Search results for: RNA folding

Authors: Paola Lecca, Lorenzo Dematte, Corrado Priami

Abstract:

The present models and simulation algorithms of intracellular stochastic kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even for small prokaryotic cells. In this work a mathematical treatment of diffusion that can be incorporated in a stochastic algorithm simulating the dynamics of a reaction-diffusion system is presented. The movement of a molecule A from a region i to a region j of the space is represented as a first order reaction Ai k- ! Aj , where the rate constant k depends on the diffusion coefficient. The diffusion coefficients are modeled as function of the local concentration of the solutes, their intrinsic viscosities, their frictional coefficients and the temperature of the system. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the intrinsic reaction kinetics and diffusion dynamics. To demonstrate the method the simulation results of the reaction-diffusion system of chaperoneassisted protein folding in cytoplasm are shown.

Keywords: Reaction-diffusion systems, diffusion coefficient, stochastic simulation algorithm.

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Authors: Hermann Kuehnle

Abstract:

Applications of the Hausdorff space and its mappings into tangent spaces are outlined, including their fractal dimensions and self-similarities. The paper details this theory set up and further describes virtualizations and atomization of manufacturing processes. It demonstrates novel concurrency principles that will guide manufacturing processes and resources configurations. Moreover, varying levels of details may be produced by up folding and breaking down of newly introduced generic models. This choice of layered generic models for units and systems aspects along specific aspects allows research work in parallel to other disciplines with the same focus on all levels of detail. More credit and easier access are granted to outside disciplines for enriching manufacturing grounds. Specific mappings and the layers give hints for chances for interdisciplinary outcomes and may highlight more details for interoperability standards, as already worked on the international level. The new rules are described, which require additional properties concerning all involved entities for defining distributed decision cycles, again on the base of self-similarity. All properties are further detailed and assigned to a maturity scale, eventually displaying the smartness maturity of a total shopfloor or a factory. The paper contributes to the intensive ongoing discussion in the field of intelligent distributed manufacturing and promotes solid concepts for implementations of Cyber Physical Systems and the Internet of Things into manufacturing industry, like industry 4.0, as discussed in German-speaking countries.

Keywords: Autonomous unit, Networkability, Smart manufacturing unit, Virtualization.

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Authors: Md Omar Faruq Howlader, Tariq Pervez Sattar, Sandra Dudley

Abstract:

This paper describes the design process of a 200 MHz Ground Penetrating Radar (GPR) and a battery powered concrete vertical concrete surface climbing mobile robot. The key design feature is a miniaturized 200 MHz dipole antenna using additional radiating arms and procedure records a reduction of 40% in length compared to a conventional antenna. The antenna set is mounted in front of the robot using a servo mechanism for folding and unfolding purposes. The robot’s adhesion mechanism to climb the reinforced concrete wall is based on neodymium permanent magnets arranged in a unique combination to concentrate and maximize the magnetic flux to provide sufficient adhesion force for GPR installation. The experiments demonstrated the robot’s capability of climbing reinforced concrete wall carrying the attached prototype GPR system and perform floor-to-wall transition and vice versa. The developed GPR’s performance is validated by its capability of detecting and localizing an aluminium sheet and a reinforcement bar (rebar) of 12 mm diameter buried under a test rig built of wood to mimic the concrete structure environment. The present robotic GPR system proves the concept of feasibility of undertaking inspection procedure on large concrete structures in hazardous environments that may not be accessible to human inspectors.

Keywords: Climbing robot, dipole antenna, Ground Penetrating Radar (GPR), mobile robots, robotic GPR.

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Authors: U. Waqas, M. F. Ahmed, A. Mehmood, M. A. Rashid

Abstract:

In geophysical exploration surveys, the quality of acquired data holds significant importance before executing the data processing and interpretation phases. In this study, 2D seismic reflection survey data of Fort Abbas area, Cholistan Desert, Pakistan was taken as test case in order to assess its quality on statistical bases by using normalized root mean square error (NRMSE), Cronbach’s alpha test (α) and null hypothesis tests (t-test and F-test). The analysis challenged the quality of the acquired data and highlighted the significant errors in the acquired database. It is proven that the study area is plain, tectonically least affected and rich in oil and gas reserves. However, subsurface 3D modeling and contouring by using acquired database revealed high degrees of structural complexities and intense folding. The NRMSE had highest percentage of residuals between the estimated and predicted cases. The outcomes of hypothesis testing also proved the biasness and erraticness of the acquired database. Low estimated value of alpha (α) in Cronbach’s alpha test confirmed poor reliability of acquired database. A very low quality of acquired database needs excessive static correction or in some cases, reacquisition of data is also suggested which is most of the time not feasible on economic grounds. The outcomes of this study could be used to assess the quality of large databases and to further utilize as a guideline to establish database quality assessment models to make much more informed decisions in hydrocarbon exploration field.

Keywords: Data quality, null hypothesis, seismic lines, seismic reflection survey.

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Authors: N. Umasuthan, S. D. N. K. Bathige, W. S. Thulasitha, I. Whang, J. Lee

Abstract:

The MyD88 is an evolutionarily conserved host-expressed adaptor protein that is essential for proper TLR/ IL1R immune-response signaling. A previously identified complete cDNA (1626 bp) of OfMyD88 comprised an ORF of 867 bp encoding a protein of 288 amino acids (32.9 kDa). The gDNA (3761 bp) of OfMyD88 revealed a quinquepartite genome organization composed of 5 exons (with the sizes of 310, 132, 178, 92 and 155 bp) separated by 4 introns. All the introns displayed splice signals consistent with the consensus GT/AG rule. A bipartite domain structure with two domains namely death domain (24-103) coded by 1^st exon, and TIR domain (151-288) coded by last 3 exons were identified through in silico analysis. Moreover, homology modeling of these two domains revealed a similar quaternary folding nature between human and rock bream homologs. A comprehensive comparison of vertebrate MyD88 genes showed that they possess a 5-exonic structure.In this structure, the last three exons were strongly conserved, and this suggests that a rigid structure has been maintained during vertebrate evolution.A cluster of TATA box-like sequences were found 0.25 kb upstream of cDNA starting position. In addition, putative 5'-flanking region of OfMyD88 was predicted to have TFBS implicated with TLR signaling, including copies of NFkB1, APRF/ STAT3, Sp1, IRF1 and 2 and Stat1/2. Using qPCR technique, a ubiquitous mRNA expression was detected in liver and blood. Furthermore, a significantly up-regulated transcriptional expression of OfMyD88 was detected in head kidney (12-24 h; >2-fold), spleen (6 h; 1.5-fold), liver (3 h; 1.9-fold) and intestine (24 h; ~2-fold) post-Fla challenge. These data suggest a crucial role for MyD88 in antibacterial immunity of teleosts.

Keywords: MyD88, Innate immunity, Flagellin, Genomic analysis.

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Authors: Sumalee B., Sirinapa L., Jenjira T., Jr., Setasak S.

Abstract:

The paper describes ergonomics problems trend of student at B5101 classroom building 2, Suranaree University of Technology. The objective to survey ergonomics problems and effect from use chairs for sitting in class room. The result from survey method 100 student they use lecture chair for sitting in classroom more than 2 hours/ day by RULA[1]. and Body discomfort survey[2]. The result from Body discomfort survey contribute fatigue problems at neck, lower back, upper back and right shoulder 2.93, 2.91, 2.33, 1.75 respectively and result from RULA contribute fatigue problems at neck, body and right upper arm 4.00, 3.75 and 3.00 respectively are consistent. After that the researcher provide improvement plan for design new chair support student fatigue reduction by prepare data of sample anthropometry and design ergonomics chair prototype 3 unit. Then sample 100 student trial to use new chair and evaluate again by RULA, Body discomfort and satisfaction. The result from trial new chair after improvement by RULA present fatigue reduction average of head and neck from 4.00 to 2.25 , body and trunk from 3.75 to 2.00 and arm force from 1.00 to 0.25 respectively. The result from trial new chair after improvement by Body discomfort present fatigue reduction average of lower back from 2.91 to 0.87, neck from 2.93 to 1.24, upper back 2.33 to 0.84 and right upper arm from 1.75 to 0.74. That statistical of RULA and Body discomfort survey present fatigue reduction after improvement significance with a confidence level of 95% (p-value 0.05). When analyzing the relationship of fatigue as part of the body by Chi – square test during RULA and Body discomfort that before and after improvements were consistent with the significant level of confidence 95% (p-value 0.05) . Moreover the students satisfaction result from trial with a new chair for 30 minutes [3]. 72 percent very satisfied of the folding of the secondary writing simple 66% the width of the writing plate, 64% the suitability of the writing plate, 62% of soft seat cushion and 61% easy to seat the chair.

Keywords: Ergonomics, Work station design, ErgonomicsChair, Student, Fatigue

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Authors: Paola Lecca, Lorenzo Dematte

Abstract:

Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.

Keywords: Reaction-diffusion systems, Fick's law, stochastic simulation algorithm.

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