Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption.

The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs' chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs' size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP's size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface.

Strong Surface Hydration and Salt Resistant Mechanism of a New Nonfouling Zwitterionic Polymer Based on Protein Stabilizer TMAO.

Zwitterionic polymers exhibit excellent nonfouling performance due to their strong surface hydrations. However, salt molecules may severely reduce the surface hydrations of typical zwitterionic polymers, making the application of these polymers in real biological and marine environments challenging. Recently, a new zwitterionic polymer brush based on the protein stabilizer trimethylamine N-oxide (TMAO) was developed as an outstanding nonfouling material. Using surface-sensitive sum frequency generation (SFG) vibrational spectroscopy, we investigated the surface hydration of TMAO polymer brushes (pTMAO) and the effects of salts and proteins on such surface hydration. It was discovered that exposure to highly concentrated salt solutions such as seawater only moderately reduced surface hydration. This superior resistance to salt effects compared to other zwitterionic polymers is due to the shorter distance between the positively and negatively charged groups, thus a smaller dipole in pTMAO and strong hydration around TMAO zwitterion. This results in strong bonding interactions between the O- in pTMAO and water, and weaker interaction between O- and metal cations due to the strong repulsion from the N+ and hydration water. Computer simulations at quantum and atomistic scales were performed to support SFG analyses. In addition to the salt effect, it was discovered that exposure to proteins in seawater exerted minimal influence on the pTMAO surface hydration, indicating complete exclusion of protein attachment. The excellent nonfouling performance of pTMAO originates from its extremely strong surface hydration that exhibits effective resistance to disruptions induced by salts and proteins.

Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface.

Fundamental understanding of biomolecular interfacial behavior, such as protein adsorption at the microscopic scale, is critical to broad applications in biomaterials, nanomedicine, and nanoparticle-based biosensing techniques. The goal of achieving both computational efficiency and accuracy presents a major challenge for simulation studies at both atomistic and molecular scales. In this work, we developed a unique, accurate, high-throughput simulation method which, by integrating discontinuous molecular dynamics (DMD) simulations with the Go-like protein-surface interaction model, not only solves the dynamics efficiently, but also describes precisely the protein intramolecular and intermolecular interactions at the atomistic scale and the protein-surface interactions at the coarse-grained scale. Using our simulation method and in-house developed software, we performed a systematic study of α-helical ovispirin-1 peptide adsorption on a graphene surface, and our study focused on the effect of surface hydrophobic interactions and π-π stacking on protein adsorption. Our DMD simulations were consistent with full-atom molecular dynamics simulations and showed that a single ovispirin-1 peptide lay down on the flat graphene surface with randomized secondary structure due to strong protein-surface interactions. Peptide aggregates were formed with an internal hydrophobic core driven by strong interactions of hydrophobic residues in the bulk environment. However, upon adsorption, the hydrophobic graphene surface can break the hydrophobic core by denaturing individual peptide structures, leading to disassembling the aggregate structure and further randomizing the ovispirin-1 peptide's secondary structures.

A novel multi-phase treatment scheme for odorous rubber effluent.

Despite the great profits of rubber latex production, its preliminary processing releases a large amount of wastewater into the water bodies from several processing steps. This rubber effluent is rich in total Kjeldahl nitrogen (TKN), total dissolved solids (TDS), biological oxygen demand (BOD) and chemical oxygen demand (COD). Therefore, the study addressed a liquid phase treatment of the effluent using an Upflow Anaerobic Sludge Blanket (UASB) reactor followed by coagu-flocculation and aeration. In addition, the gas phase (containing odorous hydrogen sulphide of 10-12% by volume) from the UASB reactor was sent to a caustic scrubber where the H2S removal efficiency of 63 ± 5% was achieved. This integrated multi-phase treatment scheme proved to be an effective approach by reducing TKN, TDS, BOD and COD by 68-87%, 61-69%, 81-84% and 81-87% respectively in the final effluent.

Determining the Potential of Mean Force for Amyloid-ß Dimerization: Combining Self-Consistent Field Theory with Molecular Dynamics Simulation.

Amyloid-ß (Aß) protein aggregates through a complex pathway to progress from monomers to soluble oligomers and ultimately insoluble fibrils. Because of the dynamic nature of aggregation, it has proven exceedingly difficult to determine the precise interactions that lead to the formation of transient oligomers. Here, a statistical thermodynamic model has been developed to elucidate these interactions. Aß1-42 was simulated using fully atomistic replica exchange molecular dynamics. We use an ensemble of approximately 5 × 105 configurations taken from simulation as input in a self-consistent field theory that explicitly accounts for the size, shape, and charge distribution of both the amino acids comprising Aß and all molecular species present in solution. The solution of the model equations provides a prediction of the probabilities of the configurations of the Aß dimer and the potential of mean force between two monomers during the dimerization process. This model constitutes a reliable methodology to elucidate the underlying physics of the Aß dimerization process as a function of pH, temperature, and salt concentration. The results obtained with this new model could be valuable in the design of Aß oligomerization inhibitors, a prospective therapeutic for Alzheimer's disease.

Atomic-Level Simulation Study of n-Hexane Pyrolysis on Silicon Carbide Surfaces.

Ethylene production plays a key role in the petrochemical industry. The severe operation conditions of ethylene thermal cracking, such as high-temperature and coke-formation, pose challenges for the development of new corrosion-resistant and coking-resistant materials for ethylene reactor radiant coils tubes (RCTs). We investigated the performance of ceramic materials such as silicon carbide (SiC) in severe pyrolysis conditions by using reactive force field molecular dynamics (ReaxFF MD) simulation method. Our results indicate that ß-SiC surface remains fully stable at 1500 K, whereas increased temperature results in melted interface. At 2500 K, fully grown cross-linked-graphene-like polycyclic aromatic hydrocarbon coking structure on SiC surfaces was observed. Such coking was particularly severe in the carbon-side of the surface slab. The coking structures were mainly derived from surface atoms at the initial 3.0 ns, as a result of the loss of interfacial hydroxyl layer and further hydrothermal corrosion. The SiC substrate surface enhances the ethylene cracking rate and also leads to different intermediate-state compounds. Our fundamental research will have significant and broad impact on both petrochemical industry and academic research in materials science, petrochemistry, and combustion chemistry.

Aromatic Polyamide Reverse-Osmosis Membrane: An Atomistic Molecular Dynamics Simulation.

Polyamide (PA) membrane-based reverse-osmosis (RO) serves as one of the most important techniques for water desalination and purification. Fundamental understanding of PA RO membranes at the atomistic level is critical to enhance their separation capabilities, leading to significant societal and commercial benefits. In this paper, a fully atomistic molecular dynamics simulation was performed to investigate PA membrane. Our simulated cross-linked membrane exhibits structural properties similar to those reported in experiments. Our results also reveal the presence of small local two-layer slip structures in PA membrane with 70% cross-linking, primarily due to short-range anisotropic interactions among aromatic benzene rings. Inside the inhomogeneous polymeric structure of the membrane, water molecules show heterogeneous diffusivities and converge adjacent to polar groups. Increased diffusion of water molecules is observed through the less cross-linked pathways. The existence of the fast pathways for water permeation has no effect on membrane's salt rejections.

Self-Assembled Monolayers of an Azobenzene Derivative on Silica and Their Interactions with Lysozyme.

The capability of the photoresponsive isomerization of azobenzene derivatives in self-assembled monolayer (SAM) surfaces to control protein adsorption behavior has very promising applications in antifouling materials and biotechnology. In this study, we performed an atomistic molecular dynamics (MD) simulation in combination with free-energy calculations to study the morphology of azobenzene-terminated SAMs (Azo-SAMs) grafted on a silica substrate and their interactions with lysozyme. Results show that the Azo-SAM surface morphology and the terminal benzene rings' packing are highly correlated with the surface density and the isomer state. Higher surface coverage and the trans-isomer state lead to a more ordered polycrystalline backbone as well as more ordered local packing of benzene rings. On the Azo-SAM surface, water retains a high interfacial diffusivity, whereas the adsorbed lysozyme is found to have extremely low mobility but a relative stable secondary structure. The moderate desorption free energy (∼60 kT) from the trans-Azo-SAM surface was estimated by using both the nonequilibrium-theorem-based Jarzynski's equality and equilibrium umbrella sampling.