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Sample records for conformable flexible large-area

  1. Semiconductor-based, large-area, flexible, electronic devices

    DOEpatents

    Goyal, Amit

    2011-03-15

    Novel articles and methods to fabricate the same resulting in flexible, large-area, triaxially textured, single-crystal or single-crystal-like, semiconductor-based, electronic devices are disclosed. Potential applications of resulting articles are in areas of photovoltaic devices, flat-panel displays, thermophotovoltaic devices, ferroelectric devices, light emitting diode devices, computer hard disc drive devices, magnetoresistance based devices, photoluminescence based devices, non-volatile memory devices, dielectric devices, thermoelectric devices and quantum dot laser devices.

  2. Flexible and mechanical strain resistant large area SERS active substrates

    NASA Astrophysics Data System (ADS)

    Singh, J. P.; Chu, Hsiaoyun; Abell, Justin; Tripp, Ralph A.; Zhao, Yiping

    2012-05-01

    We report a cost effective and facile way to synthesize flexible, uniform, and large area surface enhanced Raman scattering (SERS) substrates using an oblique angle deposition (OAD) technique. The flexible SERS substrates consist of 1 μm long, tilted silver nanocolumnar films deposited on flexible polydimethylsiloxane (PDMS) and polyethylene terephthalate (PET) sheets using OAD. The SERS enhancement activity of these flexible substrates was determined using 10-5 M trans-1,2-bis(4-pyridyl) ethylene (BPE) Raman probe molecules. The in situ SERS measurements on these flexible substrates under mechanical (tensile/bending) strain conditions were performed. Our results show that flexible SERS substrates can withstand a tensile strain (ε) value as high as 30% without losing SERS performance, whereas the similar bending strain decreases the SERS performance by about 13%. A cyclic tensile loading test on flexible PDMS SERS substrates at a pre-specified tensile strain (ε) value of 10% shows that the SERS intensity remains almost constant for more than 100 cycles. These disposable and flexible SERS substrates can be integrated with biological substances and offer a novel and practical method to facilitate biosensing applications.

  3. Scaling Up Nature: Large Area Flexible Biomimetic Surfaces.

    PubMed

    Li, Yinyong; John, Jacob; Kolewe, Kristopher W; Schiffman, Jessica D; Carter, Kenneth R

    2015-10-28

    The fabrication and advanced function of large area biomimetic superhydrophobic surfaces (SHS) and slippery lubricant-infused porous surfaces (SLIPS) are reported. The use of roll-to-roll nanoimprinting techniques enabled the continuous fabrication of SHS and SLIPS based on hierarchically wrinkled surfaces. Perfluoropolyether hybrid molds were used as flexible molds for roll-to-roll imprinting into a newly designed thiol-ene based photopolymer resin coated on flexible polyethylene terephthalate films. The patterned surfaces exhibit feasible superhydrophobicity with a water contact angle around 160° without any further surface modification. The SHS can be easily converted into SLIPS by roll-to-roll coating of a fluorinated lubricant, and these surfaces have outstanding repellence to a variety of liquids. Furthermore, both SHS and SLIPS display antibiofouling properties when challenged with Escherichia coli K12 MG1655. The current article describes the transformation of artificial biomimetic structures from small, lab-scale coupons to low-cost, large area platforms. PMID:26423494

  4. Conformational flexibility of mephenesin.

    PubMed

    Écija, Patricia; Evangelisti, Luca; Vallejo, Montserrat; Basterretxea, Francisco J; Lesarri, Alberto; Castaño, Fernando; Caminati, Walther; Cocinero, Emilio J

    2014-05-22

    The mephenesin molecule (3-(2-methylphenoxy)propane-1,2-diol) serves as a test bank to explore several structural and dynamical issues, such as conformational flexibility, the orientation of the carbon linear chain relative to the benzene plane, or the effect of substituent position on the rotational barrier of a methyl group. The molecule has been studied by rotational spectroscopy in the 4-18 GHz frequency range by Fourier-transform methods in a supersonic expansion. The experiment has been backed by a previous conformational search plus optimization of the lowest energy structures by ab initio and density functional quantum calculations. The three lowest-lying conformers that can interconvert to each other by simple bond rotations have been detected in the jet. Rotational parameters for all structures have been obtained, and methyl torsional barriers have been determined for the two lowest-lying rotamers. The lowest-lying structure of mephenesin is highly planar, with all carbon atoms lying nearly in the benzene ring plane, and is stabilized by the formation of cooperative intramolecular hydrogen bonding. An estimation of the relative abundance of the detected conformers indicates that the energetically most stable conformer will have an abundance near 80% at temperatures relevant for biological activity. PMID:24754523

  5. Conformational flexibility of aspartame.

    PubMed

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016. PMID:27038223

  6. Highly Flexible and High-Performance Complementary Inverters of Large-Area Transition Metal Dichalcogenide Monolayers.

    PubMed

    Pu, Jiang; Funahashi, Kazuma; Chen, Chang-Hsiao; Li, Ming-Yang; Li, Lain-Jong; Takenobu, Taishi

    2016-06-01

    Complementary inverters constructed from large-area monolayers of WSe2 and MoS2 achieve excellent logic swings and yield an extremely high gain, large total noise margin, low power consumption, and good switching speed. Moreover, the WSe2 complementary-like inverters built on plastic substrates exhibit high mechanical stability. The results provide a path toward large-area flexible electronics. PMID:27007295

  7. Synthesis of Large Area Graphene for High Performance in Flexible Optoelectronic Devices

    PubMed Central

    Polat, Emre O.; Balci, Osman; Kakenov, Nurbek; Uzlu, Hasan Burkay; Kocabas, Coskun; Dahiya, Ravinder

    2015-01-01

    This work demonstrates an attractive low-cost route to obtain large area and high-quality graphene films by using the ultra-smooth copper foils which are typically used as the negative electrodes in lithium-ion batteries. We first compared the electronic transport properties of our new graphene film with the one synthesized by using commonly used standard copper foils in chemical vapor deposition (CVD). We observed a stark improvement in the electrical performance of the transistors realized on our graphene films. To study the optical properties on large area, we transferred CVD based graphene to transparent flexible substrates using hot lamination method and performed large area optical scanning. We demonstrate the promise of our high quality graphene films for large areas with ~400 cm2 flexible optical modulators. We obtained a profound light modulation over a broad spectrum by using the fabricated large area transparent graphene supercapacitors and we compared the performance of our devices with the one based on graphene from standard copper. We propose that the copper foils used in the lithium-ion batteries could be used to obtain high-quality graphene at much lower-cost, with the improved performance of electrical transport and optical properties in the devices made from them. PMID:26578425

  8. Synthesis of Large Area Graphene for High Performance in Flexible Optoelectronic Devices.

    PubMed

    Polat, Emre O; Balci, Osman; Kakenov, Nurbek; Uzlu, Hasan Burkay; Kocabas, Coskun; Dahiya, Ravinder

    2015-01-01

    This work demonstrates an attractive low-cost route to obtain large area and high-quality graphene films by using the ultra-smooth copper foils which are typically used as the negative electrodes in lithium-ion batteries. We first compared the electronic transport properties of our new graphene film with the one synthesized by using commonly used standard copper foils in chemical vapor deposition (CVD). We observed a stark improvement in the electrical performance of the transistors realized on our graphene films. To study the optical properties on large area, we transferred CVD based graphene to transparent flexible substrates using hot lamination method and performed large area optical scanning. We demonstrate the promise of our high quality graphene films for large areas with ~400 cm(2) flexible optical modulators. We obtained a profound light modulation over a broad spectrum by using the fabricated large area transparent graphene supercapacitors and we compared the performance of our devices with the one based on graphene from standard copper. We propose that the copper foils used in the lithium-ion batteries could be used to obtain high-quality graphene at much lower-cost, with the improved performance of electrical transport and optical properties in the devices made from them. PMID:26578425

  9. Synthesis of Large Area Graphene for High Performance in Flexible Optoelectronic Devices

    NASA Astrophysics Data System (ADS)

    Polat, Emre O.; Balci, Osman; Kakenov, Nurbek; Uzlu, Hasan Burkay; Kocabas, Coskun; Dahiya, Ravinder

    2015-11-01

    This work demonstrates an attractive low-cost route to obtain large area and high-quality graphene films by using the ultra-smooth copper foils which are typically used as the negative electrodes in lithium-ion batteries. We first compared the electronic transport properties of our new graphene film with the one synthesized by using commonly used standard copper foils in chemical vapor deposition (CVD). We observed a stark improvement in the electrical performance of the transistors realized on our graphene films. To study the optical properties on large area, we transferred CVD based graphene to transparent flexible substrates using hot lamination method and performed large area optical scanning. We demonstrate the promise of our high quality graphene films for large areas with ~400 cm2 flexible optical modulators. We obtained a profound light modulation over a broad spectrum by using the fabricated large area transparent graphene supercapacitors and we compared the performance of our devices with the one based on graphene from standard copper. We propose that the copper foils used in the lithium-ion batteries could be used to obtain high-quality graphene at much lower-cost, with the improved performance of electrical transport and optical properties in the devices made from them.

  10. [100] or [110] aligned, semiconductor-based, large-area, flexible, electronic devices

    SciTech Connect

    Goyal, Amit

    2015-03-24

    Novel articles and methods to fabricate the same resulting in flexible, large-area, [100] or [110] textured, semiconductor-based, electronic devices are disclosed. Potential applications of resulting articles are in areas of photovoltaic devices, flat-panel displays, thermophotovoltaic devices, ferroelectric devices, light emitting diode devices, computer hard disc drive devices, magnetoresistance based devices, photoluminescence based devices, non-volatile memory devices, dielectric devices, thermoelectric devices and quantum dot laser devices.

  11. Large-area, uniform white light LED source on a flexible substrate.

    PubMed

    Sher, Chin-Wei; Chen, Kuo-Ju; Lin, Chien-Chung; Han, Hau-Vei; Lin, Huang-Yu; Tu, Zong-Yi; Tu, Hsien-Hao; Honjo, Keiji; Jiang, Hsin-Yi; Ou, Sin-Liang; Horng, Ray-Hua; Li, Xiuling; Fu, Chien-Chung; Kuo, Hao-Chung

    2015-09-21

    This study demonstrates the flexible white LED structure with high lumen efficiency and uniform optical performance for neutral white and warm white CCT. Flip-chip LEDs were attached on a polyimide substrate with copper strips as electrical and thermal conduction paths. Yellow phosphors are mixed with polydimenthysiloxane (PDMS) to provide mechanical support and flexibility. The light efficiency of this device can reach 120 lm/W and 85% of light output uniformity of the emission area can be achieved. Moreover, the optical simulation is employed to evaluate various designs of this flexible film in order to obtain uniform output. Both the pitch between the individual devices and the thickness of the phosphor film are calculated for optimization purpose. This flexible white LED with high lumen efficiency and good reliability is suitable for the large area fixture in the general lighting applications. PMID:26406747

  12. Method of making large area conformable shape structures for detector/sensor applications using glass drawing technique and postprocessing

    SciTech Connect

    Ivanov, Ilia N.; Simpson, John T.

    2012-01-24

    A method of making a large area conformable shape structure comprises drawing a plurality of tubes to form a plurality of drawn tubes, and cutting the plurality of drawn tubes into cut drawn tubes of a predetermined shape. The cut drawn tubes have a first end and a second end along the longitudinal direction of the cut drawn tubes. The method further comprises conforming the first end of the cut drawn tubes into a predetermined curve to form the large area conformable shape structure, wherein the cut drawn tubes contain a material.

  13. Large-area, flexible imaging arrays constructed by light-charge organic memories

    PubMed Central

    Zhang, Lei; Wu, Ti; Guo, Yunlong; Zhao, Yan; Sun, Xiangnan; Wen, Yugeng; Yu, Gui; Liu, Yunqi

    2013-01-01

    Existing organic imaging circuits, which offer attractive benefits of light weight, low cost and flexibility, are exclusively based on phototransistor or photodiode arrays. One shortcoming of these photo-sensors is that the light signal should keep invariant throughout the whole pixel-addressing and reading process. As a feasible solution, we synthesized a new charge storage molecule and embedded it into a device, which we call light-charge organic memory (LCOM). In LCOM, the functionalities of photo-sensor and non-volatile memory are integrated. Thanks to the deliberate engineering of electronic structure and self-organization process at the interface, 92% of the stored charges, which are linearly controlled by the quantity of light, retain after 20000 s. The stored charges can also be non-destructively read and erased by a simple voltage program. These results pave the way to large-area, flexible imaging circuits and demonstrate a bright future of small molecular materials in non-volatile memory. PMID:23326636

  14. Large-area flexible 3D optical negative index metamaterial formed by nanotransfer printing

    NASA Astrophysics Data System (ADS)

    Chanda, Debashis; Shigeta, Kazuki; Gupta, Sidhartha; Cain, Tyler; Carlson, Andrew; Mihi, Agustin; Baca, Alfred J.; Bogart, Gregory R.; Braun, Paul; Rogers, John A.

    2011-07-01

    Negative-index metamaterials (NIMs) are engineered structures with optical properties that cannot be obtained in naturally occurring materials. Recent work has demonstrated that focused ion beam and layer-by-layer electron-beam lithography can be used to pattern the necessary nanoscale features over small areas (hundreds of µm2) for metamaterials with three-dimensional layouts and interesting characteristics, including negative-index behaviour in the optical regime. A key challenge is in the fabrication of such three-dimensional NIMs with sizes and at throughputs necessary for many realistic applications (including lenses, resonators and other photonic components). We report a simple printing approach capable of forming large-area, high-quality NIMs with three-dimensional, multilayer formats. Here, a silicon wafer with deep, nanoscale patterns of surface relief serves as a reusable stamp. Blanket deposition of alternating layers of silver and magnesium fluoride onto such a stamp represents a process for `inking' it with thick, multilayer assemblies. Transfer printing this ink material onto rigid or flexible substrates completes the fabrication in a high-throughput manner. Experimental measurements and simulation results show that macroscale, three-dimensional NIMs (>75 cm2) nano-manufactured in this way exhibit a strong, negative index of refraction in the near-infrared spectral range, with excellent figures of merit.

  15. Design and fabrication of a flexible large area fabric transducer for bone healing application

    NASA Astrophysics Data System (ADS)

    Jadidian, Bahram

    The electromechanical transducers have found applications in their either passive or active modes. These applications include hydrophone, medical imaging, nondestructive evaluation, motors, sensors, actuators, civil and aerospace engineering. Other medical applications for ultrasonic transducers include therapeutics, osteosynthesis, lithotripsy, thrombolysis, and transdermal drug administration. During the past few decades, lead zirconate titanate (PZT), has been utilized in transducer applications in the form of a bulk piezoelectric ceramic and/or ceramic-polymer composites because of its high piezoelectric charge coefficient d33. The usage of piezoelectric ceramic/polymer composites allows designers to overcome some of the problems dealing with either monolithic piezoceramics or piezopolymers in transducer applications. In this work, a variety of composites with different connectivity patterns were formed. Composites with 1-3 connectivity were fabricated using bundling and collimating methods. Sized and unsized fibers were woven to form fabric. The fabric was used to form 3-3 composites and spiral structures. Square sheets of the fabric were laminated on top of each other, heat treated, and embedded in different types of polymer. The effect of applied pressure on the stack during heat treatment was studied. Plane fabric was formed in the spiral manner and used to construct piezocomposites. A piezoelectric transducer with high thickness coupling coefficient and its matching layer were exploited for bone healing application. One of the structures with the highest electromechanical properties, developed in this work, was chosen for the array fabrication. The spiral composite elements, with the best properties, were arranged in a 3 x 4 format embedded in a flexible polymer. The mechanical endurance of the elements and the array was studied. A large area flexible matching layer with low attenuation was developed. An extensive study was performed to determine the

  16. Laser Direct Write micro-fabrication of large area electronics on flexible substrates

    NASA Astrophysics Data System (ADS)

    Zacharatos, F.; Makrygianni, M.; Geremia, R.; Biver, E.; Karnakis, D.; Leyder, S.; Puerto, D.; Delaporte, P.; Zergioti, I.

    2016-06-01

    To date, Laser Direct Write (LDW) techniques, such as Laser Induced Forward Transfer (LIFT), selective laser ablation and selective laser sintering of metal nanoparticle (NP) ink layers are receiving growing attention for the printing of uniform and well-defined conductive patterns with resolution down to 10 μm. For flexible substrates in particular, selective laser sintering of such NP patterns has been widely applied, as a low temperature and high resolution process compatible with large area electronics. In this work, LDW of silver NP inks has been carried out on polyethylene-terephthalate (PET), polyethylene-naphthalate (PEN) and polyimide (PI) substrates to achieve low electrical resistivity electrodes. In more detail, high speed short pulsed (picosecond and nanosecond) lasers with repetition rates up to 1 MHz were used to print (LIFT) metal NP inks. We thus achieved uniform and continuous patterns with a minimum feature size of 1 μm and a total footprint larger than 1 cm2. Next, the printed patterns were laser sintered with ns pulses at 532 nm over a wide laser fluence window, resulting in an electrical resistivity of 10 μΩ cm. We carried out spatial beam shaping experiments to achieve a top-hat laser intensity profile and employed selective laser ablation of thin films (thickness on the order of 100 nm) to produce silver micro-electrodes with a resolution on the order of 10 μm and a low line edge roughness. Laser sintering was combined with laser ablation to constitute a fully autonomous micro-patterning technique of metallic micro-features, with a 10 μm resolution and geometrical characteristics tuned for interdigitated electrodes for sensor applications.

  17. A large-area, flexible pressure sensor matrix with organic field-effect transistors for artificial skin applications

    NASA Astrophysics Data System (ADS)

    Someya, Takao; Sekitani, Tsuyoshi; Iba, Shingo; Kato, Yusaku; Kawaguchi, Hiroshi; Sakurai, Takayasu

    2004-07-01

    It is now widely accepted that skin sensitivity will be very important for future robots used by humans in daily life for housekeeping and entertainment purposes. Despite this fact, relatively little progress has been made in the field of pressure recognition compared to the areas of sight and voice recognition, mainly because good artificial "electronic skin" with a large area and mechanical flexibility is not yet available. The fabrication of a sensitive skin consisting of thousands of pressure sensors would require a flexible switching matrix that cannot be realized with present silicon-based electronics. Organic field-effect transistors can substitute for such conventional electronics because organic circuits are inherently flexible and potentially ultralow in cost even for a large area. Thus, integration of organic transistors and rubber pressure sensors, both of which can be produced by low-cost processing technology such as large-area printing technology, will provide an ideal solution to realize a practical artificial skin, whose feasibility has been demonstrated in this paper. Pressure images have been taken by flexible active matrix drivers with organic transistors whose mobility reaches as high as 1.4 cm2/V·s. The device is electrically functional even when it is wrapped around a cylindrical bar with a 2-mm radius.

  18. Flexible, transparent and ultra-broadband photodetector based on large-area WSe2 film for wearable devices

    NASA Astrophysics Data System (ADS)

    Zheng, Zhaoqiang; Zhang, Tanmei; Yao, Jiandomg; Zhang, Yi; Xu, Jiarui; Yang, Guowei

    2016-06-01

    Although two-dimensional (2D) materials have attracted considerable research interest for use in the development of innovative wearable optoelectronic systems, the integrated optoelectronic performance of 2D materials photodetectors, including flexibility, transparency, broadband response and stability in air, remains quite low to date. Here, we demonstrate a flexible, transparent, high-stability and ultra-broadband photodetector made using large-area and highly-crystalline WSe2 films that were prepared by pulsed-laser deposition (PLD). Benefiting from the 2D physics of WSe2 films, this device exhibits excellent average transparency of 72% in the visible range and superior photoresponse characteristics, including an ultra-broadband detection spectral range from 370 to 1064 nm, reversible photoresponsivity approaching 0.92 A W‑1, external quantum efficiency of up to 180% and a relatively fast response time of 0.9 s. The fabricated photodetector also demonstrates outstanding mechanical flexibility and durability in air. Also, because of the wide compatibility of the PLD-grown WSe2 film, we can fabricate various photodetectors on multiple flexible or rigid substrates, and all these devices will exhibit distinctive switching behavior and superior responsivity. These indicate a possible new strategy for the design and integration of flexible, transparent and broadband photodetectors based on large-area WSe2 films, with great potential for practical applications in the wearable optoelectronic devices.

  19. Flexible, transparent and ultra-broadband photodetector based on large-area WSe2 film for wearable devices.

    PubMed

    Zheng, Zhaoqiang; Zhang, Tanmei; Yao, Jiandomg; Zhang, Yi; Xu, Jiarui; Yang, Guowei

    2016-06-01

    Although two-dimensional (2D) materials have attracted considerable research interest for use in the development of innovative wearable optoelectronic systems, the integrated optoelectronic performance of 2D materials photodetectors, including flexibility, transparency, broadband response and stability in air, remains quite low to date. Here, we demonstrate a flexible, transparent, high-stability and ultra-broadband photodetector made using large-area and highly-crystalline WSe2 films that were prepared by pulsed-laser deposition (PLD). Benefiting from the 2D physics of WSe2 films, this device exhibits excellent average transparency of 72% in the visible range and superior photoresponse characteristics, including an ultra-broadband detection spectral range from 370 to 1064 nm, reversible photoresponsivity approaching 0.92 A W(-1), external quantum efficiency of up to 180% and a relatively fast response time of 0.9 s. The fabricated photodetector also demonstrates outstanding mechanical flexibility and durability in air. Also, because of the wide compatibility of the PLD-grown WSe2 film, we can fabricate various photodetectors on multiple flexible or rigid substrates, and all these devices will exhibit distinctive switching behavior and superior responsivity. These indicate a possible new strategy for the design and integration of flexible, transparent and broadband photodetectors based on large-area WSe2 films, with great potential for practical applications in the wearable optoelectronic devices. PMID:27109239

  20. Nanostructured electrochromic films by inkjet printing on large area and flexible transparent silver electrodes

    NASA Astrophysics Data System (ADS)

    Layani, Michael; Darmawan, Peter; Foo, Wan Ling; Liu, Liang; Kamyshny, Alexander; Mandler, Daniel; Magdassi, Schlomo; Lee, Pooi See

    2014-04-01

    Printed electrochromic flexible films were obtained by combining transparent silver grid electrodes formed by self-assembly and inkjet printed WO3 nanoparticles. Concentrated dispersions of WO3 nanoparticles were inkjet printed on transparent plastic silver grid electrodes with a high transparency of 83% in the spectral range of 400-800 nm, and a low sheet resistance in the range of 1-5 Ω sq-1. These electrodes were used for electrochromic applications for the first time. The resultant patterned nanostructured electrochromic films maintained their coloring and bleaching performance after bending of the flexible films.Printed electrochromic flexible films were obtained by combining transparent silver grid electrodes formed by self-assembly and inkjet printed WO3 nanoparticles. Concentrated dispersions of WO3 nanoparticles were inkjet printed on transparent plastic silver grid electrodes with a high transparency of 83% in the spectral range of 400-800 nm, and a low sheet resistance in the range of 1-5 Ω sq-1. These electrodes were used for electrochromic applications for the first time. The resultant patterned nanostructured electrochromic films maintained their coloring and bleaching performance after bending of the flexible films. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr06890k

  1. Flexible and printable paper-based strain sensors for wearable and large-area green electronics.

    PubMed

    Liao, Xinqin; Zhang, Zheng; Liao, Qingliang; Liang, Qijie; Ou, Yang; Xu, Minxuan; Li, Minghua; Zhang, Guangjie; Zhang, Yue

    2016-07-14

    Paper-based (PB) green electronics is an emerging and potentially game-changing technology due to ease of recycling/disposal, the economics of manufacture and the applicability to flexible electronics. Herein, new-type printable PB strain sensors (PPBSSs) from graphite glue (graphite powder and methylcellulose) have been fabricated. The graphite glue is exposed to thermal annealing to produce surface micro/nano cracks, which are very sensitive to compressive or tensile strain. The devices exhibit a gauge factor of 804.9, response time of 19.6 ms and strain resolution of 0.038%, all performance indicators attaining and even surpassing most of the recently reported strain sensors. Due to the distinctive sensing properties, flexibility and robustness, the PPBSSs are suitable for monitoring of diverse conditions such as structural strain, vibrational motion, human muscular movements and visual control. PMID:27314505

  2. Semiconductor-based, large-area, flexible, electronic devices on {110}<100> oriented substrates

    SciTech Connect

    Goyal, Amit

    2014-08-05

    Novel articles and methods to fabricate the same resulting in flexible, oriented, semiconductor-based, electronic devices on {110}<100> textured substrates are disclosed. Potential applications of resulting articles are in areas of photovoltaic devices, flat-panel displays, thermophotovoltaic devices, ferroelectric devices, light emitting diode devices, computer hard disc drive devices, magnetoresistance based devices, photoluminescence based devices, non-volatile memory devices, dielectric devices, thermoelectric devices and quantum dot laser devices.

  3. Flexible and printable paper-based strain sensors for wearable and large-area green electronics

    NASA Astrophysics Data System (ADS)

    Liao, Xinqin; Zhang, Zheng; Liao, Qingliang; Liang, Qijie; Ou, Yang; Xu, Minxuan; Li, Minghua; Zhang, Guangjie; Zhang, Yue

    2016-06-01

    Paper-based (PB) green electronics is an emerging and potentially game-changing technology due to ease of recycling/disposal, the economics of manufacture and the applicability to flexible electronics. Herein, new-type printable PB strain sensors (PPBSSs) from graphite glue (graphite powder and methylcellulose) have been fabricated. The graphite glue is exposed to thermal annealing to produce surface micro/nano cracks, which are very sensitive to compressive or tensile strain. The devices exhibit a gauge factor of 804.9, response time of 19.6 ms and strain resolution of 0.038%, all performance indicators attaining and even surpassing most of the recently reported strain sensors. Due to the distinctive sensing properties, flexibility and robustness, the PPBSSs are suitable for monitoring of diverse conditions such as structural strain, vibrational motion, human muscular movements and visual control.Paper-based (PB) green electronics is an emerging and potentially game-changing technology due to ease of recycling/disposal, the economics of manufacture and the applicability to flexible electronics. Herein, new-type printable PB strain sensors (PPBSSs) from graphite glue (graphite powder and methylcellulose) have been fabricated. The graphite glue is exposed to thermal annealing to produce surface micro/nano cracks, which are very sensitive to compressive or tensile strain. The devices exhibit a gauge factor of 804.9, response time of 19.6 ms and strain resolution of 0.038%, all performance indicators attaining and even surpassing most of the recently reported strain sensors. Due to the distinctive sensing properties, flexibility and robustness, the PPBSSs are suitable for monitoring of diverse conditions such as structural strain, vibrational motion, human muscular movements and visual control. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02172g

  4. On the use of organic transistors in flexible large-area sensor arrays (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Cobb, Brian; Kumar, Abhishek

    2015-10-01

    While much of the OTFT activity has been display-centric there is no doubt that as the OTFT technology matures the number of applications will continue to increase. Using our most recent flexible X-ray detectors we will discuss the prospect and challenges of organic transistors in sensor backplanes. For these application, the current mobility of ~0.1-2 cm2/Vs of OTFTs is currently not a problem. Their low leakage currents give them a distinct advantage over competing technologies, such as amorphous silicon TFT. Yet, challenges remain and these will be discussed.

  5. Functionalization of nanomaterials by non-thermal large area atmospheric pressure plasmas: application to flexible dye-sensitized solar cells.

    PubMed

    Jung, Heesoo; Park, Jaeyoung; Yoo, Eun Sang; Han, Gill-Sang; Jung, Hyun Suk; Ko, Min Jae; Park, Sanghoo; Choe, Wonho

    2013-09-01

    A key challenge to the industrial application of nanotechnology is the development of fabrication processes for functional devices based on nanomaterials which can be scaled up for mass production. In this report, we disclose the results of non-thermal radio-frequency (rf) atmospheric pressure plasma (APP) based deposition of TiO2 nanoparticles on a flexible substrate for the fabrication of dye-sensitized solar cells (DSSCs). Operating at 190 °C without a vacuum enclosure, the APP method can avoid thermal damage and vacuum compatibility restrictions and utilize roll-to-roll processing over a large area. The various analyses of the TiO2 films demonstrate that superior film properties can be obtained by the non-thermal APP method when compared with the thermal sintering process operating at 450 °C. The crystallinity of the anatase TiO2 nanoparticles is significantly improved without thermal agglomeration, while the surface defects such as Ti(3+) ions are eliminated, thus providing efficient charge collecting properties for solar cells. Finally, we successfully fabricated a flexible DSSC with an energy conversion efficiency of 4.2% using a transparent plastic substrate. This work demonstrates the potential of non-thermal APP technology in the area of device-level, nano-enabled material manufacturing. PMID:23831925

  6. Conformational Flexibility in the Transmembrane Protein TSPO.

    PubMed

    Jaremko, Łukasz; Jaremko, Mariusz; Giller, Karin; Becker, Stefan; Zweckstetter, Markus

    2015-11-01

    The translocator protein (TSPO) is an integral membrane protein that interacts with a wide variety of endogenous ligands, such as cholesterol and porphyrins, and is also the target for several small molecules with substantial in vivo efficacy. When complexed with the TSPO-specific radioligand (R)-PK11195, TSPO folds into a rigid five-helix bundle. However, little is known about the structure and dynamics of TSPO in the absence of high-affinity ligands. By means of NMR spectroscopy, we show that TSPO exchanges between multiple conformations in the absence of (R)-PK11195. Extensive motions on time scales from pico- to microseconds occur all along the primary sequence of the protein, leading to a loss of stable tertiary interactions and local unfolding of the helical structure in the vicinity of the ligand-binding site. The flexible nature of TSPO highlights the importance of conformational plasticity in integral membrane proteins. PMID:26394723

  7. Ambient fabrication of flexible and large-area organic light-emitting devices using slot-die coating

    PubMed Central

    Sandström, Andreas; Dam, Henrik F.; Krebs, Frederik C.; Edman, Ludvig

    2012-01-01

    The grand vision of manufacturing large-area emissive devices with low-cost roll-to-roll coating methods, akin to how newspapers are produced, appeared with the emergence of the organic light-emitting diode about 20 years ago. Today, small organic light-emitting diode displays are commercially available in smartphones, but the promise of a continuous ambient fabrication has unfortunately not materialized yet, as organic light-emitting diodes invariably depend on the use of one or more time- and energy-consuming process steps under vacuum. Here we report an all-solution-based fabrication of an alternative emissive device, a light-emitting electrochemical cell, using a slot-die roll-coating apparatus. The fabricated flexible sheets exhibit bidirectional and uniform light emission, and feature a fault-tolerant >1-μm-thick active material that is doped in situ during operation. It is notable that the initial preparation of inks, the subsequent coating of the constituent layers and the final device operation all could be executed under ambient air. PMID:22893126

  8. Femtosecond laser rapid fabrication of large-area rose-like micropatterns on freestanding flexible graphene films.

    PubMed

    Shi, Xuesong; Li, Xin; Jiang, Lan; Qu, Liangti; Zhao, Yang; Ran, Peng; Wang, Qingsong; Cao, Qiang; Ma, Tianbao; Lu, Yongfeng

    2015-01-01

    We developed a simple, scalable and high-throughput method for fabrication of large-area three-dimensional rose-like microflowers with controlled size, shape and density on graphene films by femtosecond laser micromachining. The novel biomimetic microflower that composed of numerous turnup graphene nanoflakes can be fabricated by only a single femtosecond laser pulse, which is efficient enough for large-area patterning. The graphene films were composed of layer-by-layer graphene nanosheets separated by nanogaps (~10-50 nm), and graphene monolayers with an interlayer spacing of ~0.37 nm constituted each of the graphene nanosheets. This unique hierarchical layering structure of graphene films provides great possibilities for generation of tensile stress during femtosecond laser ablation to roll up the nanoflakes, which contributes to the formation of microflowers. By a simple scanning technique, patterned surfaces with controllable densities of flower patterns were obtained, which can exhibit adhesive superhydrophobicity. More importantly, this technique enables fabrication of the large-area patterned surfaces at centimeter scales in a simple and efficient way. This study not only presents new insights of ultrafast laser processing of novel graphene-based materials but also shows great promise of designing new materials combined with ultrafast laser surface patterning for future applications in functional coatings, sensors, actuators and microfluidics. PMID:26615800

  9. Femtosecond laser rapid fabrication of large-area rose-like micropatterns on freestanding flexible graphene films

    PubMed Central

    Shi, Xuesong; Li, Xin; Jiang, Lan; Qu, Liangti; Zhao, Yang; Ran, Peng; Wang, Qingsong; Cao, Qiang; Ma, Tianbao; Lu, Yongfeng

    2015-01-01

    We developed a simple, scalable and high-throughput method for fabrication of large-area three-dimensional rose-like microflowers with controlled size, shape and density on graphene films by femtosecond laser micromachining. The novel biomimetic microflower that composed of numerous turnup graphene nanoflakes can be fabricated by only a single femtosecond laser pulse, which is efficient enough for large-area patterning. The graphene films were composed of layer-by-layer graphene nanosheets separated by nanogaps (~10–50 nm), and graphene monolayers with an interlayer spacing of ~0.37 nm constituted each of the graphene nanosheets. This unique hierarchical layering structure of graphene films provides great possibilities for generation of tensile stress during femtosecond laser ablation to roll up the nanoflakes, which contributes to the formation of microflowers. By a simple scanning technique, patterned surfaces with controllable densities of flower patterns were obtained, which can exhibit adhesive superhydrophobicity. More importantly, this technique enables fabrication of the large-area patterned surfaces at centimeter scales in a simple and efficient way. This study not only presents new insights of ultrafast laser processing of novel graphene-based materials but also shows great promise of designing new materials combined with ultrafast laser surface patterning for future applications in functional coatings, sensors, actuators and microfluidics. PMID:26615800

  10. Femtosecond laser rapid fabrication of large-area rose-like micropatterns on freestanding flexible graphene films

    NASA Astrophysics Data System (ADS)

    Shi, Xuesong; Li, Xin; Jiang, Lan; Qu, Liangti; Zhao, Yang; Ran, Peng; Wang, Qingsong; Cao, Qiang; Ma, Tianbao; Lu, Yongfeng

    2015-11-01

    We developed a simple, scalable and high-throughput method for fabrication of large-area three-dimensional rose-like microflowers with controlled size, shape and density on graphene films by femtosecond laser micromachining. The novel biomimetic microflower that composed of numerous turnup graphene nanoflakes can be fabricated by only a single femtosecond laser pulse, which is efficient enough for large-area patterning. The graphene films were composed of layer-by-layer graphene nanosheets separated by nanogaps (~10-50 nm), and graphene monolayers with an interlayer spacing of ~0.37 nm constituted each of the graphene nanosheets. This unique hierarchical layering structure of graphene films provides great possibilities for generation of tensile stress during femtosecond laser ablation to roll up the nanoflakes, which contributes to the formation of microflowers. By a simple scanning technique, patterned surfaces with controllable densities of flower patterns were obtained, which can exhibit adhesive superhydrophobicity. More importantly, this technique enables fabrication of the large-area patterned surfaces at centimeter scales in a simple and efficient way. This study not only presents new insights of ultrafast laser processing of novel graphene-based materials but also shows great promise of designing new materials combined with ultrafast laser surface patterning for future applications in functional coatings, sensors, actuators and microfluidics.

  11. Next Generation Non-Vacuum, Maskless, Low Temperature Nanoparticle Ink Laser Digital Direct Metal Patterning for a Large Area Flexible Electronics

    PubMed Central

    Yeo, Junyeob; Hong, Sukjoon; Lee, Daehoo; Hotz, Nico; Lee, Ming-Tsang; Grigoropoulos, Costas P.; Ko, Seung Hwan

    2012-01-01

    Flexible electronics opened a new class of future electronics. The foldable, light and durable nature of flexible electronics allows vast flexibility in applications such as display, energy devices and mobile electronics. Even though conventional electronics fabrication methods are well developed for rigid substrates, direct application or slight modification of conventional processes for flexible electronics fabrication cannot work. The future flexible electronics fabrication requires totally new low-temperature process development optimized for flexible substrate and it should be based on new material too. Here we present a simple approach to developing a flexible electronics fabrication without using conventional vacuum deposition and photolithography. We found that direct metal patterning based on laser-induced local melting of metal nanoparticle ink is a promising low-temperature alternative to vacuum deposition– and photolithography-based conventional metal patterning processes. The “digital” nature of the proposed direct metal patterning process removes the need for expensive photomask and allows easy design modification and short turnaround time. This new process can be extremely useful for current small-volume, large-variety manufacturing paradigms. Besides, simple, scalable, fast and low-temperature processes can lead to cost-effective fabrication methods on a large-area polymer substrate. The developed process was successfully applied to demonstrate high-quality Ag patterning (2.1 µΩ·cm) and high-performance flexible organic field effect transistor arrays. PMID:22900011

  12. Large area in situ fabrication of poly(pyrrole)-nanowires on flexible thermoplastic films using nanocontact printing

    NASA Astrophysics Data System (ADS)

    Garcia-Cruz, Alvaro; Lee, Michael; Marote, Pedro; Zine, Nadia; Sigaud, Monique; Bonhomme, Anne; Pruna, Raquel; Lopez, Manuel; Bausells, Joan; Jaffrezic, Nicole; Errachid, Abdelhamid

    2016-08-01

    Highly efficient nano-engineering tools will certainly revolutionize the biomedical and sensing devices research and development in the years to come. Here, we present a novel high performance conducting poly(pyrrole) nanowires (PPy-NW) patterning technology on thermoplastic surfaces (poly(ethylene terephthalate (PETE), poly(ethylene 2,6-naphthalate (PEN), polyimide (PI), and cyclic olefin copolymer) using nanocontact printing and controlled chemical polymerization (nCP-CCP) technique. The technique uses a commercial compact disk as a template to produce nanopatterned polydimethylsiloxane (PDMS) stamps. The PDMS nanopatterned stamp was applied to print the PPy-NWs and the developed technology of nCP-CCP produced 3D conducting nanostructures. This new and very promising nanopatterning technology was achieved in a single step and with a low cost of fabrication over large areas.

  13. Integrating anti-reflection and superhydrophobicity of moth-eye-like surface morphology on a large-area flexible substrate

    NASA Astrophysics Data System (ADS)

    Liu, Chia-Hsing; Niu, Pei-Lun; Sung, Cheng-Kuo

    2014-01-01

    This paper proposes an ultraviolet nanoimprint lithography (UV-NIL) roll-to-roll (R2R) process with argon and oxygen (Ar-O2) plasma ashing and coating of a dilute perfluorodecyltrichlorosilane (FDTS) layer to fabricate the large-area moth-eye-like surface morphology on a polyethylene terephthalate substrate. By using Maxwell-Garnett's effective medium theory, the optimal dimensions of the moth-eye-like surface morphology was designed and fabricated with UV-NIL R2R process to obtain maximum transmittance ratio. In addition, the base angle (θ = 30.1°) of the moth-eye-like surface morphology was modified with Ar-O2 plasma ashing and coated with a dilute FDTS layer to possess both superhydrophobic and air-retention properties. This increases both the transmittance ratio of 4% and contact angle to 153°.

  14. Large-Area Monolayer MoS2 for Flexible Low-Power RF Nanoelectronics in the GHz Regime.

    PubMed

    Chang, Hsiao-Yu; Yogeesh, Maruthi Nagavalli; Ghosh, Rudresh; Rai, Amritesh; Sanne, Atresh; Yang, Shixuan; Lu, Nanshu; Banerjee, Sanjay Kumar; Akinwande, Deji

    2016-03-01

    Flexible synthesized MoS2 transistors are advanced to perform at GHz speeds. An intrinsic cutoff frequency of 5.6 GHz is achieved and analog circuits are realized. Devices are mechanically robust for 10 000 bending cycles. PMID:26707841

  15. {100}<100> or 45.degree.-rotated {100}<100>, semiconductor-based, large-area, flexible, electronic devices

    SciTech Connect

    Goyal, Amit

    2012-05-15

    Novel articles and methods to fabricate the same resulting in flexible, {100}<100> or 45.degree.-rotated {100}<100> oriented, semiconductor-based, electronic devices are disclosed. Potential applications of resulting articles are in areas of photovoltaic devices, flat-panel displays, thermophotovoltaic devices, ferroelectric devices, light emitting diode devices, computer hard disc drive devices, magnetoresistance based devices, photoluminescence based devices, non-volatile memory devices, dielectric devices, thermoelectric devices and quantum dot laser devices.

  16. Synthesis and self-assembly of large-area Cu nanosheets and their application as an aqueous conductive ink on flexible electronics.

    PubMed

    Dang, Rui; Song, Lingling; Dong, Wenjun; Li, Chaorong; Zhang, Xiaobo; Wang, Ge; Chen, Xiaobo

    2014-01-01

    Large-area Cu nanosheets are synthesized by a strategy of Cu nanocrystal self-assembly, and then aqueous conductive Cu nanosheet ink is successfully prepared for direct writing on the conductive circuits of flexible electronics. The Cu nanocrystals, as building blocks, self-assemble along the [111] direction and grow into large-area nanosheets approximately 30-100 μm in diameter and a few hundred nanometers in thickness. The laminar stackable patterns of the Cu nanosheet circuits increase the contact area of the Cu nanosheets and improve the stability of the conductor under stress, the result being that the Cu nanosheet circuits display excellent conductive performance during repeated folding and unfolding. Moreover, heterostructures of Ag nanoparticle-coated Cu nanosheets are created to improve the thermal stability of the nanosheet circuits at high temperatures. PMID:24313540

  17. Large Area Nano-transfer Printing of Sub-50-nm Metal Nanostructures Using Low-cost Semi-flexible Hybrid Templates.

    PubMed

    Nagel, Robin D; Haeberle, Tobias; Schmidt, Morten; Lugli, Paolo; Scarpa, Giuseppe

    2016-12-01

    In this work, we present a method for printing metal micro- and nanopatterns down to sub-50-nm feature sizes using replicated, defect-tolerant stamps made out of OrmoStamp®; material. The relevant parameters for a successful transfer over large areas were investigated and yields above 99 % have been achieved. Comparing our results to conventional nano-transfer printing using PDMS stamps, we find that the more rigid hybrid polymer used here prevents unintended transfer from interspaces between structures of large distance due to roof collapse and deformation of nano-sized structures due to lateral collapse. Yet, our stamps are flexible enough to ensure intimate contact with the underlying substrate over large areas even in the presence of defect particles. Additionally, the presented patterning technique is resist-, solvent-, and chemical-free and is therefore ideally suited for applications in organic nanoelectronics where standard nanostructuring methods can harm or destroy the organic material. PMID:26976429

  18. Large Area Nano-transfer Printing of Sub-50-nm Metal Nanostructures Using Low-cost Semi-flexible Hybrid Templates

    NASA Astrophysics Data System (ADS)

    Nagel, Robin D.; Haeberle, Tobias; Schmidt, Morten; Lugli, Paolo; Scarpa, Giuseppe

    2016-03-01

    In this work, we present a method for printing metal micro- and nanopatterns down to sub-50-nm feature sizes using replicated, defect-tolerant stamps made out of OrmoStamp®; material. The relevant parameters for a successful transfer over large areas were investigated and yields above 99 % have been achieved. Comparing our results to conventional nano-transfer printing using PDMS stamps, we find that the more rigid hybrid polymer used here prevents unintended transfer from interspaces between structures of large distance due to roof collapse and deformation of nano-sized structures due to lateral collapse. Yet, our stamps are flexible enough to ensure intimate contact with the underlying substrate over large areas even in the presence of defect particles. Additionally, the presented patterning technique is resist-, solvent-, and chemical-free and is therefore ideally suited for applications in organic nanoelectronics where standard nanostructuring methods can harm or destroy the organic material.

  19. A KINETIC ANALYSIS OF THE CONFORMATIONAL FLEXIBILITY OF STEROID HORMONES

    EPA Science Inventory

    For a set of 10 androgen steroids and estradiol (E2), the kinetic feasibility of conformation flexibility of the cyclic moieties was studied under the constraint of maintaining the B/C trans and C/D trans ring fusion of the natural and biologically active enantiomer. To this end,...

  20. Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata

    SciTech Connect

    Chen, Zuxu; de Serrano, Vesna; Betts, Laurie; Franzen, Stefan

    2009-01-28

    The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein which has a globin fold but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. As a hemoglobin, DHP cycles between the oxy and deoxy states as it reversibly binds oxygen for storage. Here, it is reported that the distal histidine, His55, exhibits conformational flexibility in the deoxy form and is consequently observed in two solvent-exposed conformations more than 9.5 {angstrom} away from the heme. These conformations are analogous to the open conformation of sperm whale myoglobin. The heme iron in deoxy ferrous DHP is five-coordinate and has an out-of-plane displacement of 0.25 {angstrom} from the heme plane. The observation of five-coordinate heme iron with His55 in a remote solvent-exposed conformation is consistent with the hypothesis that His55 interacts with heme iron ligands through hydrogen bonding in the closed conformation. Since His55 is also displaced by the binding of 4-iodophenol in an internal pocket, these results provide new insight into the correlation between heme iron ligation, molecular binding in the distal pocket and the conformation of the distal histidine in DHP.

  1. Flexible polyelectrolyte conformation in the presence of oppositely charged surfactants.

    PubMed

    Kuhn, P S; Diehl, A

    2007-10-01

    Conformational behavior of flexible polyelectrolytes in the presence of monovalent cationic surfactants is examined. A simple model is presented for the formation of polyelectrolyte-surfactant complexes in salt-free solutions in the framework of the Debye-Hückel-Bjerrum-Manning and Flory theories, including explicitly the hydrophobic interactions between the associated surfactant molecules on the polyelectrolyte. The distribution of complexes is calculated as a function of the surfactant concentration and a discrete conformational transition between an elongated coil and a compact globule was found, in agreement with experimental observations. PMID:17995019

  2. Inherent conformational flexibility of F1-ATPase α-subunit.

    PubMed

    Hahn-Herrera, Otto; Salcedo, Guillermo; Barril, Xavier; García-Hernández, Enrique

    2016-09-01

    The core of F1-ATPase consists of three catalytic (β) and three noncatalytic (α) subunits, forming a hexameric ring in alternating positions. A wealth of experimental and theoretical data has provided a detailed picture of the complex role played by catalytic subunits. Although major conformational changes have only been seen in β-subunits, it is clear that α-subunits have to respond to these changes in order to be able to transmit information during the rotary mechanism. However, the conformational behavior of α-subunits has not been explored in detail. Here, we have combined unbiased molecular dynamics (MD) simulations and calorimetrically measured thermodynamic signatures to investigate the conformational flexibility of isolated α-subunits, as a step toward deepening our understanding of its function inside the α3β3 ring. The simulations indicate that the open-to-closed conformational transition of the α-subunit is essentially barrierless, which is ideal to accompany and transmit the movement of the catalytic subunits. Calorimetric measurements of the recombinant α-subunit from Geobacillus kaustophilus indicate that the isolated subunit undergoes no significant conformational changes upon nucleotide binding. Simulations confirm that the nucleotide-free and nucleotide-bound subunits show average conformations similar to that observed in the F1 crystal structure, but they reveal an increased conformational flexibility of the isolated α-subunit upon MgATP binding, which might explain the evolutionary conserved capacity of α-subunits to recognize nucleotides with considerable strength. Furthermore, we elucidate the different dependencies that α- and β-subunits show on Mg(II) for recognizing ATP. PMID:27137408

  3. Investigation of robust flexible conformal THz perfect metamaterial absorber

    NASA Astrophysics Data System (ADS)

    Kim, Ju-Hyung; Hokmabadi, Mohammad P.; Balci, Soner; Rivera, Elmer; Wilbert, David; Kung, Patrick; Kim, Seongsin Margaret

    2016-04-01

    The flexible metamaterials have promised to greatly expand our ability to realize a wide range of novel applications including new methods of sensing and cloaking. In this work, flexible metamaterial absorbers, targeted to operate at terahertz frequencies, have been designed, simulated, and fabricated. The absorber structure consisted of a conducting ground plane, a dielectric spacer, and a frequency selective surface which was composed of two layers of nonconcentric, differently sized, single-ring arrays. Absorber structure was designed and simulated such that absorbers exhibited two distinct resonance frequencies with the strength of absorption for both sensitive to the center-to-center spacing of the rings and polarization. The functionality of the absorbers was seen to be similar both in planar and deformed positions, which promises robustness of the conformal flexible metamaterials device under the deformation and uneven surfaces.

  4. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.

    PubMed

    You, T J; Bashford, D

    1995-11-01

    A new method for including local conformational flexibility in calculations of the hydrogen ion titration of proteins using macroscopic electrostatic models is presented. Intrinsic pKa values and electrostatic interactions between titrating sites are calculated from an ensemble of conformers in which the positions of titrating side chains are systematically varied. The method is applied to the Asp, Glu, and Tyr residues of hen lysozyme. The effects of different minimization and/or sampling protocols for both single-conformer and multi-conformer calculations are studied. For single-conformer calculations it is found that the results are sensitive to the choice of all-hydrogen versus polar-hydrogen-only atomic models and to the minimization protocol chosen. The best overall agreement of single-conformer calculations with experiment is obtained with an all-hydrogen model and either a two-step minimization process or minimization using a high dielectric constant. Multi-conformational calculations give significantly improved agreement with experiment, slightly smaller shifts between model compound pKa values and calculated intrinsic pKa values, and reduced sensitivity of the intrinsic pKa calculations to the initial details of the structure compared to single-conformer calculations. The extent of these improvements depends on the type of minimization used during the generation of conformers, with more extensive minimization giving greater improvements. The ordering of the titrations of the active-site residues, Glu-35 and Asp-52, is particularly sensitive to the minimization and sampling protocols used. The balance of strong site-site interactions in the active site suggests a need for including site-site conformational correlations. PMID:8580316

  5. A chemical chaperone induces inhomogeneous conformational changes in flexible proteins.

    PubMed

    Hamdane, Djemel; Velours, Christophe; Cornu, David; Nicaise, Magali; Lombard, Murielle; Fontecave, Marc

    2016-07-27

    Organic osmolytes also known as chemical chaperones are major cellular compounds that favor, by an unclear mechanism, protein's compaction and stabilization of the native state. Here, we have examined the chaperone effect of the naturally occurring trimethylamine N-oxide (TMAO) osmolyte on a loosely packed protein (LPP), known to be a highly flexible form, using an apoprotein mutant of the flavin-dependent RNA methyltransferase as a model. Thermal and chemical denaturation experiments showed that TMAO stabilizes the structural integrity of the apoprotein dramatically. The denaturation reaction is irreversible indicating that the stability of the apoprotein is under kinetic control. This result implies that the stabilization is due to a TMAO-induced reconfiguration of the flexible LPP state, which leads to conformational limitations of the apoprotein likely driven by favorable entropic contribution. Evidence for the conformational perturbation of the apoprotein had been obtained through several biophysical approaches notably analytical ultracentrifugation, circular dichroism, fluorescence spectroscopy, labelling experiments and proteolysis coupled to mass spectrometry. Unexpectedly, TMAO promotes an overall elongation or asymmetrical changes of the hydrodynamic shape of the apoprotein without alteration of the secondary structure. The modulation of the hydrodynamic properties of the protein is associated with diverse inhomogenous conformational changes: loss of the solvent accessible cavities resulting in a dried protein matrix; some side-chain residues initially buried become solvent exposed while some others become hidden. Consequently, the TMAO-induced protein state exhibits impaired capability in the flavin binding process. Our study suggests that the nature of protein conformational changes induced by the chemical chaperones may be specific to protein packing and plasticity. This could be an efficient mechanism by which the cell controls and finely tunes the

  6. Large-area flexible monolithic ITO/WO3/Nb2O5/NiVOχ/ITO electrochromic devices prepared by using magnetron sputter deposition

    NASA Astrophysics Data System (ADS)

    Tang, Chien-Jen; Ye, Jia-Ming; Yang, Yueh-Ting; He, Ju-Liang

    2016-05-01

    Electrochromic devices (ECDs) have been applied in smart windows to control the transmission of sunlight in green buildings, saving up to 40-50% electricity consumption and ultimately reducing carbon dioxide emissions. However, the high manufacturing costs and difficulty of transportation of conventional massive large area ECDs has limited widespread applications. A unique design replacing the glass substrate commonly used in the ECD windows with inexpensive, light-weight and flexible polymeric substrate materials would accelerate EC adoption allowing them to be supplemented for regular windows without altering window construction. In this study, an ITO/WO3/Nb2O5/NiVOχ/ITO all-solid-state monolithic ECD with an effective area of 24 cm × 18 cm is successfully integrated on a PET substrate by using magnetron sputter deposition. The electrochromic performance and bending durability of the resultant material are also investigated. The experimental results indicate that the ultimate response times for the prepared ECD is 6 s for coloring at an applied voltage of -3 V and 5 s for bleaching at an applied voltage of +3 V, respectively. The optical transmittances for the bleached and colored state at a wavelength of 633 nm are 53% and 11%, respectively. The prepared ECD can sustain over 8000 repeated coloring and bleaching cycles, as well as tolerate a bending radius of curvature of 7.5 cm.

  7. Investigation of the interfacial adhesion of the transparent conductive oxide films to large-area flexible polymer substrates using laser-induced thermo-mechanical stresses

    NASA Astrophysics Data System (ADS)

    Park, Jin-Woo; Lee, Seung-Ho; Yang, Chan-Woo

    2013-08-01

    In this study, we investigated the interfacial adhesion strength (σint) of transparent conductive oxide (TCO) coatings on polymer substrates using a nanosecond Nd:YAG pulsed laser. We compared our results with those achieved using conventional testing methods such as bending and fragmentation tests as well as theoretical calculations. In the fragmentation and bending tests, mechanical compressive stress is induced in the film due to mismatches in Poisson's ratio and Young's modulus between the substrate and film. But, the incident laser makes the film under compression due to the mismatch in thermal expansion between the TCO and the polymer substrate. With a pulse incident to the substrate, the TCO rapidly expands by laser-induced instant heating while the transparent polymer does little, which causes the TCO to buckle and delaminate over the critical pulse energy. The critical compressive stress that scales with σint was calculated using simple equations, which agreed well with the results from previous theoretical calculations. Because the films preferentially delaminate at the defects and grain boundaries, this technique also provided useful information regarding the interface microstructures. Moreover, because the laser can scan over large areas, this method is suitable for flexible substrates that are produced by a roll-to-roll process. Nevertheless, the mechanical stress introduced by the bending and fragmentation tests causes the TCO to buckle without interfacial delamination. Hence, the stresses at the buckling disagreed with the results obtained from the laser test and the theoretical calculations.

  8. Enhanced prediction of conformational flexibility and phosphorylation in proteins.

    PubMed

    Swaminathan, Karthikeyan; Adamczak, Rafal; Porollo, Aleksey; Meller, Jarosław

    2010-01-01

    Many sequence-based predictors of structural and functional properties of proteins have been developed in the past. In this study, we developed new methods for predicting measures of conformational flexibility in proteins, including X-ray structure-derived temperature (B-) factors and the variance within NMR structural ensemble, as effectively measured by the solvent accessibility standard deviations (SASDs). We further tested whether these predicted measures of conformational flexibility in crystal lattices and solution, respectively, can be used to improve the prediction of phosphorylation in proteins. The latter is an example of a common post-translational modification that modulates protein function, e.g., by affecting interactions and conformational flexibility of phosphorylated sites. Using robust epsilon-insensitive support vector regression (ε-SVR) models, we assessed two specific representations of protein sequences: one based on the position-specific scoring matrices (PSSMs) derived from multiple sequence alignments, and an augmented representation that incorporates real-valued solvent accessibility and secondary structure predictions (RSA/SS) as additional measures of local structural propensities. We showed that a combination of PSSMs and real-valued SS/RSA predictions provides systematic improvements in the accuracy of both B-factors and SASD prediction. These intermediate predictions were subsequently combined into an enhanced predictor of phosphorylation that was shown to significantly outperform methods based on PSSM alone. We would like to stress that to the best of our knowledge, this is the first example of using predicted from sequence NMR structure-based measures of conformational flexibility in solution for the prediction of other properties of proteins. Phosphorylation prediction methods typically employ a two-class classification approach with the limitation that the set of negative examples used for training may include some sites that are

  9. Conformational flexibility and protein folding: rigid structural fragments connected by flexible joints in subtilisin BPN.

    PubMed Central

    Honig, B; Ray, A; Levinthal, C

    1976-01-01

    Conformational energy calculations are used to analyze the interactions of structural substructures in subtilisin BPN. These substructures are kept fixed or "rigid" so that the only variables in the calculations are the backbone segments that separate them. The flexible segments are assumed to be free turns. Using this representation of the protein it is possible to predict both a likely order of events along a folding pathway and preferred modes of conformational changes of the native protein. Moreover, when the native structure has been perturbed by moving the substructures apart, it is possible to assess the range of interactions that return the protein, upon energy minimization, to its original conformation. These results suggest an approach to the folding problem based on the piecemeal formation of tertiary structure from smaller prefolded fragments. PMID:1064867

  10. Flexible conformable hydrophobized surfaces for turbulent flow drag reduction

    NASA Astrophysics Data System (ADS)

    Brennan, Joseph C.; Geraldi, Nicasio R.; Morris, Robert H.; Fairhurst, David J.; McHale, Glen; Newton, Michael I.

    2015-05-01

    In recent years extensive work has been focused onto using superhydrophobic surfaces for drag reduction applications. Superhydrophobic surfaces retain a gas layer, called a plastron, when submerged underwater in the Cassie-Baxter state with water in contact with the tops of surface roughness features. In this state the plastron allows slip to occur across the surface which results in a drag reduction. In this work we report flexible and relatively large area superhydrophobic surfaces produced using two different methods: Large roughness features were created by electrodeposition on copper meshes; Small roughness features were created by embedding carbon nanoparticles (soot) into Polydimethylsiloxane (PDMS). Both samples were made into cylinders with a diameter under 12 mm. To characterize the samples, scanning electron microscope (SEM) images and confocal microscope images were taken. The confocal microscope images were taken with each sample submerged in water to show the extent of the plastron. The hydrophobized electrodeposited copper mesh cylinders showed drag reductions of up to 32% when comparing the superhydrophobic state with a wetted out state. The soot covered cylinders achieved a 30% drag reduction when comparing the superhydrophobic state to a plain cylinder. These results were obtained for turbulent flows with Reynolds numbers 10,000 to 32,500.

  11. Flexible conformable hydrophobized surfaces for turbulent flow drag reduction.

    PubMed

    Brennan, Joseph C; Geraldi, Nicasio R; Morris, Robert H; Fairhurst, David J; McHale, Glen; Newton, Michael I

    2015-01-01

    In recent years extensive work has been focused onto using superhydrophobic surfaces for drag reduction applications. Superhydrophobic surfaces retain a gas layer, called a plastron, when submerged underwater in the Cassie-Baxter state with water in contact with the tops of surface roughness features. In this state the plastron allows slip to occur across the surface which results in a drag reduction. In this work we report flexible and relatively large area superhydrophobic surfaces produced using two different methods: Large roughness features were created by electrodeposition on copper meshes; Small roughness features were created by embedding carbon nanoparticles (soot) into Polydimethylsiloxane (PDMS). Both samples were made into cylinders with a diameter under 12 mm. To characterize the samples, scanning electron microscope (SEM) images and confocal microscope images were taken. The confocal microscope images were taken with each sample submerged in water to show the extent of the plastron. The hydrophobized electrodeposited copper mesh cylinders showed drag reductions of up to 32% when comparing the superhydrophobic state with a wetted out state. The soot covered cylinders achieved a 30% drag reduction when comparing the superhydrophobic state to a plain cylinder. These results were obtained for turbulent flows with Reynolds numbers 10,000 to 32,500. PMID:25975704

  12. Flexible conformable hydrophobized surfaces for turbulent flow drag reduction

    PubMed Central

    Brennan, Joseph C; Geraldi, Nicasio R; Morris, Robert H; Fairhurst, David J; McHale, Glen; Newton, Michael I

    2015-01-01

    In recent years extensive work has been focused onto using superhydrophobic surfaces for drag reduction applications. Superhydrophobic surfaces retain a gas layer, called a plastron, when submerged underwater in the Cassie-Baxter state with water in contact with the tops of surface roughness features. In this state the plastron allows slip to occur across the surface which results in a drag reduction. In this work we report flexible and relatively large area superhydrophobic surfaces produced using two different methods: Large roughness features were created by electrodeposition on copper meshes; Small roughness features were created by embedding carbon nanoparticles (soot) into Polydimethylsiloxane (PDMS). Both samples were made into cylinders with a diameter under 12 mm. To characterize the samples, scanning electron microscope (SEM) images and confocal microscope images were taken. The confocal microscope images were taken with each sample submerged in water to show the extent of the plastron. The hydrophobized electrodeposited copper mesh cylinders showed drag reductions of up to 32% when comparing the superhydrophobic state with a wetted out state. The soot covered cylinders achieved a 30% drag reduction when comparing the superhydrophobic state to a plain cylinder. These results were obtained for turbulent flows with Reynolds numbers 10,000 to 32,500. PMID:25975704

  13. The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

    PubMed Central

    Fischer, Marcus; Coleman, Ryan G.; Fraser, James S.; Shoichet, Brian K.

    2014-01-01

    Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here, we describe a flexible-docking method that samples and weights protein conformations using experimentally-derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in Cytochrome c Peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank where similar experimental information is available. PMID:24950326

  14. A molecular dynamics description of the conformational flexibility of the L-iduronate ring in glycosaminoglycans.

    PubMed

    Angulo, Jesús; Nieto, Pedro M; Martín-Lomas, Manuel

    2003-07-01

    For a synthetic hexasaccharide model it is shown that the conformational flexibility of the L-iduronate ring in glycosaminoglycans can be adequately described by using the PME methodology together with simulation protocols suitable for highly charged systems. PMID:12868729

  15. Wormlike micelle assisted rod coating: a general method for facile fabrication of large-area conductive nanomaterial thin layer onto flexible plastics.

    PubMed

    Xie, Jingyi; Wang, Huan; Bai, Huadong; Yang, Peng; Shi, Mengxue; Guo, Peng; Wang, Chen; Yang, Wantai; Song, Huaihe

    2012-06-27

    Through combined application of wormlike-micelle and rod-coating technique, a general method was demonstrated for the facile reparation of thin transparent conductive films (TCF) of various nanomaterials and their hybrids on flexible plastics. The cetyltrimethylammonium hydroxide (CTAOH)/p-toluenesulfonic acid (CTAT) wormlike micelle system was selected for both the dispersion of different nanomaterials and the enhancement of viscosities of the coating fluids. With the single-walled carbon nanotubes (SWNTs)/wormlike micelle aqueous dispersions as coating fluid, TCFs of SWNTs on flexible poly(ethylene terephthalate) (PET) substrates made by rod-coating method were demonstrated. After doping by immersion into thionyl chloride solution, the sheet resistance of SWNTs thin films, which had a transmittance of about 78%, was as low as 480Ω/sq. This coating method was extended to the preparation of thin films or networks of other materials such as reduced graphene oxide and Ag nanowires. The obtained TCF from Ag nanowire networks has a low sheet resistance of 17Ω/sq, which is comparable to the value of best indium tin oxide (ITO) coating on plastic substrates. Finally, hybrid thin films of different nanomaterials were demonstrated by this method. PMID:22551382

  16. Consequences of conformational flexibility in hydrogen-bond-driven self-assembly processes.

    PubMed

    Berrocal, José Augusto; Di Meo, Florent; García-Iglesias, Miguel; Gosens, Ronald P J; Meijer, E W; Linares, Mathieu; Palmans, Anja R A

    2016-09-18

    We report the synthesis and self-assembly of chiral, conformationally flexible C3-symmetrical trisamides. A strong Cotton effect is observed for the supramolecular polymers in linear alkanes but not in cyclic alkanes. MD simulations suggest 2 : 1 conformations of the amides within the aggregates in both types of solvents, but a chiral bias in only linear alkanes. PMID:27525556

  17. Large area LED package

    NASA Astrophysics Data System (ADS)

    Goullon, L.; Jordan, R.; Braun, T.; Bauer, J.; Becker, F.; Hutter, M.; Schneider-Ramelow, M.; Lang, K.-D.

    2015-03-01

    Solid state lighting using LED-dies is a rapidly growing market. LED-dies with the needed increasing luminous flux per chip area produce a lot of heat. Therefore an appropriate thermal management is required for general lighting with LEDdies. One way to avoid overheating and shorter lifetime is the use of many small LED-dies on a large area heat sink (down to 70 μm edge length), so that heat can spread into a large area while at the same time light also appears on a larger area. The handling with such small LED-dies is very difficult because they are too small to be picked with common equipment. Therefore a new concept called collective transfer bonding using a temporary carrier chip was developed. A further benefit of this new technology is the high precision assembly as well as the plane parallel assembly of the LED-dies which is necessary for wire bonding. It has been shown that hundred functional LED-dies were transferred and soldered at the same time. After the assembly a cost effective established PCB-technology was applied to produce a large-area light source consisting of many small LED-dies and electrically connected on a PCB-substrate. The top contacts of the LED-dies were realized by laminating an adhesive copper sheet followed by LDI structuring as known from PCB-via-technology. This assembly can be completed by adding converting and light forming optical elements. In summary two technologies based on standard SMD and PCB technology have been developed for panel level LED packaging up to 610x 457 mm2 area size.

  18. Cyclic Constraints on Conformational Flexibility in γ-PEPTIDES: Conformation-Specific IR and UV Spectroscopy

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; Kusaka, Ryoji; Zwier, Timothy S.; Fisher, Brian F.; Gellman, Samuel H.

    2013-06-01

    Spectroscopic studies of flexible peptides in the gas phase can provide insight to their inherent structural preferences in the absence of solvent. Recently, there has been increased attention paid to synthetic foldamers containing non-natural residues that can be specifically engineered to robustly form particular secondary structures. These engineered peptides have potential in therapeutic drug design because they are resistant to enzymatic degradation. Specifically, the Gellman group has synthesized a γ-peptide with a six membered cyclic constraint in the γ^{4}-γ^{3} position and an ethyl group at the γ^{2} position (γ_{ACHC}). The three stereocenters have a well-defined chirality [S,S,S]. These two features constrain the relative orientation of adjacent amide groups, thereby favoring a particular "pitch" to the turn. Solution phase results indicate that constrained γ-peptides induce the formation of a 14-helix. Ac-γ_{ACHC}-NHBz, its monohydrate and Ac-γ_{ACHC}-γ_{ACHC}-NHBz have been studied using ultraviolet (UV) and infrared (IR) double-resonance methods to obtain conformation-specific spectra under jet-cooled conditions in the gas phase. IR spectra in the hydride stretch (3300-3750 cm^{-1}), amide I/II and OH bend (1400-1800 cm^{-1}) were recorded and compared to predictions using density functional methods (DFT) and harmonic frequency calculations. We will compare the present results on constrained γ-peptides with corresponding results on unconstrained analogs. Data obtained for the monohydrated water cluster of Ac-γ_{ACHC}-NHBz will also be presented, including assignment of the water bend fundamental, which appears in the midst of transitions due to the amide II vibrations. L. Guo, W. Zhang, A. G. Reidenbach, M. W. Giuliano, I. A. Guzei, L. C. Spencer and S. H. Gellman Angew. Chem. Int. Ed. 2011, 50, 5843-5846

  19. Flexible Near-Field Nanopatterning with Ultrathin, Conformal Phase Masks on Nonplanar Substrates for Biomimetic Hierarchical Photonic Structures.

    PubMed

    Kwon, Young Woo; Park, Junyong; Kim, Taehoon; Kang, Seok Hee; Kim, Hyowook; Shin, Jonghwa; Jeon, Seokwoo; Hong, Suck Won

    2016-04-26

    Multilevel hierarchical platforms that combine nano- and microstructures have been intensively explored to mimic superior properties found in nature. However, unless directly replicated from biological samples, desirable multiscale structures have been challenging to efficiently produce to date. Departing from conventional wafer-based technology, new and efficient techniques suitable for fabricating bioinspired structures are highly desired to produce three-dimensional architectures even on nonplanar substrates. Here, we report a facile approach to realize functional nanostructures on uneven microstructured platforms via scalable optical fabrication techniques. The ultrathin form (∼3 μm) of a phase grating composed of poly(vinyl alcohol) makes the material physically flexible and enables full-conformal contact with rough surfaces. The near-field optical effect can be identically generated on highly curved surfaces as a result of superior conformality. Densely packed nanodots with submicron periodicity are uniformly formed on microlens arrays with a radius of curvature that is as low as ∼28 μm. Increasing the size of the gratings causes the production area to be successfully expanded by up to 16 in(2). The "nano-on-micro" structures mimicking real compound eyes are transferred to flexible and stretchable substrates by sequential imprinting, facilitating multifunctional optical films applicable to antireflective diffusers for large-area sheet-illumination displays. PMID:26981613

  20. Flexibility unleashed in acyclic monoterpenes: conformational space of citronellal revealed by broadband rotational spectroscopy.

    PubMed

    Domingos, Sérgio R; Pérez, Cristóbal; Medcraft, Chris; Pinacho, Pablo; Schnell, Melanie

    2016-06-22

    Conformational flexibility is intrinsically related to the functionality of biomolecules. Elucidation of the potential energy surface is thus a necessary step towards understanding the mechanisms for molecular recognition such as docking of small organic molecules to larger macromolecular systems. In this work, we use broadband rotational spectroscopy in a molecular jet experiment to unravel the complex conformational space of citronellal. We observe fifteen conformations in the experimental conditions of the molecular jet, the highest number of conformers reported to date for a chiral molecule of this size using microwave spectroscopy. Studies of relative stability using different carrier gases in the supersonic expansion reveal conformational relaxation pathways that strongly favour ground-state structures with globular conformations. This study provides a blueprint of the complex conformational space of an important biosynthetic precursor and gives insights on the relation between its structure and biological functionality. PMID:27298210

  1. The Large Area Telescope

    SciTech Connect

    Michelson, Peter F.; /KIPAC, Menlo Park /Stanford U., HEPL

    2007-11-13

    The Large Area Telescope (LAT), one of two instruments on the Gamma-ray Large Area Space Telescope (GLAST) mission, is an imaging, wide field-of-view, high-energy pair-conversion telescope, covering the energy range from {approx}20 MeV to more than 300 GeV. The LAT is being built by an international collaboration with contributions from space agencies, high-energy particle physics institutes, and universities in France, Italy, Japan, Sweden, and the United States. The scientific objectives the LAT will address include resolving the high-energy gamma-ray sky and determining the nature of the unidentified gamma-ray sources and the origin of the apparently isotropic diffuse emission observed by EGRET; understanding the mechanisms of particle acceleration in celestial sources, including active galactic nuclei, pulsars, and supernovae remnants; studying the high-energy behavior of gamma-ray bursts and transients; using high-energy gamma-rays to probe the early universe to z {ge} 6; and probing the nature of dark matter. The components of the LAT include a precision silicon-strip detector tracker and a CsI(Tl) calorimeter, a segmented anticoincidence shield that covers the tracker array, and a programmable trigger and data acquisition system. The calorimeter's depth and segmentation enable the high-energy reach of the LAT and contribute significantly to background rejection. The aspect ratio of the tracker (height/width) is 0.4, allowing a large field-of-view and ensuring that nearly all pair-conversion showers initiated in the tracker will pass into the calorimeter for energy measurement. This paper includes a description of each of these LAT subsystems as well as a summary of the overall performance of the telescope.

  2. Large area Czochralski silicon

    NASA Technical Reports Server (NTRS)

    Rea, S. N.; Gleim, P. S.

    1977-01-01

    The overall cost effectiveness of the Czochralski process for producing large-area silicon was determined. The feasibility of growing several 12 cm diameter crystals sequentially at 12 cm/h during a furnace run and the subsequent slicing of the ingot using a multiblade slurry saw were investigated. The goal of the wafering process was a slice thickness of 0.25 mm with minimal kerf. A slice + kerf of 0.56 mm was achieved on 12 cm crystal using both 400 grit B4C and SiC abrasive slurries. Crystal growth experiments were performed at 12 cm diameter in a commercially available puller with both 10 and 12 kg melts. Several modifications to the puller hoz zone were required to achieve stable crystal growth over the entire crystal length and to prevent crystallinity loss a few centimeters down the crystal. The maximum practical growth rate for 12 cm crystal in this puller design was 10 cm/h, with 12 to 14 cm/h being the absolute maximum range at which melt freeze occurred.

  3. Thermodynamic signatures in macromolecular interactions involving conformational flexibility.

    PubMed

    Menzel, Anja; Neumann, Piotr; Schwieger, Christian; Stubbs, Milton T

    2014-07-01

    The energetics of macromolecular interactions are complex, particularly where protein flexibility is involved. Exploiting serendipitous differences in the plasticity of a series of closely related trypsin variants, we analyzed the enthalpic and entropic contributions accompanying interaction with L45K-eglin C. Binding of the four variants show significant differences in released heat, although the affinities vary little, in accordance with the principle of enthalpy-entropy compensation. Binding of the most disordered variant is almost entirely enthalpically driven, with practically no entropy change. As structures of the complexes reveal negligible differences in protein-inhibitor contacts, we conclude that solvent effects contribute significantly to binding affinities. PMID:25003391

  4. A Structure-free Method for Quantifying Conformational Flexibility in proteins

    PubMed Central

    Burger, Virginia M.; Arenas, Daniel J.; Stultz, Collin M.

    2016-01-01

    All proteins sample a range of conformations at physiologic temperatures and this inherent flexibility enables them to carry out their prescribed functions. A comprehensive understanding of protein function therefore entails a characterization of protein flexibility. Here we describe a novel approach for quantifying a protein’s flexibility in solution using small-angle X-ray scattering (SAXS) data. The method calculates an effective entropy that quantifies the diversity of radii of gyration that a protein can adopt in solution and does not require the explicit generation of structural ensembles to garner insights into protein flexibility. Application of this structure-free approach to over 200 experimental datasets demonstrates that the methodology can quantify a protein’s disorder as well as the effects of ligand binding on protein flexibility. Such quantitative descriptions of protein flexibility form the basis of a rigorous taxonomy for the description and classification of protein structure. PMID:27358108

  5. Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.

    PubMed

    Yang, Mingjun; Angles d'Ortoli, Thibault; Säwén, Elin; Jana, Madhurima; Widmalm, Göran; MacKerell, Alexander D

    2016-07-28

    The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence. PMID:27346493

  6. Inspection des pieces flexibles sans gabarit de conformation

    NASA Astrophysics Data System (ADS)

    Aidibe, Ali

    In this thesis, we focus on the automation of the fixtureless geometric inspection of non-rigid (or compliant) parts. The primary objective of this project is to handle virtually this type of component and their point cloud, which represents a scan taken in a Free State condition, by eliminating the use of very expensive and complicated specialized fixtures posing productivity problems for manufacturing companies. This topic is a very high interest in the transport sector and, more specifically, in the aerospace one in order to significantly improve its productivity and its degree of competitiveness. The thesis is organized by articles. The study is divided over four phases. The first three phases will be represented by three journal papers and the fourth phase is presented as an appendix. The first phase of this work is intended to improve the identification module of an existing inspection mathematical tool " IDI: The Iterative Displacement Inspection " which has been developed by the research team working under the supervision of professor Tahan at ETS. The identification module aims to distinguish between defects that are due to the manufacturing process and deformations that are due to the flexibility of the part (gravity and residual stress effects). We propose to replace the original module with a new one which is based on the extreme value statistical analysis. We demonstrate that the new module remarkably reduces the type I and type II errors. In addition, unlike the identification method of the IDI, the proposed one does not require a user-specified threshold based on a trial and error process. In the second phase of this study, we propose an original approach to measure the flexibility/rigidity of the mechanical components. We introduce a factor that represents the ratio between the maximum displacement resulting from the deformation of the part and its profile tolerance and we present the results in a logarithmic scale. Three different regions were

  7. Conformational flexibility of fused tetracenedione propellers obtained from one-pot reductive dimerization of acetylenic quinones.

    PubMed

    Vasilevsky, Sergei F; Baranov, Denis S; Mamatyuk, Victor I; Fadeev, Dmitry S; Gatilov, Yurii V; Stepanov, Aleksandr A; Vasilieva, Nadezhda V; Alabugin, Igor V

    2015-02-01

    Reductive dimerization of acetylenic anthraquinones provides synthetic access to flexible nonplanar polyaromatics with a tetracenedione core. In solution, these nonplanar, contorted polycycles exist as equilibrating mixtures of two symmetric conformers. The fused tetracenediones are easily reduced and exhibit rich electrochemical behavior. PMID:25575160

  8. Conformational flexibility and structural dynamics in GPCR-mediated G protein activation: a perspective

    PubMed Central

    Preininger, Anita M.; Meiler, Jens; Hamm, Heidi

    2013-01-01

    Structure and dynamics of G proteins and their cognate receptors, both alone and in complex, are becoming increasingly accessible to experimental techniques. Understanding the conformational changes and timelines which govern these changes can lead to new insights into the processes of ligand binding and associated G protein activation. Experimental systems may involve the use of, or otherwise stabilize, non-native environments. This can complicate our understanding of structural and dynamical features of processes such as the ionic lock, Tryptophan toggle, and G protein flexibility. While elements in the receptor’s transmembrane helices and the C-terminal α5 helix of Gα undergo well defined structural changes, regions subject to conformational flexibility may be important in fine-tuning the interactions between activated receptors and G proteins. The pairing of computational and experimental approaches will continue to provide powerful tools to probe the conformation and dynamics of receptor-mediated G protein activation. PMID:23602809

  9. The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains

    PubMed Central

    Münz, Márton; Hein, Jotun; Biggin, Philip C.

    2012-01-01

    In molecular recognition, it is often the case that ligand binding is coupled to conformational change in one or both of the binding partners. Two hypotheses describe the limiting cases involved; the first is the induced fit and the second is the conformational selection model. The conformational selection model requires that the protein adopts conformations that are similar to the ligand-bound conformation in the absence of ligand, whilst the induced-fit model predicts that the ligand-bound conformation of the protein is only accessible when the ligand is actually bound. The flexibility of the apo protein clearly plays a major role in these interpretations. For many proteins involved in signaling pathways there is the added complication that they are often promiscuous in that they are capable of binding to different ligand partners. The relationship between protein flexibility and promiscuity is an area of active research and is perhaps best exemplified by the PDZ domain family of proteins. In this study we use molecular dynamics simulations to examine the relationship between flexibility and promiscuity in five PDZ domains: the human Dvl2 (Dishevelled-2) PDZ domain, the human Erbin PDZ domain, the PDZ1 domain of InaD (inactivation no after-potential D protein) from fruit fly, the PDZ7 domain of GRIP1 (glutamate receptor interacting protein 1) from rat and the PDZ2 domain of PTP-BL (protein tyrosine phosphatase) from mouse. We show that despite their high structural similarity, the PDZ binding sites have significantly different dynamics. Importantly, the degree of binding pocket flexibility was found to be closely related to the various characteristics of peptide binding specificity and promiscuity of the five PDZ domains. Our findings suggest that the intrinsic motions of the apo structures play a key role in distinguishing functional properties of different PDZ domains and allow us to make predictions that can be experimentally tested. PMID:23133356

  10. Photocatalytically Active Oligomeric Graphitic Carbon Nitride: Conformational Flexibility, Electronic Levels, Carrier Localization

    NASA Astrophysics Data System (ADS)

    Blum, Volker; Lau, Vincent; Botari, Tiago; Huhn, William; Lotsch, Bettina V.

    2015-03-01

    Polymers consisting of bridged heptazine units (often called ``graphitic carbon nitride'' or ``g-C3N4'') show considerable promise as photocatalysts for solar hydrogen evolution. Recent experimental evidence suggests that oligomeric rather than fully polymerized ``g-C3N4'' exhibits increased intrinsic photocatalytic activity. Using density-functional theory (DFT; van der Waals corrected PBE functional for conformers, hybrid DFT and GW for electronic levels), we show that considerable conformational flexibility exists for the heptazine trimers and tetramers. Analysis of HOMO and LUMO locations as well as trends in photocatalytic activity among heptazine oligomers and polymers reveals the NH2 groups of the oligomers as potential charge-transfer sites. We show that conformational variations of the oligomers can lead to significant, electrostatically motivated carrier localization effects. We suggest that NH2 side groups and the intrinsic conformational variations of the oligomeric species lead to the observed enhanced catalytic activity.

  11. Conformation specific spectroscopy in the complexity gap: beta-peptides and flexible bichromophores

    NASA Astrophysics Data System (ADS)

    Baquero, Esteban Edwin

    Flexible biomolecules with many degrees of freedom have the ability to sample a great number of structural minima. The intrinsic structural preferences of these molecules are driven by stabilizations due to intramolecular interactions such as hydrogen bonding and interatomic attractive forces. These interactions become increasingly important as the atoms in the molecule come in close proximity to one another. The present work describes the conformational preferences of several model bio-relevant molecules of different sizes where different kinds of intramolecular interactions can occur. Conformation specific ultraviolet and infrared spectroscopies were utilized to obtain the spectroscopic signatures of different conformations of the jet cooled biomolecules. These experiments allowed for the assignment of conformational families and the development of a general protocol to identify the infrared signatures of amide NH stretches, which were found to vary in frequency due to their immediate chemical and structural environment. Specific examples of systems studied include molecules containing unnatural polypeptide chains and a flexible bichromophore. The unnatural polypetides (Ac-beta3-hPhe-NHMe, Ac-beta 3-hTyr-NHMe Ac-beta3-hPhe-beta3-hAla-NHMe and Ac-beta3-hAla-beta3-hPhe-NHMe) were found to have a rich conformational potential energy landscape that contained many kinds of intramolecular hydrogen bonded minima. The flexible bichromophore (HNBPA), containing two spectroscopically distinguishable chromophores (Phenol and Phenyl), was found to be an interesting case study for conformational specific electronic energy transfer and testing how well different theoretical methods manage non-covalent interactions, such as those between side-chain atoms and aromatic pi-clouds.

  12. Probing flexible conformations in molecular junctions by inelastic electron tunneling spectroscopy

    SciTech Connect

    Deng, Mingsen; Ye, Gui; Jiang, Jun; Cai, Shaohong; Sun, Guangyu

    2015-01-15

    The probe of flexible molecular conformation is crucial for the electric application of molecular systems. We have developed a theoretical procedure to analyze the couplings of molecular local vibrations with the electron transportation process, which enables us to evaluate the structural fingerprints of some vibrational modes in the inelastic electron tunneling spectroscopy (IETS). Based on a model molecule of Bis-(4-mercaptophenyl)-ether with a flexible center angle, we have revealed and validated a simple mathematical relationship between IETS signals and molecular angles. Our results might open a route to quantitatively measure key geometrical parameters of molecular junctions, which helps to achieve precise control of molecular devices.

  13. Structure of a mutant [beta] toxin from Staphylococcus aureus reveals domain swapping and conformational flexibility

    SciTech Connect

    Kruse, Andrew C.; Huseby, Medora J.; Shi, Ke; Digre, Jeff; Ohlendorf, Douglas H.; Earhart, Cathleen A.

    2011-09-16

    The 3.35 {angstrom} resolution crystal structure of a mutant form of the staphylococcal sphingomyelinase {beta} toxin in which a conserved hydrophobic {beta}-hairpin has been deleted is reported. It is shown that this mutation induces domain swapping of a C-terminal {beta}-strand, leading to the formation of dimers linked by a conformationally flexible hinge region. Eight dimers are seen in the asymmetric unit, exhibiting a broad spectrum of conformations trapped in place by intermolecular contacts within the crystal lattice. Furthermore, the 16 monomers within each asymmetric unit exhibit a remarkable heterogeneity in thermal factors, which can be accounted for by the varying degrees to which each monomer interacts with other molecules in the crystal. This structure provides a unique example of the challenges associated with crystallographic study of flexible proteins.

  14. Conformational flexibility in 2,2'-Dioxybiphenyl-chloro-cyclotetraphosphazenes and its relevance to polyphosphazene analogues.

    PubMed

    Ainscough, Eric W; Brodie, Andrew M; Chaplin, Adrian B; Derwahl, Andreas; Harrison, John A; Otter, Carl A

    2007-04-01

    The reaction of the cyclotetraphosphazene, [N4P4Cl8], with the difunctional reagent, 2,2'-biphenol, in the presence of potassium carbonate in acetone produced the spiro-substituted derivatives, 2,2'-dioxybiphenylhexachlorocyclotetraphosphazene, bis(2,2'-dioxybiphenyl)tetrachloro-cyclotetraphosphazene, and tris(2,2'-dioxybiphenyl)dichlorocyclotetraphosphazene. Both cis and trans geometrical isomers of the bis compound are observed. Although chromatographic separation of these was unsuccessful, a sample of the trans isomer was obtained by fractional crystallization. The compounds all show non-first-order 31P NMR spectra which were simulated to extract the spectral parameters. Single-crystal X-ray structures of both the trans bis and the tris compounds show that the cyclophosphazene rings exhibit conformational flexibility which gives rise to different crystalline forms being obtained from the same solvent systems. Crystals of trans-bis(2,2'-dioxybiphenyl)tetrachloro-cyclotetraphosphazene were obtained in two different space groups: Pnna (orthorhombic) and P21/n (monoclinic). In the orthorhombic structure, the dominant (72%) conformation of one phosphazene ring is a chair form, and the other (28%) resembles a boat. While for the monoclinic structure, the ring is virtually flat with an oval shape. In both cases the dioxybiphenyl groups are found in R and S configurations in the same molecule and are pi stacked in columns (Pnna) or involved in pi-pi or pi-H interactions (P21/n), thus anchoring the phosphorus atoms of the cyclotetraphosphazenes but still allowing flexibility in the ring conformations. Three crystalline modifications of tris(2,2'-dioxybiphenyl)dichloro-cyclotetraphosphazene were obtained: two in space group P (triclinic), which contained two molecules of dichloromethane in the unit cell, and one solvent-free form in space group P21/n (monoclinic). The cyclophosphazene rings exhibit puckered conformations with the trans-dioxybiphenyl moieties having

  15. Decoupling optical function and geometrical form using conformal flexible dielectric metasurfaces

    PubMed Central

    Kamali, Seyedeh Mahsa; Arbabi, Amir; Arbabi, Ehsan; Horie, Yu; Faraon, Andrei

    2016-01-01

    Physical geometry and optical properties of objects are correlated: cylinders focus light to a line, spheres to a point and arbitrarily shaped objects introduce optical aberrations. Multi-functional components with decoupled geometrical form and optical function are needed when specific optical functionalities must be provided while the shapes are dictated by other considerations like ergonomics, aerodynamics or aesthetics. Here we demonstrate an approach for decoupling optical properties of objects from their physical shape using thin and flexible dielectric metasurfaces which conform to objects' surface and change their optical properties. The conformal metasurfaces are composed of silicon nano-posts embedded in a polymer substrate that locally modify near-infrared (λ=915 nm) optical wavefronts. As proof of concept, we show that cylindrical lenses covered with metasurfaces can be transformed to function as aspherical lenses focusing light to a point. The conformal metasurface concept is highly versatile for developing arbitrarily shaped multi-functional optical devices. PMID:27193141

  16. Decoupling optical function and geometrical form using conformal flexible dielectric metasurfaces

    NASA Astrophysics Data System (ADS)

    Kamali, Seyedeh Mahsa; Arbabi, Amir; Arbabi, Ehsan; Horie, Yu; Faraon, Andrei

    2016-05-01

    Physical geometry and optical properties of objects are correlated: cylinders focus light to a line, spheres to a point and arbitrarily shaped objects introduce optical aberrations. Multi-functional components with decoupled geometrical form and optical function are needed when specific optical functionalities must be provided while the shapes are dictated by other considerations like ergonomics, aerodynamics or aesthetics. Here we demonstrate an approach for decoupling optical properties of objects from their physical shape using thin and flexible dielectric metasurfaces which conform to objects' surface and change their optical properties. The conformal metasurfaces are composed of silicon nano-posts embedded in a polymer substrate that locally modify near-infrared (λ=915 nm) optical wavefronts. As proof of concept, we show that cylindrical lenses covered with metasurfaces can be transformed to function as aspherical lenses focusing light to a point. The conformal metasurface concept is highly versatile for developing arbitrarily shaped multi-functional optical devices.

  17. Decoupling optical function and geometrical form using conformal flexible dielectric metasurfaces.

    PubMed

    Kamali, Seyedeh Mahsa; Arbabi, Amir; Arbabi, Ehsan; Horie, Yu; Faraon, Andrei

    2016-01-01

    Physical geometry and optical properties of objects are correlated: cylinders focus light to a line, spheres to a point and arbitrarily shaped objects introduce optical aberrations. Multi-functional components with decoupled geometrical form and optical function are needed when specific optical functionalities must be provided while the shapes are dictated by other considerations like ergonomics, aerodynamics or aesthetics. Here we demonstrate an approach for decoupling optical properties of objects from their physical shape using thin and flexible dielectric metasurfaces which conform to objects' surface and change their optical properties. The conformal metasurfaces are composed of silicon nano-posts embedded in a polymer substrate that locally modify near-infrared (λ=915 nm) optical wavefronts. As proof of concept, we show that cylindrical lenses covered with metasurfaces can be transformed to function as aspherical lenses focusing light to a point. The conformal metasurface concept is highly versatile for developing arbitrarily shaped multi-functional optical devices. PMID:27193141

  18. Decoupling optical function and geometrical form using conformal flexible dielectric metasurfaces

    DOE PAGESBeta

    Kamali, Seyedeh Mahsa; Arbabi, Amir; Arbabi, Ehsan; Horie, Yu; Faraon, Andrei

    2016-05-19

    Physical geometry and optical properties of objects are correlated: cylinders focus light to a line, spheres to a point and arbitrarily shaped objects introduce optical aberrations. Multifunctional components with decoupled geometrical form and optical function are needed when specific optical functionalities must be provided while the shapes are dictated by other considerations like ergonomics, aerodynamics or aesthetics. Here we demonstrate an approach for decoupling optical properties of objects from their physical shape using thin and flexible dielectric metasurfaces which conform to objects' surface and change their optical properties. The conformal metasurfaces are composed of silicon nano-posts embedded in a polymermore » substrate that locally modify near-infrared (λ = 915 nm) optical wavefronts. As proof of concept, we show that cylindrical lenses covered with metasurfaces can be transformed to function as aspherical lenses focusing light to a point. Lastly, the conformal metasurface concept is highly versatile for developing arbitrarily shaped multi-functional optical devices.« less

  19. Substrate Binding Tunes Conformational Flexibility and Kinetic Stability of an Amino Acid Antiporter*

    PubMed Central

    Bippes, Christian A.; Zeltina, Antra; Casagrande, Fabio; Ratera, Merce; Palacin, Manuel; Muller, Daniel J.; Fotiadis, Dimitrios

    2009-01-01

    We used single molecule dynamic force spectroscopy to unfold individual serine/threonine antiporters SteT from Bacillus subtilis. The unfolding force patterns revealed interactions and energy barriers that stabilized structural segments of SteT. Substrate binding did not establish strong localized interactions but appeared to be facilitated by the formation of weak interactions with several structural segments. Upon substrate binding, all energy barriers of the antiporter changed thereby describing the transition from brittle mechanical properties of SteT in the unbound state to structurally flexible conformations in the substrate-bound state. The lifetime of the unbound state was much shorter than that of the substrate-bound state. This leads to the conclusion that the unbound state of SteT shows a reduced conformational flexibility to facilitate specific substrate binding and a reduced kinetic stability to enable rapid switching to the bound state. In contrast, the bound state of SteT showed an increased conformational flexibility and kinetic stability such as required to enable transport of substrate across the cell membrane. This result supports the working model of antiporters in which alternate substrate access from one to the other membrane surface occurs in the substrate-bound state. PMID:19419962

  20. Evaluation of flexible and rigid (class solution) radiation therapy conformal prostate planning protocols

    SciTech Connect

    Coburn, Natalie; Beldham-Collins, Rachael; Westling, Jelene; Trovato, Jenny; Gebski, Val

    2012-04-01

    Protocols commonly implemented in radiotherapy work areas may be classified as being either rigid (class solution) or flexible. Because formal evaluation of these protocol types has not occurred within the literature, we evaluated the efficiency of a rigid compared with flexible prostate planning protocol by assessing a series of completed 3D conformal prostate plans. Twenty prostate cancer patients with an average age of 70 years (range, 52-77) and sizes comprising 8 small, 10 medium, and 2 large were planned on the Phillips Pinnacle treatment planning system 6 times by radiation therapists with <2 years, 2-5 years, and >5 years of experience using a rigid and flexible protocol. Plans were critiqued using critical organ doses, confirmation numbers, and conformity index. Plans were then classified as being acceptable or not. Plans produced with the flexible protocol were 53% less likely to require modification (OR 0.47, 95% CI: 0.26, 0.84, p = 0.01). Planners with >5 years of experience were 78% more likely to produce plans requiring modification (OR 1.78, 95% CI: 1.12, 2.83, P = 0.02). Plans according to the flexible protocol took longer (112 min) compared with the time taken using a rigid protocol (68 min) (p < 0.001). The results suggest that further studies are needed; however, we propose that all radiation therapy planners should start with the same limitations, and if an acceptable plan is not reached, then flexibility should be given to improve the plan to meet the desired results.

  1. Ultraflexible, large-area, physiological temperature sensors for multipoint measurements

    PubMed Central

    Yokota, Tomoyuki; Inoue, Yusuke; Terakawa, Yuki; Reeder, Jonathan; Kaltenbrunner, Martin; Ware, Taylor; Yang, Kejia; Mabuchi, Kunihiko; Murakawa, Tomohiro; Sekino, Masaki; Voit, Walter; Sekitani, Tsuyoshi; Someya, Takao

    2015-01-01

    We report a fabrication method for flexible and printable thermal sensors based on composites of semicrystalline acrylate polymers and graphite with a high sensitivity of 20 mK and a high-speed response time of less than 100 ms. These devices exhibit large resistance changes near body temperature under physiological conditions with high repeatability (1,800 times). Device performance is largely unaffected by bending to radii below 700 µm, which allows for conformal application to the surface of living tissue. The sensing temperature can be tuned between 25 °C and 50 °C, which covers all relevant physiological temperatures. Furthermore, we demonstrate flexible active-matrix thermal sensors which can resolve spatial temperature gradients over a large area. With this flexible ultrasensitive temperature sensor we succeeded in the in vivo measurement of cyclic temperatures changes of 0.1 °C in a rat lung during breathing, without interference from constant tissue motion. This result conclusively shows that the lung of a warm-blooded animal maintains surprising temperature stability despite the large difference between core temperature and inhaled air temperature. PMID:26554008

  2. Buckling assisted and lithographically micropatterned fully flexible sensors for conformal integration applications

    NASA Astrophysics Data System (ADS)

    Maji, Debashis; Das, Debanjan; Wala, Jyoti; Das, Soumen

    2015-12-01

    Development of flexible sensors/electronics over substrates thicker than 100 μm is of immense importance for its practical feasibility. However, unlike over ultrathin films, large bending stress hinders its flexibility. Here we have employed a novel technique of fabricating sensors over a non-planar ridge topology under pre-stretched condition which not only helps in spontaneous generation of large and uniform parallel buckles upon release, but also acts as stress reduction zones thereby preventing Poisson’s ratio induced lateral cracking. Further, we propose a complete lithography compatible process to realize flexible sensors over pre-stretched substrates thicker than 100 μm that are released through dissolution of a water soluble sacrificial layer of polyvinyl alcohol. These buckling assisted flexible sensors demonstrated superior performance along different flexible modalities. Based on the above concept, we also realized a micro thermal flow sensor, conformally wrapped around angiographic catheters to detect flow abnormalities for potential applications in interventional catheterization process.

  3. Buckling assisted and lithographically micropatterned fully flexible sensors for conformal integration applications

    PubMed Central

    Maji, Debashis; Das, Debanjan; Wala, Jyoti; Das, Soumen

    2015-01-01

    Development of flexible sensors/electronics over substrates thicker than 100 μm is of immense importance for its practical feasibility. However, unlike over ultrathin films, large bending stress hinders its flexibility. Here we have employed a novel technique of fabricating sensors over a non-planar ridge topology under pre-stretched condition which not only helps in spontaneous generation of large and uniform parallel buckles upon release, but also acts as stress reduction zones thereby preventing Poisson’s ratio induced lateral cracking. Further, we propose a complete lithography compatible process to realize flexible sensors over pre-stretched substrates thicker than 100 μm that are released through dissolution of a water soluble sacrificial layer of polyvinyl alcohol. These buckling assisted flexible sensors demonstrated superior performance along different flexible modalities. Based on the above concept, we also realized a micro thermal flow sensor, conformally wrapped around angiographic catheters to detect flow abnormalities for potential applications in interventional catheterization process. PMID:26640124

  4. Conformational Flexibility and Subunit Arrangement of the Modular Yeast Spt-Ada-Gcn5 Acetyltransferase Complex*

    PubMed Central

    Setiaputra, Dheva; Ross, James D.; Lu, Shan; Cheng, Derrick T.; Dong, Meng-Qiu; Yip, Calvin K.

    2015-01-01

    The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a highly conserved, 19-subunit histone acetyltransferase complex that activates transcription through acetylation and deubiquitination of nucleosomal histones in Saccharomyces cerevisiae. Because SAGA has been shown to display conformational variability, we applied gradient fixation to stabilize purified SAGA and systematically analyzed this flexibility using single-particle EM. Our two- and three-dimensional studies show that SAGA adopts three major conformations, and mutations of specific subunits affect the distribution among these. We also located the four functional modules of SAGA using electron microscopy-based labeling and transcriptional activator binding analyses and show that the acetyltransferase module is localized in the most mobile region of the complex. We further comprehensively mapped the subunit interconnectivity of SAGA using cross-linking mass spectrometry, revealing that the Spt and Taf subunits form the structural core of the complex. These results provide the necessary restraints for us to generate a model of the spatial arrangement of all SAGA subunits. According to this model, the chromatin-binding domains of SAGA are all clustered in one face of the complex that is highly flexible. Our results relate information of overall SAGA structure with detailed subunit level interactions, improving our understanding of its architecture and flexibility. PMID:25713136

  5. Conformational flexibility and subunit arrangement of the modular yeast Spt-Ada-Gcn5 acetyltransferase complex.

    PubMed

    Setiaputra, Dheva; Ross, James D; Lu, Shan; Cheng, Derrick T; Dong, Meng-Qiu; Yip, Calvin K

    2015-04-17

    The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a highly conserved, 19-subunit histone acetyltransferase complex that activates transcription through acetylation and deubiquitination of nucleosomal histones in Saccharomyces cerevisiae. Because SAGA has been shown to display conformational variability, we applied gradient fixation to stabilize purified SAGA and systematically analyzed this flexibility using single-particle EM. Our two- and three-dimensional studies show that SAGA adopts three major conformations, and mutations of specific subunits affect the distribution among these. We also located the four functional modules of SAGA using electron microscopy-based labeling and transcriptional activator binding analyses and show that the acetyltransferase module is localized in the most mobile region of the complex. We further comprehensively mapped the subunit interconnectivity of SAGA using cross-linking mass spectrometry, revealing that the Spt and Taf subunits form the structural core of the complex. These results provide the necessary restraints for us to generate a model of the spatial arrangement of all SAGA subunits. According to this model, the chromatin-binding domains of SAGA are all clustered in one face of the complex that is highly flexible. Our results relate information of overall SAGA structure with detailed subunit level interactions, improving our understanding of its architecture and flexibility. PMID:25713136

  6. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

    SciTech Connect

    Forneris, Federico; Burnley, B. Tom; Gros, Piet

    2014-03-01

    Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na{sup +} and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na{sup +} ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail.

  7. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

    Transition metal dichalcogenides (TMDs) have generated significant interest for numerous applications including sensors, flexible electronics, heterostructures and optoelectronics due to their interesting, thickness-dependent properties. Despite recent progress, the synthesis of high-quality and highly uniform TMDs on a large scale is still a challenge. In this talk, synthesis routes for WSe2 and MoS2 that achieve monolayer thickness uniformity across large area substrates with electrical properties equivalent to geological crystals will be described. Controlled doping of 2D semiconductors is also critically required. However, methods established for conventional semiconductors, such as ion implantation, are not easily applicable to 2D materials because of their atomically thin structure. Redox-active molecular dopants will be demonstrated which provide large changes in carrier density and workfunction through the choice of dopant, treatment time, and the solution concentration. Finally, several applications of these large-area, uniform 2D materials will be described including heterostructures, biosensors and strain sensors.

  8. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.

    PubMed

    Georgescu, Roxana E; Alexov, Emil G; Gunner, Marilyn R

    2002-10-01

    Protein stability and function relies on residues being in their appropriate ionization states at physiological pH. In situ residue pK(a)s also provides a sensitive measure of the local protein environment. Multiconformation continuum electrostatics (MCCE) combines continuum electrostatics and molecular mechanics force fields in Monte Carlo sampling to simultaneously calculate side chain ionization and conformation. The response of protein to charges is incorporated both in the protein dielectric constant (epsilon(prot)) of four and by explicit conformational changes. The pK(a) of 166 residues in 12 proteins was determined. The root mean square error is 0.83 pH units, and >90% have errors of <1 pH units whereas only 3% have errors >2 pH units. Similar results are found with crystal and solution structures, showing that the method's explicit conformational sampling reduces sensitivity to the initial structure. The outcome also changes little with protein dielectric constant (epsilon(prot) 4-20). Multiconformation continuum electrostatics titrations show coupling of conformational flexibility and changes in ionization state. Examples are provided where ionizable side chain position (protein G), Asn orientation (lysozyme), His tautomer distribution (RNase A), and phosphate ion binding (RNase A and H) change with pH. Disallowing these motions changes the calculated pK(a). PMID:12324397

  9. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.

    PubMed Central

    Georgescu, Roxana E; Alexov, Emil G; Gunner, Marilyn R

    2002-01-01

    Protein stability and function relies on residues being in their appropriate ionization states at physiological pH. In situ residue pK(a)s also provides a sensitive measure of the local protein environment. Multiconformation continuum electrostatics (MCCE) combines continuum electrostatics and molecular mechanics force fields in Monte Carlo sampling to simultaneously calculate side chain ionization and conformation. The response of protein to charges is incorporated both in the protein dielectric constant (epsilon(prot)) of four and by explicit conformational changes. The pK(a) of 166 residues in 12 proteins was determined. The root mean square error is 0.83 pH units, and >90% have errors of <1 pH units whereas only 3% have errors >2 pH units. Similar results are found with crystal and solution structures, showing that the method's explicit conformational sampling reduces sensitivity to the initial structure. The outcome also changes little with protein dielectric constant (epsilon(prot) 4-20). Multiconformation continuum electrostatics titrations show coupling of conformational flexibility and changes in ionization state. Examples are provided where ionizable side chain position (protein G), Asn orientation (lysozyme), His tautomer distribution (RNase A), and phosphate ion binding (RNase A and H) change with pH. Disallowing these motions changes the calculated pK(a). PMID:12324397

  10. Flexible polyelectrolyte conformation in the presence of cationic and anionic surfactants

    NASA Astrophysics Data System (ADS)

    Passos, C. B.; Kuhn, P. S.; Diehl, A.

    2015-11-01

    In this work we have studied the conformation of flexible polyelectrolyte chains in the presence of cationic and anionic surfactant molecules. We developed a simple theoretical model for the formation of the polyelectrolyte-cationic surfactant complexes and mixed micelles formed by cationic and anionic surfactant molecules, in the framework of the Debye-Hückel-Bjerrum-Manning and Flory theories, with the hydrophobic interaction included explicitly as an effective short-ranged attraction between the surfactant hydrocarbon tails. This simple model allows us to calculate the extension of the polyelectrolyte-cationic surfactant complexes as a function of the anionic surfactant concentration, for different types of cationic and anionic surfactant molecules. A discrete conformational transition from a collapsed state to an elongated coil was found, for all surfactant chain lengths we have considered, in agreement with the experimental observations for the unfolding of ​DNA-cationic surfactant complexes.

  11. 3D conformation of a flexible fiber in a turbulent flow

    NASA Astrophysics Data System (ADS)

    Verhille, Gautier; Bartoli, Adrien

    2016-07-01

    A growing number of studies is devoted to anisotropic particles in turbulent flows. In most cases, the particles are assumed to be rigid and their deformations are neglected. We present an adaptation of classical computer vision tools to reconstruct from two different images the 3D conformation of a fiber distorted by the turbulent fluctuations in a von Kármán flow. This technique allows us notably to characterize the fiber deformation by computing the correlation function of the orientation of the tangent vector. This function allows us to tackle the analogy between polymers and flexible fibers proposed by Brouzet et al. (Phys Rev Lett 112(7):074501, 2014). We show that this function depends on an elastic length ℓ _e which characterizes the particle flexibility, as is the case for polymers, but also on the fiber length L, contrary to polymers.

  12. Step-Controllable Electric-Field-Assisted Nanoimprint Lithography for Uneven Large-Area Substrates.

    PubMed

    Wang, Chunhui; Shao, Jinyou; Tian, Hongmiao; Li, Xiangming; Ding, Yucheng; Li, Ben Q

    2016-04-26

    Large-area nanostructures are widely used in various fields, but fabrication on large-area uneven substrates poses a significant challenge. This study demonstrates a step-controllable electric-field-assisted nanoimprint lithography (e-NIL) method that can achieve conformal contact with uneven substrates for high fidelity nanostructuring. Experiments are used to demonstrate the method where a substrate coated with liquid resist is brought into contact with a flexible template driven by the applied electric field. Theoretical analysis based on the elasticity theory and electro-hydrodynamic theory is carried out. Effective voltage range and the saturation voltage are also discussed. A step-controllable release of flexible template is proposed and demonstrated to ensure the continuous contact between the template and an uneven substrate. This prevents formation of air traps and allows large area conformal contact to be achieved. A combination of Vacuum-electric field assisted step-controllable e-NIL is implemented in the developed prototype. Finally, photonic crystal nanostructures are successfully fabricated on a 4 in., 158 μm bow gallium nitride light-emitting diode epitaxial wafer using the proposed method, which enhance the light extraction property. PMID:27015525

  13. Fermi's Large Area Telescope (LAT)

    NASA Video Gallery

    Fermi’s Large Area Telescope (LAT) is the spacecraft’s main scientificinstrument. This animation shows a gamma ray (purple) entering the LAT,where it is converted into an electron (red) and a...

  14. Large Area Printing of Organic Transistors

    NASA Astrophysics Data System (ADS)

    Blanchet, Graciela B.; Rogers, J. A.; Lefenfeld, M.; Fincher, C. R.; Loo, Jueh-Lin

    2003-03-01

    Organic electronic systems offer the advantage of lightweight, mechanical flexibility and large area coverage at potentially lower manufacturing cost. Although the production of functioning plastic transistors using approaches such as ink jet, screen printing and stamping, has been described in the literature, no one-transistor layer has yet been fabricated using a technique appropriate for their commercial ization. The solution processability of many organics may ultimately allow for the printing of electronic devices in a printing press at high speeds and in a reel to reel configuration. However, designing chemically compatible solutions to be printed sequentially represents a significant technical barrier to achieving all-printed plastic electronic systems. The work presented here represents a step change in the fabrication of organic electronic devices. We introduce thermal transfer, a non-lithographic technique that enables printing multi-layer electronics devices via a dry (i.e. solvent-less) additive process. This high-speed method is capable of patterning a range of organic materials over large areas ( 1 m2 ) with micron dimensions and excellent electrical performance. The 0.5 m2 transistor array backplane printed via thermal transfer represent the most advanced demonstration of a novel printing technology applied to the fabrication of large area integrated electronic devices. Dry transfer printing may provide a practical route to realizing the benefits of plastic materials for electronics.

  15. Progress on large area GEMs

    NASA Astrophysics Data System (ADS)

    Villa, Marco; Duarte Pinto, Serge; Alfonsi, Matteo; Brock, Ian; Croci, Gabriele; David, Eric; de Oliveira, Rui; Ropelewski, Leszek; Taureg, Hans; van Stenis, Miranda

    2011-02-01

    The Gas Electron Multiplier (GEM) manufacturing technique has recently evolved to allow the production of large area GEMs. A novel approach based on single mask photolithography eliminates the mask alignment issue, which limits the dimensions in the traditional double mask process. Moreover, a splicing technique overcomes the limited width of the raw material. Stretching and handling issues in large area GEMs have also been addressed. Using the new improvements it was possible to build a prototype triple-GEM detector of ˜2000 cm2 active area, aimed at an application for the TOTEM T1 upgrade. Further refinements of the single mask technique allow great control over the shape of the GEM holes and the size of the rims, which can be tuned as needed. In this framework, simulation studies can help to understand the GEM behavior depending on the hole shape.

  16. Calcium Binding Promotes Conformational Flexibility of the Neuronal Ca2+ Sensor Synaptotagmin

    PubMed Central

    Bykhovskaia, Maria

    2015-01-01

    Synaptotagmin 1 (Syt1) is a synaptic vesicle protein that serves as a calcium sensor of neuronal secretion. It is established that calcium binding to Syt1 triggers vesicle fusion and release of neuronal transmitters, however, the dynamics of this process is not fully understood. To investigate how Ca2+ binding affects Syt1 conformational dynamics, we performed prolonged molecular dynamics (MD) simulations of Ca2+-unbound and Ca2+-bound forms of Syt1. MD simulations were performed at a microsecond scale and combined with Monte Carlo sampling. We found that in the absence of Ca2+ Syt1 structure in the solution is represented by an ensemble of conformational states with tightly coupled domains. To investigate the effect of Ca2+ binding, we used two different strategies to generate a molecular model of a Ca2+-bound form of Syt1. First, we employed subsequent replacements of monovalent cations transiently captured within Syt1 Ca2+-binding pockets by Ca2+ ions. Second, we performed MD simulations of Syt1 at elevated Ca2+ levels. All the simulations produced Syt1 structures bound to four Ca2+ ions, two ions chelated at the binding pocket of each domain. MD simulations of the Ca2+-bound form of Syt1 revealed that Syt1 conformational flexibility drastically increased upon Ca2+ binding. In the presence of Ca2+, the separation between domains increased, and interdomain rotations became more frequent. These findings suggest that Ca2+ binding to Syt1 may induce major changes in the Syt1 conformational state, which in turn may initiate the fusion process. PMID:25992729

  17. Glutamate Racemase Dimerization Inhibits Dynamic Conformational Flexibility and Reduces Catalytic Rates

    SciTech Connect

    Mehboob, Shahila; Guo, Liang; Fu, Wentao; Mittal, Anuradha; Yau, Tiffany; Truong, Kent; Johlfs, Mary; Long, Fei; Fung, Leslie W.-M.; Johnson, Michael E.

    2009-09-15

    Glutamate racemase (RacE) is a bacterial enzyme that converts L-glutamate to D-glutamate, an essential precursor for peptidoglycan synthesis. In prior work, we have shown that both isoforms cocrystallize with D-glutamate as dimers, and the enzyme is in a closed conformation with limited access to the active site [May, M., et al. (2007) J. Mol. Biol. 371, 1219-1237]. The active site of RacE2 is especially restricted. We utilize several computational and experimental approaches to understand the overall conformational dynamics involved during catalysis when the ligand enters and the product exits the active site. Our steered molecular dynamics simulations and normal-mode analysis results indicate that the monomeric form of the enzyme is more flexible than the native dimeric form. These results suggest that the monomeric enzyme might be more active than the dimeric form. We thus generated site-specific mutations that disrupt dimerization and find that the mutants exhibit significantly higher catalytic rates in the D-Glu to L-Glu reaction direction than the native enzyme. Low-resolution models restored from solution X-ray scattering studies correlate well with the first six normal modes of the dimeric form of the enzyme, obtained from NMA. Thus, along with the local active site residues, global domain motions appear to be implicated in the catalytically relevant structural dynamics of this enzyme and suggest that increased flexibility may accelerate catalysis. This is a novel observation that residues distant from the catalytic site restrain catalytic activity through formation of the dimer structure.

  18. Conformational and stereochemical flexibility in cadmium(II) complexes of aza-thioether macrocycles.

    PubMed

    Glenny, Mark W; van de Water, Leon G A; Driessen, Willem L; Reedijk, Jan; Blake, Alexander J; Wilson, Claire; Schröder, Martin

    2004-07-01

    The synthesis and crystal structures of four CdII macrocyclic complexes containing mixed N-, O- and S-donors, [Cd(NO3)2([12]aneN2S2)] (1), [Cd(NO3)2([12]aneNS3)] (2), [Cd(NO3)2([15]aneNO2S2)] (3) and [Cd(NO3)([15]aneN2O2S)]NO3 (4), are presented. The metal ion is coordinated outside of the macrocyclic cavity in the complexes of the smaller macrocycles ([12]aneN2S2 and [12]aneNS3) while the flexibility of the larger macrocycles in and allows very different conformations to be adopted with a 'butterfly' geometry in and a flattened geometry in. No correlation between the number of sulfur donors and Cd-S bond distance in these types of complexes is observed, although the number and binding mode of the nitrato ligands is determined by the conformation and binding mode of the macrocycle. The position of the nitrato ligand also influences, through steric conflicts with the macrocyclic donor atoms, the bond distances in both ligand systems. PMID:15252582

  19. Investigation of the conformational flexibility of DGAT1 peptides using tryptophan fluorescence

    NASA Astrophysics Data System (ADS)

    Lopes, Jose L. S.; Araujo, Ana P. U.; Jameson, David M.

    2015-06-01

    The conformational behavior of synthetic peptides corresponding to the putative binding sites of the diacylglycerol acyltransferase 1 enzyme (a polytopic integral membrane protein) was investigated using steady-state and time-resolved fluorescence spectroscopies. Three small linear peptides with 13, 15 and 22 amino acid residues, containing one, two and three Trp residues, respectively, were studied in aqueous solution, in the absence and presence of model membranes. The high flexibility and unordered conformation of the peptides in solution were confirmed by the low Trp polarization values, the high accessibility to water-soluble quencher, and the fast rotational correlation times of the Trp residues. However, upon binding to the lipid systems, the Trp residues were incorporated within the acyl hydrophobic core and their lifetimes and rotational correlation times increased. Phasor plots were employed to analyze intensity decay of peptide-lipid binding and provided a trajectory, in phasor space, that lies along a line connecting the points of the free and bound peptide. This trajectory was analyzed to determine the association constant of the peptide to the model membrane.

  20. The Catalytic Activity of Protein-Disulfide Isomerase Requires a Conformationally Flexible Molecule

    SciTech Connect

    Tian, G.; Kober, F; Lewandrowski, U; Sickmann, A; Lennarz, W; Schindelin, H

    2008-01-01

    Protein-disulfide isomerase (PDI) catalyzes the formation of the correct pattern of disulfide bonds in secretory proteins. A low resolution crystal structure of yeast PDI described here reveals large scale conformational changes compared with the initially reported structure, indicating that PDI is a highly flexible molecule with its catalytic domains, a and a?, representing two mobile arms connected to a more rigid core composed of the b and b? domains. Limited proteolysis revealed that the linker between the a domain and the core is more susceptible to degradation than that connecting the a? domain to the core. By restricting the two arms with inter-domain disulfide bonds, the molecular flexibility of PDI, especially that of its a domain, was demonstrated to be essential for the enzymatic activity in vitro and in vivo. The crystal structure also featured a PDI dimer, and a propensity to dimerize in solution and in the ER was confirmed by cross-linking experiments and the split green fluorescent protein system. Although sedimentation studies suggested that the self-association of PDI is weak, we hypothesize that PDI exists as an interconvertible mixture of monomers and dimers in the endoplasmic reticulum due to its high abundance in this compartment.

  1. Multiple disulfide bridges modulate conformational stability and flexibility in hyperthermophilic archaeal purine nucleoside phosphorylase.

    PubMed

    Bagarolo, Maria Libera; Porcelli, Marina; Martino, Elisa; Feller, Georges; Cacciapuoti, Giovanna

    2015-10-01

    5'-Deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus is a hexameric hyperthermophilic protein containing in each subunit two pairs of disulfide bridges, a CXC motif, and one free cysteine. The contribution of each disulfide bridge to the protein conformational stability and flexibility has been assessed by comparing the thermal unfolding and the limited proteolysis of the wild-type enzyme and its variants obtained by site-directed mutagenesis of the seven cysteine residues. All variants catalyzed efficiently MTA cleavage with specific activity similar to the wild-type enzyme. The elimination of all cysteine residues caused a substantial decrease of ΔHcal (850 kcal/mol) and Tmax (39°C) with respect to the wild-type indicating that all cysteine pairs and especially the CXC motif significantly contribute to the enzyme thermal stability. Disulfide bond Cys200-Cys262 and the CXC motif weakly affected protein flexibility while the elimination of the disulfide bond Cys138-Cys205 lead to an increased protease susceptibility. Experimental evidence from limited proteolysis, differential scanning calorimetry, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing and nonreducing conditions also allowed to propose a stabilizing role for the free Cys164. PMID:26116147

  2. A relational database of protein structures designed for flexible enquiries about conformation.

    PubMed

    Islam, S A; Sternberg, M J

    1989-03-01

    A relational database of protein structure has been developed to enable rapid and flexible enquiries about the occurrence of many aspects of protein architecture. The coordinates of 294 proteins from the Brookhaven Data Bank have been processed by standard computer programs to generate many additional terms that quantify aspects of protein structure. These terms include solvent accessibility, main-chain and side-chain dihedral angles, and secondary structure. In a relational database, the information is stored in tables with columns holding the different terms and rows holding the different entries for the terms. The different relational base tables store the information about the protein coordinate set, the different chains in the protein, the amino acid residues and ligands, the atomic coordinates, the salt bridges, the hydrogen bonds, the disulphide bridges and the close tertiary contacts. The database was established under ORACLE management system. Enquiries are constructed in ORACLE using SQL (structured query language) which is simple to use and alleviates the need for extensive computer programs. A single table can be searched for entries that meet various criteria, e.g. all protein solved to better than a given resolution. The power of the database occurs when several tables, or the entries in a single table, are cross-correlated. For example the dihedral angles of proline in the fourth position in an alpha-helix in high resolution structures can be rapidly obtained. The structural database provides a powerful tool to obtain empirical rules about protein conformation. This database of protein structures is part of a joint project between Birkbeck College and Leeds University to establish an integrated data resource of protein sequences and structures (ISIS) that encodes the complex patterns of residues and coordinates that define protein conformation. The entire data resource (ISIS) will provide a system to guide all areas of protein modelling including

  3. Biophysical exploration of protein-flavonol recognition: effects of molecular properties and conformational flexibility.

    PubMed

    Ding, Fei; Peng, Wei; Peng, Yu-Kui

    2016-04-28

    The current work explores the biomolecular recognition of a series of flavonols by a protein and then uncovers the influences of the structural features of flavonols and the protein's own characteristics, e.g. the dynamics and flexibility, on the bioavailability of flavonols by using the pivotal biomacromolecule hemoglobin as a model. The experimental results revealed that flavonol may lead to a notable decrease in the steady-state fluorescence intensity of the β-37 Trp residue, and in the meantime the R-T transition of the protein transpired. Such noncovalent recognition forms the ground-state adduct, with an association intensity of 3.991 × 10(4) M(-1) in the reaction process, which has already been authenticated by the detailed analysis of time-resolved fluorescence and UV/vis absorption spectra. Furthermore, flavonol can form hydrogen bonds and π-conjugation effects with several amino acid residues on the polypeptide chain, for example, Trp-37, Arg-40, Asp-99 and Asn-102, and this event would induce self-regulation of the compact, regular conformation of the protein to a certain extent, which explicitly corroborates the results of circular dichroism. According to the study of molecular docking and structure-activity relationships, we could see that the recognition capacities of the protein-flavonols are inversely interrelated with the C log P values of the flavonol molecules. Moreover, the properties of the substituents in the structural B-ring unit of flavonols, i.e. polarity, position and number, will also prominently affect the degree of affinity and bioavailability of the protein-flavonol complexes. The analytical results of molecular dynamics (MD) simulation testified that the discussions of the structure-activity relationships are entirely logical, and the conformations of the amino acid residues forming noncovalent interactions tend to be stable in the MD simulation, as further elucidated from the dynamics data. Plainly, molecular recognition of

  4. Anion directed structural diversity in zinc complexes with conformationally flexible quinazoline ligand: structural, spectral and theoretical studies.

    PubMed

    Dwivedi, Nidhi; Panja, Sumit Kumar; Monika; Saha, Satyen; Sunkari, Sailaja S

    2016-08-14

    In this paper, we report the synthesis, structure and photophysical studies of four new complexes of conformationally flexible 6-chloro-4-phenyl-2-(pyridin-2-yl)quinazoline ligand (L) with Zn(ii). The coordinating ability of the ligand and geometrical preferences of the resultant complexes are tuned by varying the anion of the metal salt as confirmed by structural and DFT studies. The choice of the metal salt (especially anion) directs the stabilisation of different conformations of the ligand arising out of twisting of the pyridyl ring with respect to the quinazoline ring, resulting in complexes with different nuclearity (monomer/dimer) as well as different coordination geometries (tetrahedral/trigonal bipyramidal/octahedral). Photophysical properties are also found to be tuned due to conformational changes on complexation. DFT studies on the ligand establish the conformationally stable forms as observed in the reported structures. PMID:27397771

  5. Substrate-free self-assembly approach toward large-area nanomembranes.

    PubMed

    Wang, Fei; Seo, Jung-Hun; Ma, Zhenqiang; Wang, Xudong

    2012-03-27

    Free-standing two-dimensional nanostrucutures, such as graphene and semiconductor nanomembranes (NMs) featuring their integration with flexible polymer substrates, address applications in which electronic devices need to be stretchable or conformally positioned to nonplanar surfaces. We report a surfactant-directed surface assembly approach to producing large-area NMs at the water-air interface. The NMs were produced by employing the surfactants as templates as well as incorporating them in the crystal structures. By using excess amount of sodium dodecylsulfate (SDS), a tightly packed monolayer of dodecylsulfate (DS) ion was formed and directed the crystallization of submillimeter-sized zinc hydroxy dodecylsulfate (ZHDS) single-crystalline NMs over the entire water surface. This free-standing NM can be readily transferred to an arbitrary substrate and converted to ZnO via heat treatment. A flexible thin-film transistor was also fabricated using the transferred NMs and demonstrated reasonably good n-type transport properties. This approach circumvented the needs of single-crystalline substrates for making large-area NMs from materials that do not possess a laminate structure. It is a low-cost and large-scale synthesis technique and has great potential in developing NMs and flexible devices from various functional materials that are not feasible by conventional selective etching or delamination approaches. PMID:22299624

  6. Conformational flexibility of a model protein upon immobilization on self-assembled monolayers.

    PubMed

    Bigdeli, Saharnaz; Talasaz, AmirAli H; Ståhl, Patrik; Persson, Henrik H J; Ronaghi, Mostafa; Davis, Ronald W; Nemat-Gorgani, Mohsen

    2008-05-01

    The present study reports on the retention of conformational flexibility of a model allosteric protein upon immobilization on self-assembled monolayers (SAMs) on gold. Organothiolated SAMs of different compositions were utilized for adsorptive and covalent attachment of bovine liver glutamate dehydrogenase (GDH), a well-characterized allosteric enzyme. Sensitive fluorimetric assays were developed to determine immobilization capacity, specific activity, and allosteric properties of the immobilized preparations as well as the potential for repeated use and continuous catalytic transformations. The allosteric response of the free and immobilized forms towards ADP, L-leucine and high concentrations of NAD(+), some of the well-known activators for this enzyme, were determined and compared. The enzyme immobilized by adsorption or chemical binding responded similarly to the activators with a greater degree of activation, as compared to the free form. Also loss of activity involving the two immobilization procedures were similar, suggesting that residues essential for catalytic activity or allosteric properties of GDH remained unchanged in the course of chemical modification. A recently established method was used to predict GDH orientation upon immobilization, which was found to explain some of the experimental results presented. The general significance of these observations in connection with retention of native properties of protein structures upon immobilization on SAMs is discussed. PMID:18078298

  7. Conformational Flexibility Determines Selectivity and Antibacterial, Antiplasmodial, and Anticancer Potency of Cationic α-Helical Peptides*

    PubMed Central

    Vermeer, Louic S.; Lan, Yun; Abbate, Vincenzo; Ruh, Emrah; Bui, Tam T.; Wilkinson, Louise J.; Kanno, Tokuwa; Jumagulova, Elmira; Kozlowska, Justyna; Patel, Jayneil; McIntyre, Caitlin A.; Yam, W. C.; Siu, Gilman; Atkinson, R. Andrew; Lam, Jenny K. W.; Bansal, Sukhvinder S.; Drake, Alex F.; Mitchell, Graham H.; Mason, A. James

    2012-01-01

    We used a combination of fluorescence, circular dichroism (CD), and NMR spectroscopies in conjunction with size exclusion chromatography to help rationalize the relative antibacterial, antiplasmodial, and cytotoxic activities of a series of proline-free and proline-containing model antimicrobial peptides (AMPs) in terms of their structural properties. When compared with proline-free analogs, proline-containing peptides had greater activity against Gram-negative bacteria, two mammalian cancer cell lines, and intraerythrocytic Plasmodium falciparum, which they were capable of killing without causing hemolysis. In contrast, incorporation of proline did not have a consistent effect on peptide activity against Mycobacterium tuberculosis. In membrane-mimicking environments, structures with high α-helix content were adopted by both proline-free and proline-containing peptides. In solution, AMPs generally adopted disordered structures unless their sequences comprised more hydrophobic amino acids or until coordinating phosphate ions were added. Proline-containing peptides resisted ordering induced by either method. The roles of the angle subtended by positively charged amino acids and the positioning of the proline residues were also investigated. Careful positioning of proline residues in AMP sequences is required to enable the peptide to resist ordering and maintain optimal antibacterial activity, whereas varying the angle subtended by positively charged amino acids can attenuate hemolytic potential albeit with a modest reduction in potency. Maintaining conformational flexibility improves AMP potency and selectivity toward bacterial, plasmodial, and cancerous cells while enabling the targeting of intracellular pathogens. PMID:22869378

  8. Torsional flexibility of B-DNA as revealed by conformational analysis.

    PubMed Central

    Zhurkin, V B; Lysov, Y P; Florentiev, V L; Ivanov, V I

    1982-01-01

    The thermal fluctuations of a regular double helix belonging to the B-family were studied by means of atom-atomic potentials method. The winding angle fluctuation was found to be 2.4 degrees for poly(dA):poly(dT) and 3.0 degrees for poly(dG):poly(dC). The reasonable agreement of these estimations with those obtained experimentally reveals the essential role of the small-amplitude torsional vibrations of atoms in the mechanism of the double helix flexibility. The calculated equilibrium winding angle, tau 0, essentially depends on the degree of neutralization of phosphate groups, being about 35.5 degrees for the full neutralization. The deoxyribose pucker is closely related to the tau angle: while tau proceeds from 30 degrees to 45 degrees the pseudorotation phase angle, P, increases from 126 degrees to 164 degrees. Fluctuations of the angles TL and TW, which specify inclination of the bases to the helix axis, were evaluated to be 5 degrees-10 degrees. Possible correlation between conformational changes in the adjacent nucleotides is discussed. PMID:7071023

  9. Large-area Overhead Manipulator for Access of Fields

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multi-axis, cable-driven manipulators have evolved over many years providing large area suspended platform access, programmability, relatively rigid and flexibly-positioned platform control and full six degree of freedom (DOF) manipulation of sensors and tools. We describe innovations for a new six...

  10. An engineered scorpion toxin analogue with improved Kv1.3 selectivity displays reduced conformational flexibility

    PubMed Central

    Bartok, Adam; Fehér, Krisztina; Bodor, Andrea; Rákosi, Kinga; Tóth, Gábor K.; Kövér, Katalin E.; Panyi, Gyorgy; Varga, Zoltan

    2015-01-01

    The voltage-gated Kv1.3 K+ channel plays a key role in the activation of T lymphocytes. Kv1.3 blockers selectively suppress immune responses mediated by effector memory T cells, which indicates the great potential of selective Kv1.3 inhibitors in the therapy of certain autoimmune diseases. Anuroctoxin (AnTx), a 35-amino-acid scorpion toxin is a high affinity blocker of Kv1.3, but also blocks Kv1.2 with similar potency. We designed and produced three AnTx variants: ([F32T]-AnTx, [N17A]-AnTx, [N17A/F32T]-AnTx) using solid-phase synthesis with the goal of improving the selectivity of the toxin for Kv1.3 over Kv1.2 while keeping the high affinity for Kv1.3. We used the patch-clamp technique to determine the blocking potency of the synthetic toxins on hKv1.3, mKv1.1, hKv1.2 and hKCa3.1 channels. Of the three variants [N17A/F32T]-AnTx maintained the high affinity of the natural peptide for Kv1.3 but became more than 16000-fold selective over Kv1.2. NMR data and molecular dynamics simulations suggest that the more rigid structure with restricted conformational space of the double substituted toxin compared to the flexible wild-type one is an important determinant of toxin selectivity. Our results provide the foundation for the possibility of the production and future therapeutic application of additional, even more selective toxins targeting various ion channels. PMID:26689143

  11. Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel.

    PubMed

    Boiteux, Céline; Vorobyov, Igor; Allen, Toby W

    2014-03-01

    Voltage-gated Na(+) channels play an essential role in electrical signaling in the nervous system and are key pharmacological targets for a range of disorders. The recent solution of X-ray structures for the bacterial channel NavAb has provided an opportunity to study functional mechanisms at the atomic level. This channel's selectivity filter exhibits an EEEE ring sequence, characteristic of mammalian Ca(2+), not Na(+), channels. This raises the fundamentally important question: just what makes a Na(+) channel conduct Na(+) ions? Here we explore ion permeation on multimicrosecond timescales using the purpose-built Anton supercomputer. We isolate the likely protonation states of the EEEE ring and observe a striking flexibility of the filter that demonstrates the necessity for extended simulations to study conduction in this channel. We construct free energy maps to reveal complex multi-ion conduction via knock-on and "pass-by" mechanisms, involving concerted ion and glutamate side chain movements. Simulations in mixed ionic solutions reveal relative energetics for Na(+), K(+), and Ca(2+) within the pore that are consistent with the modest selectivity seen experimentally. We have observed conformational changes in the pore domain leading to asymmetrical collapses of the activation gate, similar to proposed inactivated structures of NavAb, with helix bending involving conserved residues that are critical for slow inactivation. These structural changes are shown to regulate access to fenestrations suggested to be pathways for lipophilic drugs and provide deeper insight into the molecular mechanisms connecting drug activity and slow inactivation. PMID:24550503

  12. The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility

    PubMed Central

    Linser, Rasmus; Salvi, Nicola; Briones, Rodolfo; Rovó, Petra; de Groot, Bert L.; Wagner, Gerhard

    2015-01-01

    Regulated intramembrane proteolysis (RIP) is a conserved mechanism crucial for numerous cellular processes, including signaling, transcriptional regulation, axon guidance, cell adhesion, cellular stress responses, and transmembrane protein fragment degradation. Importantly, it is relevant in various diseases including Alzheimer’s disease, cardiovascular diseases, and cancers. Even though a number of structures of different intramembrane proteases have been solved recently, fundamental questions concerning mechanistic underpinnings of RIP and therapeutic interventions remain. In particular, this includes substrate recognition, what properties render a given substrate amenable for RIP, and how the lipid environment affects the substrate cleavage. Members of the sterol regulatory element-binding protein (SREBP) family of transcription factors are critical regulators of genes involved in cholesterol/lipid homeostasis. After site-1 protease cleavage of the inactive SREBP transmembrane precursor protein, RIP of the anchor intermediate by site-2 protease generates the mature transcription factor. In this work, we have investigated the labile anchor intermediate of SREBP-1 using NMR spectroscopy. Surprisingly, NMR chemical shifts, site-resolved solvent exposure, and relaxation studies show that the cleavage site of the lipid-signaling protein intermediate bears rigid α-helical topology. An evolutionary conserved motif, by contrast, interrupts the secondary structure ∼9–10 residues C-terminal of the scissile bond and acts as an inducer of conformational flexibility within the carboxyl-terminal transmembrane region. These results are consistent with molecular dynamics simulations. Topology, stability, and site-resolved dynamics data suggest that the cleavage of the α-helical substrate in the case of RIP may be associated with a hinge motion triggered by the molecular environment. PMID:26392539

  13. Conformational variety of flexible mono-dentate ligands in coordination compounds: influence of π-involving interactions.

    PubMed

    Khavasi, Hamid Reza; Kavand, Sima

    2016-06-28

    The effect of intermolecular interactions on the conformational variety of flexible mono-dentate ligands in coordination compounds has been investigated through the preparation of two series of mercury(ii) complexes. In this regard, the molecular and structural architecture of eight complexes, [HgCl2(L(amide-Cl))2] (), [HgCl2(L(amide-Br))2] (), [HgBr2(L(amide-Br))2] (), and [HgI2(L(amide-Br))2] (), as the first series and [HgBr2(L(imine-Cl))2] (), [HgBr2(L(imine-Br))2] (), [HgI2(L(imine-Cl))]n (), and [HgI2(L(imine-Br))]n (), as the second series, using two kind of flexible ligands, N-(1-halonaphthalen-4-yl)nicotinamide, L(amide-X), and 4-halo-N-((pyridin-3-yl)methylene)naphthalen-1-amine, L(imine-X), has been studied. Inspection of the packing of these compounds clearly shows the presence of conformational changes in the arrangement of the ligands in each series. Although there are slight differences between the crystal packing of these compounds, it seems that π-involving intermolecular interactions including πnaphπnaph in the first series and πimineπpy/naph in the second series with the cooperation of Hgπpy can lock the ligand conformational variety to a single conformer. PMID:27293034

  14. Mixed Cyclic Constraints on Conformational Flexibility in β/γ-PEPTIDES: Conformation Specific IR and UV Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gord, Joseph R.; Walsh, Patrick S.; Zwier, Timothy S.; Fisher, Brian F.; Gellman, Samuel H.

    2013-06-01

    In order to further understand the intramolecular forces governing secondary structure formation in peptides and to provide benchmarks for the computational community, conformation-specific spectroscopy techniques have been applied to several model systems provided by Dr. Sam Gellman's research group at the University of Wisconsin-Madison. In the present work, two model β/γ-peptides, Ac-β_{ACPC}-γ_{ACHC}-NHBz and Ac-γ_{ACHC}-β_{ACPC}-NHBz have been investigated using single and double resonance ultraviolet and infrared spectroscopy to elucidate their intrinsic folding propensities. The β-peptide is constrained by a five-membered ring spanning the β^{3}-β^{2} positions (β_{ACPC}) and the γ-peptide is constrained by a six-membered ring spanning the γ^{4}-γ^{3} positions with an additional ethyl group at γ^{2} (γ_{ACHC}). Resonant two-photon ionization (R2PI) spectra from 37250 to 37750 cm^{-1} were obtained and subsequently interrogated using UV-UV hole-burning to reveal the presence of three conformations for Ac-β_{ACPC}-γ_{ACHC}-NHBz, and a single conformation for Ac-γ_{ACHC}-β_{ACPC}-NHBz. Resonant ion-dip infrared (RIDIR) spectra were obtained in the NH stretch region from 3300 to 3500 cm^{-1} and in both the amide I and II regions from 1400 to 1800 cm^{-1}. These spectra were compared to computational predictions given by DFT calculations using the M05-2X functional with a 6-31G+(d) basis set revealing two slightly varied iterations of a bifurcated C-8/13 double ring structure for Ac-β_{ACPC}-γ_{ACHC}-NHBz and one bifurcated C-9/13 double ring structure for Ac-γ_{ACHC}-β_{ACPC}-NHBz. The appearance of C-13 rings was also seen in solution phase studies. This work is a complement to studies performed on pure γ-peptides and α/γ-peptides. L. Guo, A. M. Almeida, W. Zhang, A. G. Reidenbach, S. H. Choi, I.. A. Guzei, and S. H. Gellman J. Am. Chem. Soc. 2010, 132, 7868-7869

  15. Modular hyperthermostable bacterial endo-β-1,4-mannanase: molecular shape, flexibility and temperature-dependent conformational changes.

    PubMed

    da Silva, Viviam M; Colussi, Francieli; de Oliveira Neto, Mario; Braz, Antonio S K; Squina, Fabio M; Oliveira, Cristiano L P; Garcia, Wanius

    2014-01-01

    Endo-β-1,4-mannanase from Thermotoga petrophila (TpMan) is a hyperthermostable enzyme that catalyzes the hydrolysis of β-1,4-mannoside linkages in various mannan-containing polysaccharides. A recent study reported that TpMan is composed of a GH5 catalytic domain joined by a linker to a carbohydrate-binding domain. However, at this moment, there is no three-dimensional structure determined for TpMan. Little is known about the conformation of the TpMan as well as the role of the length and flexibility of the linker on the spatial arrangement of the constitutive domains. In this study, we report the first structural characterization of the entire TpMan by small-angle X-ray scattering combined with the three-dimensional structures of the individual domains in order to shed light on the low-resolution model, overall dimensions, and flexibility of this modular enzyme at different temperatures. The results are consistent with a linker with a compact structure and that occupies a small volume with respect to its large number of amino acids. Furthermore, at 20°C the results are consistent with a model where TpMan is a molecule composed of three distinct domains and that presents some level of molecular flexibility in solution. Even though the full enzyme has some degree of molecular flexibility, there might be a preferable conformation, which could be described by the rigid-body modeling procedure. Finally, the results indicate that TpMan undergoes a temperature-driven transition between conformational states without a significant disruption of its secondary structure. Our results suggest that the linker can optimize the geometry between the other two domains with respect to the substrate at high temperatures. These studies should provide a useful basis for future biophysical studies of entire TpMan. PMID:24671161

  16. Modular Hyperthermostable Bacterial Endo-β-1,4-Mannanase: Molecular Shape, Flexibility and Temperature-Dependent Conformational Changes

    PubMed Central

    de Oliveira Neto, Mario; Braz, Antonio S. K.; Squina, Fabio M.; Oliveira, Cristiano L. P.; Garcia, Wanius

    2014-01-01

    Endo-β-1,4-mannanase from Thermotoga petrophila (TpMan) is a hyperthermostable enzyme that catalyzes the hydrolysis of β-1,4-mannoside linkages in various mannan-containing polysaccharides. A recent study reported that TpMan is composed of a GH5 catalytic domain joined by a linker to a carbohydrate-binding domain. However, at this moment, there is no three-dimensional structure determined for TpMan. Little is known about the conformation of the TpMan as well as the role of the length and flexibility of the linker on the spatial arrangement of the constitutive domains. In this study, we report the first structural characterization of the entire TpMan by small-angle X-ray scattering combined with the three-dimensional structures of the individual domains in order to shed light on the low-resolution model, overall dimensions, and flexibility of this modular enzyme at different temperatures. The results are consistent with a linker with a compact structure and that occupies a small volume with respect to its large number of amino acids. Furthermore, at 20°C the results are consistent with a model where TpMan is a molecule composed of three distinct domains and that presents some level of molecular flexibility in solution. Even though the full enzyme has some degree of molecular flexibility, there might be a preferable conformation, which could be described by the rigid-body modeling procedure. Finally, the results indicate that TpMan undergoes a temperature-driven transition between conformational states without a significant disruption of its secondary structure. Our results suggest that the linker can optimize the geometry between the other two domains with respect to the substrate at high temperatures. These studies should provide a useful basis for future biophysical studies of entire TpMan. PMID:24671161

  17. Flexibility.

    ERIC Educational Resources Information Center

    Humphrey, L. Dennis

    1981-01-01

    Flexibility is an important aspect of all sports and recreational activities. Flexibility can be developed and maintained by stretching exercises. Exercises designed to develop flexibility in ankle joints, knees, hips, and the lower back are presented. (JN)

  18. Emulsifying and interfacial properties of vicilins: role of conformational flexibility at quaternary and/or tertiary levels.

    PubMed

    Liang, Han-Ni; Tang, Chuan-He

    2013-11-20

    Although the functionality of plant proteins (and soy proteins in particular) has been widely investigated in the last decades, the importance of conformational characteristics to their functionalities is still far away from being understood. The aim of the present work was to unravel the role of conformational flexibility at the quaternary and/or tertiary levels in the emulsifying and interfacial properties of phaseolin, an ideal vicilin (or 7S globulin) from red kidney bean. The conformational flexibility at quaternary and tertiary levels of phaseolin was modulated by urea with increasing concentrations from 0 to 8 M, as characterized by using dynamic light scattering (DLS), intrinsic fluorescence and derivative UV spectroscopy, and differential scanning calorimetry (DSC). The emulsifying and interfacial properties, including emulsifying ability, flocculated state of oil droplets (in fresh emulsions), emulsion stability against creaming, and adsorption dynamics at the oil-water interface, were characterized at a specific protein concentration of 0.5% (w/v). The results indicated that increasing the urea concentration resulted in a progressive dissociation of trimeric phaseolin molecules into monomeric subunits, and even a structural unfolding of dissociated subunits; the urea-induced conformational changes at quaternary and/or tertiary levels were reversible, and the molecules at high urea concentrations shared similar structural features to the "molten globule state". On the other hand, increasing the urea concentration progressively improved the emulsifying ability of the protein, and flocculated extent of oil droplets in the fresh emulsions, but led to a progressive decrease in interfacial protein concentration. The improvement of the emulsifying ability was not related to diffusion (during initial adsorption) and penetration at the interface, but highly dependent on ease of structural rearrangement of the adsorbed proteins. These observations clearly

  19. Chimpanzees (Pan troglodytes) Flexibly Adjust Their Behaviour in Order to Maximize Payoffs, Not to Conform to Majorities

    PubMed Central

    Van Leeuwen, Edwin J. C.; Cronin, Katherine A.; Schütte, Sebastian; Call, Josep; Haun, Daniel B. M.

    2013-01-01

    Chimpanzees have been shown to be adept learners, both individually and socially. Yet, sometimes their conservative nature seems to hamper the flexible adoption of superior alternatives, even to the extent that they persist in using entirely ineffective strategies. In this study, we investigated chimpanzees’ behavioural flexibility in two different conditions under which social animals have been predicted to abandon personal preferences and adopt alternative strategies: i) under influence of majority demonstrations (i.e. conformity), and ii) in the presence of superior reward contingencies (i.e. maximizing payoffs). Unlike previous nonhuman primate studies, this study disentangled the concept of conformity from the tendency to maintain one’s first-learned strategy. Studying captive (n=16) and semi-wild (n=12) chimpanzees in two complementary exchange paradigms, we found that chimpanzees did not abandon their behaviour in order to match the majority, but instead remained faithful to their first-learned strategy (Study 1a and 1b). However, the chimpanzees’ fidelity to their first-learned strategy was overridden by an experimental upgrade of the profitability of the alternative strategy (Study 2). We interpret our observations in terms of chimpanzees’ relative weighing of behavioural options as a function of situation-specific trade-offs. More specifically, contrary to previous findings, chimpanzees in our study abandoned their familiar behaviour to maximize payoffs, but not to conform to a majority. PMID:24312252

  20. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    PubMed

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin. PMID:25066915

  1. Chimpanzees (Pan troglodytes) flexibly adjust their behaviour in order to maximize payoffs, not to conform to majorities.

    PubMed

    Van Leeuwen, Edwin J C; Cronin, Katherine A; Schütte, Sebastian; Call, Josep; Haun, Daniel B M

    2013-01-01

    Chimpanzees have been shown to be adept learners, both individually and socially. Yet, sometimes their conservative nature seems to hamper the flexible adoption of superior alternatives, even to the extent that they persist in using entirely ineffective strategies. In this study, we investigated chimpanzees' behavioural flexibility in two different conditions under which social animals have been predicted to abandon personal preferences and adopt alternative strategies: i) under influence of majority demonstrations (i.e. conformity), and ii) in the presence of superior reward contingencies (i.e. maximizing payoffs). Unlike previous nonhuman primate studies, this study disentangled the concept of conformity from the tendency to maintain one's first-learned strategy. Studying captive (n=16) and semi-wild (n=12) chimpanzees in two complementary exchange paradigms, we found that chimpanzees did not abandon their behaviour in order to match the majority, but instead remained faithful to their first-learned strategy (Study 1a and 1b). However, the chimpanzees' fidelity to their first-learned strategy was overridden by an experimental upgrade of the profitability of the alternative strategy (Study 2). We interpret our observations in terms of chimpanzees' relative weighing of behavioural options as a function of situation-specific trade-offs. More specifically, contrary to previous findings, chimpanzees in our study abandoned their familiar behaviour to maximize payoffs, but not to conform to a majority. PMID:24312252

  2. Influence of conformational flexibility on self-assembly and luminescence properties of lanthanide coordination polymers with flexible exo-bidentate biphenol derivatives.

    PubMed

    Guo, Yanling; Dou, Wei; Zhou, Xiaoyan; Liu, Weisheng; Qin, Wenwu; Zang, Zhipeng; Zhang, Hongrui; Wang, Daqi

    2009-04-20

    To explore how nonplanar conformational distortions affect supramolecular self-assembly and properties of lanthanide complexes, we have designed and synthesized two new flexible exo-bidentate ligands derived from biphenol featuring two salicylamide pendant arms, 2,2'-bis{[(2'-benzylaminoformyl)phenoxyl]ethoxyl}-1,1'-biphenylene (L(I)) and 5,5'-dibromo-2,2'-bis{[(2'-benzylaminoformyl)phenoxyl]ethoxyl}-1,1'-biphenylene (L(II)). These two structurally related ligands can have different conformations and are used for constructing diverse lanthanide polymers with interesting luminescence properties. Among two series of lanthanide nitrate complexes which have been characterized by elemental analysis, X-ray powder diffraction, and IR spectroscopy, four new coordination polymers have been determined using X-ray diffraction analysis. The coordination polymer type {Ln(2)(NO(3))(6)(L(I))(3).3H(2)O}(infinity) (Ln = Nd, Sm, Eu, Gd, Tb or Dy) displays a two-dimensional honeycomb-like framework in the ab plane, which can be regarded as a (6,3) topological network with neodymium atoms acting as "three-connected" centers. In contrast, the coordination polymer types {[Nd(NO(3))(3)(L(II))(CH(3)OH)] x CH(3)OH}(infinity) and [Ln(NO(3))(3)(L(II))(C(2)H(5)OH)](infinity) (Ln = Sm, Eu, Gd, Tb or Dy) possess single-stranded helix chains which can be further connected through intermolecular hydrogen bonds to form two-dimensional supramolecular sheets. The photophysical properties of trivalent Sm, Eu, Tb, and Dy complexes at room temperature were investigated. The present work substantiates the claim that the supramolecular structure as well as the luminescence properties of the coordination polymer can be tuned by controlling the conformational distortion of a nonplanar flexible ligand in the supramolecular self-assembly. PMID:19290612

  3. Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in a hormone-bound microreceptor.

    PubMed

    Vashisth, Harish

    2014-01-01

    Insulin binding to the insulin receptor (IR) is the first key step in initiating downstream signaling cascades for glucose homeostasis in higher organisms. The molecular details of insulin recognition by IR are not yet completely understood, but a picture of hormone/receptor interactions at one of the epitopes (Site 1) is beginning to emerge from recent structural evidence. However, insulin-bound structures of truncated IR suggest that crystallographic conformation of insulin cannot be accommodated in the full IR ectodomain due to steric overlap of insulin with the first two type III fibronectin domains (F1 and F2), which are contributed to the insulin binding-pocket by the second subunit in the IR homodimer. A conformational change in the F1-F2 pair has thus been suggested. In this work, we present an all-atom structural model of complex of insulin and the IR ectodomain, where no structural overlap of insulin with the receptor domains (F1 and F2) is observed. This structural model was arrived at by flexibly fitting parts of our earlier insulin/IR all-atom model into the simulated density maps of crystallized constructs combined with conformational sampling from apo-IR solution conformations. Importantly, our experimentally-consistent model helps rationalize yet unresolved Site. PMID:25309993

  4. Donor-driven conformational flexibility in a real-life catalytic dicopper(ii) peroxo complex.

    PubMed

    Hoffmann, A; Herres-Pawlis, S

    2016-03-01

    The conformers of the real-life tyrosinase model [Cu2O2{HC(3-tBuPz)2(Py)}2](2+) which displays catalytic hydroxylation reactivity were investigated by density functional theory (DFT) studies including second-order perturbation theory and charge decomposition analysis (CDA). We elucidated the donor competition between pyrazolyl and pyridinyl moieties and found that pyrazolyl units are the stronger donors in bis(pyrazolyl)pyridinylmethane copper complexes. Geometry optimisations and TD-DFT calculations on all conformers proved to be robust in the prediction of the experimental data: the XAS distances and both charge-transfer bands are well reproduced. The CDA analyses gave insights into the electronic structure of the real-life peroxo dicopper species. The donor interplay as well as the multitude of interactions within two prototypical conformers have now been dissected in detail for the first time for a catalytic real-life system without simplifications. We find that the N donor interactions to the core are extremely stabilising and that in the conformer with both pyrazolyl units in equatorial position, these interactions are more stabilising than the axial ones. In the conformer with pyridinyl/pyrazolyl equator, the picture is more mixed but the general trend keeps consistent. We relate the extraordinary catalytic activity of the [Cu2O2{HC(3-tBuPz)2(Py)}2](2+) system to the subtle interplay of the different donor moieties. PMID:26688471

  5. Protein Disorder: Conformational Distribution of the Flexible Linker in a Chimeric Double Cellulase

    PubMed Central

    von Ossowski, Ingemar; Eaton, Julian T.; Czjzek, Mirjam; Perkins, Stephen J.; Frandsen, Torben P.; Schülein, Martin; Panine, Pierre; Henrissat, Bernard; Receveur-Bréchot, Veronique

    2005-01-01

    The structural properties of the linker peptide connecting the cellulose-binding module to the catalytic module in bimodular cellulases have been investigated by small-angle x-ray scattering. Since the linker and the cellulose-binding module are relatively small and cannot be readily detected separately, the conformation of the linker was studied by means of an artificial fusion protein, Cel6BA, in which an 88-residue linker connects the large catalytic modules of the cellulases Cel6A and Cel6B from Humicola insolens. Our data showed that Cel6BA is very elongated with a maximum dimension of 178 Å, but could not be described by a single conformation. Modeling of a series of Cel6BA conformers with interdomain separations ranging between 10 Å and 130 Å showed that good Guinier and P(r) profile fits were obtained by a weighted average of the scattering curves of all the models where the linker follows a nonrandom distribution, with a preference for the more compact conformers. These structural properties are likely to be essential for the function of the linker as a molecular spring between the two functional modules. Small-angle x-ray scattering therefore provides a unique tool to quantitatively analyze the conformational disorder typical of proteins described as natively unfolded. PMID:15653742

  6. Drug-nucleic acid interactions: conformational flexibility at the intercalation site.

    PubMed Central

    Berman, H M; Neidle, S; Stodola, R K

    1978-01-01

    The conformational features of the intercalation site in polynucleotides were examined. We found that, for all the crystal structures of drug-dinucleoside complexes studied thus far, two torsion angles differ from those found in A RNA (phi and chi) and that alternate sugar puckering is not a prerequisite for intercalation. This intercalation geometry, which is the basis of helix axis displacement in a polymer, would necessitate conformational changes in the adjacent nucleotides. The base-turn angle is less sensitive to the conformation of the backbone than it is to small alterations in the base-pairing geometry. We postulate that this angle is dependent on the nature of the intercalating drug. PMID:273246

  7. Conformational flexibility of PPII-helix: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Guo, Ping; Lei, Xiaoling; Gao, Yi

    2016-05-01

    Poly-proline fragments form the distinctive PPII-helix in a high percentage in proteins and peptides, which plays an important role in signal transduction and protein complex assembly. But why and how this helical structure works is still unknown. In this work, we applied the density functional calculations to investigate the different preferences of prolines on Cγ-endo and Cγ-exo conformers, in which non-covalent interactions play important roles. As a result, Cγ-exo conformers are favored for short-oligomers with stronger n → π* interaction formed by the backbone, while Cγ-endo conformers are favored for longer oligomers with stronger dipole interactions between side groups.

  8. Conformational Flexibility in the Flap Domains of Ligand-Free HIV Protease

    SciTech Connect

    Heaslet, H.; Rosenfeld, R.; Giffin, M.; Lin, Y.-C.; Tam, K.; Torbett, B.E.; Elder, J.H.; Stout, C.D.

    2009-06-01

    The crystal structures of wild-type HIV protease (HIV PR) in the absence of substrate or inhibitor in two related crystal forms at 1.4 and 2.15 {angstrom} resolution are reported. In one crystal form HIV PR adopts an 'open' conformation with a 7.7 {angstrom} separation between the tips of the flaps in the homodimer. In the other crystal form the tips of the flaps are 'curled' towards the 80s loop, forming contacts across the local twofold axis. The 2.3 {angstrom} resolution crystal structure of a sixfold mutant of HIV PR in the absence of substrate or inhibitor is also reported. The mutant HIV PR, which evolved in response to treatment with the potent inhibitor TL-3, contains six point mutations relative to the wild-type enzyme (L24I, M46I, F53L, L63P, V77I, V82A). In this structure the flaps also adopt a 'curled' conformation, but are separated and not in contact. Comparison of the apo structures to those with TL-3 bound demonstrates the extent of conformational change induced by inhibitor binding, which includes reorganization of the packing between twofold-related flaps. Further comparison with six other apo HIV PR structures reveals that the 'open' and 'curled' conformations define two distinct families in HIV PR. These conformational states include hinge motion of residues at either end of the flaps, opening and closing the entire {beta}-loop, and translational motion of the flap normal to the dimer twofold axis and relative to the 80s loop. The alternate conformations also entail changes in the {beta}-turn at the tip of the flap. These observations provide insight into the plasticity of the flap domains, the nature of their motions and their critical role in binding substrates and inhibitors.

  9. Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2-MND1.

    PubMed

    Rampler, Evelyn; Stranzl, Thomas; Orban-Nemeth, Zsuzsanna; Hollenstein, David Maria; Hudecz, Otto; Schloegelhofer, Peter; Mechtler, Karl

    2015-12-01

    The HOP2-MND1 heterodimer is essential for meiotic homologous recombination in plants and other eukaryotes and promotes the repair of DNA double-strand breaks. We investigated the conformational flexibility of HOP2-MND1, important for understanding the mechanistic details of the heterodimer, with chemical cross-linking in combination with mass spectrometry (XL-MS). The final XL-MS workflow encompassed the use of complementary cross-linkers, quenching, digestion, size exclusion enrichment, and HCD-based LC-MS/MS detection prior to data evaluation. We applied two different homobifunctional amine-reactive cross-linkers (DSS and BS(2)G) and one zero-length heterobifunctional cross-linker (EDC). Cross-linked peptides of four biological replicates were analyzed prior to 3D structure prediction by protein threading and protein-protein docking for cross-link-guided molecular modeling. Miniaturization of the size-exclusion enrichment step reduced the required starting material, led to a high amount of cross-linked peptides, and allowed the analysis of replicates. The major interaction site of HOP2-MND1 was identified in the central coiled-coil domains, and an open colinear parallel arrangement of HOP2 and MND1 within the complex was predicted. Moreover, flexibility of the C-terminal capping helices of both complex partners was observed, suggesting the coexistence of a closed complex conformation in solution. PMID:26535604

  10. Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Structures, dynamics, and stabilities of different sized cellulosic oligomers need to be considered when designing enzymatic cocktails for the conversion of biomass to biofuels since they can be both productive substrates and inhibitors of the overall process. In the present work, the conformational...

  11. Conformer-specific vibronic spectroscopy and vibronic coupling in a flexible bichromophore: Bis-(4-hydroxyphenyl)methane

    NASA Astrophysics Data System (ADS)

    Rodrigo, Chirantha P.; Müller, Christian W.; Pillsbury, Nathan R.; James, William H.; Plusquellic, David F.; Zwier, Timothy S.

    2011-04-01

    The vibronic spectroscopy of jet-cooled bis-(4-hydroxyphenyl)methane has been explored using fluorescence excitation, dispersed fluorescence (DFL), UV-UV hole-burning, UV depletion, and fluorescence-dip infrared spectroscopies. Calculations predict the presence of three nearly isoenergetic conformers that differ in the orientations of the two OH groups in the para positions on the two aromatic rings (labeled uu, dd, and ud). In practice, two conformers (labeled A and B) are observed, with S0-S1 origins at 35 184 and 35 209 cm-1, respectively. The two conformers have nearly identical vibronic spectra and hydride stretch infrared spectra. The low-frequency vibronic structure is assigned to bands involving the phenyl torsions (T and bar T), ring-flapping (R and bar R), and butterfly (β) modes. Symmetry arguments lead to a tentative assignment of the two conformers as the C2 symmetric uu and dd conformers. The S0-S2 origins are assigned to bands located 132 cm-1 above the S0-S1 origins of both conformers. DFL spectra from the S2 origin of the two conformers display extensive evidence for vibronic coupling between the two close-lying electronic states. Near-resonant coupling from the S2 origin occurs dominantly to S1 bar R^1 and S1 bar R^1 β ^1 levels, which are located -15 and +31 cm-1 from it. Unusual vibronic activity in the ring-breathing (ν1) and ring-deformation (ν6a) modes is also attributed to vibronic coupling involving these Franck-Condon active modes. A multimode vibronic coupling model is developed based on earlier theoretical descriptions of molecular dimers [Fulton and Gouterman, J. Chem. Phys. 35, 1059 (1961)] and applied here to flexible bichromophores. The model is able to account for the ring-mode activity under conditions in which the S2 origin is strongly mixed (60%/40%) with S1 overline {6a} ^1 and bar 1^1 levels. The direct extension of this model to the T /bar T and R /bar R inter-ring mode pairs is only partially successful and required some

  12. Pax-3-DNA interaction: flexibility in the DNA binding and induction of DNA conformational changes by paired domains.

    PubMed Central

    Chalepakis, G; Wijnholds, J; Gruss, P

    1994-01-01

    The mouse Pax-3 gene encodes a protein that is a member of the Pax family of DNA binding proteins. Pax-3 contains two DNA binding domains: a paired domain (PD) and a paired type homeodomain (HD). Both domains are separated by 53 amino acids and interact synergistically with a sequence harboring an ATTA motif (binding to the HD) and a GTTCC site (binding to the PD) separated by 5 base pairs. Here we show that the interaction of Pax-3 with these two binding sites is independent of their angular orientation. In addition, the protein spacer region between the HD and the PD can be shortened without changing the spatial flexibility of the two DNA binding domains which interact with DNA. Furthermore, by using circular permutation analysis we determined that binding of Pax-3 to a DNA fragment containing a specific binding site causes conformational changes in the DNA, as indicated by the different mobilities of the Pax-3-DNA complexes. The ability to change the conformation of the DNA was found to be an intrinsic property of the Pax-3 PD and of all Pax proteins that we tested so far. These in vitro studies suggest that interaction of Pax proteins with their specific sequences in vivo may result in an altered DNA conformation. Images PMID:8065927

  13. Anthrax Edema Factor: An Ion-Adaptive Mechanism of Catalysis with Increased Transition-State Conformational Flexibility.

    PubMed

    Jara, Gabriel E; Martínez, Leandro

    2016-07-14

    Edema Factor (EF) is one of three major toxins of anthrax. EF is an adenylyl cyclase that disrupts cell signaling by accelerating the conversion of ATP into cyclic-AMP. EF has a much higher catalytic rate than that of mammalian adenylyl cyclases (mACs). Crystal structures were obtained for mACs and EF, but the molecular basis for different catalytic activities remained poorly understood. In particular, the arrangement of the active site in EF is unclear in what concerns the number of ions present and the conformation of the substrate. Here, we use quantum mechanics-molecular mechanics simulations to estimate the free-energy profiles for the reaction catalyzed by EF and a mAC. We found that EF catalysis is possible, and faster than that of mACs, in both one and two Mg(2+)-ion-binding modes, providing adaptive plasticity to host-cell environments. In both enzymes, the reaction mechanisms are highly associative. However, mechanistic differences exist. In the mAC, the nucleophile oxygen (ATP-O3') is consistently coordinated to one of the Mg(2+) ions, increasing its acidity. In EF, on the other hand, this coordination is eventual and not essential for the reaction to proceed. The persistent coordination of O3' to the ion is favored in mACs by a greater ion partial charge. In EF, the reduced acidity of the O3' oxygen is compensated by the presence of the His351 residue for proton abstraction. As proton transfer in EF does not require persistent attachment of the substrate to an ion, the substrate (ATP) and transition state display greater conformational flexibilities. These greater flexibilities allow the sampling of lower-energy conformations and might represent an entropic advantage for catalytic efficiency. PMID:27260163

  14. Ultra-flexible multiband terahertz metamaterial absorber for conformal geometry applications.

    PubMed

    Yahiaoui, Riad; Guillet, Jean Paul; de Miollis, Frédérick; Mounaix, Patrick

    2013-12-01

    Standard optical lithography relying on clean room and microelectronic facilities is used to fabricate a thin-flexible metamaterial absorber, designed to operate at submillimeter wavelengths over the 0.1-1 THz frequency band. Large terahertz absorption has been demonstrated numerically and through experimental measurements with a maximum level of about 80%. We put emphasis in this present work on the use of single-sized "meta-cells" to achieve multiple absorption peaks. Furthermore, the use of a thin-flexible dielectric spacer makes it promising for stealth technology applications in order to disguise objects and make them less visible to radar and other detection methods. PMID:24281490

  15. Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6

    SciTech Connect

    Chen, Hui; Mustafi, Sourajit M.; LeMaster, David M.; Li, Zhong; Héroux, Annie; Li, Hongmin; Hernández, Griselda

    2014-03-01

    Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80s loop, the primary site for known protein-recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances, which reflects a slow conformational transition centered in the 80s loop. The primary known physiological function of FKBP12.6 involves its role in regulating the RyR2 isoform of ryanodine receptor Ca{sup 2+} channels in cardiac muscle, pancreatic β islets and the central nervous system. With only a single previously reported X-ray structure of FKBP12.6, bound to the immunosuppressant rapamycin, structural inferences for this protein have been drawn from the more extensive studies of the homologous FKBP12. X-ray structures at 1.70 and 1.90 Å resolution from P2{sub 1} and P3{sub 1}21 crystal forms are reported for an unligated cysteine-free variant of FKBP12.6 which exhibit a notable diversity of conformations. In one monomer from the P3{sub 1}21 crystal form, the aromatic ring of Phe59 at the base of the active site is rotated perpendicular to its typical orientation, generating a steric conflict for the immunosuppressant-binding mode. The peptide unit linking Gly89 and Val90 at the tip of the protein-recognition ‘80s loop’ is flipped in the P2{sub 1} crystal form. Unlike the >30 reported FKBP12 structures, the backbone conformation of this loop closely follows that of the first FKBP domain of FKBP51. The NMR resonances for 21 backbone amides of FKBP12.6 are doubled, corresponding to a slow conformational transition centered near the tip of the 80s loop, as recently reported for 31 amides of FKBP12. The comparative absence of doubling for residues along the opposite face of the active-site pocket in FKBP12.6 may in part reflect attenuated structural coupling owing to increased conformational plasticity around the Phe59 ring.

  16. Conformational diversity of flexible ligand in metal-organic frameworks controlled by size-matching mixed ligands

    NASA Astrophysics Data System (ADS)

    Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei

    2015-12-01

    Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H2ndc) or 4,4‧-(hydroxymethylene)dibenzoic acid (H2hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd2(2,6-ndc)2(bpp)(DMF)]·2DMF (1) and [Cd3(hmdb)3(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional 'Lucky Clover' shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process.

  17. Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.

    PubMed

    Gajadeera, Chathurada S; Zhang, Xinyi; Wei, Yinan; Tsodikov, Oleg V

    2015-02-01

    Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg(2+)-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn(2+)-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn(2+) at 2.1Å resolution. The active site contains two catalytic Mn(2+) binding sites, each half-occupied, reconciling the previously observed 1:1 Mn(2+):enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme. PMID:25576794

  18. Photo-induced conformational flexibility in single solution-phase peridinin-chlorophyll-proteins.

    PubMed

    Bockenhauer, Samuel D; Moerner, W E

    2013-09-01

    The peridinin-chlorophyll-protein (PCP) is an accessory light-harvesting complex found in red-tide dinoflagellates. PCP absorbs photons primarily in the blue-green spectral region via peridinin (Per) carotenoid pigments which then transfer excitations to chlorophyll (Chl) and ultimately downstream to photosystem II (PSII). Whereas the ultrafast dynamics of PCP are well-studied, much less is known about slower protein dynamics on time scales of milliseconds and seconds. Previous single-molecule studies of spectral emission and intensity have attached PCP to surfaces, but the native environment of PCP is in the lumen, meaning that a surface-attached environment could perturb its native conformations. To address this concern, we use the anti-Brownian electrokinetic (ABEL) trap to study single PCP monomers in solution for several seconds each. We measure, for the first time, simultaneous single-molecule intensity, lifetime, and spectral emission shifts for each trapped PCP monomer. The rate of reversible spectral redshifts depends linearly on irradiance over a factor of 30, indicating a light-induced mechanism which we attribute to a protein conformational change. Independent of these spectral shifts, our measurements of intensity and lifetime show reversible Chl quenching. In contrast to previous work, we show that this quenching cannot result from isolated photobleaching of Chl. These independent mechanisms arise from distinct conformational changes which maintain relatively stable fluorescence emission. PMID:23919352

  19. Molecular structure and pronounced conformational flexibility of doxorubicin in free and conjugated state within a drug-peptide compound.

    PubMed

    Tsoneva, Yana; Jonker, Hendrik R A; Wagner, Manfred; Tadjer, Alia; Lelle, Marco; Peneva, Kalina; Ivanova, Anela

    2015-02-19

    The search for targeted drug delivery systems requires the design of drug-carrier complexes, which could both reach the malignant cells and preserve the therapeutic substance activity. A promising strategy aimed at enhancing the uptake and reducing the systemic toxicity is to bind covalently the drug to a cell-penetrating peptide. To understand the structure-activity relationship in such preparations, the chemotherapeutic drug doxorubicin was investigated by unrestrained molecular dynamics simulations, supported by NMR, which yielded its molecular geometry in aqueous environment. Furthermore, the structure and dynamics of a conjugate of the drug with a cell-penetrating peptide was obtained from molecular dynamics simulations in aqueous solution. The geometries of the unbound compounds were characterized at different temperatures, as well as the extent to which they change after covalent binding and whether/how they influence each other in the drug-peptide conjugate. The main structural fragments that affect the conformational ensemble of every molecule were found. The results show that the transitions between different substructures of the three compounds require a modest amount of energy. At increased temperature, either more conformations become populated as a result of the thermal fluctuations or the relative shares of the various conformers equalize at the nanosecond scale. These frequent structural interconversions suggest expressed conformational freedom of the molecules. Conjugation into the drug-peptide compound partially immobilizes the molecules of the parent compounds. Nevertheless, flexibility still exists, as well as an effective intra- and intermolecular hydrogen bonding that stabilizes the structures. We observe compact packing of the drug within the peptide that is also based on stacking interactions. All this outlines the drug-peptide conjugate as a prospective building block of a more complex drug-carrier system. PMID:25603129

  20. Method of Making Large Area Nanostructures

    NASA Technical Reports Server (NTRS)

    Marks, Alvin M.

    1995-01-01

    A method which enables the high speed formation of nanostructures on large area surfaces is described. The method uses a super sub-micron beam writer (Supersebter). The Supersebter uses a large area multi-electrode (Spindt type emitter source) to produce multiple electron beams simultaneously scanned to form a pattern on a surface in an electron beam writer. A 100,000 x 100,000 array of electron point sources, demagnified in a long electron beam writer to simultaneously produce 10 billion nano-patterns on a 1 meter squared surface by multi-electron beam impact on a 1 cm squared surface of an insulating material is proposed.

  1. Conformational Flexibility and Peptide Interaction of the Translocation ATPase SecA

    SciTech Connect

    Zimmer, Jochen; Rapoport, Tom A.; Harvard-Med

    2010-09-21

    The SecA ATPase forms a functional complex with the protein-conducting SecY channel to translocate polypeptides across the bacterial cell membrane. SecA recognizes the translocation substrate and catalyzes its unidirectional movement through the SecY channel. The recent crystal structure of the Thermotoga maritima SecA-SecYEG complex shows the ATPase in a conformation where the nucleotide-binding domains (NBDs) have closed around a bound ADP-BeFx complex and SecA's polypeptide-binding clamp is shut. Here, we present the crystal structure of T. maritima SecA in isolation, determined in its ADP-bound form at 3.1 {angstrom} resolution. SecA alone has a drastically different conformation in which the nucleotide-binding pocket between NBD1 and NBD2 is open and the preprotein cross-linking domain has rotated away from both NBDs, thereby opening the polypeptide-binding clamp. To investigate how this clamp binds polypeptide substrates, we also determined a structure of Bacillus subtilis SecA in complex with a peptide at 2.5 {angstrom} resolution. This structure shows that the peptide augments the highly conserved {beta}-sheet at the back of the clamp. Taken together, these structures suggest a mechanism by which ATP hydrolysis can lead to polypeptide translocation.

  2. Structure analysis and catalytic property of a microporous framework based on a flexible tripodal ligand with novel conformations

    NASA Astrophysics Data System (ADS)

    Shi, Xianju; Zhang, Xinhai; Li, Xiaoxia; Hou, Hongwei; Fan, Yaoting

    2011-06-01

    A microporous metal-organic framework {[Cu 3Cl 6(ttmb) 4]·6H 2O} n ( 1) (ttmb = 1,3,5-tris(1,2,4-triazol-1-ylmethyl)-benzene) with tetranodal (3,4)-connected topological type was prepared by the self-assembly reaction of the flexible tripodal ligand ttmb with CuCl 2·2H 2O. The ligand exhibits two infrequent coordination conformations in complex 1, and the framework has a large pore volume (remove the solvent molecules) of 1781.6 Å 3 (36.3% of the total). The test of 1 as the catalyst in the oxidative coupling reaction of 2,6-dimethylphenol indicates that it is catalytically active by showing high conversion of DMP under the optimized reaction condition.

  3. The Large Area Crop Inventory Experiment (LACIE)

    NASA Technical Reports Server (NTRS)

    Macdonald, R. B.

    1976-01-01

    A Large Area Crop Inventory Experiment (LACIE) was undertaken to prove out an economically important application of remote sensing from space. The experiment focused upon determination of wheat acreages in the U.S. Great Plains and upon the development and testing of yield models. The results and conclusions are presented.

  4. Large area space solar cell assemblies

    NASA Technical Reports Server (NTRS)

    Spitzer, M. B.; Nowlan, M. J.

    1982-01-01

    Development of a large area space solar cell assembly is presented. The assembly consists of an ion implanted silicon cell and glass cover. The important attributes of fabrication are (1) use of a back surface field which is compatible with a back surface reflector, and (2) integration of coverglass application and call fabrication.

  5. PEDOT-CNT-Coated Low-Impedance, Ultra-Flexible, and Brain-Conformable Micro-ECoG Arrays.

    PubMed

    Castagnola, Elisa; Maiolo, Luca; Maggiolini, Emma; Minotti, Antonio; Marrani, Marco; Maita, Francesco; Pecora, Alessandro; Angotzi, Gian Nicola; Ansaldo, Alberto; Boffini, Massimiliano; Fadiga, Luciano; Fortunato, Guglielmo; Ricci, Davide

    2015-05-01

    Electrocorticography (ECoG) is becoming a common tool for clinical applications, such as preparing patients for epilepsy surgery or localizing tumor boundaries, as it successfully balances invasiveness and information quality. Clinical ECoG arrays use millimeter-scale electrodes and centimeter-scale pitch and cannot precisely map neural activity. Higher-resolution electrodes are of interest for both current clinical applications, providing access to more precise neural activity localization and novel applications, such as neural prosthetics, where current information density and spatial resolution is insufficient to suitably decode signals for a chronic brain-machine interface. Developing such electrodes is not trivial because their small contact area increases the electrode impedance, which seriously affects the signal-to-noise ratio, and adhering such an electrode to the brain surface becomes critical. The most straightforward approach requires increasing the array conformability with flexible substrates while improving the electrode performance using materials with superior electrochemical properties. In this paper, we propose an ultra-flexible and conformable polyimide-based micro-ECoG array of submillimeter recording sites electrochemically coated with high surface area conductive polymer-carbon nanotube composites to improve their brain-electrical coupling capabilities. We characterized our devices both electrochemically and by recording from rat somatosensory cortex in vivo. The performance of the coated and uncoated electrodes was directly compared by simultaneously recording the same neuronal activity during multiwhisker deflection stimulation. Finally, we assessed the effect of electrode size on the extraction of somatosensory evoked potentials and found that in contrast to the normal high-impedance microelectrodes, the recording capabilities of our low-impedance microelectrodes improved upon reducing their size from 0.2 to 0.1 mm. PMID:25073174

  6. Body conformal antennas for superficial hyperthermia: the impact of bending contact flexible microstrip applicators on their electromagnetic behavior.

    PubMed

    Correia, Davi; Kok, H Petra; de Greef, Martijn; Bel, Arjan; van Wieringen, Niek; Crezee, Johannes

    2009-12-01

    Hyperthermia is a powerful radiosensitizer for treatment of superficial tumors. This requires body conformal antennas with a power distribution as homogeneous as possible over the skin area. The contact flexible microstrip applicators (CFMA) operating at 434 MHz exist in several sizes, including the large size 3H and 5H. This paper investigates the behavior of the electromagnetic fields for the 3H and 5H CFMA in both flat and curved configurations, and the impact on performance parameters like the penetration depth (PD) and the effective heating depth (EHD). The underlying theory behind the electromagnetic behavior in curved situations is presented as well as numerical simulations of both flat and curved configurations. The results are compared to measurements of the electromagnetic field distributions in a cylindrical patient model. Due to their large size multimode solutions may exist, and our results confirm their existence. These multimode solutions affect both the power distribution and PD/EHD, with a dependence on applicator curvature. Therefore, the performance parameters like PD and EHD need to be carefully assessed when bending large size CFMA applicators to conform to the patient body. This conclusion also holds for other types of large size surface current applicators. PMID:19695983

  7. Kalata B8, a novel antiviral circular protein, exhibits conformational flexibility in the cystine knot motif.

    PubMed

    Daly, Norelle L; Clark, Richard J; Plan, Manuel R; Craik, David J

    2006-02-01

    The cyclotides are a family of circular proteins with a range of biological activities and potential pharmaceutical and agricultural applications. The biosynthetic mechanism of cyclization is unknown and the discovery of novel sequences may assist in achieving this goal. In the present study, we have isolated a new cyclotide from Oldenlandia affinis, kalata B8, which appears to be a hybrid of the two major subfamilies (Möbius and bracelet) of currently known cyclotides. We have determined the three-dimensional structure of kalata B8 and observed broadening of resonances directly involved in the cystine knot motif, suggesting flexibility in this region despite it being the core structural element of the cyclotides. The cystine knot motif is widespread throughout Nature and inherently stable, making this apparent flexibility a surprising result. Furthermore, there appears to be isomerization of the peptide backbone at an Asp-Gly sequence in the region involved in the cyclization process. Interestingly, such isomerization has been previously characterized in related cyclic knottins from Momordica cochinchinensis that have no sequence similarity to kalata B8 apart from the six conserved cysteine residues and may result from a common mechanism of cyclization. Kalata B8 also provides insight into the structure-activity relationships of cyclotides as it displays anti-HIV activity but lacks haemolytic activity. The 'uncoupling' of these two activities has not previously been observed for the cyclotides and may be related to the unusual hydrophilic nature of the peptide. PMID:16207177

  8. Stabilizing a flexible interdomain hinge region harboring the SMB binding site drives uPAR into its closed conformation.

    PubMed

    Zhao, Baoyu; Gandhi, Sonu; Yuan, Cai; Luo, Zhipu; Li, Rui; Gårdsvoll, Henrik; de Lorenzi, Valentina; Sidenius, Nicolai; Huang, Mingdong; Ploug, Michael

    2015-03-27

    The urokinase-type plasminogen activator receptor (uPAR) is a multidomain glycolipid-anchored membrane protein, which facilitates extracellular matrix remodeling by focalizing plasminogen activation to cell surfaces via its high-affinity interaction with uPA. The modular assembly of its three LU (Ly6/uPAR-like) domains is inherently flexible and binding of uPA drives uPAR into its closed conformation, which presents the higher-affinity state for vitronectin thus providing an allosteric regulatory mechanism. Using a new class of epitope-mapped anti-uPAR monoclonal antibodies (mAbs), we now demonstrate that the reciprocal stabilization is indeed also possible. By surface plasmon resonance studies, we show that these mAbs and vitronectin have overlapping binding sites on uPAR and that they share Arg91 as hotspot residue in their binding interfaces. The crystal structure solved for one of these uPAR·mAb complexes at 3.0Å clearly shows that this mAb preselects the closed uPAR conformation with an empty but correctly assembled large hydrophobic binding cavity for uPA. Accordingly, these mAbs inhibit the uPAR-dependent lamellipodia formation and migration on vitronectin-coated matrices irrespective of the conformational status of uPAR and its occupancy with uPA. This is the first study to the best of our knowledge, showing that the dynamic assembly of the three LU domains in uPARwt can be driven toward the closed form by an external ligand, which is not engaging the hydrophobic uPA binding cavity. As this binding interface is also exploited by the somatomedin B domain of vitronectin, therefore, this relationship should be taken into consideration when exploring uPAR-dependent cell adhesion and migration in vitronectin-rich environments. PMID:25659907

  9. Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation.

    PubMed

    Mhashal, Anil R; Choudhury, Chandan Kumar; Roy, Sudip

    2016-03-01

    Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state. PMID:26860503

  10. Conformational flexibility in designing peptides for immunology: the molecular dynamics approach.

    PubMed

    Stavrakoudis, Athanassios

    2010-09-01

    Computational modeling techniques and computer simulations have become a routine in biological sciences and have gained great attention from researchers. Molecular dynamics simulation is a valuable tool towards an understanding of the complex structure of biological systems, especially in the study of the flexibility of the biological molecules such as peptides or proteins. Peptides play a very important role in human physiology and control many of the processes involved in the immune system response. Designing new and optimal peptide vaccines is one of the hottest challenges of the 21(st) century science and it brings together researchers from different fields. Molecular dynamics simulations have proven to be a helpful tool assisting laboratory work, saving financial sources and opening possibilities for exploring properties of the molecular systems that are hardly accessible by conventional experimental methods. Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes. PMID:20412039

  11. Heteroligand molecular "stirrups" using conformationally flexible ditopic pyridyl-pyrazolyl ligands.

    PubMed

    Lu, Jinzhen; Turner, David R; Harding, Lindsay P; Batten, Stuart R

    2009-08-17

    Heteroligand molecular "stirrups" form by the self-assembly of flexible ditopic ligands in combination with 4,4'-bipyridine and [(dppp)Pd)](2+). Crystallographic analysis shows that the ligands, bis[3-(4-pyridyl)pyrazolyl]-m-xylene (mXy(4py3pz)) and bis[4-(4-pyridyl)pyrazolyl]-p-xylene (pXy(4py4pz)) form complexes of the type [{(dppp)Pd}(2)(4,4'-bipy)(L)].4OTf (1.4OTf and 2.4OTf, respectively) in the solid state, with remarkably similar structures considering the differences in substitution patterns between the two ligands. The self-assembly of both 1(4+) and 2(4+) is assisted by face-to-face pi interactions on the exterior of the macrocycle between the phenyl rings of the dppp ligands and the pyridyl groups of the ditopic ligands. PMID:19594137

  12. Large area nanostructured arrays: optical properties of metallic nanotubes.

    PubMed

    Fröhlich, Katja; Hojati-Talemi, Pejman; Bishop, Matthew; Zuber, Kamil; Murphy, Peter; Evans, Drew

    2013-05-01

    In this study, large area metallic nanotube arrays on flexible plastic substrates are produced by templating the growth of a cosputtered alloy using anodized aluminum oxide membranes. These nanotube arrays are prepared over large areas (ca. squared centimeters) by reducing the residual stress within the thin multilayered structure. The nanotubes are approximately 20 nm in inner diameter, having walls of <10 nm in thickness, and are arranged in a close packed configuration. Optically the nanotube arrays exhibit light trapping behavior (not plasmonic), where the reflectivity is less than 15% across the visible spectra compared to >40% for a flat sample using the same alloy. When the nanotubes are exposed to high relative humidity, they spontaneously fill, with a concomitant change in their visual appearance. The filling of the nanotubes is confirmed using contact angle measurements, with the nanotubes displaying a strong hydrophilic character compared to the weak behavior of the flat sample. The ability to easily fabricate large area nanotube arrays which display exotic behavior paves the way for their uptake in real world applications such as sensors and solar energy devices. PMID:23582083

  13. GLAST Large Area Telescope Multiwavelength Planning

    NASA Technical Reports Server (NTRS)

    Reimer, O.; Michelson, P. F.; Cameron, R. A.; Digel, S. W.; Thompson, D. J.; Wood, K. S.

    2007-01-01

    Gamma-ray astrophysics depends in many ways on multiwavelength studies. The Gamma-ray Large Area Space Telescope (GLAST) Large Area Telescope (LAT) Collaboration has started multiwavelength planning well before the scheduled 2007 launch of the observatory. Some of the high-priority multiwavelength needs include: (1) availability of contemporaneous radio and X-ray timing of pulsars; (2) expansion of blazar catalogs, including redshift measurements; (3) improved observations of molecular clouds, especially at high galactic latitudes; (4) simultaneous broad-spectrum blazar monitoring; (5) characterization of gamma-ray transients, including gamma ray bursts; (6) radio, optical, X-ray and TeV counterpart searches for reliable and effective sources identification and characterization. Several of these activities are needed to be in place before launch.

  14. GLAST Large Area Telescope Multiwavelength Planning

    SciTech Connect

    Reimer, O.; Michelson, P.F.; Cameron, R.A.; Digel, S.W.; Thompson, D.J.; Wood, K.S.

    2007-01-03

    Gamma-ray astrophysics depends in many ways on multiwavelength studies. The Gamma-ray Large Area Space Telescope (GLAST) Large Area Telescope (LAT) Collaboration has started multiwavelength planning well before the scheduled 2007 launch of the observatory. Some of the high-priority multiwavelength needs include: (1) availability of contemporaneous radio and X-ray timing of pulsars; (2) expansion of blazar catalogs, including redshift measurements; (3) improved observations of molecular clouds, especially at high galactic latitudes; (4) simultaneous broad-band blazar monitoring; (5) characterization of gamma-ray transients, including gamma ray bursts; (6) radio, optical, X-ray and TeV counterpart searches for reliable and effective sources identification and characterization. Several of these activities are needed to be in place before launch.

  15. GLAST Large Area Telescope Multiwavelength Planning

    NASA Technical Reports Server (NTRS)

    Thompson, D. J.; Cameron, R. A.; Digel, S. W.; Wood, K. S.

    2006-01-01

    Because gamma-ray astrophysics depends in many ways on multiwavelength studies, the GLAST Large Area Telescope (LAT) Collaboration has started multiwavelength planning well before the scheduled 2007 launch of the observatory. Some of the high-priority needs include: (1) radio and X-ray timing of pulsars; (2) expansion of blazar catalogs, including redshift measurements (3) improved observations of molecular clouds, especially at high galactic latitudes; (4) simultaneous broad-spectrum blazar flare measurements; (5) characterization of gamma-ray transients, including gamma ray bursts; (6) radio, optical, X-ray and TeV counterpart searches for unidentified gamma-ray sources. Work on the first three of these activities is needed before launch. The GLAST Large Area Telescope is an international effort, with U.S. funding provided by the Department of Energy and NASA.

  16. Large area damage testing of optics

    SciTech Connect

    Sheehan, L.; Kozlowski, M.; Stolz, C.

    1996-04-26

    The damage threshold specifications for the National Ignition Facility will include a mixture of standard small-area tests and new large-area tests. During our studies of laser damage and conditioning processes of various materials we have found that some damage morphologies are fairly small and this damage does not grow with further illumination. This type of damage might not be detrimental to the laser performance. We should therefore assume that some damage can be allowed on the optics, but decide on a maximum damage allowance of damage. A new specification of damage threshold termed {open_quotes}functional damage threshold{close_quotes} was derived. Further correlation of damage size and type to system performance must be determined in order to use this measurement, but it is clear that it will be a large factor in the optics performance specifications. Large-area tests have verified that small-area testing is not always sufficient when the optic in question has defect-initiated damage. This was evident for example on sputtered polarizer and mirror coatings where the defect density was low enough that the features could be missed by standard small- area testing. For some materials, the scale-length at which damage non-uniformities occur will effect the comparison of small-area and large-area tests. An example of this was the sub-aperture tests on KD*P crystals on the Beamlet test station. The tests verified the large-area damage threshold to be similar to that found when testing a small-area. Implying that for this KD*P material, the dominate damage mechanism is of sufficiently small scale-length that small-area testing is capable of determining the threshold. The Beamlet test station experiments also demonstrated the use of on-line laser conditioning to increase the crystals damage threshold.

  17. Large-area thin-film modules

    NASA Technical Reports Server (NTRS)

    Tyan, Y. S.; Perez-Albuerne, E. A.

    1985-01-01

    The low cost potential of thin film solar cells can only be fully realized if large area modules can be made economically with good production yields. This paper deals with two of the critical challenges. A scheme is presented which allows the simple, economical realization of the long recognized, preferred module structure of monolithic integration. Another scheme reduces the impact of shorting defects and, as a result, increases the production yields. Analytical results demonstrating the utilization and advantages of such schemes are discussed.

  18. The Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase: A Conformationally Flexible Pharmacophore

    SciTech Connect

    Xu, Hai; Fairman, James W.; Wijerathna, Sanath R.; Kreischer, Nathan R.; LaMacchia, John; Helmbrecht, Elizabeth; Cooperman, Barry S.; Dealwis, Chris

    2008-08-19

    Eukaryotic ribonucleotide reductase (RR) catalyzes nucleoside diphosphate conversion to deoxynucleoside diphosphate. Crucial for rapidly dividing cells, RR is a target for cancer therapy. RR activity requires formation of a complex between subunits R1 and R2 in which the R2 C-terminal peptide binds to R1. Here we report crystal structures of heterocomplexes containing mammalian R2 C-terminal heptapeptide, P7 (Ac-{sup 1}FTLDADF{sup 7}) and its peptidomimetic P6 ({sup 1}Fmoc(Me)PhgLDChaDF{sup 7}) bound to Saccharomyces cerevisiae R1 (ScR1). P7 and P6, both of which inhibit ScRR, each bind at two contiguous sites containing residues that are highly conserved among eukaryotes. Such binding is quite distinct from that reported for prokaryotes. The Fmoc group in P6 peptide makes several hydrophobic interactions that contribute to its enhanced potency in binding to ScR1. Combining all of our results, we observe three distinct conformations for peptide binding to ScR1. These structures provide pharmacophores for designing highly potent nonpeptide class I RR inhibitors.

  19. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties.

    PubMed Central

    Alexov, E G; Gunner, M R

    1997-01-01

    A method for combining calculations of residue pKa's with changes in the position of polar hydrogens has been developed. The Boltzmann distributions of proton positions in hydroxyls and neutral titratable residues are found in the same Monte Carlo sampling procedure that determines the amino acid ionization states at each pH. Electrostatic, Lennard-Jones potentials, and torsion angle energies are considered at each proton position. Many acidic and basic residues are found to have significant electrostatic interactions with either a water- or hydroxyl-containing side chain. Protonation state changes are coupled to reorientation of the neighboring hydroxyl dipoles, resulting in smaller free energy differences between neutral and ionized residues than when the protein is held rigid. Multiconformation pH titration gives better agreement with the experimental pKa's for triclinic hen egg lysozyme than conventional rigid protein calculations. The hydroxyl motion significantly increases the protein dielectric response, making it sensitive to the composition of the local protein structure. More than one conformer per residue is often found at a given pH, providing information about the distribution of low-energy lysozyme structures. Images FIGURE 2 FIGURE 6 PMID:9129810

  20. Cwp84, a Clostridium difficile cysteine protease, exhibits conformational flexibility in the absence of its propeptide

    SciTech Connect

    Bradshaw, William J.; Roberts, April K.; Shone, Clifford C.; Acharya, K. Ravi

    2015-02-19

    Two structures of Cwp84, a cysteine protease from the S-layer of C. difficile, are presented after propeptide cleavage. They reveal the movement of three loops, two in the active-site groove and one on the surface of the lectin-like domain, exposing a hydrophobic pocket. In recent decades, the global healthcare problems caused by Clostridium difficile have increased at an alarming rate. A greater understanding of this antibiotic-resistant bacterium, particularly with respect to how it interacts with the host, is required for the development of novel strategies for fighting C. difficile infections. The surface layer (S-layer) of C. difficile is likely to be of significant importance to host–pathogen interactions. The mature S-layer is formed by a proteinaceous array consisting of multiple copies of a high-molecular-weight and a low-molecular-weight S-layer protein. These components result from the cleavage of SlpA by Cwp84, a cysteine protease. The structure of a truncated Cwp84 active-site mutant has recently been reported and the key features have been identified, providing the first structural insights into the role of Cwp84 in the formation of the S-layer. Here, two structures of Cwp84 after propeptide cleavage are presented and the three conformational changes that are observed are discussed. These changes result in a reconfiguration of the active site and exposure of the hydrophobic pocket.

  1. The Role of Conformational Flexibility on Protein Supercharging in Native Electrospray Ionization

    PubMed Central

    Sterling, Harry J.; Cassou, Catherine A.; Trnka, Michael J.; Burlingame, A. L.; Krantz, Bryan A.; Williams, Evan R.

    2012-01-01

    Effects of covalent intramolecular bonds, either native disulfide bridges or chemical crosslinks, on ESI supercharging of proteins from aqueous solutions were investigated. Chemically modifying cytochrome c with up to seven crosslinks or ubiquitin with up to two crosslinks did not affect the average or maximum charge states of these proteins in the absence of m-nitrobenzyl alcohol (m-NBA), but the extent of supercharging induced by m-NBA increased with decreasing numbers of crosslinks. For the model random coil polypeptide reduced/alkylated RNase A, a decrease in charging with increasing m-NBA concentration attributable to reduced surface tension of the ESI droplet was observed, whereas native RNase A electrosprayed from these same solutions exhibited enhanced charging. The inverse relationship between the extent of supercharging and the number of intramolecular crosslinks for folded proteins, as well as the absence of supercharging for proteins that are random coils in aqueous solution, indicate that conformational restrictions induced by the crosslinks reduce the extent of supercharging. These results provide additional evidence that protein and protein complex supercharging from aqueous solution is primarily due to partial or significant unfolding that occurs as a result of chemical and/or thermal denaturation induced by the supercharging reagent late in the ESI droplet lifetime. PMID:21399817

  2. Conformation of a flexible polymer in explicit solvent: Accurate solvation potentials for Lennard-Jones chains.

    PubMed

    Taylor, Mark P; Ye, Yuting; Adhikari, Shishir R

    2015-11-28

    The conformation of a polymer chain in solution is coupled to the local structure of the surrounding solvent and can undergo large changes in response to variations in solvent density and temperature. The many-body effects of solvent on the structure of an n-mer polymer chain can be formally mapped to an exact n-body solvation potential. Here, we use a pair decomposition of this n-body potential to construct a set of two-body potentials for a Lennard-Jones (LJ) polymer chain in explicit LJ solvent. The solvation potentials are built from numerically exact results for 5-mer chains in solvent combined with an approximate asymptotic expression for the solvation potential between sites that are distant along the chain backbone. These potentials map the many-body chain-in-solvent problem to a few-body single-chain problem and can be used to study a chain of arbitrary length, thereby dramatically reducing the computational complexity of the polymer chain-in-solvent problem. We have constructed solvation potentials at a large number of state points across the LJ solvent phase diagram including the vapor, liquid, and super-critical regions. We use these solvation potentials in single-chain Monte Carlo (MC) simulations with n ≤ 800 to determine the size, intramolecular structure, and scaling behavior of chains in solvent. To assess our results, we have carried out full chain-in-solvent MC simulations (with n ≤ 100) and find that our solvation potential approach is quantitatively accurate for a wide range of solvent conditions for these chain lengths. PMID:26627969

  3. Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2.

    PubMed

    Sterckx, Yann G J; Volkov, Alexander N; Vranken, Wim F; Kragelj, Jaka; Jensen, Malene Ringkjøbing; Buts, Lieven; Garcia-Pino, Abel; Jové, Thomas; Van Melderen, Laurence; Blackledge, Martin; van Nuland, Nico A J; Loris, Remy

    2014-06-10

    Antitoxins from prokaryotic type II toxin-antitoxin modules are characterized by a high degree of intrinsic disorder. The description of such highly flexible proteins is challenging because they cannot be represented by a single structure. Here, we present a combination of SAXS and NMR data to describe the conformational ensemble of the PaaA2 antitoxin from the human pathogen E. coli O157. The method encompasses the use of SAXS data to filter ensembles out of a pool of conformers generated by a custom NMR structure calculation protocol and the subsequent refinement by a block jackknife procedure. The final ensemble obtained through the method is validated by an established residual dipolar coupling analysis. We show that the conformational ensemble of PaaA2 is highly compact and that the protein exists in solution as two preformed helices, connected by a flexible linker, that probably act as molecular recognition elements for toxin inhibition. PMID:24768114

  4. Controlled synthesis of linear and cyclic liquid crystals containing conformationally flexible structural units

    NASA Astrophysics Data System (ADS)

    Asandei, Alexandru Dragos

    This thesis decribes the design, synthesis and characterization of a large variety of molecular, macromolecular and supramolecular liquid crystalline (LC) systems with linear, cyclic, and combinations of linear and cyclic architectures. These structures are based on mesogens that display conformational isomerism. Several series of macrocyclics based on 1-(4-hydroxyphenyl)-2-(2-methyl-4-hydroxyphenyl)ethane (MBPE) and various alpha,omega-dibromoalkanes were synthesized and characterized. These macrocyclics display more stable and broader LC phases than the corresponding linear polymers. Relatively minor modifications in the structure of the mesogen, spacer or microstructure of polymeric chains have a strong effect on the phase behavior of main chain polyethers. This is demonstrated for polymers based on 1-(4-hydroxyphenyl)-2-(4-hydroxy-4'-biphenylyl)butane (TPB') and alpha,omega-dibromoalkanes containing from 4 to 19 methylenic units. A stepwise synthetic procedure is described for the synthesis of a series of LC macrocyclics based of TPB' and 1,10-dibromodecane. Large increases in the yields by comparison with the one-pot method are obtained, and the procedure is also illustrated by the synthesis of the first example of a liquid crystalline bicyclic compound. The stepwise synthesis and characterization of macrocyclic monomers and of the first examples of side chain and main chain LC polymers containing supramolecular mesogens based on collapsed macrocyclics building blocks are described and discussed. An iterative stepwise procedure that allows for an exponential 2spn growth in molecular weight after n synthetic cycles is presented and applied to the synthesis of linear polyethers based on 1-(4-hydroxy-4'-biphenylyl)-2-(4-hydroxyphenyl)butane (TPB) and 1,10-dibromodecane. A library of linear monodisperse oligomers and polymers with a degree of polymerization (DP) up to 33 and with a variety of chain ends was generated, and the dependence of the phase behavior of

  5. Large area cold plasma applicator for decontamination

    NASA Astrophysics Data System (ADS)

    Konesky, G. A.

    2008-04-01

    Cold plasma applicators have been used in the Medical community for several years for uses ranging from hemostasis ("stop bleeding") to tumor removal. An added benefit of this technology is enhanced wound healing by the destruction of infectious microbial agents without damaging healthy tissue. The beam is typically one millimeter to less than a centimeter in diameter. This technology has been adapted and expanded to large area applicators of potentially a square meter or more. Decontamination applications include both biological and chemical agents, and assisting in the removal of radiological agents, with minimal or no damage to the contaminated substrate material. Linear and planar multiemitter array plasma applicator design and operation is discussed.

  6. Excimer lasers drive large-area microprocessing

    NASA Astrophysics Data System (ADS)

    Delmdahl, Ralph; Tapié, Jean-Luc

    2012-09-01

    Excimer lasers emitting in the UV to far UV region are by nature the laser sources enabling the highest optical resolution and strongest material-photon interaction. At the same time, excimer lasers deliver unmatched UV pulse energies and output powers up to the kilowatt range. Thus, they are the key to fast and effective large area processing of smallest structures with micron precision. As a consequence, excimer lasers are the UV technology of choice when it comes to high-performance microstructuring with unsurpassed quality and process repeatability in applications such as drilling advanced ink jet nozzles or patterning biomedical sensor structures.

  7. Large Area X-Ray Spectroscopy Mission

    NASA Technical Reports Server (NTRS)

    Tananbaum, H.

    1997-01-01

    The Large Area X-ray Spectroscopy (LAXS) mission concept study continues to evolve strongly following the merging of the LAXS mission with the Next Generation X-ray Observatory (NGXO, PI: Nick White) into the re-named High Throughput X-ray Spectroscopy (HTXS) Mission. HTXS retains key elements of the LAXS proposal, including the use of multiple satellites for risk-reduction and cost savings. A key achievement of the program has been the recommendation by the Structure and Evolution of the Universe (SEUS) (April 1997) for a new start for the HTXS mission in the 2000-2004 timeframe.

  8. Substrate Specificities and Conformational Flexibility of 3-Ketosteroid 9α-Hydroxylases*

    PubMed Central

    Penfield, Jonathan S.; Worrall, Liam J.; Strynadka, Natalie C.; Eltis, Lindsay D.

    2014-01-01

    KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >105 s−1 m−1 for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (KiS ∼100 μm). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue “mouth loop,” which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450. PMID:25049233

  9. PELDOR measurements on a nitroxide-labeled Cu(II) porphyrin: orientation selection, spin-density distribution, and conformational flexibility.

    PubMed

    Bode, Bela E; Plackmeyer, Jörn; Prisner, Thomas F; Schiemann, Olav

    2008-06-12

    Metal ions are functionally or structurally important centers in metalloproteins or RNAs, which makes them interesting targets for spectroscopic investigations. In combination with site-directed spin labeling, pulsed electron-electron double resonance (PELDOR or DEER) could be a well-suited method to characterize and localize them. Here, we report on the synthesis, full characterization, and PELDOR study of a copper(II) porphyrin/nitroxide model system. The X-band PELDOR time traces contain besides the distance information a convolution of orientational selectivity, conformational flexibility, exchange coupling, and spin density distribution, which can be deconvoluted by experiments with different frequency offsets and simulations. The simulations are based on the known experimental and spin Hamiltonian parameters and make use of a geometric model as employed for structurally similar bis-nitroxides and spin density parameters as obtained from density functional theory calculations. It is found that orientation selection with respect to dipolar angles is only weakly resolvable at X-band frequencies due to the large nitrogen hyperfine coupling of the copper porphyrin. On the other hand, the PELDOR time traces reveal a much faster oscillation damping than observed for structurally similar bis-nitroxides, which is mainly assigned to a small distribution in exchange couplings J. Taking the effects of orientation selectivity, distribution in J, and spin density distribution into account leads finally to a narrow distance distribution caused solely by the flexibility of the structure, which is in agreement with distributions from known bis-nitroxides of similar structure. Thus, X-band PELDOR measurements at different frequency offsets in combination with explicit time trace simulations allow for distinguishing between structural models and quantitative interpretation of copper-nitroxide PELDOR data gives access to localization of copper(II) ions. PMID:18491846

  10. GLAST Large Area Telescope Multiwavelength Opportunities

    NASA Technical Reports Server (NTRS)

    Thompson, David

    2008-01-01

    The Gamma-ray Large Area Space Telescope (GLAST) is scheduled for launch this year. Because the GLAST Large Area Telescope (LAT) has a huge field of view and the GLAST Observatory will be operated in scanning mode, it will survey the entire sky daily. The GLAST Mission and the LAT Collaboration invite cooperative efforts from theorists and observers at all wavelengths to help optimize the science. Possible topics include: (1) Blazars: These Active Galactic Nuclei are expected to be a major source class for LAT. Identifying new blazars, monitoring their variability, and joining programs to carry out planned or Target of Opportunity multiwavelength campaigns will all be important activities. The study of AGN gamma-ray jets can help link the accretion processes close to the black hole with the large-scale interaction of the AGN with its environment. (2) Unidentified Gamma-ray Sources: Modeling of possible gamma-ray sources is important to establish testable hypotheses. New gamma-ray sources need first to be identified with known objects by position, spectrum, or time variability, and then multiwavelength studies can be used to explore the astrophysical implications of high-energy radiation from these sources. The LAT team is committed to releasing a preliminary source list about six months after the start of science operations.

  11. Multi-Conformation Monte Carlo: A Method for Introducing Flexibility in Efficient Simulations of Many-Protein Systems.

    PubMed

    Prytkova, Vera; Heyden, Matthias; Khago, Domarin; Freites, J Alfredo; Butts, Carter T; Martin, Rachel W; Tobias, Douglas J

    2016-08-25

    We present a novel multi-conformation Monte Carlo simulation method that enables the modeling of protein-protein interactions and aggregation in crowded protein solutions. This approach is relevant to a molecular-scale description of realistic biological environments, including the cytoplasm and the extracellular matrix, which are characterized by high concentrations of biomolecular solutes (e.g., 300-400 mg/mL for proteins and nucleic acids in the cytoplasm of Escherichia coli). Simulation of such environments necessitates the inclusion of a large number of protein molecules. Therefore, computationally inexpensive methods, such as rigid-body Brownian dynamics (BD) or Monte Carlo simulations, can be particularly useful. However, as we demonstrate herein, the rigid-body representation typically employed in simulations of many-protein systems gives rise to certain artifacts in protein-protein interactions. Our approach allows us to incorporate molecular flexibility in Monte Carlo simulations at low computational cost, thereby eliminating ambiguities arising from structure selection in rigid-body simulations. We benchmark and validate the methodology using simulations of hen egg white lysozyme in solution, a well-studied system for which extensive experimental data, including osmotic second virial coefficients, small-angle scattering structure factors, and multiple structures determined by X-ray and neutron crystallography and solution NMR, as well as rigid-body BD simulation results, are available for comparison. PMID:27063730

  12. Large area radiation detectors based on II VI thin films

    NASA Astrophysics Data System (ADS)

    Quevedo-Lopez, Manuel

    2015-03-01

    The development of low temperature device technologies that have enabled flexible displays also present opportunities for flexible electronics and flexible integrated systems. Of particular interest are possible applications in flexible, low metal content, sensor systems for unattended ground sensors, smart medical bandages, electronic ID tags for geo-location, conformal antennas, neutron/gamma-ray/x-ray detectors, etc. In this talk, our efforts to develop novel CMOS integration schemes, circuits, memory, sensors as well as novel contacts, dielectrics and semiconductors for flexible electronics are presented. In particular, in this presentation we discuss fundamental materials properties including crystalline structure, interfacial reactions, doping, etc. defining performance and reliability of II-VI-based radiation sensors. We investigate the optimal thickness of a semiconductor diode for thin-film solid state thermal neutron detectors. Besides II-VI materials, we also evaluated several diode materials, Si, CdTe,GaAs, C (diamond), and ZnO, and two neutron converter materials,10B and 6LiF. We determine the minimum semiconductor thickness needed to achieve maximum neutron detection efficiency. By keeping the semiconductor thickness to a minimum, gamma rejection is kept as high as possible. In this way, we optimize detector performance for different thin-film semiconductor materials.

  13. Timing Characteristics of Large Area Picosecond Photodetectors

    SciTech Connect

    Adams, Bernhard W.; Elagin, Andrey L.; Frisch, H.; Obaid, Razib; Oberla, E; Vostrikov, Alexander; Wagner, Robert G.; Wang, Jingbo; Wetstein, Matthew J.; Northrop, R

    2015-09-21

    The LAPPD Collaboration was formed to develop ultralast large-area imaging photodetectors based on new methods for fabricating microchannel plates (MCPs). In this paper we characterize the time response using a pulsed, sub picosecond laser. We observe single photoelectron time resolutions of a 20 cm x 20 cm MCP consistently below 70 ps, spatial resolutions of roughly 500 pm, and median gains higher than 10(7). The RMS measured at one particular point on an LAPPD detector is 58 ps, with in of 47 ps. The differential time resolution between the signal reaching the two ends of the delay line anode is measured to be 5.1 ps for large signals, with an asymptotic limit falling below 2 ps as noise-over-signal approaches zero.

  14. Large area position sensitive β-detector

    NASA Astrophysics Data System (ADS)

    Vaintraub, S.; Hass, M.; Edri, H.; Morali, N.; Segal, T.

    2015-03-01

    A new conceptual design of a large area electron detector, which is position and energy sensitive, was developed. This detector is designed for beta decay energies up to 4 MeV, but in principle can be re-designed for higher energies. The detector incorporates one large plastic scintillator and, in general, a limited number of photomultipliers (7 presently). The current setup was designed and constructed after an extensive Geant4 simulation study. By comparison of a single hit light distribution between the various photomultipliers to a pre-measured accurate position-response map, the anticipated position resolution is around 5 mm. The first benchmark experiments have been conducted in order to calibrate and confirm the position resolution of the detector. The new method, results of the first test experiments and comparison to simulations are presented.

  15. The Large Area Pulsed Solar Simulator (LAPSS)

    NASA Technical Reports Server (NTRS)

    Mueller, R. L.

    1993-01-01

    A Large Area Pulsed Solar Simulator (LAPSS) has been installed at JPL. It is primarily intended to be used to illuminate and measure the electrical performance of photovoltaic devices. The simulator, originally manufactured by Spectrolab, Sylmar, California, occupies an area measuring about 3 meters wide by 12 meters long. The data acquisition and data processing subsystems have been modernized. Tests on the LAPSS performance resulted in better than +/- 2 percent uniformity of irradiance at the test plane and better than +/- 0.3 percent measurement repeatability after warm-up. Glass absorption filters are used to reduce the level of ultraviolet light emitted from the xenon flash lamps. This provides a close match to standard airmass zero and airmass 1.5 spectral irradiance distributions. The 2 millisecond light pulse prevents heating of the device under test, resulting in more reliable temperature measurements. Overall, excellent electrical performance measurements have been made of many different types and sizes of photovoltaic devices.

  16. The CLAS12 large area RICH detector

    SciTech Connect

    M. Contalbrigo, E. Cisbani, P. Rossi

    2011-05-01

    A large area RICH detector is being designed for the CLAS12 spectrometer as part of the 12 GeV upgrade program of the Jefferson Lab Experimental Hall-B. This detector is intended to provide excellent hadron identification from 3 GeV/c up to momenta exceeding 8 GeV/c and to be able to work at the very high design luminosity-up to 1035 cm2 s-1. Detailed feasibility studies are presented for two types of radiators, aerogel and liquid C6F14 freon, in conjunction with a highly segmented light detector in the visible wavelength range. The basic parameters of the RICH are outlined and the resulting performances, as defined by preliminary simulation studies, are reported.

  17. Large Area Sputter Coating on Glass

    NASA Astrophysics Data System (ADS)

    Katayama, Yoshihito

    Large glass has been used for commercial buildings, housings and vehicles for many years. Glass size for flat displays is getting larger and larger. The glass for the 8th generation is more than 5 m2 in area. Demand of the large glass is increasing not only in these markets but also in a solar cell market growing drastically. Therefore, large area coating is demanded to plus something else on glass more than ever. Sputtering and pyrolysis are the major coating methods on large glass today. Sputtering process is particularly popular because it can deposit a wide variety of materials in good coating uniformity on the glass. This paper describes typical industrial sputtering system and recent progress in sputtering technology. It also shows typical coated glass products in architectural, automotive and display fields and comments on their functions, film stacks and so on.

  18. Timing characteristics of Large Area Picosecond Photodetectors

    NASA Astrophysics Data System (ADS)

    Adams, B. W.; Elagin, A.; Frisch, H. J.; Obaid, R.; Oberla, E.; Vostrikov, A.; Wagner, R. G.; Wang, J.; Wetstein, M.

    2015-09-01

    The LAPPD Collaboration was formed to develop ultrafast large-area imaging photodetectors based on new methods for fabricating microchannel plates (MCPs). In this paper we characterize the time response using a pulsed, sub-picosecond laser. We observe single-photoelectron time resolutions of a 20 cm × 20 cm MCP consistently below 70 ps, spatial resolutions of roughly 500 μm, and median gains higher than 107. The RMS measured at one particular point on an LAPPD detector is 58 ps, with ± 1σ of 47 ps. The differential time resolution between the signal reaching the two ends of the delay line anode is measured to be 5.1 ps for large signals, with an asymptotic limit falling below 2 ps as noise-over-signal approaches zero.

  19. Fermi Large Area Telescope Second Source Catalog

    NASA Astrophysics Data System (ADS)

    Nolan, P. L.; Abdo, A. A.; Ackermann, M.; Ajello, M.; Allafort, A.; Antolini, E.; Atwood, W. B.; Axelsson, M.; Baldini, L.; Ballet, J.; Barbiellini, G.; Bastieri, D.; Bechtol, K.; Belfiore, A.; Bellazzini, R.; Berenji, B.; Bignami, G. F.; Blandford, R. D.; Bloom, E. D.; Bonamente, E.; Bonnell, J.; Borgland, A. W.; Bottacini, E.; Bouvier, A.; Brandt, T. J.; Bregeon, J.; Brigida, M.; Bruel, P.; Buehler, R.; Burnett, T. H.; Buson, S.; Caliandro, G. A.; Cameron, R. A.; Campana, R.; Cañadas, B.; Cannon, A.; Caraveo, P. A.; Casandjian, J. M.; Cavazzuti, E.; Ceccanti, M.; Cecchi, C.; Çelik, Ö.; Charles, E.; Chekhtman, A.; Cheung, C. C.; Chiang, J.; Chipaux, R.; Ciprini, S.; Claus, R.; Cohen-Tanugi, J.; Cominsky, L. R.; Conrad, J.; Corbet, R.; Cutini, S.; D'Ammando, F.; Davis, D. S.; de Angelis, A.; DeCesar, M. E.; DeKlotz, M.; De Luca, A.; den Hartog, P. R.; de Palma, F.; Dermer, C. D.; Digel, S. W.; Silva, E. do Couto e.; Drell, P. S.; Drlica-Wagner, A.; Dubois, R.; Dumora, D.; Enoto, T.; Escande, L.; Fabiani, D.; Falletti, L.; Favuzzi, C.; Fegan, S. J.; Ferrara, E. C.; Focke, W. B.; Fortin, P.; Frailis, M.; Fukazawa, Y.; Funk, S.; Fusco, P.; Gargano, F.; Gasparrini, D.; Gehrels, N.; Germani, S.; Giebels, B.; Giglietto, N.; Giommi, P.; Giordano, F.; Giroletti, M.; Glanzman, T.; Godfrey, G.; Grenier, I. A.; Grondin, M.-H.; Grove, J. E.; Guillemot, L.; Guiriec, S.; Gustafsson, M.; Hadasch, D.; Hanabata, Y.; Harding, A. K.; Hayashida, M.; Hays, E.; Hill, A. B.; Horan, D.; Hou, X.; Hughes, R. E.; Iafrate, G.; Itoh, R.; Jóhannesson, G.; Johnson, R. P.; Johnson, T. E.; Johnson, A. S.; Johnson, T. J.; Kamae, T.; Katagiri, H.; Kataoka, J.; Katsuta, J.; Kawai, N.; Kerr, M.; Knödlseder, J.; Kocevski, D.; Kuss, M.; Lande, J.; Landriu, D.; Latronico, L.; Lemoine-Goumard, M.; Lionetto, A. M.; Llena Garde, M.; Longo, F.; Loparco, F.; Lott, B.; Lovellette, M. N.; Lubrano, P.; Madejski, G. M.; Marelli, M.; Massaro, E.; Mazziotta, M. N.; McConville, W.; McEnery, J. E.; Mehault, J.; Michelson, P. F.; Minuti, M.; Mitthumsiri, W.; Mizuno, T.; Moiseev, A. A.; Mongelli, M.; Monte, C.; Monzani, M. E.; Morselli, A.; Moskalenko, I. V.; Murgia, S.; Nakamori, T.; Naumann-Godo, M.; Norris, J. P.; Nuss, E.; Nymark, T.; Ohno, M.; Ohsugi, T.; Okumura, A.; Omodei, N.; Orlando, E.; Ormes, J. F.; Ozaki, M.; Paneque, D.; Panetta, J. H.; Parent, D.; Perkins, J. S.; Pesce-Rollins, M.; Pierbattista, M.; Pinchera, M.; Piron, F.; Pivato, G.; Porter, T. A.; Racusin, J. L.; Rainò, S.; Rando, R.; Razzano, M.; Razzaque, S.; Reimer, A.; Reimer, O.; Reposeur, T.; Ritz, S.; Rochester, L. S.; Romani, R. W.; Roth, M.; Rousseau, R.; Ryde, F.; Sadrozinski, H. F.-W.; Salvetti, D.; Sanchez, D. A.; Saz Parkinson, P. M.; Sbarra, C.; Scargle, J. D.; Schalk, T. L.; Sgrò, C.; Shaw, M. S.; Shrader, C.; Siskind, E. J.; Smith, D. A.; Spandre, G.; Spinelli, P.; Stephens, T. E.; Strickman, M. S.; Suson, D. J.; Tajima, H.; Takahashi, H.; Takahashi, T.; Tanaka, T.; Thayer, J. G.; Thayer, J. B.; Thompson, D. J.; Tibaldo, L.; Tibolla, O.; Tinebra, F.; Tinivella, M.; Torres, D. F.; Tosti, G.; Troja, E.; Uchiyama, Y.; Vandenbroucke, J.; Van Etten, A.; Van Klaveren, B.; Vasileiou, V.; Vianello, G.; Vitale, V.; Waite, A. P.; Wallace, E.; Wang, P.; Werner, M.; Winer, B. L.; Wood, D. L.; Wood, K. S.; Wood, M.; Yang, Z.; Zimmer, S.

    2012-04-01

    We present the second catalog of high-energy γ-ray sources detected by the Large Area Telescope (LAT), the primary science instrument on the Fermi Gamma-ray Space Telescope (Fermi), derived from data taken during the first 24 months of the science phase of the mission, which began on 2008 August 4. Source detection is based on the average flux over the 24 month period. The second Fermi-LAT catalog (2FGL) includes source location regions, defined in terms of elliptical fits to the 95% confidence regions and spectral fits in terms of power-law, exponentially cutoff power-law, or log-normal forms. Also included are flux measurements in five energy bands and light curves on monthly intervals for each source. Twelve sources in the catalog are modeled as spatially extended. We provide a detailed comparison of the results from this catalog with those from the first Fermi-LAT catalog (1FGL). Although the diffuse Galactic and isotropic models used in the 2FGL analysis are improved compared to the 1FGL catalog, we attach caution flags to 162 of the sources to indicate possible confusion with residual imperfections in the diffuse model. The 2FGL catalog contains 1873 sources detected and characterized in the 100 MeV to 100 GeV range of which we consider 127 as being firmly identified and 1171 as being reliably associated with counterparts of known or likely γ-ray-producing source classes. We dedicate this paper to the memory of our colleague Patrick Nolan, who died on 2011 November 6. His career spanned much of the history of high-energy astronomy from space and his work on the Large Area Telescope (LAT) began nearly 20 years ago when it was just a concept. Pat was a central member in the operation of the LAT collaboration and he is greatly missed.

  20. Electrohydrodynamically driven large-area liquid ion sources

    DOEpatents

    Pregenzer, Arian L.

    1988-01-01

    A large-area liquid ion source comprises means for generating, over a large area of the surface of a liquid, an electric field of a strength sufficient to induce emission of ions from a large area of said liquid. Large areas in this context are those distinct from emitting areas in unidimensional emitters.

  1. Conformation of a flexible chain in explicit solvent: exact solvation potentials for short Lennard-Jones chains.

    PubMed

    Taylor, Mark P; Adhikari, Shishir R

    2011-07-28

    The average conformation of a flexible chain molecule in solution is coupled to the local solvent structure. In a dense solvent, local chain structure often mirrors the pure solvent structure, whereas, in a dilute solvent, the chain can strongly perturb the solvent structure which, in turn, can lead to either chain expansion or compression. Here we use Monte Carlo (MC) simulation to study such solvent effects for a short Lennard-Lones (LJ) chain in monomeric LJ solvent. For an n-site chain molecule in solution these many-body solvent effects can be formally mapped to an n-body solvation potential. We have previously shown that for hard-sphere and square-well chain-in-solvent systems this n-body potential can be decomposed into a set of two-body potentials. Here, we show that this decomposition is also valid for the LJ system. Starting from high precision MC results for the n = 5 LJ chain-in-solvent system, we use a Boltzmann inversion technique to compute numerically exact sets of two-body solvation potentials which map the many-body chain-in-solvent problem to a few-body single-chain problem. We have carried out this mapping across the full solvent phase diagram including the dilute vapor, dense liquid, and supercritical regions and find that these sets of solvation potentials are able to encode the complete range of solvent effects found in the LJ chain-in-solvent system. We also show that these two-site solvation potentials can be used to obtain accurate multi-site intramolecular distribution functions and we discuss the application of these exact short chain potentials to the study of longer chains in solvent. PMID:21806157

  2. Evidence That GH115 α-Glucuronidase Activity, Which Is Required to Degrade Plant Biomass, Is Dependent on Conformational Flexibility*

    PubMed Central

    Rogowski, Artur; Baslé, Arnaud; Farinas, Cristiane S.; Solovyova, Alexandra; Mortimer, Jennifer C.; Dupree, Paul; Gilbert, Harry J.; Bolam, David N.

    2014-01-01

    The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal β-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan. PMID:24214982

  3. Theory for the nonequilibrium dynamics of flexible chain molecules: Relaxation to equilibrium of pentadecane from an all-trans conformation

    NASA Astrophysics Data System (ADS)

    Tang, Wilfred H.; Kostov, Konstantin S.; Freed, Karl F.

    1998-05-01

    We extend to nonequilibrium processes our recent theory for the long time dynamics of flexible chain molecules. While the previous theory describes the equilibrium motions for any bond or interatomic separation in (bio)polymers by time correlation functions, the present extension of the theory enables the prediction of the nonequilibrium relaxation that occurs in processes, such as T-jump experiments, where there are sudden transitions between, for example, different equilibrium states. As a test of the theory, we consider the "unfolding" of pentadecane when it is transported from a constrained all-trans conformation to a random-coil state at thermal equilibrium. The time evolution of the mean-square end-to-end distance noneq after release of the constraint is computed both from the theory and from Brownian dynamics (BD) simulations. The lack of time translational symmetry for nonequilibrium processes requires that the BD simulations of the relaxation of noneq be computed from an average over a huge number of independent trajectories, rather than over successive configurations from a single trajectory, which may be used to generate equilibrium time correlation functions. Adequate convergence ensues for the nonequilibrium simulations only after averaging 9000 trajectories, each of 0.8 ns duration. In contrast, the theory requires only equilibrium averages for the initial and final states, which may be readily obtained from a few Brownian dynamics trajectories. Therefore, the new method produces enormous savings in computer time. Moreover, since both theory and simulations use identical potentials and solvent models, the theory contains no adjustable parameters. The predictions of the theory for the relaxation of noneq agree very well with the BD simulations. This work is a starting point for the application of the new method to nonequilibrium processes with biological importance such as the helix-coil transition and protein folding.

  4. Large-area lanthanum hexaboride electron emitter

    SciTech Connect

    Goebel, D.M.; Hirooka, Y.; Sketchley, T.A.

    1985-09-01

    A large-area cathode assembly which is capable of continuous, high-current electron emission is described. The cathode utilizes an indirectly heated lanthanum hexaboride (LaB/sub 6/) disk as the thermionic electron emitter. The LaB/sub 6/ cathode emits over 600 A of electrons at an average of 20 A/cm/sup 2/ continuously with no observable lifetime limits to date after about 400 h of operation in a plasma discharge. Proper clasping of the LaB/sub 6/ disk is required to avoid impurity production from chemical reactions with the holder and to provide adequate support if the disk fractures during rapid thermal cycling. Modification of the LaB/sub 6/ surface composition due to preferential sputtering of boron by hydrogen and argon ions in the plasma discharge has been observed. The surface appearance is consistent with the formation of LaB/sub 4/ as a result of boron depletion. The electron emission capability of the cathode is not significantly altered by the surface change. This surface modification by preferential sputtering is not observed in hollow cathodes where the ion energy from the cathode sheath voltage is typically less than 50 V. The electron emission by the cathode has not been affected by exposure to both air and water during operation. Utilizing thick disks of this intermediate temperature cathode material results in reliable, high-current, long-lifetime electron emitter assemblies.

  5. Airbrushed Nickel Nanoparticles for Large-Area

    SciTech Connect

    Sarac, Mehmet; ANDERSON, BRYAN; Pearce, Ryan; Railsback, Justin; Oni, Adedapo; White, Ryan M.; Hensley, Dale K; Lebeau, James M; Melechko, Anatoli; Tracy, Joseph B

    2013-01-01

    Vertically aligned carbon nanofibers (VACNFs) were grown by plasma-enhanced chemical vapor deposition (PECVD) using Ni nanoparticle (NP) catalysts that were deposited by airbrushing onto Si, Al, Cu, and Ti substrates. Airbrushing is a simple method for depositing catalyst NPs over large areas that is compatible with roll-to-roll processing. The distribution and morphology of VACNFs are affected by the airbrushing parameters and the composition of the metal foil. Highly concentrated Ni NPs in heptane give more uniform distributions than pentane and hexanes, resulting in more uniform coverage of VACNFs. For VACNF growth on metal foils, Si micropowder was added as a precursor for Si-enriched coatings formed in situ on the VACNFs that impart mechanical rigidity. Interactions between the catalyst NPs and the metal substrates impart control over the VACNF morphology. Growth of carbon nanostructures on Cu is particularly noteworthy because the miscibility of Ni with Cu poses challenges for VACNF growth, and carbon nanostructures anchored to Cu substrates are desired as anode materials for Li-ion batteries and for thermal interface materials.

  6. FERMI LARGE AREA TELESCOPE SECOND SOURCE CATALOG

    SciTech Connect

    Nolan, P. L.; Ajello, M.; Allafort, A.; Bechtol, K.; Berenji, B.; Blandford, R. D.; Bloom, E. D.; Abdo, A. A.; Ackermann, M.; Antolini, E.; Bonamente, E.; Atwood, W. B.; Belfiore, A.; Axelsson, M.; Baldini, L.; Bellazzini, R.; Ballet, J.; Bastieri, D.; Bignami, G. F. E-mail: Gino.Tosti@pg.infn.it E-mail: tburnett@u.washington.edu; and others

    2012-04-01

    We present the second catalog of high-energy {gamma}-ray sources detected by the Large Area Telescope (LAT), the primary science instrument on the Fermi Gamma-ray Space Telescope (Fermi), derived from data taken during the first 24 months of the science phase of the mission, which began on 2008 August 4. Source detection is based on the average flux over the 24 month period. The second Fermi-LAT catalog (2FGL) includes source location regions, defined in terms of elliptical fits to the 95% confidence regions and spectral fits in terms of power-law, exponentially cutoff power-law, or log-normal forms. Also included are flux measurements in five energy bands and light curves on monthly intervals for each source. Twelve sources in the catalog are modeled as spatially extended. We provide a detailed comparison of the results from this catalog with those from the first Fermi-LAT catalog (1FGL). Although the diffuse Galactic and isotropic models used in the 2FGL analysis are improved compared to the 1FGL catalog, we attach caution flags to 162 of the sources to indicate possible confusion with residual imperfections in the diffuse model. The 2FGL catalog contains 1873 sources detected and characterized in the 100 MeV to 100 GeV range of which we consider 127 as being firmly identified and 1171 as being reliably associated with counterparts of known or likely {gamma}-ray-producing source classes.

  7. Large area atmospheric-pressure plasma jet

    DOEpatents

    Selwyn, Gary S.; Henins, Ivars; Babayan, Steve E.; Hicks, Robert F.

    2001-01-01

    Large area atmospheric-pressure plasma jet. A plasma discharge that can be operated at atmospheric pressure and near room temperature using 13.56 MHz rf power is described. Unlike plasma torches, the discharge produces a gas-phase effluent no hotter than 250.degree. C. at an applied power of about 300 W, and shows distinct non-thermal characteristics. In the simplest design, two planar, parallel electrodes are employed to generate a plasma in the volume therebetween. A "jet" of long-lived metastable and reactive species that are capable of rapidly cleaning or etching metals and other materials is generated which extends up to 8 in. beyond the open end of the electrodes. Films and coatings may also be removed by these species. Arcing is prevented in the apparatus by using gas mixtures containing He, which limits ionization, by using high flow velocities, and by properly spacing the rf-powered electrode. Because of the atmospheric pressure operation, there is a negligible density of ions surviving for a sufficiently long distance beyond the active plasma discharge to bombard a workpiece, unlike the situation for low-pressure plasma sources and conventional plasma processing methods.

  8. Large area QNDE inspection for airframe integrity

    NASA Technical Reports Server (NTRS)

    Winfree, William P.; Heyman, Joseph S.

    1991-01-01

    Quantitative Nondestructive Evaluation (QNDE) technology is being developed to provide new options for cost effective inspection of airframes. An R&D effort based on five NDE technologies is addressing questions of structural bonding assessment, corrosion detection, multisite damage detection, and fatigue characterization. The research/applications are being conducted by prioritized focussing and staging of the following technologies: (1) thermal NDE; (2) ultrasonic NDE; (3) coherent optical NDE; (4) magnetic imaging NDE; and (5) radiographic NDE. The focus here is on the most recent applications of thermal NDE technology to large area inspection of lap-joint and stiffener bonds. The approach is based on pulsed radiant heating of the airframe and measurement of the surface temperature of the structure with an infrared imager. Several advantages of the technique are that it is noncontacting, inspects one square meter area in a period of less than 2 minutes and has no difficulty inspecting typical curvatures of the fuselage. Numerical models of heat flow in these geometries are used to determine appropriate techniques for reduction of the infrared images, thereby delineating regions of disbonds. These models are also used to determine the optimum heating and measurement times for maximizing the contrast between bonded and unbonded structures. Good agreement is found between these results and experimental measurements, and a comparison of the two are presented. Also presented are results of measurements on samples with fabricated defects which show the technique is able to clearly indicate regions of disbonds. Measurements on an airframe also clearly image subsurface structure.

  9. The Large Area Pulsed Solar Simulator (LAPSS)

    NASA Technical Reports Server (NTRS)

    Mueller, R. L.

    1994-01-01

    The Large Area Pulsed Solar Simulator (LAPSS) has been installed at JPL. It is primarily intended to be used to illuminate and measure the electrical performance of photovoltaic devices. The simulator, originally manufactured by Spectrolab, Sylmar, CA, occupies an area measuring about 3 m wide x 12 m long. The data acquisition and data processing subsystems have been modernized. Tests on the LAPSS performance resulted in better than plus or minus 2 percent uniformity of irradiance at the test plane and better than plus or minus 0.3 percent measurement repeatability after warm-up. Glass absorption filters reduce the ultraviolet light emitted from the xenon flash lamps. This results in a close match to three different standard airmass zero and airmass 1.5 spectral irradiances. The 2-ms light pulse prevents heating of the device under test, resulting in more reliable temperature measurements. Overall, excellent electrical performance measurements have been made of many different types and sizes of photovoltaic devices. Since the original printing of this publication, in 1993, the LAPSS has been operational and new capabilities have been added. This revision includes a new section relating to the installation of a method to measure the I-V curve of a solar cell or array exhibiting a large effective capacitance. Another new section has been added relating to new capabilities for plotting single and multiple I-V curves, and for archiving the I-V data and test parameters. Finally, a section has been added regarding the data acquisition electronics calibration.

  10. Fermi Large Area Telescope Second Source Catalog

    NASA Technical Reports Server (NTRS)

    Nolan, P. L.; Abdo, A. A.; Ackermann, M.; Ajello, M; Allafort, A.; Antolini, E; Bonnell, J.; Cannon, A.; Celik O.; Corbet, R.; Davis, D. S.; DeCesar, M. E.; Ferrara, E. C.; Gehrels, N.; Harding, A. K.; Hays, E.; Johnson, T. E.; McConville, W.; McEnery, J. E; Perkins, J. S.; Racusin, J. L; Scargle, J. D.; Stephens, T. E.; Thompson, D. J.; Troja, E.

    2012-01-01

    We present the second catalog of high-energy gamma-ray sources detected by the Large Area Telescope (LAT), the primary science instrument on the Fermi Gamma-ray Space Telescope (Fermi), derived from data taken during the first 24 months of the science phase of the mission, which began on 2008 August 4. Source detection is based on the average flux over the 24-month period. The Second Fermi-LAT catalog (2FGL) includes source location regions, defined in terms of elliptical fits to the 95% confidence regions and spectral fits in terms of power-law, exponentially cutoff power-law, or log-normal forms. Also included are flux measurements in 5 energy bands and light curves on monthly intervals for each source. Twelve sources in the catalog are modeled as spatially extended. We provide a detailed comparison of the results from this catalog with those from the first Fermi-LAT catalog (1FGL). Although the diffuse Galactic and isotropic models used in the 2FGL analysis are improved compared to the 1FGL catalog, we attach caution flags to 162 of the sources to indicate possible confusion with residual imperfections in the diffuse model. The 2FGL catalog contains 1873 sources detected and characterized in the 100 11eV to 100 GeV range of which we consider 127 as being firmly identified and 1171 as being reliably associated with counterparts of known or likely gamma-ray-producing source classes.

  11. Large area silicon sheet by EFG

    NASA Technical Reports Server (NTRS)

    Kalejs, J. P.

    1982-01-01

    Work carried out on the JPL Flat Plate Solar Array Project, for the purpose of developing a method for silicon ribbon production by Edge-defined Film-fed Growth (EEG) for use as low-cost substrate material in terrestrial solar cell manufacture, is described. A multiple ribbon furnace unit that is designed to operate on a continuous basis for periods of at least one week, with melt replenishment and automatic ribbon width control, and to produce silicon sheet at a rate of one square meter per hour, was constructed. Program milestones set for single ribbon furnace operation to demonstrate basic EEG system capabilities with respect to growth speed, thickness and cell performance were achieved for 10 cm wide ribbon: steady-state growth at 4 cm/min and 200 micron thickness over periods of an hour and longer was made routine, and a small area cell efficiency of 13+% demonstrated. Large area cells of average efficiency of 10 to 11%, with peak values of 11 to 12% were also achieved. The integration of these individual performance levels into multiple ribbon furnace operation was not accomplished.

  12. Large area silicon sheet by EFG

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Progress was made in improving ribbon flatness and reducing stress, and in raising cell performance for 10 cm wide ribbon grown in single cartridge EFG furnaces. Optimization of growth conditions resulted in improved ribbon thickness uniformity at a thickness of 200 micron, grown at 4 cm/minute, and growth at this target speed is routinely achieved over periods of the order of one hour or more. With the improved ribbon flatness, fabrication of large area (50 cm2) cells is now possible, and 10 to 11% efficiencies were demonstrated on ribbon grown at 3.5 to 4 cm/minute. Factors limiting performance of the existing multiple ribbon furnace were identified, and growth system improvements implemented to help raise throughput rates and the time percentage of simultaneous three-ribbon growth. However, it is evident that major redesign of this furnace would be needed to overcome shortfalls in its ability to achieve the Technical Features Demonstration goals of 1980. It was decided to start construction of a new multiple ribbon furnace and to incorporate the desired improvements into its design. The construction of this furnace is completed.

  13. Conformational flexibility and absolute stereochemistry of (3R)-3-hydroxy-4-aryl-β-lactams investigated by chiroptical properties and TD-DFT calculations.

    PubMed

    Tedesco, Daniele; Zanasi, Riccardo; Guerrini, Andrea; Bertucci, Carlo

    2012-09-01

    The effect of conformational flexibility on the chiroptical properties of a series of synthetic (3R)-3-hydroxy-4-aryl-β-lactams of known stereochemistry (1-6) was investigated by means of electronic circular dichroism (ECD) measurements and time-dependent density functional theory (TD-DFT) calculations. The application of the β-lactam sector rules allowed a correct stereochemical characterization of these compounds, with the exception of a thienyl-substituted derivative (cis-). TD-DFT calculations yielded accurate predictions of experimental ECD spectra and [α](D) values, allowing us to assign the correct absolute configuration to all the investigated compounds. A detailed analysis of the β-lactam ring equilibrium geometry on optimized conformers identified regular patterns for the arrangement of atoms around the amide chromophore, confirming the validity of the β-lactam sector rules. However, relevant variations in theoretical chiroptical properties were found for compounds bearing a heterocyclic substituent at C4 or a phenyl substituent at C3, whose conformers deviate from these regular geometric patterns. This behavior explains the failure of the β-lactam sector rules in cis-. This study showed the importance of conformational flexibility for the determination of chiroptical properties and highlighted the strengths and weaknesses of the different methods for the stereochemical characterization of chiral molecules in solution. PMID:22544665

  14. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

    PubMed Central

    Kurkcuoglu, Zeynep; Doruker, Pemra

    2016-01-01

    Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

  15. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins.

    PubMed

    Kurkcuoglu, Zeynep; Doruker, Pemra

    2016-01-01

    Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7-15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4-3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its "parents" up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5-2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

  16. Large Area Lunar Dust Flux Measurement Instrument

    NASA Technical Reports Server (NTRS)

    Corsaro, R.; Giovane, F.; Liou, Jer-Chyi; Burchell, M.; Stansbery, Eugene; Lagakos, N.

    2009-01-01

    The instrument under development is designed to characterize the flux and size distribution of the lunar micrometeoroid and secondary ejecta environment. When deployed on the lunar surface, the data collected will benefit fundamental lunar science as well as enabling more reliable impact risk assessments for human lunar exploration activities. To perform this task, the instrument requirements are demanding. It must have as large a surface area as possible to sample the very sparse population of the larger potentially damage-inducing micrometeorites. It must also have very high sensitivity to enable it to measure the flux of small (<10 micron) micrometeorite and secondary ejecta dust particles. To be delivered to the lunar surface, it must also be very low mass, rugged and stow compactly. The instrument designed to meet these requirements is called FOMIS. It is a large-area thin film under tension (i.e. a drum) with multiple fiber optic displacement (FOD) sensors to monitor displacements of the film. This sensor was chosen since it can measure displacements over a wide dynamic range: 1 cm to sub-Angstrom. A prototype system was successfully demonstrated using the hypervelocity impact test facility at the University of Kent (Canterbury, UK). Based on these results, the prototype system can detect hypervelocity (approx.5 km/s) impacts by particles as small as 2 microns diameter. Additional tests using slow speeds find that it can detect secondary ejecta particles (which do not penetrate the film) with momentums as small as 15 pico-gram 100m/s, or nominally 5 microns diameter at 100 m/s.

  17. Fermi Large Area Telescope Third Source Catalog

    NASA Astrophysics Data System (ADS)

    Acero, F.; Ackermann, M.; Ajello, M.; Albert, A.; Atwood, W. B.; Axelsson, M.; Baldini, L.; Ballet, J.; Barbiellini, G.; Bastieri, D.; Belfiore, A.; Bellazzini, R.; Bissaldi, E.; Blandford, R. D.; Bloom, E. D.; Bogart, J. R.; Bonino, R.; Bottacini, E.; Bregeon, J.; Britto, R. J.; Bruel, P.; Buehler, R.; Burnett, T. H.; Buson, S.; Caliandro, G. A.; Cameron, R. A.; Caputo, R.; Caragiulo, M.; Caraveo, P. A.; Casandjian, J. M.; Cavazzuti, E.; Charles, E.; Chaves, R. C. G.; Chekhtman, A.; Cheung, C. C.; Chiang, J.; Chiaro, G.; Ciprini, S.; Claus, R.; Cohen-Tanugi, J.; Cominsky, L. R.; Conrad, J.; Cutini, S.; D'Ammando, F.; de Angelis, A.; DeKlotz, M.; de Palma, F.; Desiante, R.; Digel, S. W.; Di Venere, L.; Drell, P. S.; Dubois, R.; Dumora, D.; Favuzzi, C.; Fegan, S. J.; Ferrara, E. C.; Finke, J.; Franckowiak, A.; Fukazawa, Y.; Funk, S.; Fusco, P.; Gargano, F.; Gasparrini, D.; Giebels, B.; Giglietto, N.; Giommi, P.; Giordano, F.; Giroletti, M.; Glanzman, T.; Godfrey, G.; Grenier, I. A.; Grondin, M.-H.; Grove, J. E.; Guillemot, L.; Guiriec, S.; Hadasch, D.; Harding, A. K.; Hays, E.; Hewitt, J. W.; Hill, A. B.; Horan, D.; Iafrate, G.; Jogler, T.; Jóhannesson, G.; Johnson, R. P.; Johnson, A. S.; Johnson, T. J.; Johnson, W. N.; Kamae, T.; Kataoka, J.; Katsuta, J.; Kuss, M.; La Mura, G.; Landriu, D.; Larsson, S.; Latronico, L.; Lemoine-Goumard, M.; Li, J.; Li, L.; Longo, F.; Loparco, F.; Lott, B.; Lovellette, M. N.; Lubrano, P.; Madejski, G. M.; Massaro, F.; Mayer, M.; Mazziotta, M. N.; McEnery, J. E.; Michelson, P. F.; Mirabal, N.; Mizuno, T.; Moiseev, A. A.; Mongelli, M.; Monzani, M. E.; Morselli, A.; Moskalenko, I. V.; Murgia, S.; Nuss, E.; Ohno, M.; Ohsugi, T.; Omodei, N.; Orienti, M.; Orlando, E.; Ormes, J. F.; Paneque, D.; Panetta, J. H.; Perkins, J. S.; Pesce-Rollins, M.; Piron, F.; Pivato, G.; Porter, T. A.; Racusin, J. L.; Rando, R.; Razzano, M.; Razzaque, S.; Reimer, A.; Reimer, O.; Reposeur, T.; Rochester, L. S.; Romani, R. W.; Salvetti, D.; Sánchez-Conde, M.; Saz Parkinson, P. M.; Schulz, A.; Siskind, E. J.; Smith, D. A.; Spada, F.; Spandre, G.; Spinelli, P.; Stephens, T. E.; Strong, A. W.; Suson, D. J.; Takahashi, H.; Takahashi, T.; Tanaka, Y.; Thayer, J. G.; Thayer, J. B.; Thompson, D. J.; Tibaldo, L.; Tibolla, O.; Torres, D. F.; Torresi, E.; Tosti, G.; Troja, E.; Van Klaveren, B.; Vianello, G.; Winer, B. L.; Wood, K. S.; Wood, M.; Zimmer, S.; Fermi-LAT Collaboration

    2015-06-01

    We present the third Fermi Large Area Telescope (LAT) source catalog (3FGL) of sources in the 100 MeV-300 GeV range. Based on the first 4 yr of science data from the Fermi Gamma-ray Space Telescope mission, it is the deepest yet in this energy range. Relative to the Second Fermi LAT catalog, the 3FGL catalog incorporates twice as much data, as well as a number of analysis improvements, including improved calibrations at the event reconstruction level, an updated model for Galactic diffuse γ-ray emission, a refined procedure for source detection, and improved methods for associating LAT sources with potential counterparts at other wavelengths. The 3FGL catalog includes 3033 sources above 4σ significance, with source location regions, spectral properties, and monthly light curves for each. Of these, 78 are flagged as potentially being due to imperfections in the model for Galactic diffuse emission. Twenty-five sources are modeled explicitly as spatially extended, and overall 238 sources are considered as identified based on angular extent or correlated variability (periodic or otherwise) observed at other wavelengths. For 1010 sources we have not found plausible counterparts at other wavelengths. More than 1100 of the identified or associated sources are active galaxies of the blazar class; several other classes of non-blazar active galaxies are also represented in the 3FGL. Pulsars represent the largest Galactic source class. From source counts of Galactic sources we estimate that the contribution of unresolved sources to the Galactic diffuse emission is ˜3% at 1 GeV.

  18. Large Area X-ray Spectroscopy Mission

    NASA Technical Reports Server (NTRS)

    Tananbaum, Harvey

    1996-01-01

    The Large Area X-ray Spectroscopy (LAXS) mission study concept has evolved strongly over the last year culminating in the merging of LAXS with the Goddard Space Flight Center (GSFC) proposal for a similar mission, the Next Generation X-ray Observatory (NGXO, PI: Nick White). The resulting merger, re-named the High Throughput X-rays Spectroscopy (HTXS) Mission has also expanded by the inclusion of another SAO proposed new mission concept proposal, the Hard X-Ray Telescope (PI: Paul Gorenstein). The resultant multi-instrument mission retains much of heritage from the LAXS proposal, including the use of multiple satellites for robustness. These mergers resulted from a series of contacts between various team members, via e-mail, telecons, and in-person meetings. The impetus for the mergers was the fundamental similarity between the missions, and the recognition that all three proposal teams had significant contributions to make in the effort to define the next stage in the X-ray exploration of the universe. We have enclosed four items that represent some of the work that has occurred during the first year of the study: first, a presentation at the Leicester meeting, second a presentation that was made to Dan Goldin following the merging of LAXS and NGXO, third a copy of the first announcement for the Workshop, and finally the interim report that was prepared by the HTXS study team towards the end of the first year. This last document provides the foundation for the HTXS Technology Roadmap that is being generated. The HTXS roadmap will define the near-term goals that the merged mission must achieve over the next few years. A web site has been developed and populated that contains much of the material that has been generated over the past year.

  19. Large-area mapping of biodiversity

    USGS Publications Warehouse

    Scott, J.M.; Jennings, M.D.

    1998-01-01

    The age of discovery, description, and classification of biodiversity is entering a new phase. In responding to the conservation imperative, we can now supplement the essential work of systematics with spatially explicit information on species and assemblages of species. This is possible because of recent conceptual, technical, and organizational progress in generating synoptic views of the earth's surface and a great deal of its biological content, at multiple scales of thematic as well as geographic resolution. The development of extensive spatial data on species distributions and vegetation types provides us with a framework for: (a) assessing what we know and where we know it at meso-scales, and (b) stratifying the biological universe so that higher-resolution surveys can be more efficiently implemented, coveting, for example, geographic adequacy of specimen collections, population abundance, reproductive success, and genetic dynamics. The land areas involved are very large, and the questions, such as resolution, scale, classification, and accuracy, are complex. In this paper, we provide examples from the United States Gap Analysis Program on the advantages and limitations of mapping the occurrence of terrestrial vertebrate species and dominant land-cover types over large areas as joint ventures and in multi-organizational partnerships, and how these cooperative efforts can be designed to implement results from data development and analyses as on-the-ground actions. Clearly, new frameworks for thinking about biogeographic information as well as organizational cooperation are needed if we are to have any hope of documenting the full range of species occurrences and ecological processes in ways meaningful to their management. The Gap Analysis experience provides one model for achieving these new frameworks.

  20. Development of large Area Covering Height Model

    NASA Astrophysics Data System (ADS)

    Jacobsen, K.

    2014-04-01

    Height information is a basic part of topographic mapping. Only in special areas frequent update of height models is required, usually the update cycle is quite lower as for horizontal map information. Some height models are available free of charge in the internet; for commercial height models a fee has to be paid. Mostly digital surface models (DSM) with the height of the visible surface are given and not the bare ground height, as required for standard mapping. Nevertheless by filtering of DSM, digital terrain models (DTM) with the height of the bare ground can be generated with the exception of dense forest areas where no height of the bare ground is available. These height models may be better as the DTM of some survey administrations. In addition several DTM from national survey administrations are classified, so as alternative the commercial or free of charge available information from internet can be used. The widely used SRTM DSM is available also as ACE-2 GDEM corrected by altimeter data for systematic height errors caused by vegetation and orientation errors. But the ACE-2 GDEM did not respect neighbourhood information. With the worldwide covering TanDEM-X height model, distributed starting 2014 by Airbus Defence and Space (former ASTRIUM) as WorldDEM, higher level of details and accuracy is reached as with other large area covering height models. At first the raw-version of WorldDEM will be available, followed by an edited version and finally as WorldDEM-DTM a height model of the bare ground. With 12 m spacing and a relative standard deviation of 1.2 m within an area of 1° x 1° an accuracy and resolution level is reached, satisfying also for larger map scales. For limited areas with the HDEM also a height model with 6 m spacing and a relative vertical accuracy of 0.5 m can be generated on demand. By bathymetric LiDAR and stereo images also the height of the sea floor can be determined if the water has satisfying transparency. Another method of getting

  1. Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation.

    PubMed

    Vogel, Alexander; Reuther, Guido; Roark, Matthew B; Tan, Kui-Thong; Waldmann, Herbert; Feller, Scott E; Huster, Daniel

    2010-02-01

    The lipid modified human N-Ras protein, implicated in human cancer development, is of particular interest due to its membrane anchor that determines the activity and subcellular location of the protein. Previous solid-state NMR investigations indicated that this membrane anchor is highly dynamic, which may be indicative of backbone conformational flexibility. This article aims to address if a dynamic exchange between three structural models exist that had been determined previously. We applied a combination of solid-state nuclear magnetic resonance (NMR) methods and replica exchange molecular dynamics (MD) simulations using a Ras peptide that represents the terminal seven amino acids of the human N-Ras protein. Analysis of correlations between the conformations of individual amino acids revealed that Cys 181 and Met 182 undergo collective conformational exchange. Two major structures constituting about 60% of all conformations could be identified. The two conformations found in the simulation are in rapid exchange, which gives rise to low backbone order parameters and nuclear spin relaxation as measured by experimental NMR methods. These parameters were also determined from two 300 ns conventional MD simulations, providing very good agreement with the experimental data. PMID:19819220

  2. Graphene-based large area dye-sensitized solar cell modules

    NASA Astrophysics Data System (ADS)

    Casaluci, Simone; Gemmi, Mauro; Pellegrini, Vittorio; di Carlo, Aldo; Bonaccorso, Francesco

    2016-02-01

    We demonstrate spray coating of graphene ink as a viable method for large-area fabrication of graphene-based dye-sensitized solar cell (DSSC) modules. A graphene-based ink produced by liquid phase exfoliation of graphite is spray coated onto a transparent conductive oxide substrate to realize a large area (>90 cm2) semi-transparent (transmittance 44%) counter-electrode (CE) replacing platinum, the standard CE material. The graphene-based CE is successfully integrated in a large-area (43.2 cm2 active area) DSSC module achieving a power conversion efficiency of 3.5%. The approach demonstrated here paves the way to all-printed, flexible, and transparent graphene-based large-area and cost-effective photovoltaic devices on arbitrary substrates.

  3. Graphene-based large area dye-sensitized solar cell modules.

    PubMed

    Casaluci, Simone; Gemmi, Mauro; Pellegrini, Vittorio; Di Carlo, Aldo; Bonaccorso, Francesco

    2016-03-01

    We demonstrate spray coating of graphene ink as a viable method for large-area fabrication of graphene-based dye-sensitized solar cell (DSSC) modules. A graphene-based ink produced by liquid phase exfoliation of graphite is spray coated onto a transparent conductive oxide substrate to realize a large area (>90 cm(2)) semi-transparent (transmittance 44%) counter-electrode (CE) replacing platinum, the standard CE material. The graphene-based CE is successfully integrated in a large-area (43.2 cm(2) active area) DSSC module achieving a power conversion efficiency of 3.5%. The approach demonstrated here paves the way to all-printed, flexible, and transparent graphene-based large-area and cost-effective photovoltaic devices on arbitrary substrates. PMID:26883743

  4. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  5. Gamma-Ray Large Area Space Telescope- GLAST Mission Overview

    NASA Technical Reports Server (NTRS)

    Moiseev, Alexander A.

    2007-01-01

    This viewgraph presentation reviews the Gamma-ray Large Area Space Telescope (GLAST), and the instrumentation that will be on the spacecraft: Large Area Telescope (LAT) and GLAST Burst Monitor (GBM). The presentation revierws in detail the LAT instrument.

  6. An examination of polymorphic stability and molecular conformational flexibility as a function of crystal size associated with the nucleation and growth of benzophenone.

    PubMed

    Hammond, Robert B; Pencheva, Klimentina; Roberts, Kevin J

    2007-01-01

    The polymorphic behaviour of the aromatic ketone, benzophenone, which is a conformationally flexible molecule and forms crystal structures dominated by van der Waals intermolecular interactions, is examined. Crystallization of this material from the undercooled molten state yields the two known polymorphic forms, i.e. the stable alpha-form and the metastable beta-form. The relative, energetic stabilities are examined using both crystal lattice and molecular conformational modelling techniques. Examination of nano-sized faceted molecular clusters of these forms, with cluster sizes ranging from 3 to 100 molecules, reveals that at very small cluster size (< 5 molecules) the relative energetic stability of clusters representative for the two forms become very similar, indicating that for high melting undercooling (i.e. small critical cluster size for nucleation) crystallization of the metastable beta-phase becomes more likely. Detailed analysis of the variation in molecular conformations within the simulated molecular clusters reveals more disordered three-dimensional structures at small compared to larger cluster sizes. The conformational disorder was found to be higher for the metastable beta-form. This observation, together with the lower stability of clusters for this form is indicative of the difficulty in achieving crystallization of the metastable beta-form from the melt, which requires a considerable undercooling. PMID:17955805

  7. On the role of the conformational flexibility of the active-site lid on the allosteric kinetics of glucosamine-6-phosphate deaminase.

    PubMed

    Bustos-Jaimes, Ismael; Sosa-Peinado, Alejandro; Rudiño-Piñera, Enrique; Horjales, Eduardo; Calcagno, Mario L

    2002-05-24

    The active site of glucosamine-6-phosphate deaminase from Escherichia coli (GlcN6P deaminase, EC 3.5.99.6) has a complex lid formed by two antiparallel beta-strands connected by a helix-loop segment (158-187). This motif contains Arg172, which is a residue involved in binding the substrate in the active-site, and three residues that are part of the allosteric site, Arg158, Lys160 and Thr161. This dual binding role of the motif forming the lid suggests that it plays a key role in the functional coupling between active and allosteric sites. Previous crystallographic work showed that the temperature coefficients of the active-site lid are very large when the enzyme is in its T allosteric state. These coefficients decrease in the R state, thus suggesting that this motif changes its conformational flexibility as a consequence of the allosteric transition. In order to explore the possible connection between the conformational flexibility of the lid and the function of the deaminase, we constructed the site-directed mutant Phe174-Ala. Phe174 is located at the C-end of the lid helix and its side-chain establishes hydrophobic interactions with the remainder of the enzyme. The crystallographic structure of the T state of Phe174-Ala deaminase, determined at 2.02 A resolution, shows no density for the segment 162-181, which is part of the active-site lid (PDB 1JT9). This mutant form of the enzyme is essentially inactive in the absence of the allosteric activator, N-acetylglucosamine-6-P although it recovers its activity up to the wild-type level in the presence of this ligand. Spectrometric and binding studies show that inactivity is due to the inability of the active-site to bind ligands when the allosteric site is empty. These data indicate that the conformational flexibility of the active-site lid critically alters the binding properties of the active site, and that the occupation of the allosteric site restores the lid conformational flexibility to a functional state. PMID

  8. The conformational flexibility of nucleic acid bases paired in gas phase: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Xiao, Shiyan; Liang, Haojun

    2012-05-01

    The flexibilities of pyrimidine and imidazole rings in the paired nucleobases are investigated using Car-Parrinello molecular dynamics simulation in gas phase. The pairing influence on the stiffness of rings is analyzed based on the molecular structure of the nucleobases and constraints caused by pairing. We prove that the flexibilities of pyrimidine rings in isolated state have subtle correlation with the degree of aromaticity of the rings. The pairings in nucleic base pairs cause the rings to be more rigid for G, T, and U but more flexible for A and the same for C.

  9. Fabrication of large area nanostructures with surface modified silica spheres

    NASA Astrophysics Data System (ADS)

    Kang, Kwang-Sun

    2014-03-01

    Surface modification of silica spheres with 3-(trimethoxysilyl)propylmethacrylate (TMSPM) has been performed at ambient condition. However, the FTIR spectra and field emission scanning electron microscope (FESEM) images show no evidence of the surface modification. The reaction temperatures were varied from 60 to 80 °C with various reaction periods. Small absorption shoulder of the CO stretching vibration was at 1700 cm-1, and slightly increased with the increase of the reaction time at 60 °C. The clear absorption peak appeared at 1698 cm-1 for the spheres reacted for 80 min at 70 °C and shifted toward 1720 cm-1 with the increase the reaction time. Strong absorption peak showed at 1698 cm-1 and shifted toward 1725 cm-1 with the increase of the reaction time at 80 °C. The spheres were dispersed to methanol and added photoinitiator (Irgacure-184). The solution was poured to a patterned glass substrate and exposed to the 254 nm UV-light during a self-assembly process. A large area and crack-free silica sphere film was formed. To increase the mechanical stability, a cellulose acetate solution was spin-coated to the film. The film was lift-off from the glass substrate to analyze the surface nanostructures. The surface nanostructures were maintained, and the film is stable enough to use as a mold to duplicate the nanopattern and flexible.

  10. Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

    NASA Astrophysics Data System (ADS)

    Yu, Garmay; A, Shvetsov; D, Karelov; D, Lebedev; A, Radulescu; M, Petukhov; V, Isaev-Ivanov

    2012-02-01

    Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

  11. Structural reassignment, absolute configuration, and conformation of hypurticin, a highly flexible polyacyloxy-6-heptenyl-5,6-dihydro-2H-pyran-2-one.

    PubMed

    Mendoza-Espinoza, José Alberto; López-Vallejo, Fabian; Fragoso-Serrano, Mabel; Pereda-Miranda, Rogelio; Cerda-García-Rojas, Carlos M

    2009-04-01

    The structural reassignment, absolute configuration, and conformational behavior of the highly flexible natural product hypurticin (pectinolide E), 6S-[3'S,5'R,6'S-triacetoxy-1Z-heptenyl]-5S-acetoxy-5,6-dihydro-2H-pyran-2-one (1), were ascertained by a molecular modeling protocol, which includes extensive conformational searching, geometry optimization by DFT B3LYP/DGDZVP calculations, and comparison between the theoretical (DFT) and experimental (1)H-(1)H NMR coupling constants. Hyptolide (2), a related cytotoxic 5,6-dihydro-2H-pyran-2-one that increased the S phase of the HeLa cell cycle, was employed as a reference substance to validate the theoretical protocol designed to characterize the 3D properties of compound 1. The related synthetic derivative, tri-O-acetyl-3,6-dideoxy-d-glucose diphenyldithioacetal (14), was prepared by a six-step reaction sequence starting from d-glucose and served as an enantiopure building block to reinforce the structural and configurational assignment of 1. This protocol proved to be an important tool for the structural characterization of highly flexible bioactive polyoxygenated natural products. PMID:19265396

  12. LARGE AREA LANDMARKS - DYNAMAP V.12.2

    EPA Science Inventory

    GDT Large Area Landmarks represents common landmark areas within United States including military areas, prisons, educational institutions, amusement centers, government centers, sport centers, golf courses, and cemeteries.

  13. Printable Solid-State Lithium-Ion Batteries: A New Route toward Shape-Conformable Power Sources with Aesthetic Versatility for Flexible Electronics.

    PubMed

    Kim, Se-Hee; Choi, Keun-Ho; Cho, Sung-Ju; Choi, Sinho; Park, Soojin; Lee, Sang-Young

    2015-08-12

    Forthcoming flexible/wearable electronic devices with shape diversity and mobile usability garner a great deal of attention as an innovative technology to bring unprecedented changes in our daily lives. From the power source point of view, conventional rechargeable batteries (one representative example is a lithium-ion battery) with fixed shapes and sizes have intrinsic limitations in fulfilling design/performance requirements for the flexible/wearable electronics. Here, as a facile and efficient strategy to address this formidable challenge, we demonstrate a new class of printable solid-state batteries (referred to as "PRISS batteries"). Through simple stencil printing process (followed by ultraviolet (UV) cross-linking), solid-state composite electrolyte (SCE) layer and SCE matrix-embedded electrodes are consecutively printed on arbitrary objects of complex geometries, eventually leading to fully integrated, multilayer-structured PRISS batteries with various form factors far beyond those achievable by conventional battery technologies. Tuning rheological properties of SCE paste and electrode slurry toward thixotropic fluid characteristics, along with well-tailored core elements including UV-cured triacrylate polymer and high boiling point electrolyte, is a key-enabling technology for the realization of PRISS batteries. This process/material uniqueness allows us to remove extra processing steps (related to solvent drying and liquid-electrolyte injection) and also conventional microporous separator membranes, thereupon enabling the seamless integration of shape-conformable PRISS batteries (including letters-shaped ones) into complex-shaped objects. Electrochemical behavior of PRISS batteries is elucidated via an in-depth analysis of cell impedance, which provides a theoretical basis to enable sustainable improvement of cell performance. We envision that PRISS batteries hold great promise as a reliable and scalable platform technology to open a new concept of cell

  14. Use of cysteine-reactive crosslinkers to probe conformational flexibility of human DJ-1 demonstrates that Glu18 mutations are dimers

    PubMed Central

    Prahlad, Janani; Hauser, David N.; Milkovic, Nicole M.; Cookson, Mark R.; Wilson, Mark A.

    2014-01-01

    The oxidation of a key cysteine residue (Cys106) in the parkinsonism-associated protein DJ-1 regulates its ability to protect against oxidative stress and mitochondrial damage. Cys106 interacts with a neighboring protonated Glu18 residue, stabilizing the Cys106-SO2− (sulfinic acid) form of DJ-1. To study this important post-translational modification, we previously designed several Glu18 mutations (E18N, E18D, E18Q) that alter the oxidative propensity of Cys106. However, recent results suggest these Glu18 mutations cause loss of DJ-1 dimerization, which would severely compromise the protein’s function. The purpose of this study was to conclusively determine the oligomerization state of these mutants using X-ray crystallography, NMR spectroscopy, thermal stability analysis, CD spectroscopy, sedimentation equilibrium ultracentrifugation, and crosslinking. We found that all of the Glu18 DJ-1 mutants were dimeric. Thiol crosslinking indicates that these mutant dimers are more flexible than the wild-type protein and can form multiple crosslinked dimeric species due to the transient exposure of cysteine residues that are inaccessible in the wild-type protein. The enhanced flexibility of Glu18 DJ-1 mutants provides a parsimonious explanation for their lower observed crosslinking efficiency in cells. In addition, thiol crosslinkers may have an underappreciated value as qualitative probes of protein conformational flexibility. PMID:24832775

  15. Large area x-ray detectors for cargo radiography

    NASA Astrophysics Data System (ADS)

    Bueno, C.; Albagli, D.; Bendahan, J.; Castleberry, D.; Gordon, C.; Hopkins, F.; Ross, W.

    2007-04-01

    Large area x-ray detectors based on phosphors coupled to flat panel amorphous silicon diode technology offer significant advances for cargo radiologic imaging. Flat panel area detectors provide large object coverage offering high throughput inspections to meet the high flow rate of container commerce. These detectors provide excellent spatial resolution when needed, and enhanced SNR through low noise electronics. If the resolution is reduced through pixel binning, further advances in SNR are achievable. Extended exposure imaging and frame averaging enables improved x-ray penetration of ultra-thick objects, or "select-your-own" contrast sensitivity at a rate many times faster than LDAs. The areal coverage of flat panel technology provides inherent volumetric imaging with the appropriate scanning methods. Flat panel area detectors have flexible designs in terms of electronic control, scintillator selection, pixel pitch, and frame rates. Their cost is becoming more competitive as production ramps up for the healthcare, nondestructive testing (NDT), and homeland protection industries. Typically used medical and industrial polycrystalline phosphor materials such as Gd2O2S:Tb (GOS) can be applied to megavolt applications if the phosphor layer is sufficiently thick to enhance x-ray absorption, and if a metal radiator is used to augment the quantum detection efficiency and reduce x-ray scatter. Phosphor layers ranging from 0.2-mm to 1-mm can be "sandwiched" between amorphous silicon flat panel diode arrays and metal radiators. Metal plates consisting of W, Pb or Cu, with thicknesses ranging from 0.25-mm to well over 1-mm can be used by covering the entire area of the phosphor plate. In some combinations of high density metal and phosphor layers, the metal plate provides an intensification of 25% in signal due to electron emission from the plate and subsequent excitation within the phosphor material. This further improves the SNR of the system.

  16. A large area cooled-CCD detector for electron microscopy

    NASA Astrophysics Data System (ADS)

    Faruqi, A. R.; Andrews, H. N.; Raeburn, C.

    1994-09-01

    Large area cooled-CCDs are an excellent medium for (indirectly) recording electron images and electron diffraction patterns in real time and for use in electron tomography; real-time imaging is extremely useful in making rapid adjustments in the electron microscope. CCDs provide high sensitivity (useful for minimising dosage to radiation-sensitive biological specimen), good resolution, stable performance, excellent dynamic range and linearity and a reasonably fast readout. We have built an electron imaging device based on the EEV 1152 by 814 pixel CCD which is controlled from a unix based SUN Sparestation operating under X-Windows. The incident 100 kV electrons are converted to visible light in a 0.5 mm thick YAG single crystal which is imaged through a lens on to the CCD. The CCD electronics is designed to be as flexible as possible and allows a wide variation in the readout speed to cater for the relatively fast application where readout noise is less critical and low readout noise applications where the extra few seconds of readout time are not significant. The CCD electronics is built in VME format which is controlled through a S-bus to VME driver. With two parallel channels of readout the whole image can be read out in ˜ 1 s (using the faster readout speed) with 16 bit precision and the image is displayed under X-Windows in a few seconds. The present readout works at 500 kHz and has a noise of ˜ 30 e rms per pixel. With a Peltier cooling device we can operate the CCD at ˜ -40°C which reduces the dark current adequately to allow exposures of up to several minutes. Several examples of patterns collected with the system on a Philips CM12 microscope will be presented.

  17. Uniformity of large-area bilayer graphene grown by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Sheng, Yuewen; Rong, Youmin; He, Zhengyu; Fan, Ye; Warner, Jamie H.

    2015-10-01

    Graphene grown by chemical vapor deposition (CVD) on copper foils is a viable method for large area films for transparent conducting electrode (TCE) applications. We examine the spatial uniformity of large area films on the centimeter scale when transferred onto both Si substrates with 300 nm oxide and flexible transparent polyethylene terephthalate substrates. A difference in the quality of graphene, as measured by the sheet resistance and transparency, is found for the areas at the edges of large sheets that depends on the supporting boat used for the CVD growth. Bilayer graphene is grown with uniform properties on the centimeter scale when a flat support is used for CVD growth. The flat support provides consistent delivery of precursor to the copper catalyst for graphene growth. These results provide important insights into the upscaling of CVD methods for growing high quality graphene and its transfer onto flexible substrates for potential applications as a TCE.

  18. High-performance conformal sensors employing single-crystal silicon nanomembranes

    NASA Astrophysics Data System (ADS)

    Xu, Xiaochuan; Subbaraman, Harish; Chakravarty, Swapnajit; Chen, Ray T.

    2014-03-01

    We demonstrate light-weight, conformal, and high-performance flexible sensors fabricated on a large area (>2 cm × 2 cm) silicon nanomembrane transferred onto a flexible substrate. Linear L13 photonic crystal microcavities are designed to provide high quality factors on the flexible platform. Subwavelength grating (SWG) couplers are employed in order to enable efficient light coupling to the device using a single mode fiber. Photonic crystal tapers are implemented at the strip-photonic crystal waveguide interfaces to minimize loss. Preliminary chemical sensing data suggests a sensitivity of 75nm/RIU. Bending tests are further performed in order to demonstrate sensitivityindependent operation.

  19. Protein Flexibility and Conformational State: A Comparison of Collective Vibrational Modes of Wild-Type and D96N Bacteriorhodopsin

    PubMed Central

    Whitmire, S. E.; Wolpert, D.; Markelz, A. G.; Hillebrecht, J. R.; Galan, J.; Birge, R. R.

    2003-01-01

    Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2–60 cm−1 and up to a resolution of 0.17 cm−1. The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state. PMID:12885670

  20. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink-Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling.

    PubMed

    Esquiaqui, Jackie M; Sherman, Eileen M; Ye, Jing-Dong; Fanucci, Gail E

    2016-08-01

    Site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy provides a means for a solution state description of site-specific dynamics and flexibility of large RNAs, facilitating our understanding of the effects of environmental conditions such as ligands and ions on RNA structure and dynamics. Here, the utility and capability of EPR line shape analysis and distance measurements to monitor and describe site-specific changes in the conformational dynamics of internal loop nucleobases as well as helix-helix interactions of the kink-turn motif in the Vibrio cholerae (VC) glycine riboswitch that occur upon sequential K(+)-, Mg(2+)-, and glycine-induced folding were explored. Spin-labels were incorporated into the 232-nucleotide sequence via splinted ligation strategies. Thiouridine nucleobase labeling within the internal loop reveals unambiguous differential dynamics for two successive sites labeled, with varied rates of motion reflective of base flipping and base stacking. EPR-based distance measurements for nitroxide spin-labels incorporated within the RNA backbone in the helical regions of the kink-turn motif are reflective of helical formation and tertiary interaction induced by ion stabilization. In both instances, results indicate that the structural formation of the kink-turn motif in the VC glycine riboswitch can be stabilized by 100 mM K(+) where the conformational flexibility of the kink-turn motif is not further tightened by subsequent addition of divalent ions. Although glycine binding is likely to induce structural and dynamic changes in other regions, SDSL indicates no impact of glycine binding on the local dynamics or structure of the kink-turn motif as investigated here. Overall, these results demonstrate the ability of SDSL to interrogate site-specific base dynamics and packing of helices in large RNAs and demonstrate ion-induced stability of the kink-turn fold of the VC riboswitch. PMID:27427937

  1. Smooth, seamless, and structured grid generation with flexibility in resolution distribution on a sphere based on conformal mapping and the spring dynamics method

    NASA Astrophysics Data System (ADS)

    Iga, Shin-ichi

    2015-09-01

    A generation method for smooth, seamless, and structured triangular grids on a sphere with flexibility in resolution distribution is proposed. This method is applicable to many fields that deal with a sphere on which the required resolution is not uniform. The grids were generated using the spring dynamics method, and adjustments were made using analytical functions. The mesh topology determined its resolution distribution, derived from a combination of conformal mapping factors: polar stereographic projection (PSP), Lambert conformal conic projection (LCCP), and Mercator projection (MP). Their combination generated, for example, a tropically fine grid that had a nearly constant high-resolution belt around the equator, with a gradual decrease in resolution distribution outside of the belt. This grid can be applied to boundary-less simulations of tropical meteorology. The other example involves a regionally fine grid with a nearly constant high-resolution circular region and a gradually decreasing resolution distribution outside of the region. This is applicable to regional atmospheric simulations without grid nesting. The proposed grids are compatible with computer architecture because they possess a structured form. Each triangle of the proposed grids was highly regular, implying a high local isotropy in resolution. Finally, the proposed grids were examined by advection and shallow water simulations.

  2. The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase.

    PubMed

    Montagner, Caroline; Nigen, Michaël; Jacquin, Olivier; Willet, Nicolas; Dumoulin, Mireille; Karsisiotis, Andreas Ioannis; Roberts, Gordon C K; Damblon, Christian; Redfield, Christina; Matagne, André

    2016-07-29

    Metallo-β-lactamases catalyze the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate-binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus β-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (ΔG(0)) of 32 ± 2 kJ·mol(-1) For holoBcII, a first non-cooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site, and the protein displays a well organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. Two-dimensional NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with ΔG(0) value of 65 ± 1.4 kJ·mol(-1) These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well defined conformation for both active site loops to maintain enzymatic activity. PMID:27235401

  3. Construction of helical coordination polymers via flexible conformers of bis(3-pyridyl)cyclotetramethylenesilane: metal(ii) and halogen effects on luminescence, thermolysis and catalysis.

    PubMed

    Kim, Hyeun; Park, Minwoo; Lee, Haeri; Jung, Ok-Sang

    2015-05-01

    Infinite rectangular-tubular helices, [MX2L] (M = Zn(ii), Hg(ii); X(-) = Cl(-), Br(-); L = bis(3-pyridyl)cyclotetramethylenesilane), have been efficiently constructed via the combined effects of the potential flexible conformers of L and the tetrahedral geometry of M(ii) ions. This helical molecular system affords a racemic mixture of P- and M-helices in a crystal. The helical pitches (7.8934(4)-8.1560(2) Å) that are sensitive to the nature of M(ii) ions and halide anions are attributable to subtle change in the flexible dihedral angles between the two pyridyl groups around Si and the M(ii) hinges. Their photoluminescence intensities, correspondingly, are in the order [ZnCl2L] > [ZnBr2L] ≫ [HgCl2L] > [HgBr2L]. Zinc(ii) complexes show recyclable catalytic effects on the transesterification reaction in the order [ZnCl2L] > [ZnBr2L]. Calcination of [ZnCl2L] and [ZnBr2L] at 500 °C produces uniform hexagonal tubular spire crystals of 1.2 × 1.2 × 4.0 μm(3) dimensions and spheres, respectively. PMID:25847863

  4. Laser processing system development of large area and high precision

    NASA Astrophysics Data System (ADS)

    Park, Hyeongchan; Ryu, Kwanghyun; Hwang, Taesang

    2013-03-01

    As industry of PCB (Printed Circuit Board) and display growing, this industry requires an increasingly high-precision quality so current cutting process in industry is preferred laser machining than mechanical machining. Now, laser machining is used almost "step and repeat" method in large area, but this method has a problem such as cutting quality in the continuity of edge parts, cutting speed and low productivity. To solve these problems in large area, on-the-fly (stagescanner synchronized system) is gradually increasing. On-the-fly technology is able to process large area with high speed because of stage-scanner synchronized moving. We designed laser-based high precision system with on-the-fly. In this system, we used UV nano-second pulse laser, power controller and scanner with telecentric f-theta lens. The power controller is consisted of HWP(Half Wave Plate), thin film plate polarizer, photo diode, micro step motor and control board. Laser power is possible to monitor real-time and adjust precision power by using power controller. Using this machine, we tested cutting of large area coverlay and sheet type large area PCB by applying on-the-fly. As a result, our developed machine is possible to process large area without the problem of the continuity of edge parts and by high cutting speed than competitor about coverlay.

  5. Electronic sensor and actuator webs for large-area complex geometry cardiac mapping and therapy

    PubMed Central

    Kim, Dae-Hyeong; Ghaffari, Roozbeh; Lu, Nanshu; Wang, Shuodao; Lee, Stephen P.; Keum, Hohyun; D’Angelo, Robert; Klinker, Lauren; Su, Yewang; Lu, Chaofeng; Kim, Yun-Soung; Ameen, Abid; Li, Yuhang; Zhang, Yihui; de Graff, Bassel; Hsu, Yung-Yu; Liu, ZhuangJian; Ruskin, Jeremy; Xu, Lizhi; Lu, Chi; Omenetto, Fiorenzo G.; Huang, Yonggang; Mansour, Moussa; Slepian, Marvin J.; Rogers, John A.

    2012-01-01

    Curved surfaces, complex geometries, and time-dynamic deformations of the heart create challenges in establishing intimate, nonconstraining interfaces between cardiac structures and medical devices or surgical tools, particularly over large areas. We constructed large area designs for diagnostic and therapeutic stretchable sensor and actuator webs that conformally wrap the epicardium, establishing robust contact without sutures, mechanical fixtures, tapes, or surgical adhesives. These multifunctional web devices exploit open, mesh layouts and mount on thin, bio-resorbable sheets of silk to facilitate handling in a way that yields, after dissolution, exceptionally low mechanical moduli and thicknesses. In vivo studies in rabbit and pig animal models demonstrate the effectiveness of these device webs for measuring and spatially mapping temperature, electrophysiological signals, strain, and physical contact in sheet and balloon-based systems that also have the potential to deliver energy to perform localized tissue ablation. PMID:23150574

  6. Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex

    PubMed Central

    Sewell, H.; Tanaka, T.; Omari, K. El; Mancini, E. J.; Cruz, A.; Fernandez-Fuentes, N.; Chambers, J.; Rabbitts, T. H.

    2014-01-01

    LMO2 was discovered via chromosomal translocations in T-cell leukaemia and shown normally to be essential for haematopoiesis. LMO2 is made up of two LIM only domains (thus it is a LIM-only protein) and forms a bridge in a multi-protein complex. We have studied the mechanism of formation of this complex using a single domain antibody fragment that inhibits LMO2 by sequestering it in a non-functional form. The crystal structure of LMO2 with this antibody fragment has been solved revealing a conformational difference in the positioning and angle between the two LIM domains compared with its normal binding. This contortion occurs by bending at a central helical region of LMO2. This is a unique mechanism for inhibiting an intracellular protein function and the structural contusion implies a model in which newly synthesized, intrinsically disordered LMO2 binds to a partner protein nucleating further interactions and suggests approaches for therapeutic targeting of LMO2. PMID:24407558

  7. Adjustment of local conformational flexibility and accessible surface area alterations of Serine128 and Valine183 in mnemiopsin

    NASA Astrophysics Data System (ADS)

    Hakiminia, Forough; Molakarimi, Maryam; Khalifeh, Khosrow; Jahani, Zohreh; Sajedi, Reza H.; Ranjbar, Bijan

    2016-08-01

    We used a combination of experimental and bioinformatic studies to elucidate the importance of Serine128 and Valine183 on the activity and thermal stability of mnemiopsin 1 by substitution of S128 and V183 with glycine and threonine, respectively (S128G and V183T mutants). Luminescence emissions of S128G and V183T were reduced to 71.6% and 46.6% with respect to the original activity of the wild type protein. According to circular dichroism (CD) measurements, compactness of mutants decreased in comparison with wild type (WT) protein. Differential scanning calorimetry (DSC) indicated that Tm values of thermal unfolding are not changed significantly upon mutation. Herein, we suggest that the protein variants unfold through molecular association and intermediate states. Bioinformatic studies revealed that local fluctuation of residues in S128G increased with respect to WT protein. However, S128G mutation leads to increment of the accessible surface area of lysine188. Therefore, this change is thermodynamically favorable. Finally, both experimental and theoretical studies showed a delicate balance between all structural alterations, determining total conformational stability of the protein.

  8. Optical nano-woodpiles: large-area metallic photonic crystals and metamaterials

    NASA Astrophysics Data System (ADS)

    Ibbotson, Lindsey A.; Demetriadou, Angela; Croxall, Stephen; Hess, Ortwin; Baumberg, Jeremy J.

    2015-02-01

    Metallic woodpile photonic crystals and metamaterials operating across the visible spectrum are extremely difficult to construct over large areas, because of the intricate three-dimensional nanostructures and sub-50 nm features demanded. Previous routes use electron-beam lithography or direct laser writing but widespread application is restricted by their expense and low throughput. Scalable approaches including soft lithography, colloidal self-assembly, and interference holography, produce structures limited in feature size, material durability, or geometry. By multiply stacking gold nanowire flexible gratings, we demonstrate a scalable high-fidelity approach for fabricating flexible metallic woodpile photonic crystals, with features down to 10 nm produced in bulk and at low cost. Control of stacking sequence, asymmetry, and orientation elicits great control, with visible-wavelength band-gap reflections exceeding 60%, and with strong induced chirality. Such flexible and stretchable architectures can produce metamaterials with refractive index near zero, and are easily tuned across the IR and visible ranges.

  9. Large-area functionalized CVD graphene for work function matched transparent electrodes

    PubMed Central

    Bointon, Thomas H.; Jones, Gareth F.; De Sanctis, Adolfo; Hill-Pearce, Ruth; Craciun, Monica F.; Russo, Saverio

    2015-01-01

    The efficiency of flexible photovoltaic and organic light emitting devices is heavily dependent on the availability of flexible and transparent conductors with at least a similar workfunction to that of Indium Tin Oxide. Here we present the first study of the work function of large area (up to 9 cm2) FeCl3 intercalated graphene grown by chemical vapour deposition on Nickel, and demonstrate values as large as 5.1 eV. Upon intercalation, a charge density per graphene layer of 5 ⋅ 1013 ± 5 ⋅ 1012 cm−2 is attained, making this material an attractive platform for the study of plasmonic excitations in the infrared wavelength spectrum of interest to the telecommunication industry. Finally, we demonstrate the potential of this material for flexible electronics in a transparent circuit on a polyethylene naphthalate substrate. PMID:26548711

  10. Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein

    PubMed Central

    Ng, C Leong; Waterman, David G; Koonin, Eugene V; Walters, Alison D; Chong, James PJ; Isupov, Michail N; Lebedev, Andrey A; Bunka, David HJ; Stockley, Peter G; Ortiz-Lombardía, Miguel; Antson, Alfred A

    2009-01-01

    Background Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skeletal abnormalities. This protein is highly conserved in eukaryotes and archaea but is not found in bacteria. Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown. Results We determined the crystal structure of the SBDS orthologue from Methanothermobacter thermautotrophicus (mthSBDS). This structure shows that SBDS proteins are highly flexible, with the N-terminal FYSH domain and the C-terminal ferredoxin-like domain capable of undergoing substantial rotational adjustments with respect to the central domain. Affinity chromatography identified several proteins from the large ribosomal subunit as possible interacting partners of mthSBDS. Moreover, SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments, combined with electrophoretic mobility shift assays (EMSA) suggest that mthSBDS does not interact with RNA molecules in a sequence specific manner. Conclusion It is suggested that functional interactions of SBDS proteins with their partners could be facilitated by rotational adjustments of the N-terminal and the C-terminal domains with respect to the central domain. Examination of the SBDS protein structure and domain movements together with its possible interaction with large ribosomal subunit proteins suggest that these proteins could participate in ribosome function. PMID:19454024

  11. Large-area synthesis of high-quality and uniform monolayer WS2 on reusable Au foils.

    PubMed

    Gao, Yang; Liu, Zhibo; Sun, Dong-Ming; Huang, Le; Ma, Lai-Peng; Yin, Li-Chang; Ma, Teng; Zhang, Zhiyong; Ma, Xiu-Liang; Peng, Lian-Mao; Cheng, Hui-Ming; Ren, Wencai

    2015-01-01

    Large-area monolayer WS2 is a desirable material for applications in next-generation electronics and optoelectronics. However, the chemical vapour deposition (CVD) with rigid and inert substrates for large-area sample growth suffers from a non-uniform number of layers, small domain size and many defects, and is not compatible with the fabrication process of flexible devices. Here we report the self-limited catalytic surface growth of uniform monolayer WS2 single crystals of millimetre size and large-area films by ambient-pressure CVD on Au. The weak interaction between the WS2 and Au enables the intact transfer of the monolayers to arbitrary substrates using the electrochemical bubbling method without sacrificing Au. The WS2 shows high crystal quality and optical and electrical properties comparable or superior to mechanically exfoliated samples. We also demonstrate the roll-to-roll/bubbling production of large-area flexible films of uniform monolayer, double-layer WS2 and WS2/graphene heterostructures, and batch fabrication of large-area flexible monolayer WS2 film transistor arrays. PMID:26450174

  12. Large-area synthesis of high-quality and uniform monolayer WS2 on reusable Au foils

    NASA Astrophysics Data System (ADS)

    Gao, Yang; Liu, Zhibo; Sun, Dong-Ming; Huang, Le; Ma, Lai-Peng; Yin, Li-Chang; Ma, Teng; Zhang, Zhiyong; Ma, Xiu-Liang; Peng, Lian-Mao; Cheng, Hui-Ming; Ren, Wencai

    2015-10-01

    Large-area monolayer WS2 is a desirable material for applications in next-generation electronics and optoelectronics. However, the chemical vapour deposition (CVD) with rigid and inert substrates for large-area sample growth suffers from a non-uniform number of layers, small domain size and many defects, and is not compatible with the fabrication process of flexible devices. Here we report the self-limited catalytic surface growth of uniform monolayer WS2 single crystals of millimetre size and large-area films by ambient-pressure CVD on Au. The weak interaction between the WS2 and Au enables the intact transfer of the monolayers to arbitrary substrates using the electrochemical bubbling method without sacrificing Au. The WS2 shows high crystal quality and optical and electrical properties comparable or superior to mechanically exfoliated samples. We also demonstrate the roll-to-roll/bubbling production of large-area flexible films of uniform monolayer, double-layer WS2 and WS2/graphene heterostructures, and batch fabrication of large-area flexible monolayer WS2 film transistor arrays.

  13. Large-area synthesis of high-quality and uniform monolayer WS2 on reusable Au foils

    PubMed Central

    Gao, Yang; Liu, Zhibo; Sun, Dong-Ming; Huang, Le; Ma, Lai-Peng; Yin, Li-Chang; Ma, Teng; Zhang, Zhiyong; Ma, Xiu-Liang; Peng, Lian-Mao; Cheng, Hui-Ming; Ren, Wencai

    2015-01-01

    Large-area monolayer WS2 is a desirable material for applications in next-generation electronics and optoelectronics. However, the chemical vapour deposition (CVD) with rigid and inert substrates for large-area sample growth suffers from a non-uniform number of layers, small domain size and many defects, and is not compatible with the fabrication process of flexible devices. Here we report the self-limited catalytic surface growth of uniform monolayer WS2 single crystals of millimetre size and large-area films by ambient-pressure CVD on Au. The weak interaction between the WS2 and Au enables the intact transfer of the monolayers to arbitrary substrates using the electrochemical bubbling method without sacrificing Au. The WS2 shows high crystal quality and optical and electrical properties comparable or superior to mechanically exfoliated samples. We also demonstrate the roll-to-roll/bubbling production of large-area flexible films of uniform monolayer, double-layer WS2 and WS2/graphene heterostructures, and batch fabrication of large-area flexible monolayer WS2 film transistor arrays. PMID:26450174

  14. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

    SciTech Connect

    Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino

    2014-02-01

    This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

  15. Preparation of large-area double-walled carbon nanotube films and application as film heater

    NASA Astrophysics Data System (ADS)

    Wu, Zi Ping; Wang, Jian Nong

    2009-11-01

    Large-area (larger than 30×30 cm 2) double-walled carbon nanotube (DWCNT) films are prepared and application as a heating element for film heaters is demonstrated. A high heating efficiency is observed. Measurements indicate that the use of the DWCNT film heater would save energy consumption up to 20-30% when compared with a commercial film-like metal-based heater. Morphological analysis reveals that the special surface structure, appropriate electric and high thermal conductivities of the film formed by the network of entangled nanotube bundles may lead to the high heating performance. Considering large-area, shape flexibility, negligible weight and easy manipulation, the film exhibits promising potential applications as a film heater for thermal control in aircrafts, medical equipment, home appliances and other industrial fields at low temperature (below 400 °C).

  16. Large-area fabrication of 3D petal-like nanopattern for surface enhanced Raman scattering

    NASA Astrophysics Data System (ADS)

    Zhou, Weimin; Wang, Jinhe; Zhang, Jing; Li, Xiaoli; Min, Guoquan

    2014-06-01

    A very easy and flexible approach to fabricate large area, petal-like nanopattern for surface enhanced Raman scattering using soft imprint lithography are presented here. The morphology of the petal-like nanopattern can be transferred truly using the h-PDMS and diluted PMMA molding template. By means of Au metal deposition, a SERS substrate with high enhancement factor over large area, which is still a problem, was produced easily. The morphology and Raman enhancement effect of the 3D nanopattern are characterized by SEM, AFM and SERS. The results show that the petal-like 3D nanopattern has high SERS enhancement factor (order of 1.0 × 108) and could be a promising low cost and high performance SERS active substrate.

  17. Fabrication of Large Area Periodic Nanostructures Using Nanosphere Photolithography

    NASA Astrophysics Data System (ADS)

    Wu, Wei; Dey, Dibyendu; Memis, Omer G.; Katsnelson, Alex; Mohseni, Hooman

    2008-10-01

    Large area periodic nanostructures exhibit unique optical and electronic properties and have found many applications, such as photonic band-gap materials, high dense data storage, and photonic devices. We have developed a maskless photolithography method—Nanosphere Photolithography (NSP)—to produce a large area of uniform nanopatterns in the photoresist utilizing the silica micro-spheres to focus UV light. Here, we will extend the idea to fabricate metallic nanostructures using the NSP method. We produced large areas of periodic uniform nanohole array perforated in different metallic films, such as gold and aluminum. The diameters of these nanoholes are much smaller than the wavelength of UV light used and they are very uniformly distributed. The method introduced here inherently has both the advantages of photolithography and self-assembled methods. Besides, it also generates very uniform repetitive nanopatterns because the focused beam waist is almost unchanged with different sphere sizes.

  18. Plasma and Ion Sources in Large Area Coatings: A Review

    SciTech Connect

    Anders, Andre

    2005-02-28

    Efficient deposition of high-quality coatings often requires controlled application of excited or ionized particles. These particles are either condensing (film-forming) or assisting by providing energy and momentum to the film growth process, resulting in densification, sputtering/etching, modification of stress, roughness, texture, etc. In this review, the technical means are surveyed enabling large area application of ions and plasmas, with ion energies ranging from a few eV to a few keV. Both semiconductortype large area (single wafer or batch processing with {approx} 1000 cm{sup 2}) and in-line web and glass-coating-type large area (> 10{sup 7} m{sup 2} annually) are considered. Characteristics and differences between plasma and ion sources are explained. The latter include gridded and gridless sources. Many examples are given, including sources based on DC, RF, and microwave discharges, some with special geometries like hollow cathodes and E x B configurations.

  19. Large-area metallic photonic lattices for military applications.

    SciTech Connect

    Luk, Ting Shan

    2007-11-01

    In this project we developed photonic crystal modeling capability and fabrication technology that is scaleable to large area. An intelligent optimization code was developed to find the optimal structure for the desired spectral response. In terms of fabrication, an exhaustive survey of fabrication techniques that would meet the large area requirement was reduced to Deep X-ray Lithography (DXRL) and nano-imprint. Using DXRL, we fabricated a gold logpile photonic crystal in the <100> plane. For the nano-imprint technique, we fabricated a cubic array of gold squares. These two examples also represent two classes of metallic photonic crystal topologies, the connected network and cermet arrangement.

  20. Developmental experiments on large-area silicon solar cells

    NASA Astrophysics Data System (ADS)

    Silard, Andrei P.; Nani, Gabriel

    1989-05-01

    Practical ways of attenuating the severe limitations imposed by areal inhomogeneities on the performance of large-area solar cells fabricated on both p- and n-silicon wafers are described, and the results of tests are presented. The p(+)-n-n(+) and n(+)-p-p(+) cells were processed as bifacial devices and tested under both frontside and backside AM1 illumination. It is shown that the combination of a simple design and some of the technological approaches evaluated in this study result in low-cost high-efficiency large-area bifacial silicon solar cells that exhibit with good electrooptical performance.

  1. Coatings for large-area low-cost solar concentrators and reflectors

    SciTech Connect

    Martin, P.M.; Affinito, J.D.; Gross, M.E.; Bennett, W.D.

    1994-07-01

    Seven years ago, Pacific Northwest Laboratory constructed a large-optics coating facility to develop and fabricate high-performance multilayer laser-mirror coatings on large substrates. With the reduction of DoD funding for the development of optical coatings for large optics, new applications for this chamber were sought. In addition to new DoD applications, the facility is now being used to fabricate multilayer enhanced-metal reflectors for low-cost large-area solar concentrators using both magnetron-sputtered metal and dielectric coatings, with future extension to vacuum-evaporated polymer coatings. Other new applications include: Ti/Ti:Al lamellar composites on flexible webs; EMI cladding for heater wire; EMI-shielding coatings on flexible webs; microwave-absorbing coatings on flexible webs; heat mirrors; bulk micromachining; and protective coatings on cylindrical substrates and webs. The facility has also been established as a DoD user facility for development and experimentation in large-area optical coatings. This paper describes important changes in the large-optics coating chamber and additional deposition equipment that has been added to pursue these new non-DoD technological areas. Solar reflectors and the resulting new coatings will be described. Future work and new technological areas being pursued will also be discussed.

  2. Large area, low cost solar cell development and production readiness

    NASA Technical Reports Server (NTRS)

    Michaels, D.

    1982-01-01

    A process sequence for a large area ( or = 25 sq. cm) silicon solar cell was investigated. Generic cell choice was guided by the expected electron fluence, by the packing factors of various cell envelope designs onto each panel to provide needed voltage as well as current, by the weight constraints on the system, and by the cost goals of the contract.

  3. Large area high-speed metrology SPM system

    NASA Astrophysics Data System (ADS)

    Klapetek, P.; Valtr, M.; Picco, L.; Payton, O. D.; Martinek, J.; Yacoot, A.; Miles, M.

    2015-02-01

    We present a large area high-speed measuring system capable of rapidly generating nanometre resolution scanning probe microscopy data over mm2 regions. The system combines a slow moving but accurate large area XYZ scanner with a very fast but less accurate small area XY scanner. This arrangement enables very large areas to be scanned by stitching together the small, rapidly acquired, images from the fast XY scanner while simultaneously moving the slow XYZ scanner across the region of interest. In order to successfully merge the image sequences together two software approaches for calibrating the data from the fast scanner are described. The first utilizes the low uncertainty interferometric sensors of the XYZ scanner while the second implements a genetic algorithm with multiple parameter fitting during the data merging step of the image stitching process. The basic uncertainty components related to these high-speed measurements are also discussed. Both techniques are shown to successfully enable high-resolution, large area images to be generated at least an order of magnitude faster than with a conventional atomic force microscope.

  4. Large-area cryocooling for far-infrared telescopes

    NASA Astrophysics Data System (ADS)

    Hoang, Triem T.; O'Connell, Tamara A.; Ku, Jentung; Butler, C. D.; Swanson, Theodore D.

    2003-10-01

    Requirements for cryocooling of large-area heat sources begin to appear in studies of future space missions. Examples are the cooling of (i) the entire structure/mirror of large Far Infrared space telescopes to 4-40K and (ii) cryogenic thermal bus to maintain High Temperature Superconductor electronics to below 75K. The cryocooling system must provide robust/reliable operation and not cause significant vibration to the optical components. But perhaps the most challenging aspect of the system design is the removal of waste heat over a very large area. A cryogenic Loop Heat Pipe (C-LHP)/ cryocooler cooling system was developed with the ultimate goal of meeting the aforementioned requirements. In the proposed cooling concept, the C-LHP collected waste heat from a large-area heat source and then transported it to the cryocooler coldfinger for rejection. A proof-of-concept C-LHP test loop was constructed and performance tested in a vacuum chamber to demonstrate the feasibility of the proposed C-LHP to distribute the cryocooler cooling power over a large area. The test loop was designed to operate with any cryogenic working fluid such as Oxygen/Nitrogen (60-120K), Neon (28-40K), Hydrogen (18-30K), and Helium (2.5-4.5K). Preliminary test results indicated that the test loop had a cooling capacity of 4.2W in the 30-40K temperature range with Neon as the working fluid.

  5. Toward large-area targets for “TRAKULA”

    NASA Astrophysics Data System (ADS)

    Vascon, A.; Düllmann, Ch. E.; Eberhardt, K.; Kindler, B.; Lommel, B.; Runke, J.

    2011-11-01

    TRAKULA ( Transmutationsrelevante kernphysikalische Untersuchungen langlebiger Aktinide, i.e., nuclear physical investigations of long-lived actinides with relevance to transmutation) is a joint research project of the German Federal Ministry of Science and Education (BMBF) on nuclear physics investigations with modern scientific, technological and numerical methods. Experiments concerning the transmutation of radioactive waste are a central topic of the project. For this, large-area samples (≥40 cm 2) of 235,238U and 239,242Pu compounds are required for the calibration of fission chambers and for fission yield measurements. Another topic within the project requires large-area targets for precise measurements of the half-life, t1/2, of very long-lived α-particle emitters like 144Nd ( t1/2≈2×10 15 y). Here, we report on electrodeposition tests with Gd and Nd (used as chemical homologs of the actinides), which were performed to find optimal deposition conditions for small-area targets that should be applicable to future large-area targets. The layers were produced by molecular plating. A new stirring technique, ultrasonic stirring, was adopted and found to be suitable for producing large-area targets. Moreover, two different current densities (namely 0.7 and 1.4 mA/cm 2) were studied and found appropriate for target preparation. Characterization of the layers with different analytical techniques played a major role in these studies to gain a deeper understanding of the deposition process itself: neutron activation analysis and γ-spectroscopy were used for yield measurements, radiographic imaging for homogeneity studies, scanning electron microscopy for morphology studies, and atomic force microscopy for roughness studies. According to the obtained results, a new electrochemical cell for the production of large-area targets was designed.

  6. Detection of Steel Fatigue Cracks with Strain Sensing Sheets Based on Large Area Electronics

    PubMed Central

    Yao, Yao; Glisic, Branko

    2015-01-01

    Reliable early-stage damage detection requires continuous monitoring over large areas of structure, and with sensors of high spatial resolution. Technologies based on Large Area Electronics (LAE) can enable direct sensing and can be scaled to the level required for Structural Health Monitoring (SHM) of civil structures and infrastructure. Sensing sheets based on LAE contain dense arrangements of thin-film strain sensors, associated electronics and various control circuits deposited and integrated on a flexible polyimide substrate that can cover large areas of structures. This paper presents the development stage of a prototype strain sensing sheet based on LAE for crack detection and localization. Two types of sensing-sheet arrangements with size 6 × 6 inch (152 × 152 mm) were designed and manufactured, one with a very dense arrangement of sensors and the other with a less dense arrangement of sensors. The sensing sheets were bonded to steel plates, which had a notch on the boundary, so the fatigue cracks could be generated under cyclic loading. The sensors within the sensing sheet that were close to the notch tip successfully detected the initialization of fatigue crack and localized the damage on the plate. The sensors that were away from the crack successfully detected the propagation of fatigue cracks based on the time history of the measured strain. The results of the tests have validated the general principles of the proposed sensing sheets for crack detection and identified advantages and challenges of the two tested designs. PMID:25853407

  7. Evolution of magnetically rotating arc into large area arc plasma

    NASA Astrophysics Data System (ADS)

    Wang, Cheng; Li, Wan-Wan; Zhang, Xiao-Ning; Zha, Jun; Xia, Wei-Dong

    2015-06-01

    An arc channel tends to shrink due to its conductivity increasing with the increase of temperature. In this study, to generate large area arc plasma, we construct a magnetically rotating arc plasma generator, which mainly consists of a lanthanide tungsten cathode (13 mm in diameter), a concentric cylindrical graphite anode chamber (60 mm in diameter) and a solenoid coil for producing an axial magnet field. By controlling the cold gas flow, the magnetically rotating arc evolves from constricted mode to diffuse mode, which almost fills the whole arc chamber cross section. Results show that the diffuse arc plasma has better uniformity and stability. The formation mechanism of large area arc plasma is discussed in this paper. Project supported by the National Natural Science Foundation of China (Grant Nos. 11035005, 11475174, and 50876101) and the Science Instrument Foundation of the Chinese Academy of Sciences (Grant No. Y201162).

  8. Progress on large-area polarization grating fabrication

    NASA Astrophysics Data System (ADS)

    Miskiewicz, Matthew N.; Kim, Jihwan; Li, Yanming; Komanduri, Ravi K.; Escuti, Michael J.

    2012-06-01

    Over the last several years, we have pioneered liquid crystal polarization gratings (PGs), in both switchable and polymer versions. We have also introduced their use in many applications, including mechanical/non-mechanical laser beam steering and polarization imaging/sensing. Until now, conventional holographic congurations were used to create PGs where the diameter of the active area was limited to 1-2 inches. In this paper, we discuss a new holography setup to fabricate large area PGs using spherical waves as the diverging coherent beams. Various design parameters of this setup are examined for impact on the quality of the recorded PG profile. Using this setup, we demonstrate a large area polymer PG with approximately 66 inch square area, and present detailed characterization.

  9. High Energy Astrophysics with the Fermi Large Area Telescope

    NASA Technical Reports Server (NTRS)

    Hays, Elizabeth

    2009-01-01

    This slide presentation reviews some of the findings of the Large Area Telescope (LAT) aboard the Fermi Observatory. It includes information about the LAT, and the Gamma-Ray Burst Monitor (GBM), detection of the quiet sun and the moon in gamma rays, Pulsars observed by the observatory, Globular Star Clusters, Active Galactic Nucleus, and Gamma-Ray Bursts, with specific information about GRB 080916C.

  10. Characterization of Large Area APDs for the EXO-200 Detector

    SciTech Connect

    Neilson, R.; LePort, F.; Pocar, A.; Kumar, K.; Odian, A.; Prescott, C.Y.; Tenev, V.; Ackerman, N.; Akimov, D.; Auger, M.; Benitez-Medina, C.; Breidenbach, M.; Burenkov, A.; Conley, R.; Cook, S.; deVoe, R.; Dolinski, M.J.; Fairbank, W., Jr.; Farine, J.; Fierlinger, P.; Flatt, B.; /Stanford U., Phys. Dept. /Bern U., LHEP /Stanford U., Phys. Dept. /Maryland U. /Colorado State U. /Laurentian U. /Carleton U. /SLAC /Maryland U. /Moscow, ITEP /Alabama U. /SLAC /Colorado State U. /Stanford U., Phys. Dept. /Alabama U. /Stanford U., Phys. Dept. /Alabama U. /SLAC /Carleton U. /SLAC /Maryland U. /Moscow, ITEP /Carleton U. /Stanford U., Phys. Dept. /Bern U., LHEP /SLAC /Laurentian U. /SLAC /Maryland U.

    2011-12-02

    EXO-200 uses 468 large area avalanche photodiodes (LAAPDs) for detection of scintillation light in an ultra-low-background liquid xenon (LXe) detector. We describe initial measurements of dark noise, gain and response to xenon scintillation light of LAAPDs at temperatures from room temperature to 169 K - the temperature of liquid xenon. We also describe the individual characterization of more than 800 LAAPDs for selective installation in the EXO-200 detector.