• Tribology and Lubricants
• /
• v.36 no.2
• /
• pp.55-63
• /
• 2020

Recently, graphene has attracted considerable attention owing to its unique electrical, optical, thermal, and mechanical properties. The broad spectrum of applications from optics, sensors, and electronics to biodevice have been proposed based on these properties. In particular, graphene has been proposed as a protective coating layer and solid lubricant for microdevices and nanodevices because of its high mechanical strength, chemical inertness, and low friction characteristics. During the past decade, extensive efforts have been made to explore the tribological characteristics of graphene under various conditions and to expand its applicability. In addition to the experimental approaches, the molecular simulations performed provide fundamental insights into the friction and wear characteristics of graphene resulting from molecular interactions. This work is a review of the studies conducted over the past decade on the tribological characteristics of graphene using molecular simulation. These studies demonstrate the principal mechanisms of the superlubricity of graphene and help clarify the influences of surface conditions on tribological behavior. In particular, the investigation of the effects of the number of layers, strength of adhesion to the substrate, surface roughness, and commensurability provides deeper insights into the tribological characteristics of graphene. These fundamental understandings can help elucidate the feasibility of graphene as a protective coating layer and solid lubricant for microdevices and nanodevices.

• Polymer(Korea)
• /
• v.30 no.6
• /
• pp.453-463
• /
• 2006

Molecular simulation is an exceptionally useful method for predicting self-assembled structures in various macromolecular systems, enlightening the origins of many interesting molecular events such as protein folding, polymer micellization, and ordering of molten block copolymer. The length scales of those events ranges widely from sub-nanometer scale to micron-scale or to even larger, which is the main obstacle to simulate all the events in an ab initio principle. In order to detour this major obstacle in the molecular simulation approach, a molecular model can be rebuilt by sacrificing some unimportant molecular details, based on two different perspectives with respect to the resolution of model. These two perspectives are generally referred to as 'atomistic' and 'mesoscopit'. This paper reviews various simulation methods for macromolecular self-assembly in both atomistic and mesoscopic perspectives.

• Interaction and multiscale mechanics
• /
• v.4 no.3
• /
• pp.219-237
• /
• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• YAKHAK HOEJI
• /
• v.60 no.2
• /
• pp.78-84
• /
• 2016

N-Phenylthiourea derivatives and catechol oxidase receptor complex was studied using molecular mechanics method. The starting structure was adopted from the protein databank and the calculation of energy minimization and molecular dynamics was performed with AMBER package. The molecular dynamics showed that the simulation time span of 20 ns was long enough to observe the interaction profile and stationary ligand-receptor configuration in the complex. The conformation of the ligand was related to the interaction to the receptor and the efficacy was also interpreted in this context.

• YAKHAK HOEJI
• /
• v.54 no.1
• /
• pp.67-74
• /
• 2010

Some of the benzopyrene (BP)-DNA adduct are known to build intercalated motif between flanking base pairs in damaged DNA depending on the structural condition. The size of benzopyrene itself is definitely not comparable with any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular dynamics simulation based on the theory of molecular mechanics. The specific consequences about the structural properties of the intercalated structures and benzopyrene motif in minor groove of the double helix are deduced after 5 ns simulation time.

• Proceedings of the Membrane Society of Korea Conference
• /
• 2004.05a
• /
• pp.33-38
• /
• 2004

Molecular modeling of gas permeation through zeolite membranes with/without intercrystalline region was carried out. Molecular dynamics (MD) and Monte Carlo (MC) simulations were performed to estimate the diffusion coefficient and adsorption parameters respectively, and our proposed combined method of molecular simulation techniques with a permeation theory (CMP) was used to estimate gas permeability. The calculated permeability of gases (Ar, He, Ne, $N_2$, $0_2$, $CH_4$) at 301 K for the single crystal membrane model was about one order of magnitude larger than the experiential values, although the dependence on the molecular weight of the permeating species agreed with experiments. On the other hand, the estimated permeability using the diffusivity and adsorption parameters of the intercrystalline region model was in good agreement with the experiments. The consistency between experiments and the estimated values means the importance of considering the intercrystalline region and the validity of CMP method to predict the performance of zeolite membranes.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• v.10 no.10
• /
• pp.5035-5048
• /
• 2016

Nano scale networks are futuristic networks deemed as enablers for the Internet of Nano Things, Body area nano networks, target tracking, anomaly/ abnormality detection at molecular level and neuronal therapy / drug delivery applications. Molecular communication is considered the most compatible communication technology for nano devices. However, connectivity in such networks is very low due to inter-symbol interference (ISI). Few research papers have addressed the issue of ISI mitigation in molecular communication. However, many of these methods are not adaptive to dynamic environmental conditions. This paper presents an enhancement over original Memory-1 ISI cancellation scheme using maximum likelihood estimation of a channel parameter (λ) to make it adaptable to variable channel conditions. Results of the Monte Carlo simulation show that, the connectivity (P_conn) improves by 28% for given simulation parameters and environmental conditions by using enhanced Memory-1 cancellation method. Moreover, this ISI mitigation method allows reduction in symbol time (Ts) up to 50 seconds i.e. an improvement of 75% is achieved.

• Advances in nano research
• /
• v.15 no.2
• /
• pp.105-111
• /
• 2023

Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin αvβ3 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.2
• /
• pp.321-324
• /
• 2004

• Bulletin of the Korean Chemical Society
• /
• v.22 no.12
• /
• pp.1287-1288
• /
• 2001