Matching Items (27)
Description
Viral protein U (Vpu) is a type-III integral membrane protein encoded by Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays several roles in viral progeny escape from infected cells, including down-regulation of CD4 receptors. But key structure/function questions remain regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis. Here we describe expression of Vpu in bacteria, its purification and characterization. We report the successful expression of PelB-Vpu in Escherichia coli using the leader peptide pectate lyase B (PelB) from Erwinia carotovora. The protein was detergent extractable and could be isolated in a very pure form. We demonstrate that the PelB signal peptide successfully targets Vpu to the cell membranes and inserts it as a type I membrane protein. PelB-Vpu was biophysically characterized by circular dichroism and dynamic light scattering experiments and was shown to be an excellent candidate for elucidating structural models.
ContributorsDeb, Arpan (Author) / Johnson, William (Author) / Kline, Alexander (Author) / Scott, Boston (Author) / Meador, Lydia (Author) / Srinivas, Dustin (Author) / Martin Garcia, Jose Manuel (Author) / Dorner, Katerina (Author) / Borges, Chad (Author) / Misra, Rajeev (Author) / Hogue, Brenda (Author) / Fromme, Petra (Author) / Mor, Tsafrir (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Biodesign Institute (Contributor) / School of Molecular Sciences (Contributor) / Applied Structural Discovery (Contributor) / Personalized Diagnostics (Contributor)
Created2017-02-22
Description
Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone produced antibodies against 71% (n = 17) of the bacterial and viral targets. Antibody production correlated with prior reports of target immunogenicity in host organisms, underscoring the efficiency of this DNA-gold micronanoplex approach. To generate each antigen for antibody characterization, we also developed a simple in vitro membrane protein expression and capture method. Antibody specificity was demonstrated upon identifying, for the first time, membrane-directed heterologous expression of the native sequences of the FopA and FTT1525 virulence determinants from the select agent Francisella tularensis SCHU S4. These approaches will accelerate future structural and functional investigations of therapeutically-relevant membrane proteins.
ContributorsHansen, Debra (Author) / Robida, Mark (Author) / Craciunescu, Felicia (Author) / Loskutov, Andrey (Author) / Dorner, Katerina (Author) / Rodenberry, John-Charles (Author) / Wang, Xiao (Author) / Olson, Tien (Author) / Patel, Hetal (Author) / Fromme, Petra (Author) / Sykes, Kathryn (Author) / Biodesign Institute (Contributor) / Innovations in Medicine (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor)
Created2016-02-24
Description
The Physics and Chemistry of Surfaces and Interfaces conference has maintained a focus on the interfacial and surface properties of materials since its initiation in 1974. The conference continues to be a major force in this field, bringing together scientists from a variety of disciplines to focus upon the science of interfaces and surfaces. Here, a historical view of the development of the conference and a discussion of some of the themes that have been focal points for many years are presented.
ContributorsFerry, David (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Electrical, Computer and Energy Engineering (Contributor)
Created2013
Description
Background
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
ContributorsZhang, Wenlu (Author) / Feng, Daming (Author) / Li, Rongjian (Author) / Chernikov, Andrey (Author) / Chrisochoides, Nikos (Author) / Osgood, Christopher (Author) / Konikoff, Charlotte (Author) / Newfeld, Stuart (Author) / Kumar, Sudhir (Author) / Ji, Shuiwang (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2013-12-28
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Description
Background
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
ContributorsYuan, Lei (Author) / Woodard, Alexander (Author) / Ji, Shuiwang (Author) / Jiang, Yuan (Author) / Zhou, Zhi-Hua (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / Ira A. Fulton Schools of Engineering (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2012-05-23
Description
Moore's law has been the most important driving force for the tremendous progress of semiconductor industry. With time the transistors which form the fundamental building block of any integrated circuit have been shrinking in size leading to smaller and faster electronic devices.As the devices scale down thermal effects and the short channel effects become the important deciding factors in determining transistor architecture.SOI (Silicon on Insulator) devices have been excellent alternative to planar MOSFET for ultimate CMOS scaling since they mitigate short channel effects. Hence as a part of thesis we tried to study the benefits of the SOI technology especially for lower technology nodes when the channel thickness reduces down to sub 10nm regime. This work tries to explore the effects of structural confinement due to reduced channel thickness on the electrostatic behavior of DG SOI MOSFET. DG SOI MOSFET form the Qfinfet which is an alternative to existing Finfet structure. Qfinfet was proposed and patented by the Finscale Inc for sub 10nm technology nodes.
As part of MS Thesis we developed electrostatic simulator for DG SOI devices by implementing the self consistent full band Schrodinger Poisson solver. We used the Empirical Pseudopotential method in conjunction with supercell approach to solve the Schrodinger Equation. EPM was chosen because it has few empirical parameters which give us good accuracy for experimental results. Also EPM is computationally less expensive as compared to the atomistic methods like DFT(Density functional theory) and NEGF (Non-equilibrium Green's function). In our workwe considered two crystallographic orientations of Si,namely [100] and [110].
As part of MS Thesis we developed electrostatic simulator for DG SOI devices by implementing the self consistent full band Schrodinger Poisson solver. We used the Empirical Pseudopotential method in conjunction with supercell approach to solve the Schrodinger Equation. EPM was chosen because it has few empirical parameters which give us good accuracy for experimental results. Also EPM is computationally less expensive as compared to the atomistic methods like DFT(Density functional theory) and NEGF (Non-equilibrium Green's function). In our workwe considered two crystallographic orientations of Si,namely [100] and [110].
ContributorsLaturia, Akash (Author) / Vasileska, Dragica (Thesis advisor) / Ferry, David (Committee member) / Goodnick, Stephen (Committee member) / Arizona State University (Publisher)
Created2016
Description
Thermal effects in nano-scaled devices were reviewed and modeling methodologies to deal with this issue were discussed. The phonon energy balance equations model, being one of the important previous works regarding the modeling of heating effects in nano-scale devices, was derived. Then, detailed description was given on the Monte Carlo (MC) solution of the phonon Boltzmann Transport Equation. The phonon MC solver was developed next as part of this thesis. Simulation results of the thermal conductivity in bulk Si show good agreement with theoretical/experimental values from literature.
ContributorsYoo, Seung Kyung (Author) / Vasileska, Dragica (Thesis advisor) / Ferry, David (Committee member) / Goodnick, Stephen (Committee member) / Arizona State University (Publisher)
Created2015
Description
From 2D planar MOSFET to 3D FinFET, the geometry of semiconductor devices is getting more and more complex. Correspondingly, the number of mesh grid points increases largely to maintain the accuracy of carrier transport and heat transfer simulations. By substituting the conventional uniform mesh with non-uniform mesh, one can reduce the number of grid points. However, the problem of how to solve governing equations on non-uniform mesh is then imposed to the numerical solver. Moreover, if a device simulator is integrated into a multi-scale simulator, the problem size will be further increased. Consequently, there exist two challenges for the current numerical solver. One is to increase the functionality to accommodate non-uniform mesh. The other is to solve governing physical equations fast and accurately on a large number of mesh grid points.
This research rst discusses a 2D planar MOSFET simulator and its numerical solver, pointing out its performance limit. By analyzing the algorithm complexity, Multigrid method is proposed to replace conventional Successive-Over-Relaxation method in a numerical solver. A variety of Multigrid methods (standard Multigrid, Algebraic Multigrid, Full Approximation Scheme, and Full Multigrid) are discussed and implemented. Their properties are examined through a set of numerical experiments. Finally, Algebraic Multigrid, Full Approximation Scheme and Full Multigrid are integrated into one advanced numerical solver based on the exact requirements of a semiconductor device simulator. A 2D MOSFET device is used to benchmark the performance, showing that the advanced Multigrid method has higher speed, accuracy and robustness.
This research rst discusses a 2D planar MOSFET simulator and its numerical solver, pointing out its performance limit. By analyzing the algorithm complexity, Multigrid method is proposed to replace conventional Successive-Over-Relaxation method in a numerical solver. A variety of Multigrid methods (standard Multigrid, Algebraic Multigrid, Full Approximation Scheme, and Full Multigrid) are discussed and implemented. Their properties are examined through a set of numerical experiments. Finally, Algebraic Multigrid, Full Approximation Scheme and Full Multigrid are integrated into one advanced numerical solver based on the exact requirements of a semiconductor device simulator. A 2D MOSFET device is used to benchmark the performance, showing that the advanced Multigrid method has higher speed, accuracy and robustness.
ContributorsGuo, Xinchen (Author) / Vasileska, Dragica (Thesis advisor) / Goodnick, Stephen (Committee member) / Ferry, David (Committee member) / Arizona State University (Publisher)
Created2015
Description
Understanding the interplay between the electrical and mechanical properties of single molecules is of fundamental importance for molecular electronics. The sensitivity of charge transport to mechanical fluctuations is a key problem in developing long lasting molecular devices. Furthermore, harnessing this response to mechanical perturbation, molecular devices which can be mechanically gated can be developed. This thesis demonstrates three examples of the unique electromechanical properties of single molecules.
First, the electromechanical properties of 1,4-benzenedithiol molecular junctions are investigate. Counterintuitively, the conductance of this molecule is found to increase by more than an order of magnitude when stretched. This conductance increase is found to be reversible when the molecular junction is compressed. The current-voltage, conductance-voltage and inelastic electron tunneling spectroscopy characteristics are used to attribute the conductance increase to a strain-induced shift in the frontier molecular orbital relative to the electrode Fermi level, leading to resonant enhancement in the conductance.
Next, the effect of stretching-induced structural changes on charge transport in DNA molecules is studied. The conductance of single DNA molecules with lengths varying from 6 to 26 base pairs is measured and found to follow a hopping transport mechanism. The conductance of DNA molecules is highly sensitive to mechanical stretching, showing an abrupt decrease in conductance at surprisingly short stretching distances, with weak dependence on DNA length. This abrupt conductance decrease is attributed to force-induced breaking of hydrogen bonds in the base pairs at the end of the DNA sequence.
Finally, the effect of small mechanical modulation of the base separation on DNA conductance is investigated. The sensitivity of conductance to mechanical modulation is studied for molecules of different sequence and length. Sequences with purine-purine stacking are found to be more responsive to modulation than purine-pyrimidine sequences. This sensitivity is attributed to the perturbation of &pi-&pi stacking interactions and resulting effects on the activation energy and electronic coupling for the end base pairs.
First, the electromechanical properties of 1,4-benzenedithiol molecular junctions are investigate. Counterintuitively, the conductance of this molecule is found to increase by more than an order of magnitude when stretched. This conductance increase is found to be reversible when the molecular junction is compressed. The current-voltage, conductance-voltage and inelastic electron tunneling spectroscopy characteristics are used to attribute the conductance increase to a strain-induced shift in the frontier molecular orbital relative to the electrode Fermi level, leading to resonant enhancement in the conductance.
Next, the effect of stretching-induced structural changes on charge transport in DNA molecules is studied. The conductance of single DNA molecules with lengths varying from 6 to 26 base pairs is measured and found to follow a hopping transport mechanism. The conductance of DNA molecules is highly sensitive to mechanical stretching, showing an abrupt decrease in conductance at surprisingly short stretching distances, with weak dependence on DNA length. This abrupt conductance decrease is attributed to force-induced breaking of hydrogen bonds in the base pairs at the end of the DNA sequence.
Finally, the effect of small mechanical modulation of the base separation on DNA conductance is investigated. The sensitivity of conductance to mechanical modulation is studied for molecules of different sequence and length. Sequences with purine-purine stacking are found to be more responsive to modulation than purine-pyrimidine sequences. This sensitivity is attributed to the perturbation of &pi-&pi stacking interactions and resulting effects on the activation energy and electronic coupling for the end base pairs.
ContributorsBruot, Christopher, 1986- (Author) / Tao, Nongjian (Thesis advisor) / Lindsay, Stuart (Committee member) / Mujica, Vladimiro (Committee member) / Ferry, David (Committee member) / Arizona State University (Publisher)
Created2014
Description
CMOS Technology has been scaled down to 7 nm with FinFET replacing planar MOSFET devices. Due to short channel effects, the FinFET structure was developed to provide better electrostatic control on subthreshold leakage and saturation current over planar MOSFETs while having the desired current drive. The FinFET structure has an undoped or fully depleted fin, which supports immunity from random dopant fluctuations (RDF – a phenomenon which causes a reduction in the threshold voltage and is prominent at sub 50 nm tech nodes due to lesser dopant atoms) and thus causes threshold voltage (Vth) roll-off by reducing the Vth. However, as the advanced CMOS technologies are shrinking down to a 5 nm technology node, subthreshold leakage and drain-induced-barrier-lowering (DIBL) are driving the introduction of new metal-oxide-semiconductor field-effect transistor (MOSFET) structures to improve performance. GAA field effect transistors are shown to be the potential candidates for these advanced nodes. In nanowire devices, due to the presence of the gate on all sides of the channel, DIBL should be lower compared to the FinFETs.
A 3-D technology computer aided design (TCAD) device simulation is done to compare the performance of FinFET and GAA nanowire structures with vertically stacked horizontal nanowires. Subthreshold slope, DIBL & saturation current are measured and compared between these devices. The FinFET’s device performance has been matched with the ASAP7 compact model with the impact of tensile and compressive strain on NMOS & PMOS respectively. Metal work function is adjusted for the desired current drive. The nanowires have shown better electrostatic performance over FinFETs with excellent improvement in DIBL and subthreshold slope. This proves that horizontal nanowires can be the potential candidate for 5 nm technology node. A GAA nanowire structure for 5 nm tech node is characterized with a gate length of 15 nm. The structure is scaled down from 7 nm node to 5 nm by using a scaling factor of 0.7.
A 3-D technology computer aided design (TCAD) device simulation is done to compare the performance of FinFET and GAA nanowire structures with vertically stacked horizontal nanowires. Subthreshold slope, DIBL & saturation current are measured and compared between these devices. The FinFET’s device performance has been matched with the ASAP7 compact model with the impact of tensile and compressive strain on NMOS & PMOS respectively. Metal work function is adjusted for the desired current drive. The nanowires have shown better electrostatic performance over FinFETs with excellent improvement in DIBL and subthreshold slope. This proves that horizontal nanowires can be the potential candidate for 5 nm technology node. A GAA nanowire structure for 5 nm tech node is characterized with a gate length of 15 nm. The structure is scaled down from 7 nm node to 5 nm by using a scaling factor of 0.7.
ContributorsRana, Parshant (Author) / Clark, Lawrence (Thesis advisor) / Ferry, David (Committee member) / Brunhaver, John (Committee member) / Arizona State University (Publisher)
Created2017