Scholarly Works, Mechanical Engineering
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Browsing Scholarly Works, Mechanical Engineering by Department "Electrical and Computer Engineering"
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- Energy band alignment of atomic layer deposited HfO2 on epitaxial (110)Ge grown by molecular beam epitaxyHudait, Mantu K.; Zhu, Y.; Maurya, Deepam; Priya, Shashank (AIP Publishing, 2013-03-01)The band alignment properties of atomic layer HfO2 film deposited on epitaxial (110)Ge, grown by molecular beam epitaxy, was investigated using x-ray photoelectron spectroscopy. The cross-sectional transmission electron microscopy exhibited a sharp interface between the (110)Ge epilayer and the HfO2 film. The measured valence band offset value of HfO2 relative to (110)Ge was 2.28 +/- 0.05 eV. The extracted conduction band offset value was 2.66 +/- 0.1 eV using the bandgaps of HfO2 of 5.61 eV and Ge bandgap of 0.67 eV. These band offset parameters and the interface chemical properties of HfO2/(110)Ge system are of tremendous importance for the design of future high hole mobility and low-power Ge-based metal-oxide transistor devices. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4794838]
- Establishing an immunocompromised porcine model of human cancer for novel therapy development with pancreatic adenocarcinoma and irreversible electroporationHendricks-Wenger, Alissa; Aycock, Kenneth N.; Nagai-Singer, Margaret A.; Coutermarsh-Ott, Sheryl; Lorenzo, Melvin F.; Gannon, Jessica; Uh, Kyungjun; Farrell, Kayla; Beitel-White, Natalie; Brock, Rebecca M.; Simon, Alexander; Morrison, Holly A.; Tuohy, Joanne L.; Clark-Deener, Sherrie; Vlaisavljevich, Eli; Davalos, Rafael V.; Lee, Kiho; Allen, Irving C. (Nature Research, 2021-04-07)New therapies to treat pancreatic cancer are direly needed. However, efficacious interventions lack a strong preclinical model that can recapitulate patients’ anatomy and physiology. Likewise, the availability of human primary malignant tissue for ex vivo studies is limited. These are significant limitations in the biomedical device field. We have developed RAG2/IL2RG deficient pigs using CRISPR/Cas9 as a large animal model with the novel application of cancer xenograft studies of human pancreatic adenocarcinoma. In this proof-of-concept study, these pigs were successfully generated using on-demand genetic modifications in embryos, circumventing the need for breeding and husbandry. Human Panc01 cells injected subcutaneously into the ears of RAG2/IL2RG deficient pigs demonstrated 100% engraftment with growth rates similar to those typically observed in mouse models. Histopathology revealed no immune cell infiltration and tumor morphology was highly consistent with the mouse models. The electrical properties and response to irreversible electroporation of the tumor tissue were found to be similar to excised human pancreatic cancer tumors. The ample tumor tissue produced enabled improved accuracy and modeling of the electrical properties of tumor tissue. Together, this suggests that this model will be useful and capable of bridging the gap of translating therapies from the bench to clinical application.
- The impact of sphingosine kinase inhibitor-loaded nanoparticles on bioelectrical and biomechanical properties of cancer cellsBabahosseini, Hesam; Srinivasaraghavan, Vaishnavi; Zhao, Zongmin; Gillam, Francis; Childress, Elizabeth; Strobl, Jeannine S.; Santos, Webster L.; Zhang, Chenming; Agah, Masoud (The Royal Society of Chemistry, 2015-11-19)Cancer progression and physiological changes within the cells are accompanied by alterations in the biophysical properties. Therefore, the cell biophysical properties can serve as promising markers for cancer detection and physiological activities. To aid in the investigation of the biophysical markers of cells, a microfluidic chip has been developed which consists of a constriction channel and embedded microelectrodes. Single-cell impedance magnitudes at four frequencies and entry and travel times are measured simultaneously during their transit through the constriction channel. This microchip provides a high-throughput, label-free, automated assay to identify biophysical signatures of malignant cells and monitor the therapeutic efficacy of drugs. Here, we monitored the dynamic cellular biophysical properties in response to sphingosine kinase inhibitors (SphKIs), and compared the effectiveness of drug delivery using poly lactic-co-glycolic acid (PLGA) nanoparticles (NPs) loaded with SphKIs versus conventional delivery. Cells treated with SphKIs showed significantly higher impedance magnitudes at all four frequencies. The bioelectrical parameters extracted using a model also revealed that the highly aggressive breast cells treated with SphKIs shifted electrically towards that of a less malignant phenotype; SphKI-treated cells exhibited an increase in cell-channel interface resistance and a significant decrease in specific membrane capacitance. Furthermore, SphKI-treated cells became slightly more deformable as measured by a decrease in their channel entry and travel times. We observed no significant difference in the bioelectrical changes produced by SphKI delivered conventionally or with NPs. However, NPs-packaged delivery of SphKI decreased the cell deformability. In summary, this study showed that while the bioelectrical properties of the cells were dominantly affected by SphKIs, the biomechanical properties were mainly changed by the NPs.
- Integration of lead-free ferroelectric on HfO2/Si (100) for high performance non-volatile memory applicationsKundu, Souvik; Maurya, Deepam; Clavel, Michael B.; Zhou, Yuan; Halder, Nripendra N.; Hudait, Mantu K.; Banerji, Pallab; Priya, Shashank (Nature Publishing Group, 2015-02-16)We introduce a novel lead-free ferroelectric thin film (1-x)BaTiO3-xBa(Cu1/3Nb2/3)O3 (x 5 0.025) (BT-BCN) integrated on to HfO2 buffered Si for non-volatile memory (NVM) applications. Piezoelectric force microscopy (PFM), x-ray diffraction, and high resolution transmission electron microscopy were employed to establish the ferroelectricity in BT-BCN thin films. PFMstudy reveals that the domains reversal occurs with 1806 phase change by applying external voltage, demonstrating its effectiveness forNVMdevice applications. X-ray photoelectron microscopy was used to investigate the band alignments between atomic layer deposited HfO2 and pulsed laser deposited BT-BCN films. Programming and erasing operations were explained on the basis of band-alignments. The structure offers large memory window, low leakage current, and high and low capacitance values that were easily distinguishable even after ,106 s, indicating strong charge storage potential. This study explains a new approach towards the realization of ferroelectric based memory devices integrated on Si platform and also opens up a new possibility to embed the system within current complementary metal-oxide-semiconductor processing technology.
- Label-free DNA sequence detection using oligonucleotide functionalized optical fiberWang, X. W.; Cooper, K. L.; Wang, Anbo; Xu, J. C.; Wang, Z. A.; Zhang, Y.; Tu, Zhijian Jake (AIP Publishing, 2006-10-01)The authors present a label-free method for direct detection of deoxyribonucleic acid (DNA) sequences. The capture DNA is immobilized onto the surface of a silica optical fiber tip by means of the layer-by-layer electrostatic self-assembly technique. Hybridization of target DNA with complementary capture DNA increases the optical thickness of the fiber tip. This phenomenon can be detected by demodulation of the spectrum of a Fabry-Perot cavity fabricated in the optical fiber. Experimental results demonstrate sequence specificity and sensitivity to nanogram quantities of target DNA sequences with short (similar to 5 min) hybridization time. (c) 2006 American Institute of Physics.
- A model of yeast cell-cycle regulation based on multisite phosphorylationBarik, Debashis; Baumann, William T.; Paul, Mark R.; Novak, Bela; Tyson, John J. (Nature Publishing Group, 2010-08-01)In order for the cell’s genome to be passed intact from one generation to the next, the events of the cell cycle (DNA replication, mitosis, cell division) must be executed in the correct order, despite the considerable molecular noise inherent in any protein-based regulatory system residing in the small confines of a eukaryotic cell. To assess the effects of molecular fluctuations on cell-cycle progression in budding yeast cells, we have constructed a new model of the regulation of Cln- and Clb-dependent kinases, based on multisite phosphorylation of their target proteins and on positive and negative feedback loops involving the kinases themselves. To account for the significant role of noise in the transcription and translation steps of gene expression, the model includes mRNAs as well as proteins. The model equations are simulated deterministically and stochastically to reveal the bistable switching behavior on which proper cell-cycle progression depends and to show that this behavior is robust to the level of molecular noise expected in yeast-sized cells (B50 fL volume). The model gives a quantitatively accurate account of the variability observed in the G1-S transition in budding yeast, which is governed by an underlying sizer + timer control system.
- Motion Inference Using Sparse Inertial Sensors, Self-Supervised Learning, and a New Dataset of Unscripted Human MotionGeissinger, Jack H.; Asbeck, Alan T. (MDPI, 2020-11-06)In recent years, wearable sensors have become common, with possible applications in biomechanical monitoring, sports and fitness training, rehabilitation, assistive devices, or human-computer interaction. Our goal was to achieve accurate kinematics estimates using a small number of sensors. To accomplish this, we introduced a new dataset (the Virginia Tech Natural Motion Dataset) of full-body human motion capture using XSens MVN Link that contains more than 40 h of unscripted daily life motion in the open world. Using this dataset, we conducted self-supervised machine learning to do kinematics inference: we predicted the complete kinematics of the upper body or full body using a reduced set of sensors (3 or 4 for the upper body, 5 or 6 for the full body). We used several sequence-to-sequence (Seq2Seq) and Transformer models for motion inference. We compared the results using four different machine learning models and four different configurations of sensor placements. Our models produced mean angular errors of 10–15 degrees for both the upper body and full body, as well as worst-case errors of less than 30 degrees. The dataset and our machine learning code are freely available.
- Off-chip passivated-electrode, insulator-based dielectrophoresis (O pi DEP)Zellner, Phillip; Shake, Tyler; Sahari, Ali; Behkam, Bahareh; Agah, Masoud (Springer, 2013-08-01)In this study, we report the first off-chip passivated-electrode, insulator-based dielectrophoresis microchip (OπDEP). This technique combines the sensitivity of electrode-based dielectrophoresis (eDEP) with the high throughput and inexpensive device characteristics of insulator-based dielectrophoresis (iDEP). The device is composed of a permanent, reusable set of electrodes and a disposable, polymer microfluidic chip with microposts embedded in the microchannel. The device operates by capacitively coupling the electric fields into the microchannel; thus, no physical connections are made between the electrodes and the microfluidic device. During operation, the polydimethylsiloxan (PDMS) microfluidic chip fits onto the electrode substrate as a disposable cartridge. OπDEP uses insulting structures within the channel as well as parallel electrodes to create DEP forces by the same working principle that iDEP devices use. The resulting devices create DEP forces which are larger by two orders of magnitude for the same applied voltage when compared to off-chip eDEP designs from literature, which rely on parallel electrodes alone to produce the DEP forces. The larger DEP forces allow the OπDEP device to operate at high flow rates exceeding 1 mL/h. In order to demonstrate this technology, Escherichia coli (E. coli), a known waterborne pathogen, was trapped from water samples. Trapping efficiencies of 100 % were obtained at flow rates as high as 400 μL/h and 60 % at flow rates as high as 1200 μL/h. Additionally, bacteria were selectively concentrated from a suspension of polystyrene beads.
- Stochastic simulation of enzyme-catalyzed reactions with disparate timescalesBarik, Debashis; Paul, Mark R.; Baumann, William T.; Cao, Yang; Tyson, John J. (Cell Press, 2008-10-01)Many physiological characteristics of living cells are regulated by protein interaction networks. Because the total numbers of these protein species can be small, molecular noise can have significant effects on the dynamical properties of a regulatory network. Computing these stochastic effects is made difficult by the large timescale separations typical of protein interactions (e. g., complex formation may occur in fractions of a second, whereas catalytic conversions may take minutes). Exact stochastic simulation may be very inefficient under these circumstances, and methods for speeding up the simulation without sacrificing accuracy have been widely studied. We show that the "total quasi-steady-state approximation'' for enzyme-catalyzed reactions provides a useful framework for efficient and accurate stochastic simulations. The method is applied to three examples: a simple enzyme-catalyzed reaction where enzyme and substrate have comparable abundances, a Goldbeter-Koshland switch, where a kinase and phosphatase regulate the phosphorylation state of a common substrate, and coupled Goldbeter-Koshland switches that exhibit bistability. Simulations based on the total quasi-steady-state approximation accurately capture the steady-state probability distributions of all components of these reaction networks. In many respects, the approximation also faithfully reproduces time-dependent aspects of the fluctuations. The method is accurate even under conditions of poor timescale separation.
- Ultra-high frequency photoconductivity decay in GaAs/Ge/GaAs double heterostructure grown by molecular beam epitaxyHudait, Mantu K.; Zhu, Y.; Johnston, Steve W.; Maurya, Deepam; Priya, Shashank; Umbel, Rachel (AIP Publishing, 2013-03-01)GaAs/Ge/GaAs double heterostructures (DHs) were grown in-situ using two separate molecular beam epitaxy chambers. High-resolution x-ray rocking curve demonstrates a high-quality GaAs/Ge/GaAs heterostructure by observing Pendellosung oscillations. The kinetics of the carrier recombination in Ge/GaAs DHs were investigated using photoconductivity decay measurements by the incidence excitation from the front and back side of 15 nm GaAs/100 nm Ge/0.5 mu m GaAs/(100) GaAs substrate structure. High-minority carrier lifetimes of 1.06-1.17 mu s were measured when excited from the front or from the back of the Ge epitaxial layer, suggests equivalent interface quality of GaAs/Ge and Ge/GaAs. Wavelength-dependent minority carrier recombination properties are explained by the wavelength-dependent absorption coefficient of Ge. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4794984]