• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.21-21
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• 2011

A series of Quasi-Elastic Neutron Scattering (QENS) experiments helps us to understand the single-particle (hydrogen atom) dynamics of a globular protein and its hydration water and strong coupling between them. We also performed Molecular Dynamics (MD) simulations on a realistic model of the hydrated hen-egg Lysozyme powder having two proteins in the periodic box. We found the existence of a Fragile-to-Strong dynamic Crossover (FSC) phenomenon in hydration water around a protein occurring at TL=$225{\pm}5K$ by analyzing Intermediate Scattering Function (ISF). On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the High Density Liquid (HDL) form, a more fluid state, to predominantly the Low Density Liquid (LDL) form, a less fluid state, derived from the existence of a liquid?liquid critical point at an elevated pressure. We showed experimentally and confirmed theoretically that this sudden switch in the mobility of the hydration water around a protein triggers the dynamic transition (so-called glass transition) of the protein, at a temperature TD=220 K. Mean Square Displacement (MSD) is the important factor to show that the FSC is the key to the strong coupling between a protein and its hydration water by suggesting TL${\fallingdotseq}$TD. MD simulations with TIP4P force field for water were performed to understand hydration level dependency of the FSC temperature. We added water molecules to increase hydration level of the protein hydration water, from 0.30, 0.45, 0.60 and 1.00 (1.00 is the bulk water). These confirm the existence of the FSC and the hydration level dependence of the FSC temperature: FSC temperature is decreased upon increasing hydration level. We compared the hydration water around Lysozyme, B-DNA and RNA. Similarity among those suggests that the FSC and this coupling be universal for globular proteins, biopolymers.

• 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.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.447-453
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• 2002

In this paper we have presented the results of thermodynamic, structural, and dynamic properties of model systems for liquid benzene, toluene and p-xylene in an isobaric-isothermal (NpT) ensemble at 283.15, 303.15, 323.15, and 343.15 K using molecular dynamics (MD) simulation. This work is initiated to compensate for our previous canonical (NVT) ensemble MD simulations [Bull. Kor. Chem. Soc. 2001, 23, 441] for the same systems in which the calculated pressures were too low. The calculated pressures in the NpT ensemble MD simulations are close to 1 atm and the volume of each system increases with increasing temperature. The first and second peaks in the center of mass g(r) diminish gradually and the minima increase as usual for the three liquids as the temperature increases. The three peaks of the site-site gC-C(r) at 283.15 K support the perpendicular structure of nearest neighbors in liquid benzene. Two self-diffusion coefficients of liquid benzene via the Einstein equation and via the Green-Kubo relation are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene and p-xylene are in accord with the trend that the self-diffusion coefficient decreases with increasing number of methyl group. The friction constants calculated from the force auto-correlation (FAC) function with the assumption that the fast random force correlation ends at time which the FAC has the first negative value give a correct qualitative trends: decrease with increase of temperature and increase with the number of methyl group. The friction constants calculated from the FAC's are always less than those obtained from the friction-diffusion relation which reflects that the random FAC decays slower than the total FAC as described by Kubo [Rep. Prog. Phys. 1966, 29, 255].

• Bulletin of the Korean Chemical Society
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• v.34 no.11
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• pp.3429-3443
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• 2013

Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.

• Korean Journal of Metals and Materials
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• v.47 no.1
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• pp.32-37
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• 2009

Molecular dynamic simulations on the structural evolution of the Si(001) vicinal surfaces, which are tilted with respect to [100] and [110] directions were performed by using the empirical Tersoff potential. Tersoff potential was implemented at LAMMPS code and confirmed to describe the properties of Si. When the steps are generated along [100] direction, symmetric dimer rows formed with respect to the step edges. On the other hand, when the steps are generated along [110] direction, alternating dimer rows form with respect to the step edges. The configurational differences between the two vicinal surfaces were discussed in terms of the surface diffusion and the possibility of preventing step bunching for the (001) vicinal surface tilted along [100] direction was suggested.

• Corrosion Science and Technology
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• v.21 no.1
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• pp.21-31
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• 2022

Potentiodynamic polarization, EIS measurements, quantum chemical calculations, and molecular dynamic simulations were used to investigate the corrosion behavior of mild steel in 0.5 M aqueous hydrochloric acid medium in the presence or absence of nystatin drug. Potentiodynamic tests suggested that this molecule could act as a mixed inhibitor due to its adsorption on the mild steel surface. The objective of this study was to exploit theoretical calculations to gain a better understanding mechanism of inhibition. Calculating the adsorption behavior of the investigated molecule on Fe (1 1 0) surface was accomplished using Monte Carlo simulation. Molecules were also investigated using Density Functional Theory (DFT), specifically PBE functional, in order to identify the link between molecular structure and corrosion inhibition behavior of the compound under investigation. Adsorption energies between nystatin and iron were estimated more accurately by utilizing Molecular Mechanics calculation with Periodic Boundary Conditions (PBC). Estimated theoretical parameters significantly assisted our understanding of the corrosion inhibition mechanism exhibited by this molecule. They were found to be in accord with experimental results.

• Polymer(Korea)
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• v.35 no.6
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• pp.513-519
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• 2011

Molecular simulations via the molecular dynamics method have been carried out to investigate the dynamic collision properties of penetrable-sphere model fluids. The collision frequencies, the mean free paths, the angle distributions of the hard-type reflection and the soft-type penetration, and the effective packing fractions are computed over a wide range of the packing fraction ${\phi}$ and the repulsive energy ${\varepsilon}^*$. The soft-type collisions are dominated for lower repulsive energy systems, while the hardtype collisions for higher repulsive energy systems. Very interestingly, the ratio of the soft-type (or, the hard-type) collision frequency to the total collision frequency is directly related with the Boltzmann factor of acceptance (or rejection) probabilities in the canonical ensemble Monte Carlo calculations. Such dynamic collision properties are shown to be restricted for highly repulsive and dense systems of ${\varepsilon}^*{\geqq}3.0 $and ${\phi}{\geqq}0.7$, indicating the cluster forming structures in the penetrable-sphere model.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2233-2236
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• 2011

We evaluate quantum-mechanical velocity autocorrelation functions from classical molecular dynamics simulations using quantum correction approaches. We apply recently developed approaches to supercritical argon and liquid neon. The results show that the methods provide a solution more efficient than previous methods to investigate quantum-mechanical dynamic behavior in condensed phases. Our numerical results are found to be in excellent agreement with the previous quantum-mechanical results.

• Journal of Preventive Medicine and Public Health
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• v.40 no.2
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• pp.185-190
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• 2007

Objectives : Since the first human infection from avian influenza was reported in Hong Kong in 1997, many Asian countries have confirmed outbreaks of highly pathogenic H5N1 avian influenza viruses. In addition to Asian countries, the EU authorities also held an urgent meeting in February 2006 at which it was agreed that Europe could also become the next target for H5N1 avian influenza in the near future. In this paper, we provide the general and applicable information on the avian influenza in the bioinformatics field to assist future studies in preventive medicine. Methods : We introduced some up-to-date analytical tools in bioinformatics research, and discussed the current trends of avian influenza outbreaks. Among the bioinformatics methods, we focused our interests on two topics: pattern analysis using the secondary database of avian influenza, and structural analysis using the molecular dynamics simulations in vaccine design. Results : Use of the public genome databases available in the bioinformatics field enabled intensive analysis of the genetic patterns. Moreover, molecular dynamic simulations have also undergone remarkable development on the basis of the high performance supercomputing infrastructure these days. Conclusions : The bioinformatics techniques we introduced in this study may be useful in preventive medicine, especially in vaccine and drug discovery.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.19 no.2
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• pp.116-125
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• 2006

We have presented a nanoelectromechanical (NEM) model based on atomistic simulations. Our models were applied to a NEM device as called a nanotube random access memory (NRAM) operated by an atomistic capacitive model including a tunneling current model. We have performed both static and dynamic analyses of a NRAM device. The turn-on voltage obtained from molecular dynamics simulations was less than the half of the turn-on voltage obtained from the static simulation. Since the suspended carbon nanotube (CNT) oscillated with the amplitude for the oscillation center under an externally applied force, the quantity of the CNT-gold interaction in the static analysis was different from that in the dynamic analysis. When the gate bias was applied, the oscillation centers obtained from the static analysis were different from those obtained from the dynamics analysis. Therefore, for the range of the potential difference that the CNT-gold interaction effects in the static analysis were negligible, the vibrations of the CNT in the dynamics analysis significantly affected the CNT-gold interaction energy and the turn-on voltage. The turn-on voltage and the tunneling resistance obtained from our tunneling current model were in good agreement with previous experimental and theoretical works.