Single step cell lysis/PCR detection of Escherichia coli in an independently controllable silicon microreactor

Our studies describe a novel microreactor capable of single step microbial assays involving cell lysis and DNA amplification. The device with an integrated platinum heater and temperature sensor, was fabricated using conventional silicon fabrication technologies and then anodically bonded to a Pyrex lid. Finite element analysis (FEA) and experiments have shown that the temperature uniformity in the microreactor reaction cavity is homogeneous and that the microreactor is capable of fast thermal cycling with heating and cooling rates of 11 and 2.7 °C/s, respectively. The microreactor has novel design features, such as a thermal isolation channel which eliminates thermal cross talk and an inlet/outlet port designed for ease of use. The fabricated microreactor was successfully characterised using a multifunction microbial assay involving cell lysis and PCR in a single step. An assay time of 32 min was achieved.     

Simulation and experimental validation of a SU-8 based PCR thermocycler chip with integrated heaters and temperature sensor

We present a SU-8 based polymerase chain reaction (PCR) chip with integrated platinum thin film heaters and temperature sensor. The device is fabricated in SU-8 on a glass substrate. The use of SU-8 provides a simple microfabrication process for the PCR chamber, controllable surface properties and can allow on chip integration to other SU-8 based functional elements. Finite element modeling (FEM) and experiments show that the temperature distribution in the PCR chamber is homogeneous and that the chip is capable of fast thermal cycling. With heating and cooling rates of up to 50 and 30 °C/s, respectively, the performance of the chip is comparable with the best silicon micromachined PCR chips presented in the literature. The SU-8 chamber surface was found to be PCR compatible by amplification of yeast gene ribosomal protein S3 and Campylobacter gene cadF. The PCR compatibility of the chamber surfaces was enhanced by silanization.     

Planar microreactor for biochemical application made from silicon and polymer films

Recently the progress of life science has been increasing rapidly, and the importance of the microfluidics for DNA analysis systems has been widely recognized, especially in medical fields. The polymerase chain reaction (PCR) is an essential technique for DNA assay of various diseases and it has been a strong requirement to shorten the total of PCR cycles more and more. We developed the microreactor with a single cell for PCR using fabrication technologies of MEMS. The reactor body and cover were sealed using high thickness PDMS prototyping film without using adhesive in order to achieve repeat grabbing motion for direct sample injection, resumption and cleansing the reaction cell. Good reproducibility of the heat cycling was obtained. The heating rate and cooling rate during PCR was 6.8 and 2.7°C, respectively, which well corresponds to the design parameters. The homogenous temperature distribution of variance less than 2.0°C was obtained. It is demonstrated that amplification of the DNA was successfully achieved by using the microreactor.     

Coupled flow and reaction during natural convection PCR

Polymerase chain reaction (PCR) in a microfluidic Rayleigh–Benard convection cell represents a promising route towards portable PCR for point-of-care uses. In the present contribution, the coupled fluid mechanics and heat transport processes are solved numerically for a 2-D flow cell. The resultant velocity and temperature fields serve as the inputs to a convection-diffusion-reaction model for the DNA amplification, wherein the reaction kinetics are modeled by Gaussian distributions around the conventional bulk PCR reaction temperatures. These evolution equations are integrated to determine the exponential growth rate of the double-stranded DNA concentration. The predicted doubling time is approximately 10–25 s, increasing with the Péclet number. This effect is attributed to low velocity, slow kinetics “dead zones” located at the center of the reactor. The latter observation provides an alternative rationalization for the use of loop-based natural convection PCR systems.     

Compact optical diagnostic device for isothermal nucleic acids amplification

We recently reported the successful use of the loop-mediated isothermal amplification (LAMP) reaction for hepatitis B virus (HBV) DNA amplification and its optimal primer design method. In this study, we report the development of an integrated isothermal device for both amplification and detection of targeted HBV DNA. It has two major components, a disposable polymethyl methacrylate (PMMA) micro-reactor and a temperature-regulated optical detection unit (base apparatus) for real-time monitoring of the turbidity changes due to the precipitation of DNA amplification by-product, magnesium pyrophosphate. We have established a correlation curve (R² = 0.99) between the concentration of pyrophosphate ions and the level of turbidity by using a simulated chemical reaction to evaluate the characteristics of our device. For the applications of rapid pathogens detection, we also have established a standard curve (R² = 0.96) by using LAMP reaction with a standard template in our device. Moreover, we also have successfully used the device on seven clinical serum specimens where HBV DNA levels have been confirmed by real-time PCR. The result indicates that different amounts of HBV DNA can be successfully detected by using this device within 1 h.     

A continuous-flow polymerase chain reaction microchip with regional velocity control

This paper presents a continuous-flow polymerase chain reaction (PCR) microchip with a serpentine microchannel of varying width for "regional velocity control." Varying the channel width by incorporating expanding and contracting conduits made it possible to control DNA sample velocities for the optimization of the exposure times of the sample to each temperature phase while minimizing the transitional periods during temperature transitions. A finite element analysis (FEA) and semi-analytical heat transfer model was used to determine the distances between the three heating assemblies that are responsible for creating the denaturation (96/spl deg/C), hybridization (60/spl deg/C), and extension (72/spl deg/C) temperature zones within the microchip. Predictions from the thermal FEA and semi-analytical model were compared with temperature measurements obtained from an infrared (IR) camera. Flow-field FEAs were also performed to predict the velocity distributions in the regions of the expanding and contracting conduits to study the effects of the microchannel geometry on flow recirculation and bubble nucleation. The flow fields were empirically studied using micro particle image velocimetry (/spl mu/-PIV) to validate the flow-field FEA's and to determine experimental velocities in each of the regions of different width. Successful amplification of a 90 base pair (bp) bacillus anthracis DNA fragment was achieved.     

Langasite based surface acoustic wave sensors for high temperature chemical detection in harsh environment: Design of the transducers and packaging

This work presents the design and the thermal behavior characterization of an innovative self-test portable surface acoustic wave platform for chemical detection under high temperature. Before the forthcoming deposition of the sensitive coating, the thermal behavior of the bare LGS acoustic platform has been focused on. The system includes a (0°, 140°, 25°) crystallographic cut langasite (LGS) piezoelectric substrate, a ceramic heater, and a platform with RF connections for remote measurements. The packaging consists in a hermetic stainless steel cell, which enables safe gas detection. Its thermal behavior was successfully investigated in the temperature range 25-500 °C thanks to the integrated heater, without using an external furnace. Finite element modeling aided the development of this platform structure by predicting the thermal behavior of each of its parts and their cross-influences. The structure of the platform was specifically designed so that 500 °C could be reached on the LGS acoustic device while the temperature on the PCB connections should not exceed 50 °C. Then, the temperature-dependence on the waves generated by the acoustic transducers has been investigated through numerical modeling by resolving the wave propagation equations with several sets of LGS constants. Corresponding simulations showed good agreement with experiments, Thermal cycling up to 350 °C highlighted satisfactory hardiness and response-reproducibility of the system towards thermal stress, after a first burn effect.     

A Numerical Modeling of Rayleigh–Marangoni Steady Convection in a Non-Uniform Differentially Heated 3D Cavity

A numerical study of a buoyancy driven convection flow in presence of thermocapillarity has been developed. The fluid is a silicone oil (Prandtl number equal to 105) contained in a three-dimensional box bounded by rigid and impermeable walls with top free surface exposed to a gaseous phase. At the lateral box walls a different non-uniform temperature distribution is assumed so to induce horizontal convection and to keep separated thermocapillary and buoyancy effects. The vorticity-velocity formulation of the time-dependent Navier–Stokes equations for a non-isothermal incompressible fluid is used. A procedure based on a linearized fully implicit finite difference second order scheme has been adopted. We obtained very complex steady configurations for several values of the temperature difference at the lateral walls, T=30, 40 and 50°C. Along the direction perpendicular to the lateral walls, for T increasing, we observe a physically meaningful growth of heat transfer. Confidence in these results is supported by a comparison with recent experimental and numerical observations.     

Electrical detection of DNA hybridization with multilayer gold nanoparticles between nanogap electrodes

This study presents a DNA detection method via hybridization of a probe oligonucleotide with a target DNA and with a substrate oligonucleotide, which leads to self-assembly of gold nanoparticles and a change in the observed current. In contrast to previously reported methods, the present method can be used to detect a target DNA without a silver enhancement step. The device can be washed with 0.3 M PBS below 50 °C for a few minutes, indicating the stringency of target DNA hybridization. Target DNA concentration of as low as 10 picomolar can be detected by this method. Importantly, identification of single-base-pair mismatch in the target DNA can be accomplished with this nano-gap DNA chip.The authors thank for Shu-Fen, Hos group and her assistant, Mr. Wong for useful discussions. Dr. Ho has also been supported in measuring the electricity properties.     

A new type humidity sensor using micro-air-bridge heaters

A new type absolute-humidity sensor with very quick response, very small power consumption and high sensitivity, which is based on the detection of the thermal conductivity change in humid air at heated temperature above 400°C, has been developed and demonstrated. Since this new type absolute-humidity sensor is able to be easily heated up above 400°C within 30–40 msec because of a micro-air-bridge heater structure, the surface of its sensing area is refreshed by burning out adsorbed dusts, oil, etc. Thermal conductivity _mix of mixed gas expressed by Sutherland-Wassiljewa equation is applied to the humid air to study this absolute humidity sensor. Only a single micro-air-bridge heater operation driven by double pulse-currents for this humidity sensor is also proposed.     

Micromachined jets for liquid impingement cooling of VLSI chips

Two-phase microjet impingement cooling is a potential solution for removing heat from high-power VLSI chips. Arrays of microjets promise to achieve more uniform chip temperatures and very high heat transfer coefficients. This paper presents the design and fabrication of single-jets and multijet arrays with circular orifice diameters ranging from 40 to 76 /spl mu/m, as well as integrated heater and temperature sensor test devices. The performance of the microjet heat sinks is studied using the integrated heater device as well as an industry standard 1 cm/sup 2/ thermal test chip. For single-phase, the silicon temperature distribution data are consistent with a model accounting for silicon conduction and fluid advection using convection coefficients in the range from 0.072 to 4.4 W/cm/sup 2/K. For two-phase, the experimental results show a heat removal of up to 90 W on a 1 cm/sup 2/ heated area using a four-jet array with 76 /spl mu/m diameter orifices at a flowrate of 8 ml/min with a temperature rise of 100/spl deg/C. The data indicate convection coefficients are not significantly different from coefficients for pool boiling, which motivates future work on optimizing flowrates and flow regimes. These microjet heat sinks are intended for eventual integration into a closed-loop electroosmotically pumped cooling system.     

Aluminium electrolytic cells: A computer simulator for training and supervision

A workstation-based simulator of an aluminium electrolytic cell has been constructed. A mathematical model of the cell is integrated with a database and a knowledge base, and the simulator serves as a tool for the training of personnel and for research related to cell dynamics and cell control. When used in conjunction with an expert system, it provides a powerful decision-making tool or an efficient supervisory system. The mathematical model, the simulator itself, the user environment, the interactive simulation procedure as well as examples of the use of the simulator are presented in detail.List of Symbols a _i parameters of electrolyte density calculation - AlF ₃ aluminium fluoride content [w%] - Al ₂O₃ alumina content of electrolyte [w%] - b _i parameters of electrolyte specific heat - c _i parameters of bath electrical resistivity - c _p ⁱ specific heat of electrolyte [J/kg°C] - c _p ² specific heat of freeze [J/kg°C] - c _p ³ specific heat of metal [J/kg°C] - C alumina content of electrolyte [w%] - C _s saturation concentration of alumina [w%] - CaF ₂ calcium fluoride content of electrolyte [w%] - CR cryolite ratio - H _F heat of fusion of electrolyte [J/kg] - I line current [kA] - k ₁ parameter of solution 1 [1/s w%] - k ₂ parameter of solution 2 [1/s w%] - k ₃ parameter of settling [1/s] - k ₄ parameter of alumina feeding [kg/s] - k ₅ parameter of metal production [kg/s kA] - k ₆ ratio of alumina-metal mass transformation - m ₁ mass of electrolyte [kg] - m ₂ mass of freeze [kg] - m ₃ mass of molten metal [kg] - m _a rate of alumina addition [kg/s] - m _m rate of metal production [kg/s] - m _t rate of metal tapping [kg/s] - Q total heat loss [kW] - Q _A heat flow from electrolyte to anode [kW] - Q _B heat flow from metal to cathode bottom [kW] - Q _F heat flow from freezing zone to freeze [kW] - Q _F1 heat flow from electrolyte to freezing zone [kW] - Q _F2 heat flow from metal to freezing zone [kW] - Q _Ha energy needed for alumina heatup [kW] - Q _K heat flow from electrolyte to cathode [kW] - Q _s heat flow from freeze to side-wall [kW] - S ₁ solution rate of disperesed alumina [kg/s] - S ₂ solution rate of settled alumina [kg/s] - S ₃ settling rate [kg/s] - T ₁ temperature of electrolyte [°C] - T ₂ temperature of freeze [°C] - T ₃ temperature of molten metal [°C] - T _F temperature of freezing zone [°C] - T _L cryolite liquidus temperature [°C] - U total cell voltage [V] - U _a voltage equivalent of enthalpy of metal production [V] - x ₁ mass of dispersed alumina [kg] - x ₂ mass of settled alumina [kg] - x ₃ mass of dissolved alumina [kg] - _i parameters of cryolite liquidus temperature - density of bath [kg/m³] - electrical resistivity of bath [m] - _c electrical conductivity of bath [1/m] - Note w% means percentage by weight     

Advanced automotive thermal management – Nonlinear radiator fan matrix control

Advanced automotive cooling systems for gasoline and diesel engines can improve the powertrain performance. The replacement of the mechanical driven coolant pump and radiator fans with computer controlled servo-motor actuators, and update of the wax-based thermostat valve with a 3-way variable position smart valve, allow the coolant flow rate and proportion directed through the radiator to be carefully adjusted. A smart thermal management system approach can regulate the forced convection heat transfer process to match the engine׳s cooling needs. This paper presents a Lyapunov based nonlinear control strategy to solely operate the radiator fan matrix for transient engine temperature tracking. A reduced order mathematical model serves as the basis for the closed-loop feedback system. An adaptive backstepping method was implemented to derive the control law. An experimental test bench with multiple radiator fans, heat exchanger, wind tunnel, coolant pump, three way valve, and engine thermal load has been fabricated. Representative numerical and experimental tests demonstrate that the advanced control strategy can regulate the engine temperature tracking error within 0.12 °C and compensate the unknown heat load. The nonlinear controller provided superior performance in terms of power consumption and temperature tracking as evident by the reduced magnitude when compared to a classical PI with lookup table based controller and a bang bang controller.     

Prediction and optimization of unsteady forced convection around a rounded cornered square cylinder in the range of Re

An unsteady two-dimensional laminar forced convection heat transfer around a square cylinder with the rounded corner edge is numerically investigated for Re = 80–180 and non-dimensional corner radius, r = 0.50–0.71 at Pr = 0.71 (Air). A structured non-uniform mesh is used for the computational domain discretization, and the finite-volume-method-based commercial code FLUENT is used for numerical simulation. The heat transfer characteristics over the rounded corner square cylinder are analyzed with average Nusselt number (Nu _avg) at various Re and various corner radii. The heat transfer characteristic is predicted by gene expression programming (GEP), and the GEP-generated explicit equation of Nu _avg is utilized in particle swarm optimization to optimize the corner radii for maximum heat transfer rate. The data required for the training the GEP model have been collected from the authors’ recent published article (Neural Comput Appl, 2015. doi:10.1007/s00521-015-2023-8). It is found that the heat transfer rate of a circular cylinder can be enhanced 12 % by introducing a new cylinder geometry of corner radius r = 0.51.

     

A preliminary study of a diagonal channel-routing model

The layout of two-terminal nets in a VLSI channel is realized in a new diagonal channel-routing model (DCRM), where the tracks are segments respectively displayed at +45 ° and –45 ° on the two layers of the channel. A new definition of channel density is introduced, and a lower bound to the channel width is derived by the application of an algorithm, whose complexity is evaluated as a function of the channel density, and other parameters of the problem.A simple linear-time algorithm is proposed, which produces an optimal layout (i.e., it requires a channel of minimum width) if the length of the longest net equals the lower bound for the channel width. In any case, the number of vias is at most one for each net. Some particular solutions are proposed for problems with long nets.Specific problems are much easier in DCRM than in the classical Manhattan model. For example, any shift-by-i can be realized in DCRM in a channel of widthi.This work has been supported by Consiglio Nazionale delle Ricerche of Italy under a research grant.     

Adaptive control of brain temperature for brain hypothermia treatment using Stolwijk-Hardy model

An automatic thermal control system is proposed for the treatment of cerebral injury and inflammation. The system is based on the reference model adaptive control method. It works adaptively according to the difference between individuals, and chronic change of the patients physiological state, and changes in the environmental conditions. Using the human thermal system of the Stolwijk-Hardy model, the brain temperature is dynamically related to the ambient temperature of the head, trunk, and extremities and their metabolic heat production. The dynamic characteristics of brain temperature under various physical conditions, as examined by simulation experiments, provide improved understanding of clinical brain cooling treatment, which simultaneously give good evidence for the validity of the model. The brain temperature is adaptively controlled in accordance with the appropriate physiological state suggested by various clinical experiences. This kind of adaptive control system is useful for the practical implementation of automatic hypothermia control in seriously injured or inflamed brain.     

Decreasing microfluidic evaporation loss using the HMDL method: open systems for nucleic acid amplification and analysis

Evaporation is of great importance when dealing with microfluidic devices with open air/liquid interfaces due to the large surface-to-volume ratio. For devices utilizing a thermal reaction (TR) reservoir to perform a series of biological and chemical reactions, excessive heat-induced microfluidic evaporation can quickly lead to reaction reservoir dry out and failure of the overall device. In this study, we present a simple, novel method to decrease heat-induced fluid evaporation within microfluidic systems, which is termed as heat-mediated diffusion-limited (HMDL) method. This method does not need complicated thermal isolation to reduce the interfacial temperature, or external pure water to be added continuously to the TR chamber to compensate for evaporation loss. The principle of the HMDL method is to make use of the evaporated reaction content to increase the vapor concentration in the diffusion channel. The experimental results have shown that the relative evaporation loss (V _loss/V _ini) based on the HMDL method is not only dependent on the HMDL and TR region’s temperatures (T _HMDL and T _TR), but also on the HMDL and TR’s channel geometries. Using the U-shaped uniform channel with a diameter of 200 μm, the V _loss/V _ini within 60 min is low to 5% (T _HMDL = 105°C, T _TR = 95°C). The HMDL method can be used to design open microfluidic systems for nucleic acid amplification and analysis such as isothermal amplification and PCR thermocycling amplification, and a PCR process has been demonstrated by amplifying a 135-bp fragment from Listeria monocytogenes genomic DNA.     

Improved upper and lower bounds on the optimization of mixed chordal ring networks

Recently, Chen, Hwang and Liu [S.K. Chen, F.K. Hwang, Y.C. Liu, Some combinatorial properties of mixed chordal rings, J. Interconnection Networks 1 (2003) 3-16] introduced the mixed chordal ring network as a topology for interconnection networks. In particular, they showed that the amount of hardware and the network structure of the mixed chordal ring network are very comparable to the (directed) double-loop network, yet the mixed chordal ring network can achieve a better diameter than the double-loop network. More precisely, the mixed chordal ring network can achieve diameter about as compared to for the (directed) double-loop network, where N is the number of nodes in the network. One of the most important questions in interconnection networks is, for a given number of nodes, how to find an optimal network (a network with the smallest diameter) and give the construction of such a network. Chen et al. [S.K. Chen, F.K. Hwang, Y.C. Liu, Some combinatorial properties of mixed chordal rings, J. Interconnection Networks 1 (2003) 3-16] gave upper and lower bounds for such an optimization problem on the mixed chordal ring network. In this paper, we improve the upper and lower bounds as and , respectively. In addition, we correct some deficient contexts in [S.K. Chen, F.K. Hwang, Y.C. Liu, Some combinatorial properties of mixed chordal rings, J. Interconnection Networks 1 (2003) 3-16].     

Bead-based polymerase chain reaction on a microchip

We present a bead-based approach to microfluidic polymerase chain reaction (PCR), enabling fluorescent detection and sample conditioning in a single microchamber. Bead-based PCR, while not extensively investigated in microchip format, has been used in a variety of bioanalytical applications in recent years. We leverage the ability of bead-based PCR to accumulate fluorescent labels following DNA amplification to explore a novel DNA detection scheme on a microchip. The microchip uses an integrated microheater and temperature sensor for rapid control of thermal cycling temperatures, while the sample is held in a microchamber fabricated from (poly)dimethylsiloxane and coated with Parylene. The effects of key bead-based PCR parameters, including annealing temperature and concentration of microbeads in the reaction mixture, are studied to achieve optimized device sensitivity and detection time. The device is capable of detecting a synthetically prepared section of the Bordetella pertussis genome in as few as 10 temperature cycles with times as short as 15?min. We then demonstrate the use of the procedure in an integrated device; capturing, amplifying, detecting, and purifying template DNA in a single microfluidic chamber. These results show that this method is an effective method of DNA detection which is easily integrated in a microfluidic device to perform additional steps such as sample pre-conditioning.