• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.828-832
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• 2012

We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (betahairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins.

• Bulletin of the Korean Chemical Society
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• 제24권12호
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• pp.1742-1750
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• 2003

In order to characterize the hydrophobic parameters of N-acetyl amino acid amides in 1-octanol/water, a theoretical calculation was carried out using a solvation free energy density model. The hydrophobicity parameters of the molecules are obtained with the consideration of the solvation free energy over the solvent volume surrounding the solute, using a grid model. Our method can account for the solvent accessible surface area of the molecules according to conformational variations. Through a comparison of the hydrophobicity of our calculation and that of other experimental/theoretical works, the solvation free energy density model is proven to be a useful tool for the evaluation of the hydrophobicity of amino acids and peptides. In order to evaluate the solvation free energy density model as a method of calculating the activity of drugs using the hydrophobicity of its building blocks, the contracture of Bradykinin potentiating pentapeptide was also predicted from the hydrophobicity of each residue. The solvation free energy density model can be used to employ descriptors for the prediction of peptide activities in drug discovery, as well as to calculate the hydrophobicity of amino acids.

• 신재생에너지
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• 제1권1호
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• pp.54-63
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• 2005

A critical issue in the field of the rotor aerodynamics is the treatment of the wake. The wake is of primary importance in determining overall aerodynamic behavior, especially, a wind turbine blade includes the unsteady airloads problem. In this study, the wake generated by blades are depicted by a free wake model to analyse unsteady loading on blade and a new free wake model named Finite Vortex Element(FVE hereafter) is devised in order to include a wake-tower interaction. In this new free wake model, blade-wake-tower interaction is described by cutting a vortex filament when the filament collides with a tower. This FVE model is compared with a conventional free wake model and verified by a comparison with NRELand SNU wind tunnel model. A comparison with NREL and SNU data shows validity and effectiveness of devised FVE free wake model and an efficient.

• Bulletin of the Korean Chemical Society
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• 제32권spc8호
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• pp.3051-3056
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• 2011

We calculate the free energy surfaces for two small proteins and a protein-RNA complex system by using a lattice model approach. In particular, we employ the Munoz-Eaton model, which is a native-structure based statistical mechanical model for studying protein folding problem. The model can provide very useful insights into the folding mechanisms by allowing one to calculate the free energy surfaces efficiently. We first calculate the free energy surfaces of ubiquitin and BBL, using both approximate and recently developed exact solutions of the model. Ubiquitin exhibits a typical two-state folding behavior, while BBL downhill folding in our study. We then extend the method to study of a protein-RNA complex. In particular, we focus on PAZ-siRNA complex. In order to elucidate the interplay between folding and binding kinetics for this system we perform comparative studies of PAZ only, PAZ-siRNA complex and two mutated complexes. We find that folding and binding are strongly coupled with each other and the bound PAZ is more stable than the unbound PAZ. Our results also suggest that the binding sites of the siRNA may serve act as a nucleus in the folding process.

• Bulletin of the Korean Chemical Society
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• 제11권2호
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• pp.144-149
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• 1990

Conformational free energy calculations using an empirical potential function (ECEPP/2) and the hydration shell model were carried out on the sulfonylurea herbicides of bensulfuron methyl (Londax) and metsulfuron methyl (Ally). The conformational energy was minimized from starting conformations which included possible combinations of torsion angles in the molecule. The conformational entropy of each conformation was computed using a harmonic approximation. To understand the hydration effect on the conformation of the molecule in aqueous solution, the hydration free energy of each group was calculated and compared each other. It was found that the low-free-energy conformations of two molecules in aqueous solution prefer the overall folded structure, in which an interaction between the carbonyl group of ester in aryl ring and the first amido group of urea bridge plays an important role. From the analysis of total free energy, the hydration and conformational entropy are known to be essential in stabilizing low-free-energy conformations of Londax, whereas the conformational energy is proved to be a major contribution to the total free energy of low-free-energy conformations of Ally.

• Bulletin of the Korean Chemical Society
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• 제31권5호
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• pp.1247-1251
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• 2010

We propose an improved solvent contact model to estimate the solvation free energies of amino acids from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 17 atom types are developed by the operation of a standard genetic algorithm in such a way to minimize the difference between experimental and calculated solvation free energies. The present solvation model is able to predict the experimental solvation free energies of amino acids with the squared correlation coefficients of 0.94 and 0.93 for the parameterization with Gaussian and screened Coulomb potential as the envelope functions, respectively. This result indicates that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for the estimation of the molecular solvation free energy of a protein in aqueous solution.

• 천문학회보
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• 제39권1호
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• pp.69.2-69.2
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• 2014

To estimate free magnetic energy stored in an active region is a key to the quantitative prediction of activity observed on the Sun. This energy is defined as an excess over the potential energy that is the lowest energy taken by a magnetic structure formed in the solar atmosphere including the solar corona. It is, however still difficult to derive the configuration of a coronal magnetic field only by observations, so we have to use some observable quantity to estimate free magnetic energy. Recently, by performing a coordinated series of three-dimensional magnetohydrodynamic simulations of an emerging flux tube that transfers intense magnetic flux to the solar atmosphere we have found an universal power-law relation between free magnetic energy and emerged magnetic flux, the latter of which is a possibly observed quantity. We further investigate what causes this relation through a comparison with a model of linear force-free field.

• Bulletin of the Korean Chemical Society
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• 제26권4호
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• pp.589-593
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• 2005

The solvation free energy of proton in methanol was calculated by B3LYP flavor of density functional calculations in combination with the Poisson-Boltzmann continuum solvation model. In order to check the adequacy of the computation level, the free energies of clustering in the gas phase were compared with the experimental data. The solvents were taken into account in a hybrid manner, i.e. one to five molecules of methanol were explicitly considered while other solvent molecules were represented with an implicit solvation model.

• Bulletin of the Korean Chemical Society
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• 제14권2호
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• pp.220-225
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• 1993

The influence of temperature and pressure on the free energy of the ion hydration has been considered. The ion radii measured by conductometric method and the saturated dielectric constant cited from other works were used to calculate the free energy in the hydration shell. The Born equation was modified in order to fit in our model. In our model, the environment of ion consists of three regions. The innermost one is the hydration shell in which water is immobilized and electrostricted, the middle one is the one which contains less ordered waters than the bulk medium, and the outermost one is the bulk water which is under the influence of the electric field of ion. Our results for the free energy of ion hydration were compared with those of other attempts. Especially, ${\Delta}$G$_{hyd}$ of $Li^+$ ion is considerably too negative in this study at given temperature, comparing with those of other attempts. But ${\Delta}$G$_{hyd}$ of other ions coincides with each other.

• 전기학회논문지
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• 제66권6호
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• pp.905-910
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• 2017

As the development of BESS(Battery Energy Storage System), the application of BESS in load frequency control is considered as effective method. So, KEPCO(Korea Electric Power Corporation) have installed about 236MW ESS for GF(Govner Free) function from 2014. In this paper, we implemented Simulink Model for KEPCO GF ESS and analyzed one year historical operation data generated by Simulink model and actually measured frequency data. The operation results were divided into action for maintaining SOC and frequency. In addition, we also analyzed cycle life of GF ESS using two ESS cycle life model. We concluded the ESS cycle life models are not appropriate, because Most of the SOC swing in operation results are below 10%.