dependent protein-surface interactions from intrinsic solvent response.

The phyllosilicate mineral muscovite mica is widely used as a surface template for the patterning of macromolecules, yet a molecular understanding of its surface chemistry under varying solution conditions, required to predict and control the self-assembly of adsorbed species, is lacking. We utilize all-atom molecular dynamics simulations in conjunction with an electrostatic analysis based in local molecular field theory that affords a clean separation of long-range and short-range electrostatics. Using water polarization response as a measure of the electric fields that arise from patterned, surface-bound ions that direct the adsorption of charged macromolecules, we apply a Landau theory of forces induced by asymmetrically polarized surfaces to compute protein-surface interactions for two muscovite-binding proteins (DHR10-mica6 and C98RhuA). Comparison of the pressure between surface and protein in high-concentration KCl and NaCl aqueous solutions reveals ion-specific differences in far-field protein-surface interactions, neatly capturing the ability of ions to modulate the surface charge of muscovite that in turn selectively attracts one binding face of each protein over all others.

Expanding the Scope of Sortase-Mediated Ligations by Using Sortase Homologues.

Sortase-catalyzed transacylation reactions are widely used for the construction of non-natural protein derivatives. However, the most commonly used enzyme for these strategies (sortase A from Staphylococcus aureus) is limited by its narrow substrate scope. To expand the range of substrates compatible with sortase-mediated reactions, we characterized the in vitro substrate preferences of eight sortase A homologues. From these studies, we identified sortase A enzymes that recognize multiple substrates that are unreactive toward sortase A from S. aureus. We further exploited the ability of sortase A from Streptococcus pneumoniae to recognize an LPATS substrate to perform a site-specific modification of the N-terminal serine residue in the naturally occurring antimicrobial peptide DCD-1L. Finally, we unexpectedly observed that certain substrates (LPATXG, X=Nle, Leu, Phe, Tyr) were susceptible to transacylation at alternative sites within the substrate motif, and sortase A from S. pneumoniae was capable of forming oligomers. Overall, this work provides a foundation for the further development of sortase enzymes for use in protein modification.