Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association

Ligand–protein association is the first and critical step for many biological and chemical processes. This study investigated the molecular association processes under different environments. In biology, cells have different compartments where ligand–protein binding may occur on a membrane. In experiments involving ligand–protein binding, such as the surface plasmon resonance and continuous flow biosynthesis, a substrate flow and surface are required in experimental settings. As compared with a simple binding condition, which includes only the ligand, protein, and solvent, the association rate and processes may be affected by additional ligand transporting forces and other intermolecular interactions between the ligand and environmental objects. We evaluated these environmental factors by using a ligand xk263 binding to HIV protease (HIVp) with atomistic details. Using Brownian dynamics simulations, we modeled xk263 and HIVp association time and probability when a system has xk263 diffusion flux and a non-polar self-assembled monolayer surface. We also examined different protein orientations and accessible surfaces for xk263. To allow xk263 to access to the dimer interface of immobilized HIVp, we simulated the system by placing the protein 20Å above the surface because immobilizing HIVp on a surface prevented xk263 from contacting with the interface. The non-specific interactions increased the binding probability while the association time remained unchanged. When the xk263 diffusion flux increased, the effective xk263 concentration around HIVp, xk263–HIVp association time and binding probability decreased non-linearly regardless of interacting with the self-assembled monolayer surface or not. The work sheds light on the effects of the solvent flow and surface environment on ligand–protein associations and provides a perspective on experimental design.

Numerical Study on the Flow and Heat Transfer Coupled in a Rectangular Mini-Channel by Finite Element Method for Industrial Micro-Cooling Technologies

Nowadays, cooling high thermal flows in compact volumes continues to be one of the crucial problems in the industry. With the advent of advanced technologies, much more attention has been paid to how to improve the performance of cooling systems in the area of micro-technologies. Rectangular mini-channels are typical representatives which commonly used for cooling applications. However, micro-technologies still face the problem of low performance due to the low productivity of cooling related to unbefitting physical parameter values. Here, this work studies the applicability of the heat transfer scheme of convective flow and flow boiling in a rectangular mini-channel for satisfying the cooling requirement of industrial micro-technologies, through a simulation model governed by the coupled mechanism from Navier-Stokes (N-S) equation and heat transfer equations with phase change effect. In this work, various hydraulic diameters and different inlet fluid speed are used to calculate the different velocity profiles, pressure drops, coefficients of friction and finally, the distribution of the temperatures and dissipated heat flux. The simulation results show the applicability of the rectangular mini-channel in diverse applications such as engine cooling, electronic components, automotive on-board electronics and aerospace engineering. Flow boiling simulation results reveal that the obtained patterns were smooth mixture flow and discrete flow. The dissipated heat flux can reach 1.02–5.34 MW/m2 for a hydraulic diameter of 0.5 mm. We show that the system with the gradient temperature that evolves increasingly along the top and bottom walls of the channels presents the highest heat flux dissipated in flow boiling. Additionally, the fin efficiency of the system is 0.88 and the coefficient value of convective heat transfer is in the range between 5000 < h < 100,000, which indicates the flow boiling heat transfer is effective in the mini-channel when the Reynolds number is less than 400. It provides a significant heat exchange for cooling in these application areas.