Molecular dynamics simulations of ovalbumin adsorption at squalene/water interface

The adsorption of protein molecules to oil/water(O/W)interface is of critical importance for the product design in a wide range of technologies and industries such as biotechnology,food industry and pharmaceutical industry.In this work,with ovalbumin(OVA)as the model protein,the adsorption conformations at the O/W interface and the adsorption stability have been systematically studied via multiple simulation methods,including all-atom molecular dynamic(AAMD)simulations,coarse-grained molecular dynamic(CGMD)simulations and enhanced sampling methods.The computational results of AAMD and CGMD show that the hydrophobic tail of OVA tends to be folded under long time relaxation in aqueous phase,and multiple adsorption conformations can exist at the interface due to heterogeneous interactions raising from oil and water respectively.To further study the adsorption sites of the protein,the adsorption kinetics of OVA at the O/W interface is simulated using metadynamics method combined with CGMD simulations,and the result suggests the existence of multiple adsorption conformations of OVA at interface with the head-on conformation as the most stable one.In all,this work focuses on the adsorption behaviors of OVA at squalene/water interface,and provides a theoretical basis for further functionalization of the proteins in emulsion-based products and engineering.

Concentration fluctuation caused by reaction-diffusion coupling near catalytic active sites

The coupling of reaction and diffusion between neighboring active sites in the catalyst pore leads to the spatiotemporal fluctuation in component concentration,which is very importa nt to catalyst performance and hence its optimal design.Molecular dynamics simulation with hard-sphere and pseudo-particle modeling has previously revealed the non-stochastic concentration fluctuation of the reactant/product near isolated active site due to such coupling,using a simple model reaction of A→B in 2D pores.The topic is further developed in this work by studying the concentration fluctuation due to such coupling between neighboring active sites in 3D pores.Two 3D pore models containing an isolated active site and two adjacent active sites were constructed,respectively.For the isolated site,the concentration fluctuation intensifies for larger pores,but the product yield decreases,and for a given pore size,the product yield reaches a peak at a certain reactant concentration.For two neighboring sites,their distance(d)is found to have little effect on the reaction,but significant to the diffusion.For the same reaction competing at both sites,larger d leads to more efficient diffusion and better overall performance.However,for sequential reactions at the two sites,higher overall performance presents at a smaller d.The results should be helpful to the catalyst design and reaction control in the relevant processes.

Effect of amorphous lamella on the crack propagation behavior of crystalline Mg/amorphous Mg–Al nanocomposites

The effects of amorphous lamella on the crack propagation behavior in crystalline/amorphous（C/A） Mg/Mg–Al nanocomposites under tensile loading are investigated using the molecular dynamics simulation method. The sample with an initial crack of orientation（1210） [0001] is considered here. For the nano-monocrystal Mg, the crack growth exhibits brittle cleavage. However, for the C/A Mg/Mg–Al nanocomposites, the ‘double hump＇ behavior can be observed in all the stress–strain curves regardless of the amorphous lamella thickness. The results indicate that the amorphous lamella plays a critical role in the crack deformation, and it can effectively resist the crack propagation. The above mentioned crack deformation behaviors are also disclosed and analyzed in the present work. The results here provide a strategy for designing the high-performance hexagonal-close-packed metal and alloy materials.

The Phase Transition during Post Annealing

We have studied why PA （post-annealing） takes a long time to restore damaged crystallinity, which corresponds to repeat 10 10 times of lattice vibrations. Using a MD （molecular dynamics） simulation, we monitored the time-series of the LRO （long-range order） parameter as LRO pattern, in the case of a type IIa diamond, from the beginning of ion impact by a sub-keV N2 beam implantation to a few nanoseconds, i.e., close to the feasible time limit for MD simulations. Due to the ion impact, the LRO parameter changed gradually from ＂LRO = 1＂ （crystal） to ＂LRO = 0＂ （amorphous）, showing the so-called critical slowing-down phenomenon. However, since PA was started the LRO pattern was not unique. The LRO patterns were grouped into more than three types of phases and the transition between them was also found. From the viewpoint of statistical dynamics, such chaotic variations in the LRO pattern may present that the system is a GCM （globally coupled map） of a complex system in a closed system. A GCM composed of coupled oscillators develops slowly to exhibit several different phases or ‘chaotic itinerancy＇ over time. Therefore, the long duration required for PA may be attributable to the nature of a complex system.

Molecular dynamics simulations of the electric double layer capacitance of graphene electrodes in mono-valent aqueous electrolytes

Electrical double layer （EDL） capacitors based on recently emergent graphene materials have shown several folds performance improvement compared to conventional porous carbon materials, driving a wave of technology breakthrough in portable and renewable energy storage. Accordingly, much interest has been generated to pursue a comprehensive understanding of the fundamental yet elusive double layer structure at file electrode^electrolyte interface. In this paper, we carried out comprehensive molecular dynamics simulations to obtain a com- prehensive picture of how ion type, solvent properties, and charging conditions affect the EDL structure at the graphene electrode surface, and thereby its contribution to capacitance. We show that different symmetrical monovalent aqueous electrolytes M^X- （M~ = Na~, K~, Rb＋, and Cs＋; X- = F-, CI-, and I ） indeed have distinctive EDL structures. Larger ions, such as, Rb＊, Cs＊, C1, and I, undergo partial dehydration and penetrate through the first water layer next to the graphene electrode surfaces under charging. As such, the electrical potential distribution through the EDL strongly depends on the ion type. Interestingly, we further reveal that the water can play a critical role in determining the capacitance value. The change of dielectric constant of water in different electrolytes largely cancels out the variance in electric potential drop across the EDL of different ion type. Our simulation sheds new lights on how the interplay between solvent molecules and EDL structure cooperatively contributes to capacitance, which agrees with our experimental results well.

Novel Dual-Site-Binding Neuraminidase Inhibitor from Virtual Screening by Pharmacophore and Molecular Dynamics Methods

Neuraminidase is a significant anti-influenza target that plays crucial role in virus replication cycle. The discov- ery of 150-cavity in Group-1 neuraminidase provides us a novel mentality of designing inhibitor which can bind with both conserved site and 150-cavity. In order to discover novel dual-site-binding inhibitors, a 3D chemi- cal-feature-based pharmacophore model was established to cover dual-site in neuraminidase. The dual-site-binding model was consistent in predicting the binding conformation of Group-1 neuraminidase inhibitor and applied for virtual screening of Specs database. Compound 4 （ZINC05790048） that aligned well to the model was selected after multiple filtrations for molecular dynamics simulations, indicating improved binding energy with neuraminidase. It can sever as the lead compound for a novel series of inhibitors.