Study of Dynamics on the Interfaces of Carbon-Based Nanomaterials and Nanobiosensor



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Carbon-based nanomaterials have promising applications spanning areas from the oil industry to healthcare due to their special attributes to interface with molecules in their local environments. The investigation on nano-interfaces can open in-depth visions of chemical, physical and biological mechanisms that mediate the functions of the nanodevices designed for drug delivery and biodetection. To study properties of the surface at nanoscales poses challenges to current detection techniques, such as infrared absorption spectroscopy (IR) and transmission electron microscopy (TEM). They are either not appropriate for detecting materials in aqueous environments or lack of ability to resolve dynamics at the interface with a sufficient temporal recording rate. The computation technology fueled by the latest progress in software and hardware has shown capabilities to accurately simulate molecular binding processes in biophysics for instance. In this study, we seek the power of molecular dynamics simulation and computational docking to analyze the dynamics at various nano-interfaces including graphene amphiphilic Janus nanosheet (AJN), carbon nanotubes (CNTs), and CNT array biosensor. Rational design of the functional interface is explored by comparison of experimental results and the theoretical predictions. In the study of AJN, we discovered (1) a facile, cheap, and scalable synthesis method of AJN with graphene oxide and tapioca starch, and (2) an additive poly (sodium 4-styrenesulfonate) (PSS) that improves the stability of AJN in brine. Regarding the study of biocompatibility and biodegradation mechanism of CNTs, we found that immunoglobulin G (IgG) was susceptible to bind with CNTs that could contribute to reduce CNTs’ cytotoxicity and accelerate their biodegradation. In the biorecognition study, we identified an array of phenolic oligomers with different polymerization structures could facilitate the interaction with the protein template and self-assemble to form recognition interfaces. By establishing a cascading molecular dynamics and docking analysis, a preliminary protocol of rational design for protein imprinting was proposed and had shown an efficient screening of a chemical library. This study provides opportunities to understand molecular interactions on the interface in atomistic details, and demonstrates the combination of molecular dynamics simulation and docking is an effective approach for the development of novel nanomaterials and nanosensors.



Nanodevice, Carbon nanotubes, Computational methods


Portions of this document appear in: Ding, Yun, Rong Tian, Zhen Yang, Jianfa Chen, and Naihao Lu. "Binding of human IgG to single-walled carbon nanotubes accelerated myeloperoxidase-mediated degradation in activated neutrophils." Biophysical chemistry 218 (2016): 36-41. And in: Ding, Yun, Rong Tian, Zhen Yang, Jianfa Chen, and Naihao Lu. "Effects of serum albumin on the degradation and cytotoxicity of single-walled carbon nanotubes." Biophysical chemistry 222 (2017): 1-6. And in: Ding, Yun, Rong Tian, Zhen Yang, Jianfa Chen, and Naihao Lu. "NADPH oxidase-dependent degradation of single-walled carbon nanotubes in macrophages." Journal of Materials Science: Materials in Medicine 28, no. 1 (2017): 7. And in: Chen, Jianfa, Cale Lewis, D. Balamurugan, Zhen Yang, Liqiang Ai, and Dong Cai. "Theoretical analysis of a high performance protein imprint on a nanosensor." Sensing and bio-sensing research 7 (2016): 12-19.