CAP Profiles

Bio

Current Role at Stanford

Deputy Director, Center for Cancer Nanotechnology Excellence

Projects

  • Nanomedicine/Diagnostic and Therapeutic Nanodevices (2002 - Present)

    Location

    CA

  • Cancer Theranostics for Brain, Lung, Breast and Prostate (2012 - Present)

    This project involves several sub-projects wherein nano-based or nano-enabled approaches are used for evaluating response to anti-cancer therapy as well as intraoperative/minimally invasive phothermal and RF-based tumor ablation

    Location

    CA

  • Wearable/Implantable Devices (2013 - Present)

    Location

    CA

  • Health Monitoring, Precision Medicine, Microbiome (2013 - Present)

    Location

    CA

Contact

Links

Professional

Professional Interests

RESEARCH INTERESTS

* Biological Engineering and Micro/Nanomedicine *
- Chip-based biomedical micro and nano-integrated systems for sensing, diagnosis, and therapy; micro and nano-scale biosensors for cells, proteins, DNA
- Biomimetically Inspired Engineered Systems
- Biosensors, Intelligent Medical Devices utilizing machine learning, artificial intelligence and expert systems to improve functionality and performance
- Polymer-based microfludic and silicon micromachined chips for infectious agent detection and re-emerging diseases
- Single molecule imaging and image analysis to study cell:pathogen interactions, molecular beacons for intracellular gene expression analysis, Atomic Force Microscopy, study of viral capsid biomechanics and assembly
- Microbial and cellular engineering for Cancer applications
- Stimuli responsive polymers such as hydrogels for development of micro/nano-devices for drug delivery and biomedical sensing applications.
- Wireless Passive Theranostic Devices for medical monitoring and intervention

* Genomics/Systems Biology *
- Reverse Engineering of Signal Transduction Networks and Molecular Pathways: SilicoCyte, Virtual Cellular communities
- Applications of genomics and bioinformatics in molecular profiling of cancer. Identification of predictive tumor markers and anti-cancer small molecule drug leads.
- Artificial intelligence-based collaborative software development for Systems Biology: Fuzzy logic, Neural Nets, Genetic Algorithms, Expert Systems, Pattern Finding, Data Warehousing

* Gene Therapy/Microbiology/Virology *
- Microbial and cellular engineering
- Experimental Therapeutics and Diagnostics: Endogenously (Self)-Regulated Gene Therapy; Cellular Re-programming, Therapeutic Transgenics, Correction of genetic defects by via gene replacement
- Molecular basis of disease resistance , susceptibility and coordinated gene regulation. Enhancement of disease resistance via manipulation of host immune components, DNA vaccines and therapeutic modulation of signal transduction pathways by small molecule drugs
- Prediction and computational modeling of genome evolution of RNA viruses (Coronaviridae, influenza). Forced evolution of viruses and emergence of new strains or quasi-species formation
- MEMS and Nano-based Biosensors for detection and continious monitoring of airborne biothreat agents

Work Experience

  • Deputy Director, Center for Cancer Nanotechnology Excellence and Translation (CCNE-T), Stanford University (9/1/2010)

    http://mips.stanford.edu/grants/ccne-t/

    Location

    Stanford, CA 94305

  • Deputy Director, Center for Cancer Nanotechnology Excellence focused on Therapy Response (CCNE-TR), Stanford University (5/1/2008)

    http://mips.stanford.edu/grants/ccne/

    Location

    Stanford, CA 94305

  • Assistant Research Professor (Nanomedicine), Purdue University (4/1/2005 - 5/1/2008)

    Faculty member in the Weldon School of Biomedical Engineering (BME) at Purdue University.

    Carried out Nanotechnology research.

    Location

    West Lafayette, IN

  • Manager, BioMEMS and BioNano Laboratories, Birck Nanotechnology Center, Purdue University (1/1/2005 - 5/1/2008)

    http://nano.purdue.edu/

    Location

    West Lafayette, IN

  • Senior Research Scientist, School of Electrical and Computer Engineering, Purdue University (1/1/2002 - 12/30/2006)

    Location

    West Lafayette, IN

  • Manager, BioMEMS Laboratory, School of Electrical and Computer Engineering, Purdue University (1/1/2002 - 12/30/2006)

    Location

    West Lafayette, IN

  • Research Scientist-Genomics, Applied Intelligent Systems Lab, School of Nuclear Engineering, Purdue University (1/1/2000 - 12/30/2001)

    Location

    West Lafayette, IN

  • Research Associate, Indiana State ADDL, Purdue University (1/1/1998 - 12/30/2000)

    Location

    West Lafayette, IN

  • Research Assistant (Molecular Virology), Department of Comparative Pathobiology, Purdue University (1/1/1993 - 7/30/1998)

    Location

    West Lafayette, IN

Publications

All Publications

  • Rapid and specific labeling of single live Mycobacterium tuberculosis with a dual-targeting fluorogenic probe SCIENCE TRANSLATIONAL MEDICINE Cheng, Y., Xie, J., Lee, K., Gaur, R. L., Song, A., Dai, T., Ren, H., Wu, J., Sun, Z., Banaei, N., Akin, D., Rao, J. 2018; 10 (454)

    Abstract

    Tuberculosis (TB) remains a public health crisis and a leading cause of infection-related death globally. Although in high demand, imaging technologies that enable rapid, specific, and nongenetic labeling of live Mycobacterium tuberculosis (Mtb) remain underdeveloped. We report a dual-targeting strategy to develop a small molecular probe (CDG-DNB3) that can fluorescently label single bacilli within 1 hour. CDG-DNB3 fluoresces upon activation of the β-lactamase BlaC, a hydrolase naturally expressed in Mtb, and the fluorescent product is retained through covalent modification of the Mtb essential enzyme decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1). This dual-targeting probe not only discriminates live from dead Bacillus Calmette-Guérin (BCG) but also shows specificity for Mtb over other bacterial species including 43 nontuberculosis mycobacteria (NTM). In addition, CDG-DNB3 can image BCG phagocytosis in real time, as well as Mtb in patients' sputum. Together with a low-cost, self-driven microfluidic chip, we have achieved rapid labeling and automated quantification of live BCG. This labeling approach should find many potential applications for research toward TB pathogenesis, treatment efficacy assessment, and diagnosis.

    View details for PubMedID 30111644

  • Internalization of subcellular-scale microfabricated chips by healthy and cancer cells. PloS one Parizi, K. B., Akin, D., Wong, H. P. 2018; 13 (3): e0194712

    Abstract

    Continuous monitoring of physiological parameters inside a living cell will lead to major advances in our understanding of biology and complex diseases, such as cancer. It also enables the development of new medical diagnostics and therapeutics. Progress in nanofabrication and wireless communication has opened up the potential of making a wireless chip small enough that it can be wholly inserted into a living cell. To investigate how such chips could be internalized into various types of living single cells and how this process might affect cells' physiology, we designed and fabricated a series of multilayered micron-scale tag structures with different sizes as potential RFID (Radio Frequency IDentification) cell trackers. While the present structures are test structures that do not resonate, the tags that do resonate have similar structure from device fabrication, material properties, and device size point of view. The structures are in four different sizes, the largest with the lateral dimension of 9 mum * 21 mum. The thickness for these structures is kept constant at 1.5 mum. We demonstrate successful delivery of our fabricated chips into various types of living cells, such as melanoma skin cancer, breast cancer, colon cancer and healthy/normal fibroblast skin cells. To our surprise, we observed a remarkable internalization rate difference between each cell type; the uptake rate was faster for more aggressive cancer cells than the normal/healthy cells. Cell viability before and after tag cellular internalization and persistence of the internalized tags have also been recorded over the course of five days of incubation. These results establish the foundations of the possibility of long term, wireless, intracellular physiological signal monitoring.

    View details for PubMedID 29601607

  • Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics. Proceedings of the National Academy of Sciences of the United States of America Inci, F., Filippini, C., Baday, M., Ozen, M. O., Calamak, S., Durmus, N. G., Wang, S., Hanhauser, E., Hobbs, K. S., Juillard, F., Kuang, P. P., Vetter, M. L., Carocci, M., Yamamoto, H. S., Takagi, Y., Yildiz, U. H., Akin, D., Wesemann, D. R., Singhal, A., Yang, P. L., Nibert, M. L., Fichorova, R. N., Lau, D. T., Henrich, T. J., Kaye, K. M., Schachter, S. C., Kuritzkes, D. R., Steinmetz, L. M., Gambhir, S. S., Davis, R. W., Demirci, U. 2015; 112 (32): E4354-63

    Abstract

    Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients' homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE(2)RD), which addresses all these impediments on a single platform. The NE(2)RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE(2)RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE(2)RD's broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients' homes.

    View details for DOI 10.1073/pnas.1510824112

    View details for PubMedID 26195743

    View details for PubMedCentralID PMC4538635

  • Fluorescent Magnetic Nanoparticles for Magnetically Enhanced Cancer Imaging and Targeting in Living Subjects ACS NANO Fu, A., Wilson, R. J., Smith, B. R., Mullenix, J., Earhart, C., Akin, D., Guccione, S., Wang, S. X., Gambhir, S. S. 2012; 6 (8): 6862-6869

    Abstract

    Early detection and targeted therapy are two major challenges in the battle against cancer. Novel imaging contrast agents and targeting approaches are greatly needed to improve the sensitivity and specificity of cancer theranostic agents. Here, we implemented a novel approach using a magnetic micromesh and biocompatible fluorescent magnetic nanoparticles (FMN) to magnetically enhance cancer targeting in living subjects. This approach enables magnetic targeting of systemically administered individual FMN, containing a single 8 nm superparamagnetic iron oxide core. Using a human glioblastoma mouse model, we show that nanoparticles can be magnetically retained in both the tumor neovasculature and surrounding tumor tissues. Magnetic accumulation of nanoparticles within the neovasculature was observable by fluorescence intravital microscopy in real time. Finally, we demonstrate that such magnetically enhanced cancer targeting augments the biological functions of molecules linked to the nanoparticle surface.

    View details for DOI 10.1021/nn301670a

    View details for Web of Science ID 000307988900039

    View details for PubMedID 22857784

    View details for PubMedCentralID PMC3601027

  • Theranostics. NCI Cancer Nanotechnology Plan (2010-2020) Akin D., S.S. Gambhir 2010
  • Nanotechnology Research Directions for Societal Needs in 2020. Nanobiosystems, Medicine and Health. M.C. Roco, C.A. Mirkin and M.C. Hersham eds. Mirkin C.A., A. Nel, C. S. Thaxton, B.A. Baird, C. Batt, D. Grainger, S.S.Gambhir, D. Akin, O. Zhou, J.F. Stoddart, T.J. Meade, P. Grodzinski, D. Farrell, H.F. Tibbals, J. De Simone 2010; NSF
  • A cellular Trojan horse for delivery of therapeutic nanoparticles into tumors NANO LETTERS Choi, M., Stanton-Maxey, K. J., Stanley, J. K., Levin, C. S., Bardhan, R., Akin, D., Badve, S., Sturgis, J., Robinson, J. P., Bashir, R., Halas, N. J., Clare, S. E. 2007; 7 (12): 3759-3765

    Abstract

    Destruction of hypoxic regions within tumors, virtually inaccessible to cancer therapies, may well prevent malignant progression. The tumor's recruitment of monocytes into these regions may be exploited for nanoparticle-based delivery. Monocytes containing therapeutic nanoparticles could serve as "Trojan Horses" for nanoparticle transport into these tumor regions. Here we report the demonstration of several key steps toward this therapeutic strategy: phagocytosis of Au nanoshells, and photoinduced cell death of monocytes/macrophages as isolates and within tumor spheroids.

    View details for DOI 10.1021/nl072209h

    View details for Web of Science ID 000251581600037

    View details for PubMedID 17979310

  • Bacteria-mediated delivery of nanoparticles and cargo into cells NATURE NANOTECHNOLOGY Akin, D., Sturgis, J., Ragheb, K., Sherman, D., Burkholder, K., Robinson, J. P., Bhunia, A. K., Mohammed, S., Bashir, R. 2007; 2 (7): 441-449

    Abstract

    Nanoparticles and bacteria can be used, independently, to deliver genes and proteins into mammalian cells for monitoring or altering gene expression and protein production. Here, we show the simultaneous use of nanoparticles and bacteria to deliver DNA-based model drug molecules in vivo and in vitro. In our approach, cargo (in this case, a fluorescent or a bioluminescent gene) is loaded onto the nanoparticles, which are carried on the bacteria surface. When incubated with cells, the cargo-carrying bacteria ('microbots') were internalized by the cells, and the genes released from the nanoparticles were expressed in the cells. Mice injected with microbots also successfully expressed the genes as seen by the luminescence in different organs. This new approach may be used to deliver different types of cargo into live animals and a variety of cells in culture without the need for complicated genetic manipulations.

    View details for DOI 10.1038/nnano.2007.149

    View details for Web of Science ID 000248302500016

    View details for PubMedID 18654330

  • Solid-state nanopore channels with DNA selectivity NATURE NANOTECHNOLOGY Iqbal, S. M., Akin, D., Bashir, R. 2007; 2 (4): 243-248

    Abstract

    Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be determined by measuring how the forces on the DNA molecules, and also the ion currents through the nanopore, change as the molecules pass through the nanopore. Unlike their biological counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solutions and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a 'probe' of hair-pin loop DNA can, under an applied electrical field, selectively transport short lengths of 'target' ssDNA that are complementary to the probe. Even a single base mismatch between the probe and the target results in longer translocation pulses and a significantly reduced number of translocation events. Our single-molecule measurements allow us to measure separately the molecular flux and the pulse duration, providing a tool to gain fundamental insight into the channel-molecule interactions. The results can be explained in the conceptual framework of diffusive molecular transport with particle-channel interactions.

    View details for DOI 10.1038/nnano.2007.78

    View details for Web of Science ID 000245920900016

    View details for PubMedID 18654270

  • Anomalous resonance in a nanomechanical biosensor PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Gupta, A. K., Nair, P. R., Akin, D., Ladisch, M. R., Broyles, S., Alam, M. A., Bashir, R. 2006; 103 (36): 13362-13367

    Abstract

    The decrease in resonant frequency (-Deltaomega(r)) of a classical cantilever provides a sensitive measure of the mass of entities attached on its surface. This elementary phenomenon has been the basis of a new class of bio-nanomechanical devices as sensing components of integrated microsystems that can perform rapid, sensitive, and selective detection of biological and biochemical entities. Based on classical analysis, there is a widespread perception that smaller sensors are more sensitive (sensitivity approximately -0.5omega(r)/m(C), where m(C) is the mass of the cantilever), and this notion has motivated scaling of biosensors to nanoscale dimensions. In this work, we show that the response of a nanomechanical biosensor is far more complex than previously anticipated. Indeed, in contrast to classical microscale sensors, the resonant frequencies of the nanosensor may actually decrease or increase after attachment of protein molecules. We demonstrate theoretically and experimentally that the direction of the frequency change arises from a size-specific modification of diffusion and attachment kinetics of biomolecules on the cantilevers. This work may have broad impact on microscale and nanoscale biosensor design, especially when predicting the characteristics of bio-nanoelectromechanical sensors functionalized with biological capture molecules.

    View details for DOI 10.1073/pnas.0602022103

    View details for Web of Science ID 000240512700021

    View details for PubMedID 16938886

  • Single virus particle mass detection using microresonators with nanoscale thickness Applied Physics Letters Gupta A., D. Akin, R. Bashir 2004; 84: 1976-1978
  • Nanomedicine for Spontaneous Brain Tumors: A Companion Clinical Trial. ACS nano Arami, H., Patel, C. B., Madsen, S. J., Dickinson, P. J., Davis, R. M., Zeng, Y., Sturges, B. K., Woolard, K. D., Habte, F. G., Akin, D., Sinclair, R., Gambhir, S. S. 2019

    Abstract

    Nanoparticles' enhanced permeation and retention (EPR) variations due to tumor heterogeneity in naturally occurring brain tumors are commonly neglected in preclinical nanomedicine studies. Recent pathological studies have shown striking similarities between brain tumors in humans and dogs, indicating that canine brain tumors may be a valuable model to evaluate nanoparticles' EPR in this context. We recruited canine clinical cases with spontaneous brain tumors to investigate nanoparticles' EPR in different brain tumor pathologies using surface-enhanced Raman spectroscopy (SERS). We used gold nanoparticles due to their surface plasmon effect that enables their sensitive and microscopic resolution detection using the SERS technique. Raman microscopy of the resected tumors showed heterogeneous EPR of nanoparticles into oligodendrogliomas and meningiomas of different grades, without any detectable traces in necrotic parts of the tumors or normal brain. Raman observations were confirmed by scanning electron microscopy (SEM) and X-ray elemental analyses, which enabled localization of individual nanoparticles embedded in tumor tissues. Our results demonstrate nanoparticles' EPR and its variations in clinically relevant, spontaneous brain tumors. Such heterogeneities should be considered alongside routine preoperative imaging and histopathological analyses in order to accelerate clinical management of brain tumors using nanomedicine approaches.

    View details for PubMedID 30714717

  • Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device ((NERD)-R-2) for diagnostics PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Inci, F., Filippini, C., Baday, M., Ozen, M. O., Calamak, S., Durmus, N. G., Wang, S., Hanhauser, E., Hobbs, K. S., Juillard, F., Kuang, P. P., Vetter, M. L., Carocci, M., Yamamoto, H. S., Takagi, Y., Yildiz, U. H., Akin, D., Wesemann, D. R., Singhal, A., Yang, P. L., Nibert, M. L., Fichorova, R. N., Lau, D. T., Henrich, T. J., Kaye, K. M., Schachter, S. C., Kuritzkes, D. R., Steinmetz, L. M., Gambhir, S. S., Davis, R. W., Demirci, U. 2015; 112 (32): E4354-E4363

    Abstract

    Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients' homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE(2)RD), which addresses all these impediments on a single platform. The NE(2)RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE(2)RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE(2)RD's broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients' homes.

    View details for DOI 10.1073/pnas.1510824112

    View details for Web of Science ID 000359285100006

    View details for PubMedID 26195743

    View details for PubMedCentralID PMC4538635

  • Biotargeted nanomedicines for cancer: six tenets before you begin NANOMEDICINE Goldberg, M. S., Hook, S. S., Wang, A. Z., Bulte, J. W., Patri, A. K., Uckun, F. M., Cryns, V. L., Hanes, J., Akin, D., Hall, J. B., Gharkholo, N., Mumper, R. J. 2013; 8 (2): 299-308

    Abstract

    Biotargeted nanomedicines have captured the attention of academic and industrial scientists who have been motivated by the theoretical possibilities of the 'magic bullet' that was first conceptualized by Paul Ehrlich at the beginning of the 20th century. The Biotargeting Working Group, consisting of more than 50 pharmaceutical scientists, engineers, biologists and clinicians, has been formed as part of the National Cancer Institute's Alliance for Nanotechnology in Cancer to harness collective wisdom in order to tackle conceptual and practical challenges in developing biotargeted nanomedicines for cancer. In modern science and medicine, it is impossible for any individual to be an expert in every aspect of biology, chemistry, materials science, pharmaceutics, toxicology, chemical engineering, imaging, physiology, oncology and regulatory affairs. Drawing on the expertise of leaders from each of these disciplines, this commentary highlights six tenets of biotargeted cancer nanomedicines in order to enable the translation of basic science into clinical practice.

    View details for DOI 10.2217/NNM.13.3

    View details for Web of Science ID 000314791200022

    View details for PubMedID 23394158

    View details for PubMedCentralID PMC3643633

  • Capture and alignment of phi29 viral particles in sub-40 nanometer porous alumina membranes BIOMEDICAL MICRODEVICES Moon, J., Akin, D., Xuan, Y., Ye, P. D., Guo, P., Bashir, R. 2009; 11 (1): 135-142

    Abstract

    Bacteriophage phi29 virus nanoparticles and its associated DNA packaging nanomotor can provide for novel possibilities towards the development of hybrid bio-nano structures. Towards the goal of interfacing the phi29 viruses and nanomotors with artificial micro and nanostructures, we fabricated nanoporous Anodic Aluminum Oxide (AAO) membranes with pore size of 70 nm and shrunk the pores to sub 40 nm diameter using atomic layer deposition (ALD) of Aluminum Oxide. We were able to capture and align particles in the anodized nanopores using two methods. Firstly, a functionalization and polishing process to chemically attach the particles in the inner surface of the pores was developed. Secondly, centrifugation of the particles was utilized to align them in the pores of the nanoporous membranes. In addition, when a mixture of empty capsids and packaged particles was centrifuged at specific speeds, it was found that the empty capsids deform and pass through 40 nm diameter pores whereas the particles packaged with DNA were mainly retained at the top surface of the nanoporous membranes. Fluorescence microscopy was used to verify the selective filtration of empty capsids through the nanoporous membranes.

    View details for DOI 10.1007/s10544-008-9217-0

    View details for Web of Science ID 000263114000014

    View details for PubMedID 18770041

  • Dielectrophoresis-based cell manipulation using electrodes on a reusable printed circuit board LAB ON A CHIP Park, K., Suk, H., Akin, D., Bashir, R. 2009; 9 (15): 2224-2229

    Abstract

    Particle manipulation based on dielectrophoresis (DEP) can be a versatile and useful tool in lab-on-chip systems for a wide range of cell patterning and tissue engineering applications. Even though there are extensive reports on the use of DEP for cell patterning applications, the development of approaches that make DEP even more affordable and common place is still desirable. In this study, we present the use of interdigitated electrodes on a printed circuit board (PCB) that can be reused to manipulate and position HeLa cells and polystyrene particles over 100 microm thick glass cover slips using DEP. An open-well or a closed microfluidic channel, both made of PDMS, was placed on the glass coverslip, which was then placed directly over the PCB. An AC voltage was applied to the electrodes on the PCB to induce DEP on the particles through the thin glass coverslip. The HeLa cells patterned with DEP were subsequently grown to confirm the lack of any adverse affects from the electric fields. This alternative and reusable platform for DEP particle manipulation can provide a convenient and rapid method for prototyping a DEP-based lab-on-chip system, cost-sensitive lab-on-chip applications, and a wide range of tissue engineering applications.

    View details for DOI 10.1039/b904328d

    View details for Web of Science ID 000268033900015

    View details for PubMedID 19606300

  • Real-time detection of airborne viruses on a mass-sensitive device APPLIED PHYSICS LETTERS Lee, J., Jang, J., Akin, D., Savran, C. A., Bashir, R. 2008; 93 (1)

    View details for DOI 10.1063/1.2956679

    View details for Web of Science ID 000258184600069

  • Effects of inlet/outlet configurations on the electrostatic capture of airborne nanoparticles and viruses MEASUREMENT SCIENCE & TECHNOLOGY Jang, J., Akin, D., Bashir, R. 2008; 19 (6)

    View details for DOI 10.1088/0957-0233/19/6/065204

    View details for Web of Science ID 000256907700014

  • Real-time detection of air-borne viruses on a mass-sensitive device Applied Physics Letters Lee, J., J. Jang, D. Akin, C.A. Savran, R. Bashir 2008; 93 (1): 13901
  • PCR-based detection in a micro-fabricated platform LAB ON A CHIP Bhattacharya, S., Salamat, S., Morisette, D., Banada, P., Akin, D., Liu, Y., Bhunia, A. K., Ladisch, M., Bashir, R. 2008; 8 (7): 1130-1136

    Abstract

    We present a novel, on-chip system for the electrokinetic capture of bacterial cells and their identification using the polymerase chain reaction (PCR). The system comprises a glass-silicon platform with a set of micro-channels, -chambers, and -electrodes. A platinum thin film resistor, placed in the proximity of the chambers, is used for temperature monitoring. The whole chip assembly is mounted on a Printed Circuit Board (PCB) and wire-bonded to it. The PCB has an embedded heater that is utilized for PCR thermal cycle and is controlled by a Lab-View program. Similar to our previous work, one set of electrodes on the chip inside the bigger chamber (0.6 microl volume) is used for diverting bacterial cells from a flowing stream into to a smaller chamber (0.4 nl volume). A second set of interdigitated electrodes (in smaller chamber) is used to actively trap and concentrate the bacterial cells using dielectrophoresis (DEP). In the presence of the DEP force, with the cells still entrapped in the micro-chamber, PCR mix is injected into the chamber. Subsequently, PCR amplification with SYBR Green detection is used for genetic identification of Listeria monocytogenes V7 cells. The increase in fluorescence is recorded with a photomultiplier tube module mounted over an epifluorescence microscope. This integrated micro-system is capable of genetic amplification and identification of as few as 60 cells of L. monocytogenes V7 in less than 90 min, in 600 nl volume collected from a sample of 10(4) cfu ml(-1). Specificity trials using various concentrations of L. monocytogenes V7, Listeria innocua F4248, and Escherichia coli O157:H7 were carried out successfully using two different primer sets specific for a regulatory gene of L. monocytogenes, prfA and 16S rRNA primer specific for the Listeria spp., and no cross-reactivity was observed.

    View details for DOI 10.1039/b802227e

    View details for Web of Science ID 000257236900020

    View details for PubMedID 18584089

  • Effects of inlet/outlet configurations on the electrostatic capture of airborne nanoparticles and viruses Measurement Science and Technology Jang J., D. Akin, R. Bashir 2008; 19: 065204-065212
  • Ultrananocrystalline diamond film as an optimal cell interface for biomedical applications BIOMEDICAL MICRODEVICES Bajaj, P., Akin, D., Gupta, A., Sherman, D., Shi, B., Auciello, O., Bashir, R. 2007; 9 (6): 787-794

    Abstract

    Surfaces of materials that promote cell adhesion, proliferation, and growth are critical for new generation of implantable biomedical devices. These films should be able to coat complex geometrical shapes very conformally, with smooth surfaces to produce hermetic bioinert protective coatings, or to provide surfaces for cell grafting through appropriate functionalization. Upon performing a survey of desirable properties such as chemical inertness, low friction coefficient, high wear resistance, and a high Young's modulus, diamond films emerge as very attractive candidates for coatings for biomedical devices. A promising novel material is ultrananocrystalline diamond (UNCD) in thin film form, since UNCD possesses the desirable properties of diamond and can be deposited as a very smooth, conformal coating using chemical vapor deposition. In this paper, we compared cell adhesion, proliferation, and growth on UNCD films, silicon, and platinum films substrates using different cell lines. Our results showed that UNCD films exhibited superior characteristics including cell number, total cell area, and cell spreading. The results could be attributed to the nanostructured nature or a combination of nanostructure/surface chemistry of UNCD, which provides a high surface energy, hence promoting adhesion between the receptors on the cell surface and the UNCD films.

    View details for DOI 10.1007/s10544-007-9090-2

    View details for Web of Science ID 000250462200002

    View details for PubMedID 17530409

  • Electrical capture and lysis of vaccinia virus particles using silicon nano-scale probe array BIOMEDICAL MICRODEVICES Park, K., Akin, D., Bashir, R. 2007; 9 (6): 877-883

    Abstract

    A probe array with nano-scale tips, integrated into a micro-fluidic channel was developed for the capture and lysing of small number of vaccinia virus particles using dielectrophoresis. The nano-scale probe array was fabricated in Silicon on Insulator (SOI) wafers, and sharpened with repeated oxidation steps. The gap between each probe ranged from 100 nm to 1.5 microm depending on fabrication parameters. The probe array was used to capture vaccinia virus using positive dielectrophoresis (DEP) from a flow within the microfluidic channel, and then the same probe array was used to apply high electric field to lyse the virus particles. It was shown that under electric field strengths of about 10(7)V/m, the permeability of ethidium bromide into the vaccinia virus particles was increased. Upon SEM analysis, the particles were found to be damaged and exhibited tubules networks, indicating disintegration of the virus outer layer. In addition, elongated strands of DNA were clearly observed on the chip surface after the application of the high electric field, demonstrating the possibility of electrical lysis of virus particles.

    View details for DOI 10.1007/s10544-007-9101-3

    View details for Web of Science ID 000250462200013

    View details for PubMedID 17610069

  • Biomems and nanotechnology-based approaches for rapid detection of biological entities JOURNAL OF RAPID METHODS AND AUTOMATION IN MICROBIOLOGY Bhattacharya, S., Jang, J., Yang, L., Akin, D., Bashir, R. 2007; 15 (1): 1-32

    View details for Web of Science ID 000245613100001

  • Capture of airborne nanoparticles in swirling flows using non-uniform electrostatic fields for bio-sensor applications SENSORS AND ACTUATORS B-CHEMICAL Jang, J., Akin, D., Lim, K. S., Broyles, S., Ladisch, M. R., Bashira, R. 2007; 121 (2): 560-566

    View details for DOI 10.1016/j.sub.2006.04.097

    View details for Web of Science ID 000244545100030

  • Nanotechnology in Biology and Medicine: Methods, Devices, and Applications. Edited by Tuan Vo-Dinh, Book Review. ChemMedChem Akin D. 2007; 2 (10): 1534-1535
  • Biomems and Nanotechnology based approaches for rapid detection of biological entities J. Rapid Methods & Automation in Microbiology Bhattacharya, S., J. Jang, L. Yang, D. Akin, R. Bashir 2007; 15: 1-32
  • Capture of airborne nanoparticles in swirling flows using non-uniform electrostatic fields for bio-sensor applications Sensors and Actuators B Jang J., D. Akin, K.S. Lim, S. Broyles, M.R. Ladisch, R. Bashir 2007; 121: 560-566
  • Characterization of vaccinia virus particles using microscale silicon cantilever resonators and atomic force microscopy SENSORS AND ACTUATORS B-CHEMICAL Johnson, L., Gupta, A. T., Ghafoor, A., Akin, D., Bashir, R. 2006; 115 (1): 189-197

    View details for DOI 10.1016/j.snb.2005.08.047

    View details for Web of Science ID 000236929100027

  • Characterization of vaccinia virus particles using microscale silicon cantilever resonators and atomic force microscopy Sensors and Actuators B Johnson, L., A. Gupta, D. Akin, A. Ghafoor, R. Bashir 2006; 115: 189-197
  • Characterization and modeling of a microfluidic dielectrophoresis filter for biological species JOURNAL OF MICROELECTROMECHANICAL SYSTEMS Li, H. B., Zheng, Y. N., Akin, D., Bashir, R. 2005; 14 (1): 103-112

    View details for DOI 10.1109/JMEMS.2004.839124

    View details for Web of Science ID 000226965200012

  • Bacterial delivery of smart nanoparticles-loaded with therapeutic molecules into cancer cells Nanomedicine Akin D., K. Ragheb, J. Sturgis, A.K. Bhunia, J.P. Robinson, R. Bashir 2005; 1: 250
  • Delocalization of vaccinia virus components observed by Atomic Force and Fluorescence Microscopy NanoBiotechnology Ghafoor, A*., D. Akin*, R. Bashir 2005; 4: 337-346
  • Characterization and modeling of a microfluidic dielectrophoresis filter for biological species J. Microelectromechanical Systems Li, H., Y. Zheng, D. Akin, R. Bashir 2005; 143: 103-112
  • Detection of bacterial cells and antibodies using surface micromachined thin silicon cantilever resonators JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B Gupta, A., Akin, D., Bashir, R. 2004; 22 (6): 2785-2791

    View details for DOI 10.1116/1.1824047

    View details for Web of Science ID 000226439800041

  • Single virus particle mass detection using microresonators with nanoscale thickness APPLIED PHYSICS LETTERS Gupta, A., Akin, D., Bashir, R. 2004; 84 (11): 1976-1978

    View details for DOI 10.1063/1.1667011

    View details for Web of Science ID 000220182600054

  • Real-time virus trapping and fluorescent imaging in microfluidic devices NANO LETTERS Akin, D., Li, H. B., Bashir, R. 2004; 4 (2): 257-259

    View details for DOI 10.1021/nl034987p

    View details for Web of Science ID 000188965700013

  • Detection of bacterial cells and antibodies using surface micromachined thin silicon cantilever resonators. J. Vacuum Sci. & Tech. B: Microelectronics and Nanometer Structures Gupta A., D. Akin, R. Bashir 2004; 22: 2785-2791
  • Real-time virus trapping and fluorescent imaging in micro-fluidic devices Nano Letters Demir Akin, H. Li, R. Bashir 2004; 4: 257-259
  • Integrated nanoscale silicon sensors using top-down fabrication APPLIED PHYSICS LETTERS Elibol, O. H., Morisette, D., Akin, D., Denton, J. P., Bashir, R. 2003; 83 (22): 4613-4615

    View details for DOI 10.1063/1.1630853

    View details for Web of Science ID 000186787100049

  • Poly(dimethylsiloxane) (PDMS) and silicon hybrid biochip for bacterial culture BIOMEDICAL MICRODEVICES Chang, W. J., Akin, D., Sedlak, M., Ladisch, M. R., Bashir, R. 2003; 5 (4): 281-290

    View details for Web of Science ID 000186331900002

  • Microfiber assisted fabrication of microfluidic channels using poly(dimethylsiloxane) AICHE JOURNAL Huang, T. T., Chang, W. J., Akin, D., Gomez, R., Bashir, R., Mosier, N., Ladisch, M. R. 2003; 49 (11): 2984-2987

    View details for Web of Science ID 000186664000028

  • Micro-assembly of functionalized particulate monolayer on C-18-derivatized SiO2 surfaces BIOTECHNOLOGY AND BIOENGINEERING Huang, T. T., Geng, T., Akin, D., Chang, W. J., Sturgis, J., Bashir, R., Bhunia, A. K., Robinson, J. P., Ladisch, M. R. 2003; 83 (4): 416-427

    Abstract

    This work describes a simple approach to immobilize functionalized colloidal microstructures onto a C(18)-coated SiO(2) substrate via specific or non-specific bio-mediated interactions. Biotinylated bovine serum albumin pre-adsorbed onto a C(18) surface was used to mediate the surface assembly of streptavidin-coated microbeads (2.8 microm), while a bare C(18) surface was used to immobilize anti-Listeria antibody-coated microbeads (2.8 microm) through hydrophobic interactions. For a C(18) surface pre-adsorbed with bovine serum albumin, hydrophobic polystyrene microbeads (0.8 microm) and positively charged dimethylamino microbeads (0.8 microm) were allowed to self-assemble onto the surface. A monolayer with high surface coverage was observed for both polystyrene and dimethylamino microbeads. The adsorption characteristics of Escherichia coli and Listeria monocytogenes on these microbead-based surfaces were studied using fluorescence microscopy. Both streptavidin microbeads pre-adsorbed with biotinylated anti-Listeria antibody and anti-Listeria antibody-coated microbeads showed specific capture of L. monocytogenes, while polystyrene and dimethylamino microbeads captured both E. coli and L. monocytogenes non-specifically. The preparation of microbead-based surfaces for the construction of microfluidic devices for separation, detection, or analysis of specific biological species is discussed.

    View details for DOI 10.1002/bit.10680

    View details for Web of Science ID 000183993000006

    View details for PubMedID 12800136

  • Integrated nanoscale silicon sensors using top-down fabrication Applied Physics Letters Elibol O.H., D. Morisette, D. Akin, J. P. Denton, R. Bashir 2003; 83: 4613-4615
  • Poly(dimethylsiloxane) (PDMS) and silicon hybrid biochip for bacterial culture Biomedical Microdevices Chang W.J., D. Akin, R. Bashir 2003; 5: 281-290
  • Resonant mass biosensor for ultrasensitive detection of bacterial cells Microfluidics, BioMEMS, and Medical Microsystems, Holger Becker, Peter Woias, Editors Gupta A., D. Akin, R. Bashir 2003; 4982: 21-27