• Title/Summary/Keyword: Derivative-free methods

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Density Functional Theory (DFT) Study of Gas-phase O.C Bond Dissociation Energy of Models for o-TEMPO-Bz-C(O)-Peptide: A Model Study for Free Radical Initiated Peptide Sequencing

  • Kwon, Gyemin;Kwon, Hyuksu;Lee, Jihye;Han, Sang Yun;Moon, Bongjin;Oh, Han Bin;Sung, Bong June
    • Bulletin of the Korean Chemical Society
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    • v.35 no.3
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    • pp.770-774
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    • 2014
  • The bond dissociation energy (BDE) of the chemical bond between the carbon and oxygen atoms of a simple TEMPO-derivative is calculated by employing the density functional theory, the $2^{nd}$ order M${\phi}$ller-Plesset (MP2) perturbation theory, and complete basis set (CBS) methods. We find that BDE of the positive ion of the TEMPO-derivative is larger at least by 7 kcal/mol than that of the negative ion, which implies that the dissociation reaction rate of the positive ion should be slower than that of the negative ion. Such theoretical predictions are contrary to the results of our previous experiments (Anal. Chem. 2013, 85, 7044), in which the larger energy was required for negative o-TEMPO-Bz-C(O)-peptides to undergo the dissociation reactions than for the positive ones. By comparing our theoretical results to those of the experiments, we conclude that the dissociation reaction of o-TEMPO-Bz-C(O)-peptide should occur in a complicated fashion with a charge, either positive or negative, probably being located on the amino acid residues of the peptide.

Comparison of Inhibitory Effects of 17-AAG Nanoparticles and Free 17-AAG on HSP90 Gene Expression in Breast Cancer

  • Ghalhar, Masoud Gandomkar;Akbarzadeh, Abolfazl;Rahmati, Mohammad;Mellatyar, Hassan;Dariushnejad, Hassan;Zarghami, Nosratallah;Barkhordari, Amin
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.17
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    • pp.7113-7118
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    • 2014
  • Background: HSP90 may be overexpressed in cancer cells which are greatly dependent on Hsp90 function. Geldanamycin derivative 17 allylamino-17-demethoxygeldanamycin (17-AAG) inhibits the function and expression of HSP90. 17-AAG has poor water-solubility which is a potential problem for clinical practice. In this study for improving the stability and solubility of molecules in drug delivery systems we used a ${\beta}$-cyclodextrin-17AAG complex. Materials and Methods: To assess cytotoxic effects of ${\beta}$-cyclodextrin-17AAG complexes and free 17AAG, colorimetric cell viability (MTT) assays were performed. Cells were treated with equal concentrations of ${\beta}$-cyclodextrin- 17AAG complex and free 17AAG and Hsp90 gene expression levels in the two groups was compared by real-time PCR. Results: MTT assay confirmed that ${\beta}$-cyclodextrin- 17AAG complex enhanced 17AAG cytotoxicity and drug delivery in T47D breast cancer cells. The level of Hsp90 gene expression in cells treated with ${\beta}$-cyclodextrin- 17AAG complex was lower than that of cells treated with free 17AAG (P=0.001). Conclusions: The results demonstrated that ${\beta}$-cyclodextrin- 17AAG complexes are more effective than free 17AAG in down-regulating HSP90 expression due to enhanced ${\beta}$-cyclodextrin-17AAG uptake by cells. Therefore, ${\beta}$-cyclodextrin could be superior carrier for this kind of hydrophobic agent.

Experimental and numerical study of autopilot using Extended Kalman Filter trained neural networks for surface vessels

  • Wang, Yuanyuan;Chai, Shuhong;Nguyen, Hung Duc
    • International Journal of Naval Architecture and Ocean Engineering
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    • v.12 no.1
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    • pp.314-324
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    • 2020
  • Due to the nonlinearity and environmental uncertainties, the design of the ship's steering controller is a long-term challenge. The purpose of this study is to design an intelligent autopilot based on Extended Kalman Filter (EKF) trained Radial Basis Function Neural Network (RBFNN) control algorithm. The newly developed free running model scaled surface vessel was employed to execute the motion control experiments. After describing the design of the EKF trained RBFNN autopilot, the performances of the proposed control system were investigated by conducting experiments using the physical model on lake and simulations using the corresponding mathematical model. The results demonstrate that the developed control system is feasible to be used for the ship's motion control in the presences of environmental disturbances. Moreover, in comparison with the Back-Propagation (BP) neural networks and Proportional-Derivative (PD) based control methods, the EKF RBFNN based control method shows better performance regarding course keeping and trajectory tracking.

Comparison of different iterative schemes for ISPH based on Rankine source solution

  • Zheng, Xing;Ma, Qing-wei;Duan, Wen-yang
    • International Journal of Naval Architecture and Ocean Engineering
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    • v.9 no.4
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    • pp.390-403
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    • 2017
  • Smoothed Particle Hydrodynamics (SPH) method has a good adaptability for the simulation of free surface flow problems. There are two forms of SPH. One is weak compressible SPH and the other one is incompressible SPH (ISPH). Compared with the former one, ISPH method performs better in many cases. ISPH based on Rankine source solution can perform better than traditional ISPH, as it can use larger stepping length by avoiding the second order derivative in pressure Poisson equation. However, ISPH_R method needs to solve the sparse linear matrix for pressure Poisson equation, which is one of the most expensive parts during one time stepping calculation. Iterative methods are normally used for solving Poisson equation with large particle numbers. However, there are many iterative methods available and the question for using which one is still open. In this paper, three iterative methods, CGS, Bi-CGstab and GMRES are compared, which are suitable and typical for large unsymmetrical sparse matrix solutions. According to the numerical tests on different cases, still water test, dam breaking, violent tank sloshing, solitary wave slamming, the GMRES method is more efficient than CGS and Bi-CGstab for ISPH method.

Numerical Evaluation of 2nd Derivatives of the Potential in the Panel method for the Unsteady Potential Flow Problem (비정상 포텐셜 유동의 패널법 해석에서 포텐셜의 2차 미분값의 수치계산)

  • 양진호;전호환
    • Journal of Ocean Engineering and Technology
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    • v.14 no.3
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    • pp.41-45
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    • 2000
  • In solving the unsteady potential flow problem of the ship in waves with the panel method, in general one can consider the basic flow as the free stream or double body solution. For the double body solution, the body boundary condition has the 2nd derivatives of the velocity potential. Low order panel methods are known to suffer from the significant error in the 2nd derivatives computed at the body surface. This paper analyzes the numerical error in the 2nd derivatives for a 2-D cylinder and a 3-D sphere problem, and an extrapolation method to obtain the correct derivatives on the body surface is suggested.

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A study for the- reconstruction of free field sound source from the measured data in a closed wall by using Boundary Element Method (경계요소법을 이용한 음원의 자유음장 복원에 대한 연구)

  • Choi, Han-Lim;Lee, Duck-Joo
    • Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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    • 2000.06a
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    • pp.1747-1751
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    • 2000
  • It is well known that acoustic signals, even measured in an anechoic chamber, can be contaminated due to the wall interference. Therefore, it is necessary to reconstruct the original signal from the measured data, which is very critical for the case of measurement of source signal in a water tunnel. In this thesis, new methods for the reconstruction of sound sources are proposed and validated by using Boundary Element Method from measured data in a closed space. The inverse Helmholtz integral equation and its normal derivative are used for the reconstruction of sound sources in a closed space. An arbitrary Kirchhoff surface over the sources is proposed to solve the surface information instead of direct solution for the source. Although sound sources are not directly known by the inverse Helmholtz equation, the original sound source of pressure-field outside of the wall can be indirectly obtained by using this new method.

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Antioxidative and Cytoprotective Effects of Isoflavones Isolated from Pueraria thunbergiana Flowers (갈화에서 분리한 이소플라본의 항산화 및 세포보호효과)

  • 이경태;손일철;공은아;김동현;최승기;최종원;박희준
    • YAKHAK HOEJI
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    • v.43 no.6
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    • pp.736-742
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    • 1999
  • Antioxidative and cytoprotective effects of tectorigenin and glycitein isolated from the pueraria thunbergiana and its derivative, genistein, were determined. Among these three compounds, tectorigenin and glycitein bearing 6-methoxyl groups in both isoflavones showed significant free radical scavenging activities on 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical and xanthine/xanthine oxidase (XOD) generating superoxide anion radical. Tectorigenin only showed a slight inhibitory effect on XOD. We further studied the inhibitory effects of these isoflavones on the lipid peroxidation in rat liver microsomes induced by enzymatic and non-enzymatic methods. Each of them exhibited inhibitory effect on both ascorbic $acid/Fe^{2+}-{\;}and{\;}ADP/NADPH/Fe^{+3}-induced$ lipid peroxidation. Moreover, tectorigenin exhibited the highest protection of hydrogen peroxide damage on HepG2 and Vero cells among the three isoflavones, in the cytoprotective assay. It was suggested that the pattern of antioxidative and cytoprotective effect of isoflavones could be crucially by the aromatic substitution of oxygen-containing groups.

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Economic Power Dispatch with Valve Point Effects Using Bee Optimization Algorithm

  • Kumar, Rajesh;Sharma, Devendra;Kumar, Anupam
    • Journal of Electrical Engineering and Technology
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    • v.4 no.1
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    • pp.19-27
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    • 2009
  • This paper presents a newly developed optimization algorithm, the Bee Optimization Algorithm (BeeOA), to solve the economic power dispatch (EPD) problem. The authors have developed a derivative free and global optimization technique based on the working of the honey bee. The economic power dispatch problem is a nonlinear constrained optimization problem. Classical optimization techniques fail to provide a global solution and evolutionary algorithms provide only a good enough solution. The proposed approach has been examined and tested on two test systems with different objectives. A simple power dispatch problem is tested first on 6 generators and then the algorithm is demonstrated on 13 thermal unit systems whose incremental fuel cost function takes into account the value point loading effect. The results are promising and show the effectiveness and robustness of the proposed approach over recently reported methods.

An Analysis of the Gyungokgo's Ingredients and a Comparison Study on Anti-oxidation Effects According to the Kinds of Extract (경옥고(瓊玉膏)의 성분 분석 및 추출물별 항산화(抗酸化) 효능 비교)

  • Lee, So-Yeon;Shin, Yoo-Jeong;Park, Jong-Hyuk;Kim, Seung-Mo;Park, Chi-Sang
    • The Korea Journal of Herbology
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    • v.23 no.2
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    • pp.123-136
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    • 2008
  • Objectives : To estimate the value of the Gyungokgo as therapeutic agent preventing against aging with an analysis of the ingredients and the bio-activating effects by enzymologic methods. Methods : A quantitative analysis of general ingredients' of the Gyungokgo's extract was done first. The effects on electronic donating ability, SOD-like activity, nitric oxide inhibition, xanthine oxidase inhibition, whitening effect have been investigated in the physiological activity measurement of function experiment. Results : The contained hydrolyzed amino acid is Valine, Aspartic acid, Arginine, Isoleucine and the contained free amino acid is Arginine, Phenylalanine, Valine, Glycine. The derivative of free amino acid is Phosphoserine, Carnocine, ${\gammer}$-Aminoisobutyric acid. And the Gyungokgo contains 14 species of minerals, K>Na>Ca>Mg>Fe>Al>Mn. Then, to assure of the Gyungokgo's anti-oxidation, these following subjects -polyphenol, electronic donating ability, SOD-like activity, nitric oxide inhibition, xanthine oxidase inhibition, tyrosinase inhibation- are analyzed and show high activity especially the most in chloroform extracts, (every ingredients written by the order of high amount) Conclusions : The Gyungokgo contains many materials functioning as anti-oxidation, neurotransmitter, anti-fatigue and immune agent.

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An analysis of the Gongjindan's ingredients and its efficacy on anti-oxidation (공진단(拱辰丹)의 성분 분석 및 갱산화(坑酸化) 작용에 미치는 영향)

  • Choi, Kum-Hee;Park, Chi-Sang
    • The Korea Journal of Herbology
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    • v.22 no.2
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    • pp.51-63
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    • 2007
  • Objectives : For the congenital feeble, the Gongjindan is useful medicine. The experiment is to estimate the value of the Gongjindan as therapeutic agent preventing against aging with an analysis of the ingredients and the bio-activating effects by enzymologic methods. Methods : General ingredients' of the Gongjindan's extract were analyzed first and the quantitative analysis of a reducing sugar, a soluble protein, an amino acid and minerals was made. The Gongjindan, which is extracted, concentrated, and freeze drying with water, ethanol and chloroform, have got applied for the experiment. The effects on electronic donating ability, SOD-like activity, nitric oxide inhibition, xanthine oxidase inhibition, whitening effect have been investigated in the physiological activity measurement of function experiment. Results : The contained amino acid, in order of high amount, is Arginine, Alanine, Glutamic acid, Proline and the contained free amino acid is Glutamic acid, Leucine, Lysine, Phenylalanine. The derivative of free amino acid is ${\gamma}-Aminoisobutyric$ acid, Phosphoserine, Taurine. And the Gongjindan is containing 13 species of minerals in order of Ca>K>Na>Mg>Fe>AI>Mn. Then, to assure of the Gongjindan's capability of anti-oxidation, these following subjects-polyphenol, electronic donating ability, SOD-like activity, nitric oxide inhibition, xanthine oxidase inhibition, tyrosinase inhibition- are analyzed and show high activity especially the most in ethanol extracts. Conclusion : With this analysis of ingredients, the Gongjindan is containing many materials functioning as anti-oxidation, anti-aging, anti-fatigue, neurotransmitter and immune agent. Moreover, In every water, ethanol, chloroform extracts, the Gongjindan's capability of anti-oxidation is confirmed so that we can apply to patients' treatment clinically.

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