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  • Open Access

    ABSTRACT

    A Lattice Boltzmann Method for modeling the oscillation of Min proteins: Oscillation pattern due to the initial copy of MinD and MinE

    Somchai Sriyab1, Wannapong Triampo2

    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 51-52, 2009, DOI:10.3970/icces.2009.013.051

    Abstract Understanding of Bacteria cell division is essential for an understanding of microorganism as well as the origin of the life. Particularly, in cell division process of \emph {E. coli}, Min proteins (MinD and MinE) play crucial roles to regulate the dividing dynamics physically via their oscillatory dynamics from pole to pole. In this work, we have developed a numerical scheme based on the mesoscopic Lattice Boltzmann Method (LBM) to simulate the coarse-grained coupled reaction-diffusion equations model used to describe the MinD/MinE interaction in two dimensions. Biologically, we have focused on investigating how the protein copies affect the oscillation patterns as… More >

  • Open Access

    ABSTRACT

    Effects of boundary conditions on Min-Protein Oscillation in \emph {E. coli} using mesoscopic lattice Boltzmann method

    Waipot Ngamsaad, Wannapong Triampo1

    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.2, pp. 49-50, 2009, DOI:10.3970/icces.2009.013.049

    Abstract The Min-proteins oscillation in \emph {E. coli} has an essential role in controlling the accuracy placement of cell-division septum at the middle cell zone of the bacteria. This biochemical process has been successfully described by a set of reaction-diffusion equation at the macroscopic level [1]. Recently, a mesoscopic modeling by the lattice Boltzmann method (LBM) has been proposed to simulate the Min-proteins oscillation [2]. However, as pointed out by Zhang et al., the standard boundary conditions are not accuracy for a class of dispersion transport modeled by LBM [3]. In this present work, we investigated the boundary effects in LBM… More >

  • Open Access

    ABSTRACT

    Mechanical insights into the physiological functions of intercellular adhesion proteins

    S.R.K Vedula1, T.S. Lim2, W. Hunziker3, C.T. Lim1

    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.1, pp. 29-30, 2009, DOI:10.3970/icces.2009.013.029

    Abstract The structural integrity as well as the regulation of paracellular diffusion of solutes across epithelial monolayers is critically regulated by the intercellular adhesion complex. The intercellular adhesion complex consists of a variety of proteins that perform different physiological functions. While proteins localizing at adherens junctions (nectins and e-cadherins) are important for initiating and stabilizing cell adhesion, proteins localizing at the tight junctions (occludin, claudins and junctional adhesion molecules) act as gates to regulate the diffusion of solutes across the epithelial monolayer. Despite significant advancement in the understanding of the biological roles of these cell adhesion proteins in regulating various cellular… More >

  • Open Access

    ABSTRACT

    DNA Cracks at the Region of Protein Binding Under the Action of Stretch

    Qingjia Chi*, Xinge Geng

    The International Conference on Computational & Experimental Engineering and Sciences, Vol.22, No.1, pp. 118-118, 2019, DOI:10.32604/icces.2019.05168

    Abstract The binding of DNA to protein in the cellular nucleus is a common phenomenon. DNA molecules will soften at the binding region when they adhere to proteins. Softening will affect the mechanical properties significantly. However, the mechanism underlying the mechanical softening remains to be explored. To understand the changes in the mechanical properties of DNA, the peridynamics technique can effectively capture the stress of the softened DNA under tensile forces. And later the results were verified by finite element computations. Utilizing the computations of perydynamics to reveal the stretch of the double-stranded DNA. The results demonstrated DNA was easy to… More >

  • Open Access

    ARTICLE

    ZnSe Nanoparticles Reinforced Biopolymeric Soy Protein Isolate Film

    Rakesh Kumar1,*, Reshma Praveen1, Shikha Rani1, K. Sharma2, K. P. Tiwary3,*, K. Dinesh Kumar4

    Journal of Renewable Materials, Vol.7, No.8, pp. 749-761, 2019, DOI:10.32604/jrm.2019.06286

    Abstract ZnSe nanoparticles have been synthesized by microwave assisted method by using zinc chloride, selenium powder and ethylene diamine. The synthesized nanoparticles have been characterized structurally by FT-IR and XRD as well as morphological characterization was done by scanning electron microscope (SEM). The crystallite size after synthesis was obtained around 30 nm for pure ZnSe nanocrystallites. However, from SEM micrograph, agglomerated ZnSe nanoparticles of irregular shapes were observed. The as-synthesized ZnSe nanoparticles at different contents (1 to 5% w/w w.r.t SPI) were incorporated into soy protein isolate (SPI) to produce reinforced SPI films by solution casting method. The ZnSe nanoparticles incorporated… More >

  • Open Access

    ARTICLE

    Soy Protein Isolate Film by Incorporating Mandelic Acid as Well as Through Fermentation Mediated by Bacillus Subtilis

    Rakesh Kumar1,*, Priya Rani1, K. Dinesh Kumar2

    Journal of Renewable Materials, Vol.7, No.2, pp. 103-115, 2019, DOI:10.32604/jrm.2019.00027

    Abstract Soy protein isolate (SPI) biopolymeric films were prepared by adding different contents of mandelic acid (1 to 5% wrt SPI) to glycerol plasticized SPI by solution casting method. Also, SPI was fermented by Bacillus subtilis to get fermented SPI films by solution casting. Molecular mass determination of mandelic acid incorporated and fermented SPI films was carried out by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Mandelic acid incorporated and fermented SPI films were characterized by Fourier-transform infrared spectroscopy (FT-IR), dynamic mechanical analysis (DMA), tensile strength, water uptake and optical transmittance studies. Results indicated that incorporation of mandelic acid in SPI resulted… More >

  • Open Access

    ABSTRACT

    Multi-Component Modal Analysis of Protein Structure

    G. Yoon1, K. Bong2, J. Kim3, I.H. Ahn4, K. Eom5, S. Na6

    The International Conference on Computational & Experimental Engineering and Sciences, Vol.2, No.2, pp. 53-60, 2007, DOI:10.3970/icces.2007.002.053

    Abstract This paper presents multi-component mode methodology applicable to biomolecular structures for understanding the dynamics of proteins. Even though the conventional normal mode analysis has been contributed for analyzing the dynamics and thermal fluctuations of proteins, it frequently encounters with the computational prohibition for large proteins due to memory requirement. To overcome the conventional computational limitations, the drawback motivates one to develop various model reduction methods, which reduces the degrees of freedom of the full model so as to decrease the computational expense, while the computational accuracy is maintained. Our results demonstrate that the multi-component modal analysis applied to the biomolecular… More >

  • Open Access

    ARTICLE

    Protein Secondary Structure Prediction with Dynamic Self-Adaptation Combination Strategy Based on Entropy

    Yuehan Du1,2, Ruoyu Zhang1, Xu Zhang1, Antai Ouyang3, Xiaodong Zhang4, Jinyong Cheng1, Wenpeng Lu1,*

    Journal of Quantum Computing, Vol.1, No.1, pp. 21-28, 2019, DOI:10.32604/jqc.2019.06063

    Abstract The algorithm based on combination learning usually is superior to a single classification algorithm on the task of protein secondary structure prediction. However, the assignment of the weight of the base classifier usually lacks decision-making evidence. In this paper, we propose a protein secondary structure prediction method with dynamic self-adaptation combination strategy based on entropy, where the weights are assigned according to the entropy of posterior probabilities outputted by base classifiers. The higher entropy value means a lower weight for the base classifier. The final structure prediction is decided by the weighted combination of posterior probabilities. Extensive experiments on CB513… More >

  • Open Access

    ARTICLE

    New Closed- and Open-Cell, Aldehyde-Free Protein Foams

    María Cecilia Basso1*, Antonio Pizzi1,2

    Journal of Renewable Materials, Vol.5, No.1, pp. 48-53, 2017, DOI:10.7569/JRM.2016.634124

    Abstract New aldehyde-free and isocyanate-free biofoams have been obtained by reacting albumin chicken egg white and dimethyl carbonate (DMC). The optimized formulations yielded lightweight foams whose densities were evaluated as 0.016–0.16 g/cm3. Mechanical resistance was 0.023–0.34 MPa and residual pH nearly neutral. The new foams presented up to 57% of closed cells as measured by helium pycnometry and good thermal insulation. These new natural foams are environmentally friendly materials and show very promising properties. More >

  • Open Access

    ARTICLE

    Chitin Preparation by Demineralizing Deproteinized Lobster Shells with CO2 and a Cationite

    Miguel Ángel Ramírez1, Patricia González2, Juan Reinerio Fagundo2, Margaret Suarez3, Clara Melian3, Tania Rodríguez1, Carlos Peniche4*

    Journal of Renewable Materials, Vol.5, No.1, pp. 30-37, 2017, DOI:10.7569/JRM.2016.634121

    Abstract The inorganic components of crustacean shells are usually removed using HCl solutions. This provokes undesirable modifications in the extracted chitin. In the present procedure, deproteinized lobster shells were demineralized with CO2 and a cationic resin (cationite). The resulting chitin (CHI-CO2) is compared in terms of degree of acetylation (DA), crystallinity index (CrI) and thermal stability with chitins obtained by demineralization procedures with HCl (CHI-HCl) and ethylenediaminetetraacetic acid (CHI-EDTA). The ash content of chitins demineralized with CO2 was similar to that of chitins prepared using HCl or EDTA. However, the resultant DA and CrI of CHI-HCl and CHI-EDTA were lower than… More >

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