• Title/Summary/Keyword: chain conformation

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Conformational changes of short, discrete Rouse chain during creep and recovery processes

  • Watanabe, Hiroshi;Inoue, Tadashi
    • Korea-Australia Rheology Journal
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    • v.16 no.2
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    • pp.91-99
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    • 2004
  • For the Rouse chain composed of infinite number of beads (continuous limit), conformational changes during the creep and creep recovery processes was recently analyzed to reveal the interplay among all Rouse eigenmodes under the constant stress condition (Watanabe and Inoue, Rheol. Acta, 2004). For completeness of the analysis of the Rouse model, this paper analyzes the conformational changes of the discrete Rouse chain having a finite number of beads (N = 3 and 4). The analysis demonstrates that the chain of finite N exhibits the affine deformation on imposition/removal of the stress and this deformation gives the instantaneous component of the recoverable compliance, $J_{R}$(0) = 1/(N-l)v $k_{B}$T with v and $k_{B}$ being the chain number density and Boltzmann constant, respectively. (This component vanishes for N\longrightarrow$\infty$.) For N = 2, it is known that the chain has only one internal eigenmode so that the affinely deformed conformation at the onset of the creep process does not change with time t and $J_{R}$(t) coincides with $J_{R}$(0) at any t (no transient increase of $J_{R}$(t)). However, for N$\geq$3, the chain has N-l eigenmodes (N-l$\geq$2), and this coincidence vanishes. For this case, the chain conformation changes with t to the non-affine conformation under steady flow, and this change is governed by the interplay of the Rouse eigenmodes (under the constant stress condition). This conformational change gives the non-instantaneous increase of $J_{R}$(t) with t, as also noted in the continuous limit (N\longrightarrow$\infty$).X>).TEX>).X>).

A Novel Simulation Architecture of Configurational-Bias Gibbs Ensemble Monte Carlo for the Conformation of Polyelectrolytes Partitioned in Confined Spaces

  • Chun, Myung-Suk
    • Macromolecular Research
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    • v.11 no.5
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    • pp.393-397
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    • 2003
  • By applying a configurational-bias Gibbs ensemble Monte Carlo algorithm, priority simulation results regarding the conformation of non-dilute polyelectrolytes in solvents are obtained. Solutions of freely-jointed chains are considered, and a new method termed strandwise configurational-bias sampling is developed so as to effectively overcome a difficulty on the transfer of polymer chains. The structure factors of polyelectrolytes in the bulk as well as in the confined space are estimated with variations of the polymer charge density.

Conformation of single polymer molecule in a slot coating flow

  • Lee, Jeong-Yong;Ryu, Bo-Kyung;Lee, Joo-Sung;Jung, Hyun-Wook;Hyun, Jae-Chun
    • Korea-Australia Rheology Journal
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    • v.20 no.2
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    • pp.89-94
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    • 2008
  • To satisfy good mechanical and optical properties of polymer-coated film products, it will be indispensable to elucidate the molecular orientation of polymer chains within coating liquids in coating flows. Using hybridized numerical method between computational fluid dynamics (CFD) and Brownian dynamics (BD) simulations can provide the useful information for the better quality control of coated films. Flexible polymer chains, e.g., ${\lambda}$-DNA molecules here, change their conformation according to the flow strength and the flow type. The molecular conformation within the coated film on the web or substrate is quite different, because the polymer chains experience the complicated flow strength and flow types in flow field. Especially in the slot coating flow, these chains are more extended by the extension-like flow field generated in the free surface curvature just beyond the downstream die region. Also, the polymer chain extension beneath the free surface can be affected by the die geometry, e.g., the coating gap, changing flow field.

Isolation and Characterization of $\beta$-Galactoside Specific Lectin from Korean Mistletoe (Viscum album var. coloratum with Lactose-BSA-Sepharose 4B and Changes of Lectin Conformation

  • Park, Won-Bong;Ju, Yeun-Jin;Han, Seon-Kyu
    • Archives of Pharmacal Research
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    • v.21 no.4
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    • pp.429-435
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    • 1998
  • Lectins and its A- and B-chains from Korean mistletoe (Viscum album var. coloratum) were isolated by affinity chromatography on the Sepharose 4B modified by lactose-BSA conjugate synthesized by reductive amination of ligand (lactose) to .epsilon.-amino groups of lysine residues of spacer (BSA) after reduction by $NaCNBH_3$. The lactose-BSA conjugate was coupled to Sepharose 4B activated by cyanogen bromide. The molecular weight determined by SDS-PAGE were a 31 kD of A-chain and a 35kD of B-chain. Amino acid analysis and N-terminal sequencing were performed. The effects of pH, temperature and guanidine chloride on the conformation of the lectin were investigated by measuring its intrinsic fluorescence and compared with its hemagglutinating activities. Blue shift was detected on the acidic pH and there was a close relationship between activities and conformation of the lectin. Under denaturing conditions, the tryptophan emission profile of lectin showed typical denaturaiional red shift which also correspond to the conformations and activity of lectin.

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An Algorithm for Computing Valid Side Chain Conformations for Finding Transformed Channels in a Protein Molecule (단백질 분자에서 변형된 채널 발견을 위한 유효 사이드 체인 배치 알고리즘)

  • Choi, Jihoon;Kim, Byungjoo;Kim, Ku-Jin
    • KIPS Transactions on Computer and Communication Systems
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    • v.4 no.1
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    • pp.1-4
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    • 2015
  • This paper presents an algorithm for finding valid side chain conformations of amino acids, when given channel is transformed. The suggested algorithm implements a protein molecule with flexible side chains based on the flexibility of amino acids, and extracts adjacent amino acids that affect the formation of the channel. We detect the collision between adjacent amino acids and neighbors, in order to exclude invalid side chain conformations. Then, we construct the rotation angle combination tree to choose valid side chain conformations.

A Design of ATP Model Related eCRM Using LTV (LTV를 이용한 eCRM을 연계한 ATP 모델구현에 관한 연구)

  • 박재현;양광모;강경식
    • Journal of Korean Society of Industrial and Systems Engineering
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    • v.25 no.4
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    • pp.54-60
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    • 2002
  • In the Supply chain, The ATP(Available to Promise) function doesn't only give customers to conformation of delivery. It can be used by the core function with ATP rule that can reconcile supplies and demands on the supply chain. Therefore We can be acquire the conformation about on the due date of supplier by using the ATP function of management about real and concurrent access on the supply chain, also decide the affect about product availability due to forecasting or customer's orders through the ATP. In this paper, It consolidates the necessity on a ATP and analyzes data which is concerned of ATP. tinder the these environments, defines the ATP nile that can improve the customer value and data flow related the eCRM and builds on a algorithm.

Investigations on the Chain Conformation of Weakly Charged Polyelectrolyte in Solvents by Using Efficient Hybrid Molecular Simulations

  • Chun, Myung-Suk;Lee, Hyun-Su
    • Macromolecular Research
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    • v.10 no.6
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    • pp.297-303
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    • 2002
  • We have investigated the microstructural properties of a weakly charged polyelectrolyte modeled with both Hookean spring and Debye-Huckel potential, by employing a novel hybrid scheme of molecular dynamics (MD) and Monte Carlo (MC) simulations. Although the off-lattice pivot step facilitates the earlier computations stage, it gives rise to oscillations and hinders the stable equilibrium state. In order to overcome this problem, we adopt the MC off-lattice pivot step in early stage only, and then switch the computation to a pure MD step. The result shows that the computational speed-up compared to the previous method is entirely above 10 to 50, without loss of the accuracy. We examined the conformations of polyelectrolyte in solvents in terms of the end-to-end distance, radius of gyration, and structure factor with variations of the screening effects of solvent and the monomer charges. The emphasis can favorably be given on the elongation behavior of a polyelectrolyte chain, with observing the simultaneous snapshots.