Pavel Neuzil - Academia.edu (original) (raw)
Papers by Pavel Neuzil
Lab on a Chip, 2016
World's smallest, fully autonomous, handheld real-time PCR was shown in this contribution. Th... more World's smallest, fully autonomous, handheld real-time PCR was shown in this contribution. The device can quickly process up to four samples at a time with detection capability of a single DNA copy. The fully integrated system includes all required electronics for fluorescence measurement, data viewing (LCD display) and processing, and is ideal for use in small clinics and point-of-care applications.
Scientific Reports, 2015
The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, du... more The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, due to its ability to multiply a number of copies of DNA sequences (known as amplicons). Here we report on a method to double the throughput of quantitative PCR which could be especially useful for PCRbased mass screening. We concurrently amplified two target genes using only single fluorescent dye. A FAM probe labelled olionucleotide was attached to a quencher for one amplicon while the second one was without a probe. The PCR was performed in the presence of the intercalating dye SYBR Green I. We collected the fluorescence amplitude at two points per PCR cycle, at the denaturation and extension steps. The signal at denaturation is related only to the amplicon with the FAM probe while the amplitude at the extension contained information from both amplicons. We thus detected two genes within the same well using a single fluorescent channel. Any commercial realtime PCR systems can use this method doubling the number of detected genes. The method can be used for absolute quantification of DNA using a known concentration of housekeeping gene at one fluorescent channel.
Journal of Microelectromechanical Systems
Here, we introduce a microchip for differential measurements of aqueous samples in twin calorimet... more Here, we introduce a microchip for differential measurements of aqueous samples in twin calorimetric arms with a sub-nL enclosed space. Each arm features a fluidic microchannel located in close proximity to a thin-film resistance thermometer and heater patterned on a low-stress SiN membrane held over a Si cavity with suspension beams. The chip exhibits a rapid response with a thermal time constant of less than 10 ms in atmosphere and a residual thermal conductance below 6 µW•K −1 , one of the lowest reported and accounts for the excellent sensitivity registered in vacuum up to 11 V•W −1. These values are in good agreement with those ones predicted by modeling using finite element method, lumped-capacitance analysis, and calorimeter electrothermal circuit simulation together with the measurement system. Long suspension beams in each arm ensure uniform temperature maintained across its membrane as revealed by the fluorescence-based melting curve analysis. We share the specific heat capacity values of water, glycerin, and mineral oil accurately measured by the chip. Lastly, we demonstrate the chip calorimeter utility on the measurement of the photothermal transduction efficiency of
We report on the application as well as microfabrication process of batch-fabricated optical near... more We report on the application as well as microfabrication process of batch-fabricated optical near-field sensors using cantilevered scanning force microscopy tips. The process includes implementation of a coaxial conductive geometry into a silicon sensor tip, along with electrical connections on the cantilever and chip body. The coaxial guide structure is used as electric lead to a sub-micron Schottky photodetector at
Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures, 2001
... astronomy. Mechanical instruments and equipment. Micromechanical devices andsystems. Electron... more ... astronomy. Mechanical instruments and equipment. Micromechanical devices andsystems. Electronic and magnetic devices; microelectronics . Micro-and nano-electromechanical systems (MEMS/NEMS) and devices. Instruments ...
This paper reports the development of a silicon-based microfluidic device that enables ultra fast... more This paper reports the development of a silicon-based microfluidic device that enables ultra fast melting curve analysis (MCA) for genomic studies (DNA) and drug discovery (proteins). The system relies on the flow of nanoliter-sized discrete phase samples through a buried silicon channel. The samples are subjected to a temperature gradient generated by two external heaters along the channel. The channel also simultaneously serves as a light guide to illuminate the droplets and guide the emitted fluorescence to the detector outside the channel. The system provides a simple melting analysis of fluorescent-labeled molecular complexes, with high multiplexing capability and throughput. The chip-based solution is attractive due to nanolitre sized samples handling, resulting in fast heat transfer thus achieving ultra fast MCA for genomic studies and drug discoveries .
Journal of the Chemical Society, Faraday Transactions, 1996
ABSTRACT
Lab Chip, 2015
We present the online coupling of a free-flow isotachophoresis (FFITP) device to an electrospray ... more We present the online coupling of a free-flow isotachophoresis (FFITP) device to an electrospray ionization mass spectrometer (ESI-MS) for continuous analysis without extensive sample preparation. Free-flowelectrophoresis techniques are used for continuous electrophoretic separations using an electric field applied perpendicular to the buffer and sample flow, with FFITP using a discontinuous electrolyte system to concurrently focus a target analyte and remove interferences. The online coupling of FFITP to ESI-MS decouples the separation and detection timeframe because the electrophoretic separation takes place perpendicular to the flow direction, which can be beneficial for monitoring bio)chemical changes and/or extensive MS n studies. We demonstrated the coupling of FFITP with ESI-MS for simultaneous concentration of target analytes and sample clean-up. Furthermore, we show hydrodynamic control of the fluidic fraction injected into the MS, allowing for fluidically controlled scanning of the ITP window. Future applications of this approach are expected in monitoring biochemical changes and proteomics. Lab Chip, 2015, 15, 3495-3502 | 3495
Physical Review B, 2002
Domain formation during magnetization reversal in arrays of square holes in Fe films is investiga... more Domain formation during magnetization reversal in arrays of square holes in Fe films is investigated using the diffracted magneto-optic kerr effect (DMOKE). The shape of the domains can, in some cases, be extracted from hysteresis loops measured at various diffraction orders. We find that the shape of the domains depends strongly on: the direction of the applied field relative to the holes, the size of the square holes, and also the small intrinsic anisotropy of the unpatterned film. DMOKE results are compared with those obtained with magnetic force microscopy. In the saturated state Brillouin spectroscopy shows that square holes induce a fourfold anisotropy in the film.
Physical Review B, 2000
The magnetic properties of an array of elliptical holes in an Fe film have been investigated usin... more The magnetic properties of an array of elliptical holes in an Fe film have been investigated using the diffracted magneto-optical Kerr effect (D-MOKE), Lorentz scanning transmission electron microscopy (LSTEM), and Brillouin scattering. In the absence of a comprehensive theory for magnetization or magnons in these materials, we find that our results can be fit by a semiquantitative analysis treating the
1998 IEEE MTT-S International Microwave Symposium Digest (Cat. No.98CH36192), 1998
ABSTRACT We present the first scanned probe Schottky diode used as a detector of microwave power.... more ABSTRACT We present the first scanned probe Schottky diode used as a detector of microwave power. This technique enables direct sensing of local fields without the use of a high frequency receiver, and it can accommodate simultaneous measurement of sample topography, as well. Applications for this probe range from field mapping on planar filters to failure analysis of MMIC's
Atherosclerosis Supplements, 2011
Our model is able to reproduce measured lipid data of humans with normal lipoprotein values. Furt... more Our model is able to reproduce measured lipid data of humans with normal lipoprotein values. Furthermore, certain lipoprotein-associated diseases like hypercholesterolemia may be simulated by modifying the associated parameters of the metabolism. As particular lipoproteins are simulated, we are able to get information about the distribution and metabolic rates of lipoproteins in all density classes. Hence it is possible to simulate kinetic measurements. Discussion: The model is capable to investigate associated diseases of lipid metabolism and to provide a powerful tool for possible therapeutic approaches. However, there is still need for further improvements.
RSC Adv., 2014
In this paper we report a method of continuous electroextraction of amino acids as model samples ... more In this paper we report a method of continuous electroextraction of amino acids as model samples using a caseinate-poly(ethylene-glycol) -PEGtwo phase system in a microchip able to separate compounds based on their differences in electrophoretic mobility and solvent affinity. Fundamentally, the phase boundary replaces a physical membrane, suppressing the diffusion. When external potential is applied, the molecules selectively cross this barrier. The selectivity of the amino acids extraction is the result of their electrochemical properties and applied voltage. We applied this method to amino acids extraction and the results suggest the possibility of high levels of purification by controlling the electric field strength across the liquid barrier. It is a promising method for complex sample separation as well as for the purification of individual compounds.
Biosensors & bioelectronics, 2002
An ion-sensitive field effect transistor (ISFET)-based immunosensor was developed to detect/quant... more An ion-sensitive field effect transistor (ISFET)-based immunosensor was developed to detect/quantitate beta-Bungarotoxin (beta-BuTx), a potent presynaptic neurotoxin from the venom of Bungarus multicinctus. A murine monoclonal antibody (mAb 15) specific to beta-BuTx was immobilized onto silicon nitride wafers after silanization and activation with glutaraldehyde. A chip based enzyme linked-immunosorbantassay (ELISA) was performed to ascertain antigen binding to the immobilized antibody. To develop an electrochemical immunosensing system for the detection/quantitation of beta-BuTx, an ISFET was used as a solid phase detector. MAb 15 was immobilized on the gate region of the ISFET. The antigen antibody reaction was monitored by the addition of urease conjugated rabbit anti-beta-BuTx antibodies. The sensor can detect toxin level as low as 15.6 ng/ml. The efficacy of the sensor for the determination of beta-BuTx from B. multicinctus venom was demonstrated in mouse model. Toxin concentra...
Controlling and Using Light in Nanometric Domains, 2001
ABSTRACT We report on the application as well as microfabrication process of batch-fabricated opt... more ABSTRACT We report on the application as well as microfabrication process of batch-fabricated optical near-field sensors using cantilevered scanning force microscopy tips. The process includes implementation of a coaxial conductive geometry into a silicon sensor tip, along with electrical connections on the cantilever and chip body. The coaxial guide structure is used as electric lead to a sub-micron Schottky photodetector at the end of the tip, formed at the junction of the protruding silicon core and a recessed aluminum coating. The I-V curves of these sensors are consistent with numerical studies for such constricted geometries. Optical near-field data gathered by this sensor in topography-following mode is presented.
1996 International Integrated Reliability Workshop Final Report, 1996
ABSTRACT We introduce a new concept for combined probing of topography and local AC fields and re... more ABSTRACT We introduce a new concept for combined probing of topography and local AC fields and report some early results of tip fabrication and measurements. Because this instrument can be used to measure both AC fields and topography with nanometer-level localization, we call it a Nanoscilloscope. This new instrument promises to be particularly useful for proactive reliability engineering because it can simultaneously image dynamic electric fields (i.e. signals) and sample topography, but unlike electron-beam probing, it operates in ambient conditions
Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures, 1996
ABSTRACT
Lab on a Chip, 2016
World's smallest, fully autonomous, handheld real-time PCR was shown in this contribution. Th... more World's smallest, fully autonomous, handheld real-time PCR was shown in this contribution. The device can quickly process up to four samples at a time with detection capability of a single DNA copy. The fully integrated system includes all required electronics for fluorescence measurement, data viewing (LCD display) and processing, and is ideal for use in small clinics and point-of-care applications.
Scientific Reports, 2015
The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, du... more The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, due to its ability to multiply a number of copies of DNA sequences (known as amplicons). Here we report on a method to double the throughput of quantitative PCR which could be especially useful for PCRbased mass screening. We concurrently amplified two target genes using only single fluorescent dye. A FAM probe labelled olionucleotide was attached to a quencher for one amplicon while the second one was without a probe. The PCR was performed in the presence of the intercalating dye SYBR Green I. We collected the fluorescence amplitude at two points per PCR cycle, at the denaturation and extension steps. The signal at denaturation is related only to the amplicon with the FAM probe while the amplitude at the extension contained information from both amplicons. We thus detected two genes within the same well using a single fluorescent channel. Any commercial realtime PCR systems can use this method doubling the number of detected genes. The method can be used for absolute quantification of DNA using a known concentration of housekeeping gene at one fluorescent channel.
Journal of Microelectromechanical Systems
Here, we introduce a microchip for differential measurements of aqueous samples in twin calorimet... more Here, we introduce a microchip for differential measurements of aqueous samples in twin calorimetric arms with a sub-nL enclosed space. Each arm features a fluidic microchannel located in close proximity to a thin-film resistance thermometer and heater patterned on a low-stress SiN membrane held over a Si cavity with suspension beams. The chip exhibits a rapid response with a thermal time constant of less than 10 ms in atmosphere and a residual thermal conductance below 6 µW•K −1 , one of the lowest reported and accounts for the excellent sensitivity registered in vacuum up to 11 V•W −1. These values are in good agreement with those ones predicted by modeling using finite element method, lumped-capacitance analysis, and calorimeter electrothermal circuit simulation together with the measurement system. Long suspension beams in each arm ensure uniform temperature maintained across its membrane as revealed by the fluorescence-based melting curve analysis. We share the specific heat capacity values of water, glycerin, and mineral oil accurately measured by the chip. Lastly, we demonstrate the chip calorimeter utility on the measurement of the photothermal transduction efficiency of
We report on the application as well as microfabrication process of batch-fabricated optical near... more We report on the application as well as microfabrication process of batch-fabricated optical near-field sensors using cantilevered scanning force microscopy tips. The process includes implementation of a coaxial conductive geometry into a silicon sensor tip, along with electrical connections on the cantilever and chip body. The coaxial guide structure is used as electric lead to a sub-micron Schottky photodetector at
Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures, 2001
... astronomy. Mechanical instruments and equipment. Micromechanical devices andsystems. Electron... more ... astronomy. Mechanical instruments and equipment. Micromechanical devices andsystems. Electronic and magnetic devices; microelectronics . Micro-and nano-electromechanical systems (MEMS/NEMS) and devices. Instruments ...
This paper reports the development of a silicon-based microfluidic device that enables ultra fast... more This paper reports the development of a silicon-based microfluidic device that enables ultra fast melting curve analysis (MCA) for genomic studies (DNA) and drug discovery (proteins). The system relies on the flow of nanoliter-sized discrete phase samples through a buried silicon channel. The samples are subjected to a temperature gradient generated by two external heaters along the channel. The channel also simultaneously serves as a light guide to illuminate the droplets and guide the emitted fluorescence to the detector outside the channel. The system provides a simple melting analysis of fluorescent-labeled molecular complexes, with high multiplexing capability and throughput. The chip-based solution is attractive due to nanolitre sized samples handling, resulting in fast heat transfer thus achieving ultra fast MCA for genomic studies and drug discoveries .
Journal of the Chemical Society, Faraday Transactions, 1996
ABSTRACT
Lab Chip, 2015
We present the online coupling of a free-flow isotachophoresis (FFITP) device to an electrospray ... more We present the online coupling of a free-flow isotachophoresis (FFITP) device to an electrospray ionization mass spectrometer (ESI-MS) for continuous analysis without extensive sample preparation. Free-flowelectrophoresis techniques are used for continuous electrophoretic separations using an electric field applied perpendicular to the buffer and sample flow, with FFITP using a discontinuous electrolyte system to concurrently focus a target analyte and remove interferences. The online coupling of FFITP to ESI-MS decouples the separation and detection timeframe because the electrophoretic separation takes place perpendicular to the flow direction, which can be beneficial for monitoring bio)chemical changes and/or extensive MS n studies. We demonstrated the coupling of FFITP with ESI-MS for simultaneous concentration of target analytes and sample clean-up. Furthermore, we show hydrodynamic control of the fluidic fraction injected into the MS, allowing for fluidically controlled scanning of the ITP window. Future applications of this approach are expected in monitoring biochemical changes and proteomics. Lab Chip, 2015, 15, 3495-3502 | 3495
Physical Review B, 2002
Domain formation during magnetization reversal in arrays of square holes in Fe films is investiga... more Domain formation during magnetization reversal in arrays of square holes in Fe films is investigated using the diffracted magneto-optic kerr effect (DMOKE). The shape of the domains can, in some cases, be extracted from hysteresis loops measured at various diffraction orders. We find that the shape of the domains depends strongly on: the direction of the applied field relative to the holes, the size of the square holes, and also the small intrinsic anisotropy of the unpatterned film. DMOKE results are compared with those obtained with magnetic force microscopy. In the saturated state Brillouin spectroscopy shows that square holes induce a fourfold anisotropy in the film.
Physical Review B, 2000
The magnetic properties of an array of elliptical holes in an Fe film have been investigated usin... more The magnetic properties of an array of elliptical holes in an Fe film have been investigated using the diffracted magneto-optical Kerr effect (D-MOKE), Lorentz scanning transmission electron microscopy (LSTEM), and Brillouin scattering. In the absence of a comprehensive theory for magnetization or magnons in these materials, we find that our results can be fit by a semiquantitative analysis treating the
1998 IEEE MTT-S International Microwave Symposium Digest (Cat. No.98CH36192), 1998
ABSTRACT We present the first scanned probe Schottky diode used as a detector of microwave power.... more ABSTRACT We present the first scanned probe Schottky diode used as a detector of microwave power. This technique enables direct sensing of local fields without the use of a high frequency receiver, and it can accommodate simultaneous measurement of sample topography, as well. Applications for this probe range from field mapping on planar filters to failure analysis of MMIC's
Atherosclerosis Supplements, 2011
Our model is able to reproduce measured lipid data of humans with normal lipoprotein values. Furt... more Our model is able to reproduce measured lipid data of humans with normal lipoprotein values. Furthermore, certain lipoprotein-associated diseases like hypercholesterolemia may be simulated by modifying the associated parameters of the metabolism. As particular lipoproteins are simulated, we are able to get information about the distribution and metabolic rates of lipoproteins in all density classes. Hence it is possible to simulate kinetic measurements. Discussion: The model is capable to investigate associated diseases of lipid metabolism and to provide a powerful tool for possible therapeutic approaches. However, there is still need for further improvements.
RSC Adv., 2014
In this paper we report a method of continuous electroextraction of amino acids as model samples ... more In this paper we report a method of continuous electroextraction of amino acids as model samples using a caseinate-poly(ethylene-glycol) -PEGtwo phase system in a microchip able to separate compounds based on their differences in electrophoretic mobility and solvent affinity. Fundamentally, the phase boundary replaces a physical membrane, suppressing the diffusion. When external potential is applied, the molecules selectively cross this barrier. The selectivity of the amino acids extraction is the result of their electrochemical properties and applied voltage. We applied this method to amino acids extraction and the results suggest the possibility of high levels of purification by controlling the electric field strength across the liquid barrier. It is a promising method for complex sample separation as well as for the purification of individual compounds.
Biosensors & bioelectronics, 2002
An ion-sensitive field effect transistor (ISFET)-based immunosensor was developed to detect/quant... more An ion-sensitive field effect transistor (ISFET)-based immunosensor was developed to detect/quantitate beta-Bungarotoxin (beta-BuTx), a potent presynaptic neurotoxin from the venom of Bungarus multicinctus. A murine monoclonal antibody (mAb 15) specific to beta-BuTx was immobilized onto silicon nitride wafers after silanization and activation with glutaraldehyde. A chip based enzyme linked-immunosorbantassay (ELISA) was performed to ascertain antigen binding to the immobilized antibody. To develop an electrochemical immunosensing system for the detection/quantitation of beta-BuTx, an ISFET was used as a solid phase detector. MAb 15 was immobilized on the gate region of the ISFET. The antigen antibody reaction was monitored by the addition of urease conjugated rabbit anti-beta-BuTx antibodies. The sensor can detect toxin level as low as 15.6 ng/ml. The efficacy of the sensor for the determination of beta-BuTx from B. multicinctus venom was demonstrated in mouse model. Toxin concentra...
Controlling and Using Light in Nanometric Domains, 2001
ABSTRACT We report on the application as well as microfabrication process of batch-fabricated opt... more ABSTRACT We report on the application as well as microfabrication process of batch-fabricated optical near-field sensors using cantilevered scanning force microscopy tips. The process includes implementation of a coaxial conductive geometry into a silicon sensor tip, along with electrical connections on the cantilever and chip body. The coaxial guide structure is used as electric lead to a sub-micron Schottky photodetector at the end of the tip, formed at the junction of the protruding silicon core and a recessed aluminum coating. The I-V curves of these sensors are consistent with numerical studies for such constricted geometries. Optical near-field data gathered by this sensor in topography-following mode is presented.
1996 International Integrated Reliability Workshop Final Report, 1996
ABSTRACT We introduce a new concept for combined probing of topography and local AC fields and re... more ABSTRACT We introduce a new concept for combined probing of topography and local AC fields and report some early results of tip fabrication and measurements. Because this instrument can be used to measure both AC fields and topography with nanometer-level localization, we call it a Nanoscilloscope. This new instrument promises to be particularly useful for proactive reliability engineering because it can simultaneously image dynamic electric fields (i.e. signals) and sample topography, but unlike electron-beam probing, it operates in ambient conditions
Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures, 1996
ABSTRACT