• Genomics & Informatics
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• v.11 no.4
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• pp.282-288
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• 2013

The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated by structure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. The resulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram result produced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study of adenosine receptor agonism and antagonism. The tree that was produced by clustering analysis of molecular vibration patterns showed its potential for the functional classification of adenosine receptor ligands.

• Genomics & Informatics
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• v.10 no.2
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• pp.128-132
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• 2012

To learn the differences between the structure-activity relationship and molecular vibration-activity relationship in the ligand-receptor interaction of the histamine receptor, 47 ligands of the histamine receptor were analyzed by structural similarity and molecular vibrational frequency patterns. The radial tree that was produced by clustering analysis of molecular vibrational frequency patterns shows its potential for the functional classification of histamine receptor ligands.

• Bulletin of the Korean Chemical Society
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• v.7 no.2
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• pp.124-129
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• 1986

The effects of molecular attraction and orientations for the energy mismatch variance, vibrational energy level and double-quantum transition, in the vibration-vibration energy exchange, have been considered. The contribution of molecular attraction increases the exchange rate of the purely repulsive interaction, in general, significantly, but which becomes smaller as the temperature is increased. As the energy mismatch is increased, its contribution is also increased, but which is small. However, its contribution for the double-quantum transition is very paramount. At each orientation, the exchange rate constants have been calculated and compared with the results for rotational average, and it is found that the exchange rate is a strong function of the orientation angles of colliding molecules. We have also discussed about the system having the strong interaction such as the hydrogen bond, and it is found that for this system the preferred orientation should be considered in order to calculate the exchange rates.

• The Science & Technology
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• v.8 no.12 s.79
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• pp.61-64
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• 1975

An expression for the vibrational frequency of diatomic molecular is obtained by using molecular gas temperature T and molecular gas mean-free path λ. And when λ/T →2.59, beca use of the damped vibration, a diatomic molecular gas is Impeded about transportation. If transfortation is not attained with this condition, rectilinear motion of a diatomic molecular gas can't maintain for the equilibrium state.

• 한국정보디스플레이학회:학술대회논문집
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• 2003.07a
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• pp.1112-1117
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• 2003

Polarized Fourier transform infrared (IR) absorption is used to probe molecular conformation in a ferroelectric liquid crystal (FLC) during the reorientation induced by the external field. Spectra of planar aligned cells of FLC W314 are measured as functions of IR polarizer orientation and electric field applied to the FLC. The time evolution of the dichroism of the absorbance due to biphenyl core and alkyl tail molecular vibration modes, is observed. Static IR dichroism experiments show a W314 dichroism structure in which the principal axis of dielectric tensor from molecular core vibration are tilted further from the smectic layer normal than those of the tail. This structure indicates the effective binding site in which the molecules are confined in the Sm-C phase has, on average, "zig-zag" shape and this zig-zag binding site structure is rigidly maintained while the molecular axis rotates about the layer normal during field-induced switching.

• Current Applied Physics
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• v.18 no.11
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• pp.1388-1392
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• 2018

Metal thin films are used widely to solve the vibration problem. However, damping mechanism is still not clear, which limits the further improvement of the damping properties for film and the development of multi-functional damping coating. In this paper, Damping microscopic mechanism of porous metal films was investigated at both macroscopically and microscopically mixed levels. Molecular dynamics simulation method was used to model and simulate the loading-unloading numerical experiment on the micro-pore and vacancy model to get the stress-strain curve and the microstructure diagram of different defects. And damping factor was calculated by the stress-strain curve. The results show that dislocations and new vacancies appear in the micro-pores when metal film is stretched. The energetic consumption from the motion of dislocation is the main reason for the damping properties of materials. Micro-mechanism of damping properties is discussed with the results of in-situ experiment.

• Steel and Composite Structures
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• v.34 no.2
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• pp.261-277
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• 2020

The main objective of this research paper is to consider vibration analysis of vacancy defected graphene sheet as a nonisotropic structure via molecular dynamic and continuum approaches. The influence of structural defects on the vibration of graphene sheets is considered by applying the mechanical properties of defected graphene sheets. Molecular dynamic simulations have been performed to estimate the mechanical properties of graphene as a nonisotropic structure with single- and double- vacancy defects using open source well-known software i.e., large-scale atomic/molecular massively parallel simulator (LAMMPS). The interactions between the carbon atoms are modelled using Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential. An isogeometric analysis (IGA) based upon non-uniform rational B-spline (NURBS) is employed for approximation of single-layered graphene sheets deflection field and the governing equations are derived using nonlocal elasticity theory. The dependence of small-scale effects, chirality and different defect types on vibrational characteristic of graphene sheets is investigated in this comprehensive research work. In addition, numerical results are validated and compared with those achieved using other analysis, where an excellent agreement is found. The interesting results indicate that increasing the number of missing atoms can lead to decrease the natural frequencies of graphene sheets. It is seen that the degree of the detrimental effects differ with defect type. The Young's and shear modulus of the graphene with SV defects are much smaller than graphene with DV defects. It is also observed that Single Vacancy (SV) clusters cause more reduction in the natural frequencies of SLGS than Double Vacancy (DV) clusters. The effectiveness and the accuracy of the present IGA approach have been demonstrated and it is shown that the IGA is efficient, robust and accurate in terms of nanoplate problems.

• Advances in nano research
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• v.8 no.2
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• pp.103-114
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• 2020

In this research, buckling and free vibration of rectangular polymeric laminate reinforced by graphene sheets are investigated. Various patterns are considered for augmentation of each laminate. Critical buckling load is evaluated for different parameters, including boundary conditions, reinforcement pattern, loading regime, and laminate geometric states. Furthermore, vibration analysis is investigated for square laminate. Elastic properties of the composite are calculated using a combination of both molecular dynamics (MD) and the rule of mixture (MR). Kinematics of the plate is approximated based on the first shear deformation theory (FSDT). The current analysis is performed based on the energy method. For the numerical investigation, Ritz method is applied, and for shape functions, Chebyshev polynomials are utilized. It is found that the number of layers is effective on the buckling load and natural frequency of laminates which made from non-uniform layers.

• Tribology and Lubricants
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• v.36 no.5
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• pp.290-296
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• 2020

When two layers of carbon nanotube (CNT) arrays are loaded to mate, the free ends of individual CNTs come into contact at the interface of the two layers. This leads to a higher contact resistance due to a smaller contact region. However, when the free CNT ends of one array penetrate into the mating array, the contact region increases, effectively lowering the contact resistance. To explore the penetration of mating CNTs, we perform molecular dynamic simulations of a simple unit cell model, incorporating four CNTs in the lower array layer coupled with a single moving CNT on the upper layer. The interaction with neighboring CNTs is modelled by long-range carbon bond order potential (LCBOP I). The model structure is optimized by energy minimization through the conjugate gradient method. A NVT ensemble is used for maintain a room temperature during simulation. The time integration is performed through the velocity-Verlet algorithm. A significant vibrational motion of CNTs is captured when penetration is not available, resulting in a specific vibration mode with a high frequency. Due to this vibrational behavior, the random behaviors of CNT motion for predicting the penetration are confirmed under the specific gap distances between CNTs. Thus, the probability of penetration is examined according to the gap distance between CNTs in the lower array and the aspect ratio of CNTs. The penetration is significantly affected by the vibration mode due to the van der Waals forces between CNTs.

• Current Applied Physics
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• v.18 no.11
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• pp.1327-1337
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• 2018

This paper investigates the vibration behavior of pristine and defected triangular graphene sheets; which has recently attracted the attention of researchers and compare these two types in natural frequencies and sensitivity. Here, the molecular dynamics method has been employed to establish a virtual laboratory for this purpose. After measuring the different parameters obtained by the molecular dynamics approach, these data have been analyzed by using the frequency domain decomposition (FDD) method, and the dominant frequencies and mode shapes of the system have been extracted. By analyzing the vibration behaviors of pristine triangular graphene sheets in four cases (right angle of 45-90-45 configuration, right angle of 60-90-30 configuration, equilateral triangle and isosceles triangle), it has been demonstrated that the natural frequencies of these sheets are higher than the natural frequency of a square sheet, with the same number of atoms, by a minimum of 7.6% and maximum of 26.6%. Therefore, for increasing the resonance range of sensors based on 2D materials, nonrectangular structures, and especially the triangular structure, can be considered as viable candidates. Although the pristine and defective equilateral triangular sheets have the highest values of resonance, the sensitivity of defective (45,90,45) triangular sheet is more than other configurations and then, defective (45,90,45) sheet is the worst choice for sensor applications.