Waseem Asghar - Academia.edu (original) (raw)

Papers by Waseem Asghar

Cancer Targeted Drug Delivery, 2013

Nanotechnology, 2011

Solid-state nanopores have emerged as sensors for single molecules and these have been employed t... more Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.

Materials Today, 2015

The natural microenvironment of tumors is composed of extracellular matrix (ECM), blood vasculatu... more The natural microenvironment of tumors is composed of extracellular matrix (ECM), blood vasculature, and supporting stromal cells. The physical characteristics of ECM as well as the cellular components play a vital role in controlling cancer cell proliferation, apoptosis, metabolism, and differentiation. To mimic the tumor microenvironment outside the human body for drug testing, two-dimensional (2-D) and murine tumor models are routinely used. Although these conventional approaches are employed in preclinical studies, they still present challenges. For example, murine tumor models are expensive and difficult to adopt for routine drug screening. On the other hand, 2-D in vitro models are simple to perform, but they do not recapitulate natural tumor microenvironment, because they do not capture important three-dimensional (3-D) cell-cell, cell-matrix signaling pathways, and multi-cellular heterogeneous components of the tumor microenvironment such as stromal and immune cells. The three-dimensional (3-D) in vitro tumor models aim to closely mimic cancer microenvironments and have emerged as an alternative to routinely used methods for drug screening. Herein, we review recent advances in 3-D tumor model generation and highlight directions for future applications in drug testing.

Scientific reports, Jan 6, 2015

The need for sensitive, robust, portable, and inexpensive biosensing platforms is of significant ... more The need for sensitive, robust, portable, and inexpensive biosensing platforms is of significant interest in clinical applications for disease diagnosis and treatment monitoring at the point-of-care (POC) settings. Rapid, accurate POC diagnostic assays play a crucial role in developing countries, where there are limited laboratory infrastructure, trained personnel, and financial support. However, current diagnostic assays commonly require long assay time, sophisticated infrastructure and expensive reagents that are not compatible with resource-constrained settings. Although paper and flexible material-based platform technologies provide alternative approaches to develop POC diagnostic assays for broad applications in medicine, they have technical challenges integrating to different detection modalities. Here, we address the limited capability of current paper and flexible material-based platforms by integrating cellulose paper and flexible polyester films as diagnostic biosensing ma...

2011 11th IEEE International Conference on Nanotechnology, 2011

Solid-state nanopore systems have emerged as novel platforms for DNA, RNA and protein analysis. I... more Solid-state nanopore systems have emerged as novel platforms for DNA, RNA and protein analysis. In the state of the art, the nanopores are made using electron beam induced shrinking of larger pores, drilling in thin membranes or deposition of material on fabricated nanopores. These processes have slow deposition rates, provide poor control of surface composition of deposited layers and the

Cancer Targeted Drug Delivery, 2013

2010 IEEE Frontiers in Education Conference (FIE), 2010

The applications of nanotechnology in biology and medicine have seen unprecedented growth. Nanore... more The applications of nanotechnology in biology and medicine have seen unprecedented growth. Nanoresearch encompasses many areas of science and engineering. This paper reports the development of innovative methods and approaches to teach Bio-Nanotechnology, with similar relevance for biologists and engineers. The course work is approached from an engineering perspective offering insights on the details of nano-scale fabrication processes as well as cell biology. The basics of biology and chemistry, with focus on how to engineer the behavior of molecules at the nano-scale, are also introduced and analyzed. The course is designed so as to (1) focus on broad accessibility (for students from engineering and natural sciences), (2) build designproblems of interest that cross the traditional boundaries, (3) accelerate assimilation of new knowledge spanning multiple domains through individual and construct-centered design problems, and (4) effectively exchange knowledge of state of the art developments and capabilities using collaborative learning projects.

American Journal of Biomedical Sciences, 2009

A major challenge in using solid-state nanopores for DNA detection and sequencing is the molecula... more A major challenge in using solid-state nanopores for DNA detection and sequencing is the molecular selectivity and sensitivity resolution through proper control of DNA-nanopore interface. This paper explores the interaction mechanisms between DNA and nanopores through molecular dynamics simulations. The DNA translocation dynamics through nanopores of various diameters and under various applied biasvoltages are characterized. Such property-function relationship can be used for the optimal designs of the lab-on-chip DNA diagnostic devices.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2011

Deposition of polymeric and biocompatible nanolayers on the solid-state substrates is done using ... more Deposition of polymeric and biocompatible nanolayers on the solid-state substrates is done using a simple vacuum chamber. The chemical characteristics of the deposited nanolayer are analyzed using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. The surface morphology of the nanolayers is analyzed using contact angle goniometer and scanning electron microscopy. The coated nanolayers show excellent stability in different chemical surroundings including the physiological pH therefore making it applicable in coating 3D MEMS devices and body implants which need medicated coating. A micropore is coated with this approach and results depict uniform coating of the structure.

Advanced Healthcare Materials, 2014

Fertilization and reproduction are central to the survival and propagation of a species. Couples ... more Fertilization and reproduction are central to the survival and propagation of a species. Couples who cannot reproduce naturally have to undergo in vitro clinical procedures. An integral part of these clinical procedures includes isolation of healthy sperm from raw semen. Existing sperm sorting methods are not effi cient and isolate sperm having high DNA fragmentation and reactive oxygen species (ROS), and suffer from multiple manual steps and variations between operators. Inspired by in vivo natural sperm sorting mechanisms where vaginal mucus becomes less viscous to form microchannels to guide sperm towards egg, a chip is presented that effi ciently sorts healthy, motile and morphologically normal sperm without centrifugation. Higher percentage of sorted sperm show signifi cantly lesser ROS and DNA fragmentation than the conventional swim-up method. The presented chip is an easy-to-use highthroughput sperm sorter that provides standardized sperm sorting assay with less reliance on operators's skills, facilitating reliable operational steps.

Biotechnology Journal, 2014

Cell cryopreservation maintains cellular life at sub-zero temperatures by slowing down biochemica... more Cell cryopreservation maintains cellular life at sub-zero temperatures by slowing down biochemical processes. Various cell types are routinely cryopreserved in modern reproductive, regenerative, and transfusion medicine. Current cell cryopreservation methods involve freezing (slow/rapid) or vitrifying cells in the presence of a cryoprotective agent (CPA). Although these methods are clinically utilized, cryo-injury due to ice crystals, osmotic shock, and CPA toxicity cause loss of cell viability and function. Recent approaches using minimum volume vitrification provide alternatives to the conventional cryopreservation methods. Minimum volume vitrification provides ultra-high cooling and rewarming rates that enable preserving cells without ice crystal formation. Herein, we review recent advances in cell cryopreservation technology and provide examples of techniques that are utilized in oocyte, stem cell, and red blood cell cryopreservation.

2011 IEEE/NIH Life Science Systems and Applications Workshop (LiSSA), 2011

Break junctions have emerged as an important tool to interrogate electrical transport properties ... more Break junctions have emerged as an important tool to interrogate electrical transport properties of molecules. A number of approaches have been reported for the fabrication of break junctions, including optical/e-beam lithography, electromigration, and electrochemical deposition of conductive materials. All of these are either time consuming (due to slow e-beam writing) or give low yield. We report a novel method to fabricate a nanogap between two gold electrodes. A scratch made by focused ion beam (FIB) milling followed by electromigration provides rapid and high throughput break junctions. These nanogap break junctions are used to selectively capture and electrically detect cancer biomarker protein.

Micro- and Nanotechnology Sensors, Systems, and Applications III, 2011

Translocation of DNA through a silicon nanopore with an applied voltage bias causes the ionic cur... more Translocation of DNA through a silicon nanopore with an applied voltage bias causes the ionic current signal to spike sharply downward as molecules block the flow of ions through the pore. Proper processing of the sampled signal is paramount in obtaining accurate translocation kinetics from the negative peaks, but manual analysis is time-consuming. Here, an algorithm is reported that automates the process. It imports the signal from a tab-delimited text file, automatically zero-baselines, filters noise, detects negative peaks, and estimates each peak's start and end time. The imported signal is processed using a zero-overlap sampling window. Peaks are detected by comparison of the window's standard deviation to a threshold standard deviation in addition to a comparison against a peak magnitude threshold. Zero-baselining and noise removal is accomplished through calculation of the mean of non-peak window values. The start and end times of a peak are approximated by checking where the signal becomes positive on either side of the peak. The program then stores the magnitude, sample number, approximate start time, and approximate end time of each peak in a matrix. All these tasks are automatically done by the program, requiring only the following initial input from the user: window size, file path to sampled signal data file, standard deviation threshold, peak magnitude threshold, and sampling frequency of the sampled signal. Trials with signals from an 11-micron pore sampled at 100 kHz for 30 seconds yielded a high rate of successful peak detection with a magnitude threshold of 600, a standard deviation threshold of 1.25, and a window size of 100.

Biosensors and Bioelectronics, 2014

Early stage detection and precise quantification of circulating tumor cells (CTCs) in the periphe... more Early stage detection and precise quantification of circulating tumor cells (CTCs) in the peripheral blood of cancer patients are important for early diagnosis. Early diagnosis improves the effectiveness of the therapy and results in better prognosis. Several techniques have been used for CTC detection but are limited by their need for dye tagging, low throughput and lack of statistical reliability at single cell level. Solid-state micropores can characterize each cell in a sample providing interesting information about cellular populations. We report a multi-channel device which utilized solid-state micropores array assembly for simultaneous measurement of cell translocation. This increased the throughput of measurement and as the cells passed the micropores, tumor cells showed distinctive current blockade pulses, when compared to leukocytes. The ionic current across each micropore channel was continuously monitored and recorded. The measurement system not only increased throughput but also provided on-chip cross-relation. The whole blood was lysed to get rid of red blood cells, so the blood dilution was not needed. The approach facilitated faster processing of blood samples with tumor cell detection efficiency of about 70%. The design provided a simple and inexpensive method for rapid and reliable detection of tumor cells without any cell staining or surface functionalization. The device can also be used for high throughput electrophysiological analysis of other cell types.

The Journal of Physical Chemistry B, 2011

Nanotechnology, 2011

Solid-state nanopores have emerged as sensors for single molecules and these have been employed t... more Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.

Nanotechnology, 2012

Epidermal growth factor receptor (EGFR) is a cell surface protein overexpressed in cancerous cell... more Epidermal growth factor receptor (EGFR) is a cell surface protein overexpressed in cancerous cells. It is known to be the most common oncogene. EGFR concentration also increases in the serum of cancer patients. The detection of small changes in the concentration of EGFR can be critical for early diagnosis, resulting in better treatment and improved survival rate of cancer patients. This article reports an RNA aptamer based approach to selectively capture EGFR protein and an electrical scheme for its detection. Pairs of gold electrodes with nanometer separation were made through confluence of focused ion beam scratching and electromigration. The aptamer was hybridized to a single stranded DNA molecule, which in turn was immobilized on the SiO(2) surface between the gold nanoelectrodes. The selectivity of the aptamer was demonstrated by using control chips with mutated non-selective aptamer and with no aptamer. Surface functionalization was characterized by optical detection and two orders of magnitude increase in direct current (DC) was measured when selective capture of EGFR occurred. This represents an electronic biosensor for the detection of proteins of interest for medical applications.

Nanotechnology, 2012

Cell adhesion, morphology and growth are influenced by surface topography at nano and micrometer ... more Cell adhesion, morphology and growth are influenced by surface topography at nano and micrometer scales. Nano-textured surfaces are prepared using photolithography, plasma etching and long polymer chemical etching which are cost prohibitive and require specialized equipment. This article demonstrates a simple approach to synthesize nano-textured scaffolds from chicken eggshells. Varieties of pattern are made on the eggshells like micro-needle forests and nanopores, giving very uniform nano-textures to the surfaces. The surfaces are characterized for chemical composition and crystal phase. The novel patterns are transferred to PDMS surfaces and the nano-textured PDMS surfaces are used to study the effect of texturing on human fibroblast cell growth and attachment. The effects of surface topographies, along with laminin coating on cell cultures, are also studied. We find an exciting phenomenon that the initial seeding density of the fibroblast cells affects the influence of the nano-texturing on cell growth. These nano-textured surfaces give 16 times more fibroblast growth when compared to flat PDMS surfaces. The novel nano-textured patterns also double the laminin adsorption on PDMS.

Nanoscale Research Letters, 2011

Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A nove... more Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A novel and simple technique for solid-state nanopore fabrication is reported here. The process involves direct thermal heating of 100 to 300 nm nanopores, made by focused ion beam (FIB) milling in free-standing membranes. Direct heating results in shrinking of the silicon dioxide nanopores. The free-standing silicon dioxide membrane is softened and adatoms diffuse to a lower surface free energy. The model predicts the dynamics of the shrinking process as validated by experiments. The method described herein, can process many samples at one time. The inbuilt stress in the oxide film is also reduced due to annealing. The surface composition of the pore walls remains the same during the shrinking process. The linear shrinkage rate gives a reproducible way to control the diameter of a pore with nanometer precision.

Nano Today, 2013

Circulating tumor cells (CTCs) originate from the primary tumor mass and enter into the periphera... more Circulating tumor cells (CTCs) originate from the primary tumor mass and enter into the peripheral bloodstream. CTCs hold the key to understanding the biology of metastasis and also play a vital role in cancer diagnosis, prognosis, disease monitoring, and personalized therapy. However, CTCs are rare in blood and hard to isolate. Additionally, the viability of CTCs can easily be compromised under high shear stress while releasing them from a surface. The heterogeneity of CTCs in biomarker expression makes their isolation quite challenging; the isolation efficiency and specificity of current approaches need to be improved. Nanostructured substrates have emerged as a promising biosensing platform since they provide better isolation sensitivity at the cost of specificity for CTC isolation. This review discusses major challenges faced by CTC isolation techniques and focuses on nanostructured substrates as a platform for CTC isolation.

Cancer Targeted Drug Delivery, 2013

Nanotechnology, 2011

Solid-state nanopores have emerged as sensors for single molecules and these have been employed t... more Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.

Materials Today, 2015

The natural microenvironment of tumors is composed of extracellular matrix (ECM), blood vasculatu... more The natural microenvironment of tumors is composed of extracellular matrix (ECM), blood vasculature, and supporting stromal cells. The physical characteristics of ECM as well as the cellular components play a vital role in controlling cancer cell proliferation, apoptosis, metabolism, and differentiation. To mimic the tumor microenvironment outside the human body for drug testing, two-dimensional (2-D) and murine tumor models are routinely used. Although these conventional approaches are employed in preclinical studies, they still present challenges. For example, murine tumor models are expensive and difficult to adopt for routine drug screening. On the other hand, 2-D in vitro models are simple to perform, but they do not recapitulate natural tumor microenvironment, because they do not capture important three-dimensional (3-D) cell-cell, cell-matrix signaling pathways, and multi-cellular heterogeneous components of the tumor microenvironment such as stromal and immune cells. The three-dimensional (3-D) in vitro tumor models aim to closely mimic cancer microenvironments and have emerged as an alternative to routinely used methods for drug screening. Herein, we review recent advances in 3-D tumor model generation and highlight directions for future applications in drug testing.

Scientific reports, Jan 6, 2015

The need for sensitive, robust, portable, and inexpensive biosensing platforms is of significant ... more The need for sensitive, robust, portable, and inexpensive biosensing platforms is of significant interest in clinical applications for disease diagnosis and treatment monitoring at the point-of-care (POC) settings. Rapid, accurate POC diagnostic assays play a crucial role in developing countries, where there are limited laboratory infrastructure, trained personnel, and financial support. However, current diagnostic assays commonly require long assay time, sophisticated infrastructure and expensive reagents that are not compatible with resource-constrained settings. Although paper and flexible material-based platform technologies provide alternative approaches to develop POC diagnostic assays for broad applications in medicine, they have technical challenges integrating to different detection modalities. Here, we address the limited capability of current paper and flexible material-based platforms by integrating cellulose paper and flexible polyester films as diagnostic biosensing ma...

2011 11th IEEE International Conference on Nanotechnology, 2011

Solid-state nanopore systems have emerged as novel platforms for DNA, RNA and protein analysis. I... more Solid-state nanopore systems have emerged as novel platforms for DNA, RNA and protein analysis. In the state of the art, the nanopores are made using electron beam induced shrinking of larger pores, drilling in thin membranes or deposition of material on fabricated nanopores. These processes have slow deposition rates, provide poor control of surface composition of deposited layers and the

Cancer Targeted Drug Delivery, 2013

2010 IEEE Frontiers in Education Conference (FIE), 2010

The applications of nanotechnology in biology and medicine have seen unprecedented growth. Nanore... more The applications of nanotechnology in biology and medicine have seen unprecedented growth. Nanoresearch encompasses many areas of science and engineering. This paper reports the development of innovative methods and approaches to teach Bio-Nanotechnology, with similar relevance for biologists and engineers. The course work is approached from an engineering perspective offering insights on the details of nano-scale fabrication processes as well as cell biology. The basics of biology and chemistry, with focus on how to engineer the behavior of molecules at the nano-scale, are also introduced and analyzed. The course is designed so as to (1) focus on broad accessibility (for students from engineering and natural sciences), (2) build designproblems of interest that cross the traditional boundaries, (3) accelerate assimilation of new knowledge spanning multiple domains through individual and construct-centered design problems, and (4) effectively exchange knowledge of state of the art developments and capabilities using collaborative learning projects.

American Journal of Biomedical Sciences, 2009

A major challenge in using solid-state nanopores for DNA detection and sequencing is the molecula... more A major challenge in using solid-state nanopores for DNA detection and sequencing is the molecular selectivity and sensitivity resolution through proper control of DNA-nanopore interface. This paper explores the interaction mechanisms between DNA and nanopores through molecular dynamics simulations. The DNA translocation dynamics through nanopores of various diameters and under various applied biasvoltages are characterized. Such property-function relationship can be used for the optimal designs of the lab-on-chip DNA diagnostic devices.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2011

Deposition of polymeric and biocompatible nanolayers on the solid-state substrates is done using ... more Deposition of polymeric and biocompatible nanolayers on the solid-state substrates is done using a simple vacuum chamber. The chemical characteristics of the deposited nanolayer are analyzed using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. The surface morphology of the nanolayers is analyzed using contact angle goniometer and scanning electron microscopy. The coated nanolayers show excellent stability in different chemical surroundings including the physiological pH therefore making it applicable in coating 3D MEMS devices and body implants which need medicated coating. A micropore is coated with this approach and results depict uniform coating of the structure.

Advanced Healthcare Materials, 2014

Fertilization and reproduction are central to the survival and propagation of a species. Couples ... more Fertilization and reproduction are central to the survival and propagation of a species. Couples who cannot reproduce naturally have to undergo in vitro clinical procedures. An integral part of these clinical procedures includes isolation of healthy sperm from raw semen. Existing sperm sorting methods are not effi cient and isolate sperm having high DNA fragmentation and reactive oxygen species (ROS), and suffer from multiple manual steps and variations between operators. Inspired by in vivo natural sperm sorting mechanisms where vaginal mucus becomes less viscous to form microchannels to guide sperm towards egg, a chip is presented that effi ciently sorts healthy, motile and morphologically normal sperm without centrifugation. Higher percentage of sorted sperm show signifi cantly lesser ROS and DNA fragmentation than the conventional swim-up method. The presented chip is an easy-to-use highthroughput sperm sorter that provides standardized sperm sorting assay with less reliance on operators's skills, facilitating reliable operational steps.

Biotechnology Journal, 2014

Cell cryopreservation maintains cellular life at sub-zero temperatures by slowing down biochemica... more Cell cryopreservation maintains cellular life at sub-zero temperatures by slowing down biochemical processes. Various cell types are routinely cryopreserved in modern reproductive, regenerative, and transfusion medicine. Current cell cryopreservation methods involve freezing (slow/rapid) or vitrifying cells in the presence of a cryoprotective agent (CPA). Although these methods are clinically utilized, cryo-injury due to ice crystals, osmotic shock, and CPA toxicity cause loss of cell viability and function. Recent approaches using minimum volume vitrification provide alternatives to the conventional cryopreservation methods. Minimum volume vitrification provides ultra-high cooling and rewarming rates that enable preserving cells without ice crystal formation. Herein, we review recent advances in cell cryopreservation technology and provide examples of techniques that are utilized in oocyte, stem cell, and red blood cell cryopreservation.

2011 IEEE/NIH Life Science Systems and Applications Workshop (LiSSA), 2011

Break junctions have emerged as an important tool to interrogate electrical transport properties ... more Break junctions have emerged as an important tool to interrogate electrical transport properties of molecules. A number of approaches have been reported for the fabrication of break junctions, including optical/e-beam lithography, electromigration, and electrochemical deposition of conductive materials. All of these are either time consuming (due to slow e-beam writing) or give low yield. We report a novel method to fabricate a nanogap between two gold electrodes. A scratch made by focused ion beam (FIB) milling followed by electromigration provides rapid and high throughput break junctions. These nanogap break junctions are used to selectively capture and electrically detect cancer biomarker protein.

Micro- and Nanotechnology Sensors, Systems, and Applications III, 2011

Translocation of DNA through a silicon nanopore with an applied voltage bias causes the ionic cur... more Translocation of DNA through a silicon nanopore with an applied voltage bias causes the ionic current signal to spike sharply downward as molecules block the flow of ions through the pore. Proper processing of the sampled signal is paramount in obtaining accurate translocation kinetics from the negative peaks, but manual analysis is time-consuming. Here, an algorithm is reported that automates the process. It imports the signal from a tab-delimited text file, automatically zero-baselines, filters noise, detects negative peaks, and estimates each peak's start and end time. The imported signal is processed using a zero-overlap sampling window. Peaks are detected by comparison of the window's standard deviation to a threshold standard deviation in addition to a comparison against a peak magnitude threshold. Zero-baselining and noise removal is accomplished through calculation of the mean of non-peak window values. The start and end times of a peak are approximated by checking where the signal becomes positive on either side of the peak. The program then stores the magnitude, sample number, approximate start time, and approximate end time of each peak in a matrix. All these tasks are automatically done by the program, requiring only the following initial input from the user: window size, file path to sampled signal data file, standard deviation threshold, peak magnitude threshold, and sampling frequency of the sampled signal. Trials with signals from an 11-micron pore sampled at 100 kHz for 30 seconds yielded a high rate of successful peak detection with a magnitude threshold of 600, a standard deviation threshold of 1.25, and a window size of 100.

Biosensors and Bioelectronics, 2014

Early stage detection and precise quantification of circulating tumor cells (CTCs) in the periphe... more Early stage detection and precise quantification of circulating tumor cells (CTCs) in the peripheral blood of cancer patients are important for early diagnosis. Early diagnosis improves the effectiveness of the therapy and results in better prognosis. Several techniques have been used for CTC detection but are limited by their need for dye tagging, low throughput and lack of statistical reliability at single cell level. Solid-state micropores can characterize each cell in a sample providing interesting information about cellular populations. We report a multi-channel device which utilized solid-state micropores array assembly for simultaneous measurement of cell translocation. This increased the throughput of measurement and as the cells passed the micropores, tumor cells showed distinctive current blockade pulses, when compared to leukocytes. The ionic current across each micropore channel was continuously monitored and recorded. The measurement system not only increased throughput but also provided on-chip cross-relation. The whole blood was lysed to get rid of red blood cells, so the blood dilution was not needed. The approach facilitated faster processing of blood samples with tumor cell detection efficiency of about 70%. The design provided a simple and inexpensive method for rapid and reliable detection of tumor cells without any cell staining or surface functionalization. The device can also be used for high throughput electrophysiological analysis of other cell types.

The Journal of Physical Chemistry B, 2011

Nanotechnology, 2011

Solid-state nanopores have emerged as sensors for single molecules and these have been employed t... more Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.

Nanotechnology, 2012

Epidermal growth factor receptor (EGFR) is a cell surface protein overexpressed in cancerous cell... more Epidermal growth factor receptor (EGFR) is a cell surface protein overexpressed in cancerous cells. It is known to be the most common oncogene. EGFR concentration also increases in the serum of cancer patients. The detection of small changes in the concentration of EGFR can be critical for early diagnosis, resulting in better treatment and improved survival rate of cancer patients. This article reports an RNA aptamer based approach to selectively capture EGFR protein and an electrical scheme for its detection. Pairs of gold electrodes with nanometer separation were made through confluence of focused ion beam scratching and electromigration. The aptamer was hybridized to a single stranded DNA molecule, which in turn was immobilized on the SiO(2) surface between the gold nanoelectrodes. The selectivity of the aptamer was demonstrated by using control chips with mutated non-selective aptamer and with no aptamer. Surface functionalization was characterized by optical detection and two orders of magnitude increase in direct current (DC) was measured when selective capture of EGFR occurred. This represents an electronic biosensor for the detection of proteins of interest for medical applications.

Nanotechnology, 2012

Cell adhesion, morphology and growth are influenced by surface topography at nano and micrometer ... more Cell adhesion, morphology and growth are influenced by surface topography at nano and micrometer scales. Nano-textured surfaces are prepared using photolithography, plasma etching and long polymer chemical etching which are cost prohibitive and require specialized equipment. This article demonstrates a simple approach to synthesize nano-textured scaffolds from chicken eggshells. Varieties of pattern are made on the eggshells like micro-needle forests and nanopores, giving very uniform nano-textures to the surfaces. The surfaces are characterized for chemical composition and crystal phase. The novel patterns are transferred to PDMS surfaces and the nano-textured PDMS surfaces are used to study the effect of texturing on human fibroblast cell growth and attachment. The effects of surface topographies, along with laminin coating on cell cultures, are also studied. We find an exciting phenomenon that the initial seeding density of the fibroblast cells affects the influence of the nano-texturing on cell growth. These nano-textured surfaces give 16 times more fibroblast growth when compared to flat PDMS surfaces. The novel nano-textured patterns also double the laminin adsorption on PDMS.

Nanoscale Research Letters, 2011

Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A nove... more Solid-state nanopores have emerged as useful single-molecule sensors for DNA and proteins. A novel and simple technique for solid-state nanopore fabrication is reported here. The process involves direct thermal heating of 100 to 300 nm nanopores, made by focused ion beam (FIB) milling in free-standing membranes. Direct heating results in shrinking of the silicon dioxide nanopores. The free-standing silicon dioxide membrane is softened and adatoms diffuse to a lower surface free energy. The model predicts the dynamics of the shrinking process as validated by experiments. The method described herein, can process many samples at one time. The inbuilt stress in the oxide film is also reduced due to annealing. The surface composition of the pore walls remains the same during the shrinking process. The linear shrinkage rate gives a reproducible way to control the diameter of a pore with nanometer precision.

Nano Today, 2013

Circulating tumor cells (CTCs) originate from the primary tumor mass and enter into the periphera... more Circulating tumor cells (CTCs) originate from the primary tumor mass and enter into the peripheral bloodstream. CTCs hold the key to understanding the biology of metastasis and also play a vital role in cancer diagnosis, prognosis, disease monitoring, and personalized therapy. However, CTCs are rare in blood and hard to isolate. Additionally, the viability of CTCs can easily be compromised under high shear stress while releasing them from a surface. The heterogeneity of CTCs in biomarker expression makes their isolation quite challenging; the isolation efficiency and specificity of current approaches need to be improved. Nanostructured substrates have emerged as a promising biosensing platform since they provide better isolation sensitivity at the cost of specificity for CTC isolation. This review discusses major challenges faced by CTC isolation techniques and focuses on nanostructured substrates as a platform for CTC isolation.