• Title/Summary/Keyword: Molecular Modeling

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Mechanical Properties of Hydrated Cement Paste: Development of Structure-property Relationships

  • Ghebrab, Tewodros T.;Soroushian, Parviz
    • International Journal of Concrete Structures and Materials
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    • 제4권1호
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    • pp.37-43
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    • 2010
  • Theoretical models based on modern interpretations of the morphology and interactions of cement hydration products are developed for prediction of the mechanical properties of hydrated cement paste (hcp). The models are based on the emerging nanostructural vision of calcium silicate hydrate (C-S-H) morphology, and account for the intermolecular interactions between nano-scale calcium C-S-H particles. The models also incorporate the effects of capillary porosity and microcracking within hydrated cement paste. The intrinsic modulus of elasticity and tensile strength of hydrated cement paste are determined based on intermolecular interactions between C-S-H nano-particles. Modeling of fracture toughness indicates that frictional pull-out of the micro-scale calcium hydroxide (CH) platelets makes major contributions to the fracture energy of hcp. A tensile strength model was developed for hcp based on the linear elastic fracture mechanics theories. The predicted theoretical models are in reasonable agreements with empirical models developed based on the experimental performance of hcp.

피발산비닐과 아세트산비닐의 공중합에 관한 이론적 고찰 (Theoretical Investigations on the Copolymerization of Vinyl Pivalate and Vinyl Acetate)

  • Ghim, Han-Do;Kim, Jae-Pil;Lyo, Won-Seok
    • 한국섬유공학회:학술대회논문집
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    • 한국섬유공학회 2002년도 봄 학술발표회 논문집
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    • pp.29-32
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    • 2002
  • Thermodynamics of copolymerization is one of the fundamental elements for studying the effects of copolymerization parameters on the copolymer characteristics. Up until now, it has not been easy work not because there are not effective models but because the known thermodynamic values are limited to some copolymer pairs. Recently, owing to the development of molecular modeling methods, some thermodynamic parameters can be calculated and estimated on computer. (omitted)

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Structure-based Functional Discovery of Proteins: Structural Proteomics

  • Jung, Jin-Won;Lee, Weon-Tae
    • BMB Reports
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    • 제37권1호
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    • pp.28-34
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    • 2004
  • The discovery of biochemical and cellular functions of unannotated gene products begins with a database search of proteins with structure/sequence homologues based on known genes. Very recently, a number of frontier groups in structural biology proposed a new paradigm to predict biological functions of an unknown protein on the basis of its three-dimensional structure on a genomic scale. Structural proteomics (genomics), a research area for structure-based functional discovery, aims to complete the protein-folding universe of all gene products in a cell. It would lead us to a complete understanding of a living organism from protein structure. Two major complementary experimental techniques, X-ray crystallography and NMR spectroscopy, combined with recently developed high throughput methods have played a central role in structural proteomics research; however, an integration of these methodologies together with comparative modeling and electron microscopy would speed up the goal for completing a full dictionary of protein folding space in the near future.

Kinetic Study of the Lipase-Catalyzed Interesterification of Triolein and Stearic Acid in Nonpolar Media

  • Chi, Young-Min
    • BMB Reports
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    • 제30권1호
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    • pp.7-12
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    • 1997
  • The kinetics of the interesterification of triolein and stearic acid catalyzed by immobilized Rhizopus delemar lipase were studied in a batch operation. In order to clarify the mechanisms of this reaction, three models are discussed under various conditions in terms of the ratio of triolein and stearic acid. The rate constants involved in the proposed model were determined by combining the numerical Gauss-elemination method, and the trial-and-error method so as to fit the calculated results with the experimental data. The accuracy of the obtained rate constants was confirmed after they were substituted for simultaneous differential equations and the equations simulated using an adaptive step-size Runge-Kutta method. Finally, the model which agrees with the calculated results and the experimental data was selected.

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Structure studies of Pulmonary Surfactant Protein B(SP-B(3,4)) by NMR Spectroscopy and Molecular Modeling

  • Kim, Yangmee;Dongha Baek;Kang, Joo-Hyun;Shin, Song-Yub;Hahm, Kyung-Soo
    • 한국자기공명학회논문지
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    • 제5권1호
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    • pp.37-45
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    • 2001
  • Synthetic pulmonary surfactants consisting of a mixture of phospholipids with synthetic peptides based on human surfactant-associated protein SP-B were prepared. These surfactants were analyzed f3r their secondary structures by circular dichroism (CD) spectroscopy and NMR spectroscopy. Two synthetic peptides (SP-B(3), SP-B(4)) combined with the phospholipid mixture displayed significant surfactant properties. The CD spectra showed that the u-helical propensities of the peptides in DPC micelles. In the NMR spectroscopy, the tertiary structures of SP-B(3) show that it has $\alpha$-helical structure from Gln5 to Arg13 in DPC micelle and SP-B(4) show that they have $\alpha$-helical structure from Gln5 to Leu12 in DPC micelle. Based on these structures, truncated peptides originated from SP-B protein, can be designed as effective synthetic surfactants for clinical use.

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Pseudoreceptor: Concept and an Overview

  • Kothandan, Gugan;Madhavan, Thirumurthy;Gadhe, Changdev G.;Cho, Seung Joo
    • 통합자연과학논문집
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    • 제3권3호
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    • pp.162-167
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    • 2010
  • A pseudoreceptor combines structure-based and ligand-based techniques to represent a unifying concept for both receptor mapping and ligand matching. In this molecular modeling approach, there are opportunities to construct the pseudoreceptor models using a set of small molecules. To build a reliable pseudoreceptor model, we need a set of ligand molecules with known affinity (biological activity) to generate 3D bioactive conformation for each of these ligand molecules. Several software packages are available to generate a pseudoreceptor model and this can provide an entry point for structure based drug discovery in cases where receptor structure information is not available. In this review, we presented the concept of pseudoreceptor, as well as discussed about various software packages available to generate a pseudoreceptor model.

Styren과 acrylonitrile의 과상 공중합을 위한 회분식 반응기의 모델링 및 모사 (Modeling and simulation of a batch reactor for bulk copolymerization of styrene and acrylonitirle)

  • 유기윤;황우현;백종은;이현구
    • 제어로봇시스템학회:학술대회논문집
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    • 제어로봇시스템학회 1994년도 Proceedings of the Korea Automatic Control Conference, 9th (KACC) ; Taejeon, Korea; 17-20 Oct. 1994
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    • pp.207-212
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    • 1994
  • A mathematical model is developed for a batch reactor in which the free radical bulk copolymerization of styrene and acrylonitrile takes place. In this model, we introduce the free volume theory to quantify the diffusion controlled termination and propagation reactions, and develop a model for the chain length dependent termination reaction in the context of the pseudo kinetic rate constant method(PKRCM). The simulation results from this model are found to be in good agreement with experimental data under different copolymerization conditions. The present model can predict both the copolymer composition and the number and weight average molecular weights. These kinetic approaches provide greater insight into the performance of the batch reactor used for the free radical bulk copolymerization of styrene and acrylonitirle.

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Applications of Tandem Mass Spectrometry in the Structure Determination of Permethylated Sialic Acid-containing Oligosaccharides

  • Yoo, Eun-Sun;Yoon, In-Mo
    • Bulletin of the Korean Chemical Society
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    • 제26권9호
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    • pp.1347-1353
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    • 2005
  • Sets of sialic acid-containing trisaccharides having different internal and terminal linkages have been synthesized to develop a sensitive method for analysis of the reducing terminal linkage positions. The trisaccharides, sialyl($\alpha$ 2-3)Gal($\beta$ 1-3)GalNAc and sialyl($\alpha$ 2-3)Gal($\beta$ 1-X)GlcNAc where X=3, 4 and 6, were synthesized and examined using electrospray ionization (ESI)-collision induced dissociation (CID) tandem mass spectrometry (MS/MS). The compounds chosen for this study are related to terminal groups likely to be found on polylactosamine-like glycoproteins and glycolipids which occur on the surface of mammalian cells. The purpose of this study is to develop tandem mass spectrometral methods to determine detailed carbohydrate structures on permethylated or partially methylated oligosaccharides for future applications on biologically active glycoconjugates and to exploit a faster method of synthesizing a series of structural isomeric oligosaccharides to be used for further mass spectrometry and instrumental analysis.

Solubility of Hydrogen Sulfide in Aqueous Solutions of Methyldiethanolamine and diethanolamine

  • Park, Moon-Ki;Moon, Yung-Soo;Kim, Jung-Ho
    • Environmental Sciences Bulletin of The Korean Environmental Sciences Society
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    • 제3권2호
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    • pp.131-136
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    • 1999
  • The solubility of H2S is an important parameter for modeling H2S absorption. Since the direct measurement of H2S solubility in aqueous amine solutions is impossible, this work initially attempted to develop an H2S analogy method, however, this was unsuccessful. Consequently, H2S solubilities were measured in aqueous amines which were completely protonated with HCI over a temperature range of 25-60℃. The solvents investigated in this work included 0-50% aqueous solutions of methyldiethanolamine and diethanolamine. Thereafter, a new empirical correlation was developed that can predict Henry's constant for H2S using only the solubility of H2S in water and t도 molecular weight of the aqueous solvent.

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Molecular Modeling for the Crystal Structure of Stereoregular Poly(vinyl Alcohol) (I) - New Crystal Dimension of Syndiotactic Poly(vinyl Alcohol) -

  • Lyoo, Won-Seok;Sergei Chvalun;John Blackwell
    • 한국섬유공학회:학술대회논문집
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    • 한국섬유공학회 1998년도 봄 학술발표회 논문집
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    • pp.135-139
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    • 1998
  • Poly(vinyl acetate) (PVAc) from which atactic poly(vinyl alcohol) (PVA) is derived, is always noncrystalline. This was attributed to the irregular steric arrangement of the acetyl groups in PVAc. However, the X-ray diffraction patterns of atactic PVA, a derivative of PVAc, were found to show distinct crystallinity, and to give an identity period of 2,52 ${\AA}$ along the fiber axis, despite the expectation of an irregular arrangement of the hydroxyl groups in atactic PVA, in the same manner as that of the acetyl groups in PVAc.(omitted)

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