• 제목/요약/키워드: Molecular modelling

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Understanding the connection between O32 and LyC escape based on numerical simulations

  • Choe, Suhyeon;Kimm, Taysun;Katz, Harley;Yoo, Teahwa
    • The Bulletin of The Korean Astronomical Society
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    • v.46 no.1
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    • pp.56.1-56.1
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    • 2021
  • Identifying the main source of reionization is one of the essential astrophysical problems that remain to be solved. But there are difficulties in directly measuring the Lyman continuum (LyC) escape fraction (fesc) from high-z galaxies, and other indirect methods have been suggested to identify potential LyC leakers. The O32 ratio ([OIII] λ5007 / [OII] λ3727) is one of those examples, which appear to positively correlate with fesc according to some observations and photoionization modelling of HII regions. However, recent studies fail to find such a correlation. Here we exploit a set of radiation-hydrodynamic simulations of giant molecular clouds to understand the physical connection between O32 and fesc. We post-process our simulations with the photo-ionization code Cloudy, and discuss the results obtained from the runs with different metallicities and input SEDs.

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Optimization and Elucidation of Interactions between Ammonium, Nitrate and Phosphate in Centella asiatica Cell Culture Using Response Surface Methodology

  • Omar Rozita;Abdullah M. A.;Hasan M. A.;Marziah M.;Mazlina M.K.Siti
    • Biotechnology and Bioprocess Engineering:BBE
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    • v.10 no.3
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    • pp.192-197
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    • 2005
  • The effects of macronutrients $(NO_3^-,\; NH_4^+\;and\;PO_4^{3-})$ on cell growth and triterpenoids production in Centella asiatica cell suspension cultures were analyzed using the Box­Behnken response surface model experimental design. In screening and optimization experiments, $PO_4^{3-}$ as a single factor significantly influenced cell growth where increasing the phosphate level from 0.1 to 2.4 or 2.6 mM, elevated cell growth from 3.9 to $14\~16g/L$. The optimum values predicted from the response surface model are 5.05mM $NH_4^+$, 15.0mM $NO_3^-$ and 2.6mM $PO_4^{3-}$, yielding 16.0g/L cell dry weight with $99\%$ fitness to the experimental data. While the $NH_4^+-NO_3^-$ interaction influenced cell growth positively in the optimization experiment, $NH_4^+$ and $NO_3^-$ as single factors; and interactions of $NO_3^--PO_4^{3-},\;NH_4^+-PO_4^{3-}$ and $NH_4^+-NO_3^-$ were all negative in the screening experiment. Cell growth and the final pH level were positively affected by $PO_4^{3-}$, but negatively affected by $NH_4^+\;and\;NH_4^+-PO_4^{3-}$ interactions. The different effects of factors and their interactions on cell growth and final pH are influenced by a broad or narrow range of macronutrient concentrations. The productions of triterpenoids however were lower than 4mg/g cell dry weight.

Review on the Computer Simulation Tools for Polymeric Membrane Researches (고분자 분리막 연구를 위한 전산모사 도구 소개)

  • Choi, Chan Hee;Park, Chi Hoon
    • Membrane Journal
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    • v.30 no.4
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    • pp.242-251
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    • 2020
  • Computer simulation tools mainly used for polymer materials and polymeric membranes are divided into various fields depending on the size of the object to be simulated and the time to be simulated. The computer simulations introduced in this review are classified into three categories: Quantum mechanics (QM), molecular dynamics (MD), and mesoscale modeling, which are mainly used in computational material chemistry. The computer simulation used in polymer research has different research target for each kind of computational simulation. Quantum mechanics deals with microscopic phenomena such as molecules, atoms, and electrons to study small-sized phenomena, molecular dynamics calculates the movement of atoms and molecules calculated by Newton's equation of motion when a potential or force of is given, and mesoscale simulation is a study to determine macroscopically by reducing the computation time with large molecules by forming beads by grouping atoms together. In this review, various computer simulation programs mainly used for polymers and polymeric membranes divided into the three types classified above will be introduced according to each feature and field of use.

Optimization-based method for structural damage detection with consideration of uncertainties- a comparative study

  • Ghiasi, Ramin;Ghasemi, Mohammad Reza
    • Smart Structures and Systems
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    • v.22 no.5
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    • pp.561-574
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    • 2018
  • In this paper, for efficiently reducing the computational cost of the model updating during the optimization process of damage detection, the structural response is evaluated using properly trained surrogate model. Furthermore, in practice uncertainties in the FE model parameters and modelling errors are inevitable. Hence, an efficient approach based on Monte Carlo simulation is proposed to take into account the effect of uncertainties in developing a surrogate model. The probability of damage existence (PDE) is calculated based on the probability density function of the existence of undamaged and damaged states. The current work builds a framework for Probability Based Damage Detection (PBDD) of structures based on the best combination of metaheuristic optimization algorithm and surrogate models. To reach this goal, three popular metamodeling techniques including Cascade Feed Forward Neural Network (CFNN), Least Square Support Vector Machines (LS-SVMs) and Kriging are constructed, trained and tested in order to inspect features and faults of each algorithm. Furthermore, three wellknown optimization algorithms including Ideal Gas Molecular Movement (IGMM), Particle Swarm Optimization (PSO) and Bat Algorithm (BA) are utilized and the comparative results are presented accordingly. Furthermore, efficient schemes are implemented on these algorithms to improve their performance in handling problems with a large number of variables. By considering various indices for measuring the accuracy and computational time of PBDD process, the results indicate that combination of LS-SVM surrogate model by IGMM optimization algorithm have better performance in predicting the of damage compared with other methods.

Next-generation gene targeting in the mouse for functional genomics

  • Gondo, Yoichi;Fukumura, Ryutaro;Murata, Takuya;Makino, Shigeru
    • BMB Reports
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    • v.42 no.6
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    • pp.315-323
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    • 2009
  • In order to elucidate ultimate biological function of the genome, the model animal system carrying mutations is indispensable. Recently, large-scale mutagenesis projects have been launched in various species. Especially, the mouse is considered to be an ideal model to human because it is a mammalian species accompanied with well-established genetic as well as embryonic technologies. In 1990', large-scale mouse mutagenesis projects firstly initiated with a potent chemical mutagen, N-ethyl-N-nitrosourea (ENU) by the phenotype-driven approach or forward genetics. The knockout mouse mutagenesis projects with trapping/conditional mutagenesis have then followed as Phase II since 2006 by the gene-driven approach or reverse genetics. Recently, the next-generation gene targeting system has also become available to the research community, which allows us to establish and analyze mutant mice carrying an allelic series of base substitutions in target genes as another reverse genetics. Overall trends in the large-scale mouse mutagenesis will be reviewed in this article particularly focusing on the new advancement of the next-generation gene targeting system. The drastic expansion of the mutant mouse resources altogether will enhance the systematic understanding of the life. The construction of the mutant mouse resources developed by the forward and reverse genetic mutagenesis is just the beginning of the annotation of mammalian genome. They provide basic infrastructure to understand the molecular mechanism of the gene and genome and will contribute to not only basic researches but also applied sciences such as human disease modelling, genomic medicine and personalized medicine.

Preparation and Evaluation of Inclusion Complex of Muscone with ${\beta}-Cyclodextrin$ (무스콘의 ${\beta}$-시클로덱스트린 포접 복합체의 제조 및 평가)

  • Kwack, Eun-Sun;Cho, In-Sook;Lee, Gye-Won;Jee, Ung-Kil;Park, Dae-Kyu
    • Journal of Pharmaceutical Investigation
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    • v.27 no.4
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    • pp.265-269
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    • 1997
  • An inclusion complex of muscone with ${\beta}-cyclodextrin$ (CD), as a solid form of muscone, was prepared to increase the solubility of muscone. The molar ratio of muscone to ${\beta}-CD$ in complex was in the range of $1:1{\sim}1:5$ when prepared by freeze-drying method. The interaction of muscone with ${\beta}-CD$ in solid state was investigated by Infrared (IR) spectroscopy and differential scanning calorimetry (DSC). IR and DSC studies between $muscone-{\beta}-CD$ inclusion complex and physical mixture showed that $muscone-{\beta}-CD$ inclusion complex was prepared stably. From the amount of muscone incorporated in the inclusion complex, it was found that the molar ratio of muscone : ${\beta}-CD$ was 1:1. Relative spatial position of muscone and ${\beta}-CD$ was observed by Hyperchem molecular modelling program.

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A Study on Monte Carlo Simulation by beam scattering in Resin of New Austria Tunnel Method for Safety of Industrial Disaster (산업재해 방지를 위한 New Austria Tunnel Method 수지에서 빔산란에 의한 Monte Carlo 시뮬레이션에 관한 연구)

  • Nam, Sang-Sung;Lee, Joo-Youb
    • Journal of the Korean Applied Science and Technology
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    • v.30 no.3
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    • pp.444-450
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    • 2013
  • The influences of scatterer and absorber in turbid material by light scattering on silica fume of additive were interpreted for the scattered intensity and wavelength. The molecular properties have been studied by Monte Carlo simulation in resin of New Austria Tunnel Method. It has been found that the effects of optical properties in scattering media could be investigated by the optical parameters(${\mu}_s$, ${\mu}_a$,${\mu}_t$). Monte Carlo Simulation method for modelling of light transport in the civil engineering and construction field was applied. The results using a phantom were discussed that the distance from source to detector is closer, and scattering intensity is stronger with those obtained through Monte Carlo Simulation. It may also aid in designing the best model for coatings and corrosion for the durability of metal constructions.

NEUTRON SCATTERING INVESTIGATIONS OF PROTON DYNAMICS OF WATER AND HYDROXYL SPECIES IN CONFINED GEOMETRIES

  • Chen, S.H.;Loong, C.K.
    • Nuclear Engineering and Technology
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    • v.38 no.3
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    • pp.201-210
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    • 2006
  • This article presents a brief overview of an important area of neutron scattering: the general principles and techniques of elastic, quasielastic and inelastic scattering from a system composed predominately of incoherent scatterers. The methodology is then applied to the study of water, specifically when it is confined in nanometer-scale environments. The confined water exhibits uniquely anomalous properties in the supercooled state. It also nourishes biological functions, and supports essential chemical reactions in living systems. We focus on recent investigations of water encapsulated in nanoporous silica and carbon nanotubes, hydrated water in proteins and water or hydroxyl species incorporated in nanostructured minerals. Through these scientific examples, we demonstrate the advantages derived from the high sensitivity of incoherent neutron spectroscopy to hydrogen atom motions and hydrogen-bond dynamics, aided by rigorous data interpretation method using molecular dynamics simulations or theoretical modelling. This enables us to probe the inter-/intramolecular vibrations and relaxation/diffusion processes of water molecules in a complex environment.

Verification on Diffusion of Beam Propagation in Randomly Distributed Scattering Medium (무질서하게 분포된 산란매질에서 빔전파의 확산에 관한 검증)

  • Kim, Ki-Jun;Lee, Hoo-Seol
    • Journal of the Korean Applied Science and Technology
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    • v.24 no.4
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    • pp.354-361
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    • 2007
  • The distribution of light in a randomly scattering medium can represent problems found in many area. Particularly, in the clinical application of lasers for Photodynamic therapy(PDT) or in the fluorescence spectroscopy for biological tissue, turbidity plays a very important role. The influences of fluorophor, scatterer, and absorber in turbid material by light scattering were interpreted for the scattered fluorescence intensity and wavelength. The molecular properties have been studied by laser induced fluorescence spectroscopy in scattering medium as tissue. It has been found that the effects of optical properties in scattering media could be investigated by the optical $parameters({\mu}_s$, ${\mu}_a$ ,${\mu}t)$. Experimental and Monte Carlo simulation method for modelling light transport in tissue was applied. The experimental results using a randomly distributed scattering medium were discussed and compared with those obtained through Monte Carlo simulation. It'll be also important in designing the best model for oil chemistry, medicine and application of medical engineering.

Modelling the Hydrogen-Bonding Interactions in a Copolymer/Biodegradable Homopolymer Blend through Excess Functions

  • Garcia-Lopera, Rosa;Monzo, Isidro S.;Campos, Agustin;Abad, Concepcion
    • Macromolecular Research
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    • v.16 no.5
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    • pp.446-456
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    • 2008
  • A recent theoretical approach based on the coupling of both the Flory-Huggins (FH) and the Association Equilibria thermodynamic (AET) theories was modified and adapted to study the miscibility properties of a multi-component system formed by two polymers (a proton-donor and a proton-acceptor) and a proton-acceptor solvent, named copolymer(A)/solvent(B)/polymer(C). Compatibility between polymers was mainly attained by hydrogen-bonding between the hydroxyl group on the phenol unit of the poly(styrene-co-vinyl phenol) (PSVPh) and the carbonyl group of the biodegradable and environmentally friendly poly(3-hydroxybutyrate) (PHB). However, the self-association of PSVPh and specific interactions between the PSVPh and the H-acceptor group (an ether oxygen atom) of the epichlorohydrin (ECH) solvent were also established in a lower extension, which competed with the polymer-polymer association. All the binary specific interactions and their dependence with the system composition as well as with the copolymer content were evaluated and quantified by means of two excess functions of the Gibbs tree energy, ${\Delta}g_{AB}$ and ${\Delta}g_{AC}$. Experimental results from fluorescence spectroscopy were consistent with the theoretical simulations derived with the model, which could also be applied and extended to predict the miscibility in solution of any polymer blend with specific interactions.