• Molecules and Cells
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• v.46 no.8
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• pp.513-525
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• 2023

Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.

• Journal of applied mathematics & informatics
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• v.25 no.1_2
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• pp.435-443
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• 2007

Computing the interior spectrum of large sparse generalized eigenvalue problems $Ax\;=\;{\lambda}Bx$, where A and b are large sparse and SPD(Symmetric Positive Definite), is often required in areas such as structural mechanics and quantum chemistry, to name a few. Recently, CG-type methods have been found useful and hence, very amenable to parallel computation for very large problems. Also, as in the case of linear systems proper choice of preconditioning is known to accelerate the rate of convergence. After the smallest eigenpair is found we use the orthogonal deflation technique to find the next m-1 eigenvalues, which is also suitable for parallelization. This offers advantages over Jacobi-Davidson methods with partial shifts, which requires re-computation of preconditioner matrx with new shifts. We consider as preconditioners Incomplete LU(ILU)(0) in two variants, ever-relaxation(SOR), and Point-symmetric SOR(SSOR). We set m to be 5. We conducted our experiments on matrices from discretizations of partial differential equations by finite difference method. The generated matrices has dimensions up to 4 million and total number of processors are 32. MPI(Message Passing Interface) library was used for interprocessor communications. Our results show that in general the Multi-Color ILU(0) gives the best performance.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1499-1504
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• 2008

Pyrazine derivatives bind to b-RAF receptor which is important in cancer therapy. The ligand-receptor interactions have been studied by comparative molecular field analysis (CoMFA) and molecular docking methods. Applying conventional ligand-based alignment schemes for the whole set was not successful. However, QM and DFT results suggested that some ligands have electrostatic interaction while others have steric interactions. On the basis of these results, we divided the dataset into two subsets. Electrostatic effect was found to be important in one set while steric effect for the other. Best docking modes were obtained for each subset based on the available crystal structure. These receptor-guided CoMFA models propose an interesting possibility which is difficult to obtain otherwise. i.e., in one binding mode the electrostatic interaction plays a key role for one subset ($q^2$ = 0.46, $r^2$ = 0.98), while in another binding mode steric effect is important with another subset ($q^2$ = 0.43, $r^2$ = 0.74).

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.763-770
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• 2003

The $BH_5$ molecule, which is suggested as an intermediate of the acidolysis of $BH_4^-$, contains a weak two-electron-three-center bond and it requires extremely high-level of theories to calculate the energy and structure correctly. The structures and energies of $BH_5$ and the transition state for the hydrogen scrambling have been studied using recently developed multi-coefficient correlated quantum mechanical methods (MCCMs). The dissociation energies and the barrier heights agree very well with the previous results at the CCSD(T)/ TZ(3d1f1g, 2p1d) level. We have also calculated the potential energy curves for the dissociation of $BH_5$ to $BH_3$ and $H_2$. The lower levels of theory were unable to plot correct potential curves, whereas the MCCM methods give very good potential energy curves and requires much less computing resources than the CCSD(T)/ TZ(3d1f1g,2p1d) level. The potential energy of the $BH_5$ scrambling has been obtained by the multiconfiguration molecular mechanics algorithm (MCMM), and the rates are calculated using the variational transition state theory including multidimensional tunneling approximation. The rate constant at 300 K is 2.1 × $10^9s^{-1}$, and tunneling is very important.

• Proceedings of the Korea Contents Association Conference
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• 2009.05a
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• pp.141-145
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• 2009

Lee Sang, a poet and a architect, made new experimental poems that was influenced by quantum mechanics and theory of relativity that were published in the early 1900's, and he showed his new view of the world that transcended time and space limit through his poems. In this essay, I studied and analyzed on the links between his view of the world and modern design view with as the central figure his text, 'A Written Promise of The Line' The result is that he fellow the cyclic world view which the world consisted of cycles within cycles, of immense duration and the scientific view of the world which the universe and me are one flesh.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.17 no.3
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• pp.540-545
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• 2013

The Fractional Fourier transform, as a generalization of the classical Fourier Transform, was first introduced in quantum mechanics. Because of its simple and useful properties of Fractional Fourier transform in time-frequency plane, various research results in sonar and radar signal processing have been introduced and shown superior results to conventional method utilizing Fourier transform until now. In this paper, we applied Fractional Fourier transform to sonar signal processing to detect and separate the overlapping linear frequency modulated signals. Experimental results show that received overlapping LFM(Linear Frequency Modulation) signals can be detected and separated effectively in Fractional Fourier transform domain.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.399-408
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• 2014

신약을 개발하거나 단백질 구조를 예측하는데 Molecular Mechanics (MM)의 방법을 사용한다. 하지만, MM 만으로는 자연현상에서 일어나는 결과를 정확하게 기술하기 어렵다. 본 연구는 기존의 MM 방법으로는 정확히 예측이 불가능한 비 공유결합 중 하나인 ${\pi}-{\pi}$ interaction을 양자역학 계산을 통해 정확한 예측이 가능한지 알아보았다. ${\pi}-{\pi}$ interaction이란 생채 내, 의약 화합물에서 발견되는 결합이기 때문에, 단백질과 결합하는 구조의 예측에 중요하다고 할 수 있다. 본 실험은 ${\pi}-{\pi}$ interaction을 갖는 Sandwich, T shape, 그리고 Parallel displaced 세 가지 모형과 각각의 모형 아래에 분자를 하나 더 쌓은 모형을 추가하여 양자역학 재산을 수행하였다. 양자역학 계산은 DFT의 세가지 함수 M06_2X, M05_2X, B3LYP를 이용하였다. 실험결과에서 세 가지 함수가 각기 다른 결과를 보였는데, 상대적으로 B3LYP의 경우에는 세가지 모델에서 모두 제대로 된 에너지 변화를 계산하지 못하였으며, M06_2X와 M05_2X의 결과에서는 거리에 따른 ${\pi}-{\pi}$ interaction 에너지의 변화를 정확하게 계산하였다. 이러한 결과를 바탕으로, 양자역학의 방법을 통해 MM에서는 예측이 불가능한 ${\pi}-{\pi}$ interaction을 계산 할 수 있고 이 부분을 고려하여 화합물 간의 결합구조를 예측을 향상시킬 수 있다.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.89-100
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• 2013

생물정보학의 다양한 이론적 내용과 계산적 방법들이 갈수록 전문화 되어짐에 따라 신약 개발, 신 물질 합성, 단백질의 구조 예측 등 다양한 분야에서 필요성이 커져가고 있다. 이 중 molecular docking 기술은 단백질과 특정 분자간의 결합 형태를 분자 모델링 기법을 통해 알아내는 방법이며 신약개발 연구에 큰 영향을 미치고 있다. Molecular docking을 통하여 분자간의 결합 형태를 예측하는 과정에서 Protein-ligand complex의 정확한 에너지 측정을 가능하게 하는 scoring function이 필요하다. 그런데 본 연구에서 사용한 B-Raf kinase protein 은 active site 부분에서 ligand와 receptor 간에 aromatic ring로 인한 ${\pi}-{\pi}$ interaction이 정확한 에너지 계산을 어렵게 한다. 이러한 ${\pi}-{\pi}$ interaction 부분의 에너지를 정확하게 계산하기 위해 양자역학 계산을 실시하였다. Active site 부분에서 ligand와 receptor에서 발생하는 각각 다른 5개의 ${\pi}-{\pi}$ interaction 구조를 준비하여 Gaussian을 통해 양자역학 에너지를 계산하였다. 그리고 이러한 결과 값들이 ligand의 활성 값과 어떤 상관관계를 갖는지 살펴보았다. 그 결과 ${\pi}-{\pi}$ interaction을 양자역학으로 계산한 값이 그렇지 않은 것보다 더 좋은 상관관계를 보여주었다. 이는 특별한 구조의 영향으로 ligand와 receptor 간의 결합에너지를 정확하게 계산하기 어려운 문제에서 양자역학을 적용할 경우 더욱 좋은 결과값을 얻을 수 있었다. 또한 이러한 데이터가 신 물질 개발이나 신약 개발 등의 다양한 분야에서 계산화학 방법이 신뢰성을 얻는데 도움 될 수 있다고 생각된다.

• The Korean Journal of Food & Health Convergence
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• v.4 no.3
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• pp.1-5
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• 2018

In today's technological development of human society more and more influence on the lives of biological organisms different electromagnetic radiation. Therefore, the study and analysis of the mechanisms of their effects is an urgent task. The purpose of research - the study of the primary mechanisms of interaction of photons of optical radiation with the structures of biological objects, using the laws of quantum mechanics and biophysics. Photobiological basis of the mechanism of action of EMR optical range is the energy absorption of light quanta (photons) by atoms and molecules of biological structures (law Grotgus-Draper), which resulted in the formation of electronically excited states of these molecules with the transfer of photon energy (internal photoeffect). This is accompanied by electrolytic dissociation and ionization of biological molecules. The degree of manifestation of photobiological effects in the body depends on the intensity of the optical radiation, which is inversely proportional to the square of the distance from the source to the irradiated surface. Accordingly, in practice, determine not the intensity and irradiation dose at a certain distance from the source of exposure by the exposure time.

• International Journal of Advanced Culture Technology
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• v.11 no.2
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• pp.170-177
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• 2023

In quantum mechanics, uncertainty refers to the uncertainty of a measurement physical quantity, because some mechanical quantity can only be in its eigenstate under certain conditions, and the values shown are discrete.The exact value can only be obtained by measuring it in the eigenstate of this mechanical quantity.Uncertainty is like a double-edged sword, which has both advantages and disadvantages in art itself and in the process of artistic creation. In this study, it is divided into three main parts. First, the existence of uncertainties in contemporary art is sorted out in two broad parts, the definition of the uncertainties in art and the specific expression in contemporary art, respectively, with examples from four aspects of psychological impact, accidental presentation effect, expression form and connection with the viewer. The purpose is to understand how uncertainties are expressed in the process of artistic creation. Second, the role of the uncertainties in artistic creation is analyzed through examples, and then it is proposed that artists should use uncertainties to serve art with a scientific and rational attitude. Thirdly, the application of uncertainties in my creative practice and their influences on my painting creation. In summary, every artistic creator should take art seriously and sincerely. The relationship among the creative subject, society and life is an eternal and continuous interaction, and art is a carrier of reflection. For the problems brought by uncertainties in artistic creation, from choosing new certainty by thinking to the emergence of uncertainties, such a cycle is the process of art sublimating from life and being closely related to life.