A Molecular Dynamics Study of Nanowire Resonator Bio-Object Detection

Abstract

This paper presents a comprehensive analysis, carried out by the molecular dynamics (MD) simulations, of the vibrations of silicon nanowire (SiNW) resonators, having diverse applications including biological and medical fields. The chosen approach allows us to obtain a better understanding of the nanowire (NW) materials’ characteristics, providing a more detailed insight into the behavior of nanostructures, especially when the topic of interest is relevant to their dynamics, interatomic interactions, and atoms trajectories’ prediction. We first simulate a SiNW to study its frequency of vibrations using MD simulations. Then, we add a molecule of human immunodeficiency virus as an example to investigate the potential of the SiNW resonator for the detection of tiny bio-objects. The developed technique and its application to the detection of tiny objects, such as viruses, are discussed in the context of several key effects pertinent to the design of SiNW.

Coupled Multiphysics Modelling of Sensors for Chemical, Biomedical, and Environmental Applications with Focus on Smart Materials and Low-Dimensional Nanostructures

“…More generally, the development of micro and nanomechanical resonators can be viewed as part of the advancements made in micro-electromechanical systems/nano-electromechanical systems (MEMS/NEMS) because such resonators can perform a dual function of detection and sensing. Recently developed models, based on comprehensive nonlinear vibration analysis and supported by molecular dynamics simulations [ 147 , 148 ], present an important tool in this respect. In this context, we also mention recent work [ 149 ] where the focus has been made on mass sensing applications while using boron nitride nanotubes (BNNTs) and carbon nanotubes (CNT) as the strongest lightweight nanomaterials.…”

“…Further, the biocompatibility of SWCNTs, as well as their unique optical properties, where fluorescent nanoparticles’ emission signal can serve as an optical reporter for a location or environmental properties, lead to the multifaceted applicability of SWCNT sensors in different biosystems, ranging from single-molecules to in-vivo sensing and providing a deeper insight into many biological phenomena and processes [ 227 ]. Clearly, the importance of molecular recognition of small molecules (e.g., DNAs, RNAs) proteins and viruses goes well beyond biomedical and healthcare applications, aiming at improved clinical diagnostics and treatments, as it also includes other diverse areas such as environmental and food sciences, to name just a few [ 147 , 148 ]. In a generic sense, the success of the sensors in these fields is based on the combination of recognition capabilities with signal transduction, contributing to their sensitivity and selectivity.…”

“…While continuum-type models remain a computationally efficient and practical tool in these fields [ 147 ], in a number of cases more refined models such as those based on molecular dynamics simulations are required to complement such models [ 148 , 229 ]. Among other applications, this includes the development of nanoelectromechanical systems working in the terahertz range, where the employment of CNTs has opened up new areas related to drug delivery, atomic transportation, and detection of atoms and molecules.…”

“…As we saw in the previous sections, there are innovative designs of sensors based on low-dimensional nanostructures, such as nanowires, for detecting tiny bio-particles such as DNA, RNA, proteins, viruses, and bacteria [ 147 , 148 ]. In the analysis and modelling of such sensors, a combination of continuum mechanics methods and molecular dynamics simulations are applied to quantitatively characterize frequency shifts due to the added bio-object mass.…”