Advances in nanotechnology lead to the development of nano-electro-mechanical systems (NEMS) such as nanomechanical resonators with ultra-high resonant frequencies. The ultra-high-frequency resonators have recently received significant attention for wide-ranging applications such as molecular separation, molecular transportation, ultra-high sensitive sensing, high-frequency signal processing, and biological imaging. It is well known that for micrometer length scale, first-principles technique, the most accurate approach, poses serious limitations for comparisons with experimental studies. For such larger size, classical molecular dynamics (MD) simulations are desirable, which require interatomic potentials. Additionally, a mesoscale method such as the coarse-grained (CG) method is another useful method to support simulations for even larger system sizes. Furthermore, quasi-two-dimensional (Q2D) materials have attracted intensive research interest due to their many novel properties over the past decades. However, the energy dissipation mechanisms of nanomechanical resonators based on several Q2D materials are still unknown. In this work, the addressed main issues include the development of the CG models for molybdenum disulphide (MoS2), investigation of the mechanism effects on black phosphorus (BP) nanoresonators and the application of graphene nanoresonators. The primary coverage and results of the dissertation are as follows: Method development. Firstly, a two-dimensional (2D) CG model for single layer MoS2 (SLMoS2) is analytically developed. The Stillinger-Weber (SW) potential for this 2D CG model is further parametrized, in which all SW geometrical parameters are determined analytically according to the equilibrium condition for each individual potential term, while the SW energy parameters are derived analytically based on the valence force field model. Next, the 2D CG model is further simplified to one-dimensional (1D) CG model, which describes the 2D SLMoS2 structure using a 1D chain model. This 1D CG model is applied to investigate the relaxed configuration and the resonant oscillation of the folded SLMoS2. Owning to the simplicity nature of the 1D CG model, the relaxed configuration of the folded SLMoS2 is determined analytically, and the resonant oscillation frequency is derived analytically. Considering the increasing interest in studying the properties of other 2D layered materials, and in particular those in the semiconducting transition metal dichalcogenide class like MoS2, the CG models proposed in current work provide valuable simulation approaches. Mechanism understanding. Two energy dissipation mechanisms of BP nanoresonators are focused exclusively, i.e. mechanical strain effects and defect effects (including vacancy and oxidation). Vacancy defect is intrinsic damping factor for the quality (Q)-factor, while mechanical strain and oxidation are extrinsic damping factors. Intrinsic dissipation (induced by thermal vibrations) in BP resonators (BPRs) is firstly investigated. Specifically, classical MD simulations are performed to examine the temperature dependence for the Q-factor of the single layer BPR (SLBPR) along the armchair and zigzag directions, where two-step fitting procedure is used to extract the frequency and Q-factor from the kinetic energy time history. The Q-factors of BPRs are evaluated through comparison with those of graphene and MoS2 nanoresonators. Next, effects of mechanical strain, vacancy and oxidation on BP nanoresonators are investigated in turn. Considering the increasing interest in studying the properties of BP, and in particular the lack of theoretical study for the BPRs, the results in current work provide a useful reference. Application. A novel application for graphene nanoresonators, using them to self-assemble small nanostructures such as water chains, is proposed. All of the underlying physics enabling this phenomenon is elucidated. In particular, by drawing inspiration from macroscale self-assembly using the higher order resonant modes of Chladni plates, classical MD simulations are used to investigate the self-assembly of water molecules using graphene nanoresonators. An analytic formula for the critical resonant frequency based on the interaction between water molecules and graphene is provided. Furthermore, the properties of the water chains assembled by the graphene nanoresonators are studied.