• Journal of Korean Ophthalmic Optics Society
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• v.2 no.1
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• pp.17-24
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• 1997

The Voight function which results from the convolution of the Gauss and Lorentz function is applied the MAS-NMR simulation of mixed alkali glasses and the glasses doped transition metal oxides. It is well known that the convolution of the Gauss and Lorentz function cannot be integrated in closed form for arbitrary values. So we make the new computer simulation program from which the Voight lineshape is obtained. The results are accorded well with the MAS-NMR spectra and we can find out the very small change of MAS-NMR lineshape.

• Geophysics and Geophysical Exploration
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• v.16 no.2
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• pp.97-105
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• 2013

Nuclear magnetic resonance (NMR) logging has become an important technique for formation evaluation, detecting interaction signals between H protons and applied magnetic fields. Measured decay signals called relaxation, contain important information about density of H protons and different decay rate due to its fluid type in the sensitive area. Thus, petrophysical information such as porosity, permeability and wettability can be estimated through the interpretation of the decay signals. Many researches on random walk simulation have been published, since a simulation method based on random walk for solving exponential decays was adapted in the early of 1950. This study first makes a review on NMR simulation researches, explains two most important methods: simulation with or without considering magnetic field gradient. Lastly, the study makes a comparison between NMR simulation responses with and without magnetic field gradient to show the importance to consider magnetic gradient to analyze the effects of magnetic gradients on NMR responses.

• Bulletin of the Korean Chemical Society
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• v.25 no.2
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• pp.198-202
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• 2004

Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

• Journal of the Korean Magnetic Resonance Society
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• v.10 no.1
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• pp.1-37
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• 2006

General expressions for solid state NMR lines are described for transitions under static, magic angle spinning, and variable angle spinning conditions in the case where the principal axis system for the anisotropic chemical shift tensor is noncoincident with that of the quadrupole coupling tensor. It is demonstrated that solid state NMR powder pattern simulation program VMAS based on the conventional grid point method of integrating over the Euler angle space is fast enough in comparison with the POWDER simulation package and Gauss-point method.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• Journal of the Korean Magnetic Resonance Society
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• v.10 no.1
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• pp.46-58
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• 2006

With a simple pulse sequence ($\pi/2$-{gradient, duration T}-acquisition) in solution NMR, detected signal has slowly grown up to percents of the equilibrium magnetization. The source of this unusual resurrection of dephased magnetization after a crushed gradient is cross-correlated effects of radiation damping and the distant dipolar field, which has been demonstrated by a numerical simulation and theoretical analysis.

• Journal of the Korean Magnetic Resonance Society
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• v.9 no.1
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• pp.67-73
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• 2005

$^{27}AI$ triple quantum magic angle spinning (3QMAS) NMR spectra of several mordenite (MOR) sample were simulated with the point charge model method and compared with experimental 3QMAS spectra. Signal positions from different tetrahedral (T) sites in 3QMAS spectra are mainly governed by local structures of T sites such as T-O-T angles and T-O bond lengths. When preparation methods, cations in addition to Si/Al rations vary, the local structures of T sites in MOR change enough to alter signal patterns in 3QMAS of MOR. This inhibits to study the of Al distribution variation over 4 different T sites in mordenite during process such as dealumination by 3QMAS spectra.

• Bulletin of the Korean Chemical Society
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• v.30 no.5
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• pp.1139-1142
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• 2009

Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.

• Progress in Superconductivity and Cryogenics
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• v.18 no.3
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• pp.21-24
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• 2016

Recently, production technique and property of the High-Temperature Superconductor (HTS) tape have been improved. Thus, the study on applying an HTS magnet to the high magnetic field application is rapidly increased. A Nuclear Magnetic Resonance (NMR) spectrometer requires high magnitude and homogeneous of central magnetic field. However, the HTS magnet has fabrication errors because shape of HTS is tape and HTS magnet is manufactured by winding HTS tape to the bobbin. The fabrication errors are winding error, bobbin diameter error, spacer thickness error and so on. The winding error occurs when HTS tape is departed from the arranged position on the bobbin. The bobbin diameter and spacer thickness error occur since the diameter of bobbin and spacer are inaccurate. These errors lead magnitude and homogeneity of central magnetic field to be different from its ideal design. The purpose of this paper is to investigate the effect of winding error, bobbin diameter error and spacer thickness error on the central field and field homogeneity of HTS magnet using the virtual NMR signals in MATLAB simulation.