• Journal of the Korean Physical Society
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• v.73 no.10
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• pp.1466-1472
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• 2018

A key comparison has been made between the air-kerma standards of the National Institute of Metrology (NIM), China, and other Asia Pacific Metrology Programme (APMP) members in the medium-energy X-ray. This paper reviews the primary standard Free-air ionization chamber correction factor experimental method and Monte Carlo simulation method in the NIM. The experimental method and the Monte Carlo simulation method are adopted to obtain the correction factor for the medium-energy X-ray primary standard free-air ionization chamber at 100 kV, 135 kV, 180 kV, 250 kV four CCRI reference qualities. The correction factor has already been submitted to the APMP as key comparison data and the results are in good agreement with those obtained in previous studies. This study shows that the experimental method and the EGSnrc simulation method are usually used in the measurement of the correction factor. In particular, the application of the simulation methods is more common.

• Bulletin of the Korean Chemical Society
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• v.21 no.12
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• pp.1207-1212
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• 2000

The free energy simulation technique is used to evaluate the relative binding affinity of a set of hydroxyethylene isostere inhibitors of the HIV-1 protease. The binding reactions and an alchemical mutation construct the thermodynamic cycle, which reduces the free energy difference of the binding interactions into that of the alchemical processes. In the alchemical process, a methyl group is mutated into a hydrogen atom. Albeit the change is a small perturbation to the inhibitor-protease complex, it results in 25 fold difference in the binding constants. The simulation reproduces the experimentally measured binding affinities within 2% of the free energy difference. The protonation state of the catalytic aspartic acid residues is also investigated through the free energy simulations.

• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.2823-2829
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• 2010

We investigated the solvent effects on the relative free energies of binding of $Na^+$ and $Li^+$ ions to 12-crown-4 and ${\Delta}log\;K_s$ (the difference of stability constant of binding) by a Monte Carlo simulation of statistical perturbation theory (SPT) in several solvents. Comparing the relative free energies of binding of $Na^+$ and $Li^+$ ions to 12-crown-4, in $CH_3OH$ of this study with experimental works, there is a good agreement among the studies. We have reported the quantitative free energy polarity (of solvent) relationships (QFPR) of the relationship between the relative free energies and solvent polarity studied on the solvent effects on the relative free energies of binding of $Na^+$ and $Li^+$ ions to 12-crown-4.

• Bulletin of the Korean Chemical Society
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• v.22 no.8
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• pp.877-882
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• 2001

The solvent effects on the relative free energies of Eu3+ to Yb3+ ion mutation in solution have been investigated using a Monte Carlo simulation of statistical perturbation theory (SPT). Our results agree well with available data that were obtained by others. Particularly, the results of water (SPC/E) solvent are almost identical with experimental data. For the present Eu3+ and Yb3+ ions, the relative free energies of solvation vs. Born’s function of bulk solvents decrease with increasing Born’s function of bulk solvents. There is also good agreement between the calculated structural properties in this study and the published works obtained by computer simulation and experimental work.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.363-371
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• 2008

As a computational method for the discovery of the effective agonists for PPARd, we address the usefulness of molecular dynamics free energy (MDFE) simulation with explicit solvent in terms of the accuracy and the computing cost. For this purpose, we establish an efficient computational protocol of thermodynamic integration (TI) that is superior to free energy perturbation (FEP) method in parallel computing environment. Using this protocol, the relative binding affinities of GW501516 and its derivatives for PPARd are calculated. The accuracy of our protocol was evaluated in two steps. First, we devise a thermodynamic cycle to calculate the absolute and relative hydration free energies of test molecules. This allows a self-consistent check for the accuracy of the calculation protocol. Second, the calculated relative binding affinities of the selected ligands are compared with experimental IC50 values. The average deviation of the calculated binding free energies from the experimental results amounts at the most to 1 kcal/mol. The computational efficiency of current protocol is also assessed by comparing its execution times with those of the sequential version of the TI protocol. The results show that the calculation can be accelerated by 4 times when compared to the sequential run. Based on the calculations with the parallel computational protocol, a new potential agonist of GW501516 derivative is proposed.

• Bulletin of the Korean Chemical Society
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• v.33 no.12
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• pp.3939-3940
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• 2012

• KIEAE Journal
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• v.4 no.4
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• pp.19-26
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• 2004

The purpose of this study was to evaluate the thermal environment of present state and energy consumption and to verify the improvement of energy performance applying free cooling in 5ESS-2000 telecommunication equipment room. Analysis program is used the DOE-2.1E and commercial CFD code, Star-CD. The results of the simulation show that free cooling could reduce 42.1% of cooling energy, increase 48.5% of heating energy because introduced outdoor air must heating and humidification. Therefore free cooling could reduce yearly 34,609.9 kWh of heating and cooling energy and this is reaching to 21.6% of total energy.

• Bulletin of the Korean Chemical Society
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• v.20 no.7
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• pp.815-818
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• 1999

The method of calculating the excess Helmholtz free energy from the averaged effective acceptance ratio for the Lennard-Jones fluid and the inverse twelve fluid has been slightly modified and applied to the two-center-Lennard-Jones liquid. The excess Helmholtz free energy is calculated directly from the average of the modified effective acceptance ratio through a single Metropolis Monte Carlo simulation. Therefore this method does not need any reference system. The results of the present method were satisfactory compared with those of the perturbation theories and the overlap ratio method.

• Journal of the Semiconductor & Display Technology
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• v.17 no.4
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• pp.1-5
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• 2018

Atomic force microscopy (AFM) simulation for Si (001) surface defects was conducted by using density functional theory (DFT). Three major defects on the Si (001) surface are difficult to analyze due to external noises that are always present in the images obtained by AFM. Noise-free surface defects obtained by simulation can help identify the real surface defects on AFM images. The surface defects were first optimized by using a DFT code. The AFM tip was designed by using five carbon atoms and positioned on the surface to calculate the system's energy. Forces between tip and surface were calculated from the energy data and converted into an AFM image. The simulated AFM images are noise-free and, therefore, can help evaluate the real surface defects present on the measured AFM images.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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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.