Modeling and Experiment of Shuttling Speed Effects on the Oscillatory Thermal Cycler Chamber (OSTRYCH)

2010 ◽  
Author(s):  
Jyh Jian Chen ◽  
Yao Tsung Yang ◽  
Tse Yu Hsieh
Keyword(s):  
Boundary Conditions ◽  
Reaction Chamber ◽  
Operational Parameters ◽  
Thermal Cycles ◽  
Time Duration ◽  
Temperature Distributions ◽  
Pcr Products ◽  
Rectangular Chamber ◽  
Thermal Cycler ◽  
Moving Speed

Polymerase chain reaction (PCR) has emerged as a powerful tool in genetic analysis. The PCR products are closely linked with thermal cycles. Therefore, to reduce the reaction time and make temperature distribution uniform in the reaction chamber, a novel oscillatory thermal cycler (OSTRYCH) is designed. The sample is placed in a fixed chamber, and three constant isothermal zones are established and lined in the system. The sample is oscillated and contacted with three different isothermal zones to complete thermal cycles. This study presents the analyses of the operational parameters of the chamber. The commercial software CFD-ACE+™ is utilized to investigate the influences of various chamber materials, boundary conditions and moving speed of the chamber on the temperature distributions inside the chamber. The chamber moves at a specific speed and the boundary conditions with time variations are related to the moving speed. Whereas the chamber moves, the boundary is specified at the conditions of the convection or the uniform temperature. The user subroutines compiled by the FORTRAN language are used to make the numerical results realistically. The effects of various chamber materials, boundary conditions, moving speeds of the rectangular chamber on the temperature distributions are examined. Results show that regarding to the temperature profiles and the standard deviation of the temperature at the Y-cut cross section; the effects of various moving speeds of the chamber on the temperature distributions are negligible at the assigned time duration. The central temperatures of the chamber with various moving speeds are measured. The repeatability and stability of the OSTRYCH are examined. Finally, the experimental results and numerical simulations are compared.

The Effect of Thermal Contact Resistance on Heat Management in a Shuttling PCR System

2013 ◽  
Vol 284-287 ◽  
pp. 1941-1945
Author(s):  
Jyh Jian Chen ◽  
Wei Hua Chen ◽  
Yi Shiang Shie
Keyword(s):  
Pid Controller ◽  
Thermal Contact Resistance ◽  
Thermal Contact ◽  
Computer Code ◽  
Reaction Chamber ◽  
Operational Parameters ◽  
Heat Management ◽  
Dna Templates ◽  
Polymerase Chain ◽  
The Stability

A novel shuttling polymerase chain reaction (PCR) system is assembled to make temperature uniform in the reaction chamber. The chamber is oscillated by a servo motor and contacted with three different isothermal zones to complete several thermal cycles. The home-made computer code is utilized to investigate the influences of operational parameters on the temperature inside the chamber. Numerical results show that the contact resistances between the heating blocks and the reaction chamber dominate the temperatures inside the PCR chamber. In this work a PCR system that is composed of the PID controller, the moving stage, three aluminum blocks for three different isothermal zones and a reaction chamber is also developed. Experimental results demonstrated that the stability of this shuttling PCR system is confirmed. And results show that DNA templates provided with the yT&A® cloning vector are amplified successfully in this PCR system.

scholarly journals The role of infectious agent in development of tooth decay

2020 ◽  
Vol 10 (4) ◽  
pp. 747-754
Author(s):  
A. V. Liubimova ◽  
T. V. Brodina ◽  
A. E. Goncharov ◽  
A. V. Silin ◽  
L. P. Zueva ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Uv Light ◽  
Infectious Agent ◽  
Caries Experience ◽  
Oligonucleotide Primer ◽  
Index Number ◽  
Tooth Decay ◽  
Pcr Products ◽  
Dmft Index ◽  
Thermal Cycler

Aim: to assess the relationship between colonization of the oral cavity with S. mutans and different genotypic characteristics and the degree of tooth decay in children.Materials and methods. 274 children aged 5 to 17 years (153 girls and 121 boys) who received a preventive dental checkup were included in the study. The dental caries experience was assessed by the DMFT index (number of decayed, missing due to caries, and filled teeth), according to WHO recommendations. The plaque was collected with sterile wooden toothpicks from the buccal gingival margin or from fissures of the first molars and placed in 1.5 mL Eppendorf tubes, and then plated on Mitis Salivarius Agar medium (HiMedia, India). 481 strains of S. mutans were selected for further study. DNA was extracted by an express method. Amplification was performed in the CFX-96 thermal cycler (Bio-Rad, USA). Serotyping was performed by multiplex PCR. PCR products were analyzed by gel electrophoresis in 1.5% agarose gel with ethidium bromide (10 mg/mL) manufactured by Helicon, Moscow, and visualized in UV light in transilluminator UVT1 by Biokom. Genotyping was performed according to the methodology (Saarela et al., 1996) with the oligonucleotide primer OPA-02 (5’-TGCCGAGCTG-3’). Strains of S. mutans were studied for the presence of the following genes: gtfB, spaP, cnm, fruA, gtfB, htrA, comE, mutA x(I), mutA (II), mutA (III), nlmAB (IV), adcA, Smu.399, Smu.583, Smu.761, Smu.940c, Smu.1449, Smu.2130.Results. S. mutans was isolated from all the examined children. Dental decay was detected in 82.4% of the children. Among the strains studied, all 4 serotypes were found: in children with a DMFT = 0 only serotypes k and f were detected; the predominant serotype in children with tooth decay was serotype c (74.7%). 19 genotypes of S. mutans were identified. In children without caries (DMFT = 0), S. mutans did not contain the genes spaP, comE, adcA, Smu.2130, Smu.1449, gtfB, htrA. With the increase in the DMFT index, the frequency of their detection increased. 9 genotypes of S. mutans had all 7 virulence factors. In 94.9% of children colonized by these “virulent” genotypes, high DMFT index scores were observed.Conclusion. The data obtained indicate that only a limited number of specific strains have a cariogenic potential. Strains of S. mutans belonging to serotypes e and c with a combination of virulence genes spaP, gtfB, comE, adcA, Smu.2130, Smu.1449, and htrA were isolated from children with tooth decay. Strains without these factors did not cause any damage to the teeth. The degree of tooth decay increases with colonization by several genotypes with the combination of virulence factors described above.

scholarly journals Research on Flow and Temperature Fields in Aircraft Engines

2014 ◽  
Vol 8 (1) ◽  
pp. 731-738 ◽  
Author(s):  
Guochang Zhao ◽  
Daniel X. Zhao ◽  
Jing Li ◽  
Xia Du ◽  
Xianyi Tong ◽  
...  
Keyword(s):  
Numerical Simulation ◽  
Boundary Layer ◽  
Boundary Conditions ◽  
Analytical Solutions ◽  
Temperature Fields ◽  
Dimensionless Temperature ◽  
Wedge Flow ◽  
Dimensionless Velocity ◽  
Temperature Distributions ◽  
Wall Boundary Conditions

The similarity criteria which ensure the similarity between flow and temperature fields of both the lowtemperature turbine cavity model and the actual high-temperature turbine cavity are derived and then verified using numerical simulation of two different sized rotor-stator system turbine cavities. The analytical solution of threedimensional dimensionless velocity distribution and the numerical solutions of both the three-dimensional dimensionless velocity and temperature distributions of the free disk flow field are obtained. Using these solutions as a foundation, the analytical solutions of the dimensionless temperature distribution within the boundary layer of the isothermal and nonisothermal free disk model are obtained. The numerical and analytical solutions of velocity and temperature are compared to ensure that the solutions are consistent with each other. The analytical solutions of the dimensionless velocity and temperature fields within the laminar boundary layer of the wedge flow are obtained. The approximation solutions of the dimensionless temperature of the wedge flow under subsonic speed and isothermal wall boundary conditions and the dimensionless temperature of the wedge flow under supersonic speed and adiabatic wall boundary conditions are provided. The velocity and temperature distributions of the airflow outside the strut are obtained through numerical simulation and the pattern of changes in the velocity and temperature within the laminar boundary layer of the strut is revealed. Numerical simulation on gas jet cooling and regenerative cooling for the strut are simulated and shown to be effective for thermal protection. Using a strut with rough internal surface and aviation kerosene as the cooling medium is effective at cooling. The experiment fixture used to simulate the outlet temperature of the combustor and the experimental fixture used to simulate the dynamic temperature of the compressor are designed and built. The dynamic temperature of the compressor airflow is measured using combined thermocouples. Experimental results show that the dynamic error caused by the thermal inertia of the thermocouple can be eliminated by the compensation algorithm.

scholarly journals Calculations of Velocity and Temperature in a Polar Glacier using the Finite-Element Method

1979 ◽  
Vol 24 (90) ◽  
pp. 131-146 ◽  
Author(s):  
Roger LeB. Hooke ◽  
Charles F. Raymond ◽  
Richard L. Hotchkiss ◽  
Robert J. Gustafson
Keyword(s):  
Finite Element ◽  
Steady State ◽  
Temperature Distribution ◽  
Differential Equations ◽  
Boundary Conditions ◽  
Velocity Distribution ◽  
Vertical Velocity ◽  
Measured Temperature ◽  
Temperature Distributions ◽  
Flow Law

AbstractNumerical methods based on quadrilateral finite elements have been developed for calculating distributions of velocity and temperature in polar ice sheets in which horizontal gradients transverse to the flow direction are negligible. The calculation of the velocity field is based on a variational principle equivalent to the differential equations governing incompressible creeping flow. Glen’s flow law relating effective strain-rateε̇ and shear stressτbyε̇ = (τ/B)nis assumed, with the flow law parameterBvarying from element to element depending on temperature and structure. As boundary conditions, stress may be specified on part of the boundary, in practice usually the upper free surface, and velocity on the rest. For calculation of the steady-state temperature distribution we use Galerkin’s method to develop an integral condition from the differential equations. The calculation includes all contributions from vertical and horizontal conduction and advection and from internal heat generation. Imposed boundary conditions are the temperature distribution on the upper surface and the heat flux elsewhereFor certain simple geometries, the flow calculation has been tested against the analytical solution of Nye (1957), and the temperature calculation against analytical solutions of Robin (1955) and Budd (1969), with excellent results.The programs have been used to calculate velocity and temperature distributions in parts of the Barnes Ice Cap where extensive surface and bore-hole surveys provide information on actual values. The predicted velocities are in good agreement with measured velocities if the flow-law parameterBis assumed to decrease down-glacier from the divide to a point about 2 km above the equilibrium line, and then remain constant nearly to the margin. These variations are consistent with observed and inferred changes in fabric from fine ice with randomc-axis orientations to coarser ice with single- or multiple-maximum fabrics. In the wedge of fine-grained deformed superimposed ice at the margin,Bincreases again.Calculated and measured temperature distributions do not agree well if measured velocities and surface temperatures are used in the model. The measured temperature profiles apparently reflect a recent climatic warming which is not incorporated into the finite-element model. These profiles also appear to be adjusted to a vertical velocity distribution which is more consistent with that required for a steady-state profile than the present vertical velocity distribution.

Fluorescent Melting Curve Analysis Compatible With a Flowing Polymerase Chain Reactor

2005 ◽  
Author(s):  
Tara M. Dalton ◽  
David J. Kinahan ◽  
Mark R. Davies
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Melting Curve ◽  
Curve Analysis ◽  
Melting Curve Analysis ◽  
Pair Composition ◽  
Pcr Product ◽  
Pcr Products ◽  
Dna Strand ◽  
Thermal Cycler

A primary tool for analysing PCR product is the Fluorescent Melting Curve Analysis (FMCA). The temperature at which a double helix DNA strand denatures depends both on its length and base pair composition. Accurate measurement of this melting temperature using fluorescence allows estimations be made regarding DNA product length and composition. Current progress in development of PCR thermal cyclers has been primarily aimed at micro-channel based flowing devices. This paper addresses the challenges associated with performing FMCA analysis which is compatible with the output from a flowing PCR thermocycler. Two PCR products of significantly different lengths and base pair composition are compared using space domain FMCA. Results allow for differentiation of the PCR product, and compare favourably with results from a commercial thermal cycler. The successful application of FMCA within a channel shows its potential for use in high throughput flow based total analysis systems (μTAS).

Flow and Heat Transfer in Ducts of Arbitrary Shape With Arbitrary Thermal Boundary Conditions

1966 ◽  
Vol 88 (4) ◽  
pp. 351-357 ◽  
Author(s):  
E. M. Sparrow ◽  
A. Haji-Sheikh
Keyword(s):  
Heat Transfer ◽  
Boundary Conditions ◽  
Cross Section ◽  
Arbitrary Cross Section ◽  
Space Technology ◽  
Closed Form Solutions ◽  
Thermal Boundary Conditions ◽  
Flow And Heat Transfer ◽  
Temperature Distributions ◽  
Circular Segment

A computation-oriented method of analysis is presented for determining closed-form solutions for fully developed laminar flow and heat transfer in ducts of arbitrary cross section. The analytical method can accommodate both uniform and circumferentially varying thermal boundary conditions. The solutions provide information for local quantities such as the velocity and the temperature distributions as well as for overall quantities such as the friction factor and the Nusselt number. As an application of the method, solutions are presented for flow and for heat transfer in ducts of circular-segment cross section, a configuration that is of current interest in space technology.

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